Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE165703
Status 2021/9/3
Title Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV (ATAC-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is mainly the result of recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to disease. Alveolar macrophages (AM) are the first cells of the innate immune system that engage Mtb, but how HIV and antiretroviral therapy (ART) impact on the anti-mycobacterial response of AM is not known. In this study AM were challenged in vitro with Mtb, and their epigenetic and transcriptomic responses were determined for PLWH receiving ART, control subjects who were HIV-free (HC) and subjects who received pre-exposure prophylaxis (PrEP) with ART to prevent HIV infection. Compared to HC subjects’ response to Mtb, we showed that AM isolated from PLWH and PrEP subjects displayed substantially weaker transcriptomic response and no significant changes in their chromatin state. These findings revealed a previously unknown adverse effect of ART.
Samples
GSM ID Sample info Characteristics Description
GSM5048426 ATAC-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 49;medical.history: hypertension, diabetes, gout;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 500;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/05/03;mtb challenged: no;average tagmented library size: 1887;fragments in clean bam: 40024972;sequencing run: 1;lane: 1,2,3,4 Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048427 ATAC-Seq Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 49;medical.history: hypertension, diabetes, gout;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 500;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/05/03;mtb challenged: yes;average tagmented library size: 1783;fragments in clean bam: 45844418;sequencing run: 1;lane: 1,2,3,4 Healthy control sample 7, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048428 ATAC-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 58;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1173;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: no;average tagmented library size: 1168;fragments in clean bam: 29933483;sequencing run: 6;lane: 3,4 Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048429 ATAC-Seq Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 58;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1173;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: yes;average tagmented library size: 1215;fragments in clean bam: 23713146;sequencing run: 6;lane: 3,4 Healthy control sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048430 ATAC-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 29;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1091;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/01/11;mtb challenged: no;average tagmented library size: 880;fragments in clean bam: 8996363;sequencing run: 3,4;lane: 2,2 Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048431 ATAC-Seq Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 29;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1091;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/01/11;mtb challenged: yes;average tagmented library size: 872;fragments in clean bam: 10255215;sequencing run: 3,4;lane: 2,2 Healthy control sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048432 ATAC-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 27;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/11/29;mtb challenged: no;average tagmented library size: 874;fragments in clean bam: 51471183;sequencing run: 6;lane: 1,2 Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048433 ATAC-Seq Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 27;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/11/29;mtb challenged: yes;average tagmented library size: 944;fragments in clean bam: 37654633;sequencing run: 6;lane: 1,2 Healthy control sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048434 ATAC-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1263;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/13;mtb challenged: no;average tagmented library size: 1020;fragments in clean bam: 11131668;sequencing run: 3,4;lane: 4,4 Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048435 ATAC-Seq Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1263;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/13;mtb challenged: yes;average tagmented library size: 617;fragments in clean bam: 11687787;sequencing run: 3,4;lane: 4,4 Healthy control sample 12, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048436 ATAC-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 31;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 871;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/12;mtb challenged: no;average tagmented library size: 710;fragments in clean bam: 12895757;sequencing run: 3,4;lane: 5,5 Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048437 ATAC-Seq Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 31;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 871;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/12/12;mtb challenged: yes;average tagmented library size: 787;fragments in clean bam: 10954886;sequencing run: 3,4;lane: 5,5 Healthy control sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048438 ATAC-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1023;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/12/20;mtb challenged: no;average tagmented library size: 1051;fragments in clean bam: 17501089;sequencing run: 2;lane: 3,4 Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048439 ATAC-Seq Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1023;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/12/20;mtb challenged: yes;average tagmented library size: 1526;fragments in clean bam: 25887464;sequencing run: 2;lane: 3,4 Healthy control sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048440 ATAC-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 41;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 843;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/17;mtb challenged: no;average tagmented library size: 846;fragments in clean bam: 11006774;sequencing run: 3,4;lane: 1,1 Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048441 ATAC-Seq Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 41;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 843;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/17;mtb challenged: yes;average tagmented library size: 1265;fragments in clean bam: 16142385;sequencing run: 3,4;lane: 1,1 Healthy control sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048424 ATAC-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 495;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/02/01;mtb challenged: no;average tagmented library size: 1527;fragments in clean bam: 28419005;sequencing run: 1;lane: 1,2,3,4 Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048442 ATAC-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 37;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: yes;cd4 count: 1249;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/02/21;mtb challenged: no;average tagmented library size: 941;fragments in clean bam: 12990608;sequencing run: 3,4;lane: 4,4 Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048443 ATAC-Seq Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 37;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: yes;cd4 count: 1249;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/02/21;mtb challenged: yes;average tagmented library size: 1109;fragments in clean bam: 16205485;sequencing run: 3,4;lane: 4,4 Healthy control sample 16, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048425 ATAC-Seq Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 495;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/02/01;mtb challenged: yes;average tagmented library size: 1590;fragments in clean bam: 45656306;sequencing run: 1;lane: 1,2,3,4 Healthy control sample 2, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048444 ATAC-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 27;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 826;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/06/20;mtb challenged: no;average tagmented library size: 1107;fragments in clean bam: 32382439;sequencing run: 3,4;lane: 1,1 Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048445 ATAC-Seq Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 27;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 826;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/06/20;mtb challenged: yes;average tagmented library size: 1013;fragments in clean bam: 20603291;sequencing run: 3,4;lane: 1,1 Healthy control sample 18, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048446 ATAC-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 53;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 692;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/09/19;mtb challenged: no;average tagmented library size: 768;fragments in clean bam: 21637984;sequencing run: 6;lane: 3,4 Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048447 ATAC-Seq Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 53;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 692;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/09/19;mtb challenged: yes;average tagmented library size: 916;fragments in clean bam: 28265830;sequencing run: 6;lane: 3,4 Healthy control sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048467 ATAC-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 25;medical.history: None;sexually transmitted infections: Chlamydia 2018;quantiferon tb reagent: no;cd4 count: 832;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2018;recreational drugs: cocaine;cigarette smoker: yes;bal sampling date: 2019/11/06;mtb challenged: yes;average tagmented library size: 1107;fragments in clean bam: 35143253;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048468 ATAC-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 28;medical.history: None;sexually transmitted infections: gonorrhea PCR+;quantiferon tb reagent: no;cd4 count: 1009;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: ketamine;cigarette smoker: yes;bal sampling date: 2019/11/06;mtb challenged: no;average tagmented library size: 1095;fragments in clean bam: 39268870;sequencing run: 6;lane: 3,4 Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048448 ATAC-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: hypertension, type.2.diabetes;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1077;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/10/12;mtb challenged: no;average tagmented library size: 1426;fragments in clean bam: 26122895;sequencing run: 5;lane: 5.6 Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048469 ATAC-Seq Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 28;medical.history: None;sexually transmitted infections: gonorrhea PCR+;quantiferon tb reagent: no;cd4 count: 1009;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: ketamine;cigarette smoker: yes;bal sampling date: 2019/11/06;mtb challenged: yes;average tagmented library size: 1019;fragments in clean bam: 31326758;sequencing run: 6;lane: 3,4 Pre-exposure prophylaxis sample 36, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048470 ATAC-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1454;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2017;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2019/11/27;mtb challenged: no;average tagmented library size: 1063;fragments in clean bam: 41476497;sequencing run: 6;lane: 3,4 Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048449 ATAC-Seq Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: hypertension, type.2.diabetes;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1077;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/10/12;mtb challenged: yes;average tagmented library size: 1518;fragments in clean bam: 19135976;sequencing run: 5;lane: 5.6 Healthy control sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048471 ATAC-Seq Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 40;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1454;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2017;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2019/11/27;mtb challenged: yes;average tagmented library size: 1282;fragments in clean bam: 35696820;sequencing run: 6;lane: 3,4 Pre-exposure prophylaxis sample 37, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048472 ATAC-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 52;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 382;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 1998;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/05/31;mtb challenged: no;average tagmented library size: 1616;fragments in clean bam: 26856196;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048473 ATAC-Seq Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 52;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 382;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 1998;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/05/31;mtb challenged: yes;average tagmented library size: 1708;fragments in clean bam: 44699498;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 3, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048450 ATAC-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 42;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1248;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/10/12;mtb challenged: no;average tagmented library size: 1350;fragments in clean bam: 29582416;sequencing run: 5;lane: 5.6 Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048474 ATAC-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1172;prescription drugs: Biktarvy;active ingredient: Emtricitabine, Tenofovir_AF, Bictegravir;art start year: 2002;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: no;average tagmented library size: 1245;fragments in clean bam: 43512856;sequencing run: 6;lane: 1,2 Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048475 ATAC-Seq Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1172;prescription drugs: Biktarvy;active ingredient: Emtricitabine, Tenofovir_AF, Bictegravir;art start year: 2002;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2019/12/04;mtb challenged: yes;average tagmented library size: 1350;fragments in clean bam: 39616792;sequencing run: 6;lane: 1,2 Person living with HIV sample 4, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048451 ATAC-Seq Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 42;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1248;prescription drugs: none;active ingredient: none;art start year: none;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/10/12;mtb challenged: yes;average tagmented library size: 1333;fragments in clean bam: 24249131;sequencing run: 5;lane: 5.6 Healthy control sample 22, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048476 ATAC-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: HIV (1995);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 606;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2009;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/06/21;mtb challenged: no;average tagmented library size: 1496;fragments in clean bam: 27619275;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048477 ATAC-Seq Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: HIV (1995);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 606;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2009;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/06/21;mtb challenged: yes;average tagmented library size: 1435;fragments in clean bam: 35166491;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 5, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048452 ATAC-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Hispanic;Sex: M;age: 36;medical.history: None;sexually transmitted infections: chlamydia PCR+ and gonorrhea PCR+;quantiferon tb reagent: no;cd4 count: 961;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2014;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/11/21;mtb challenged: no;average tagmented library size: 1360;fragments in clean bam: 20898937;sequencing run: 5;lane: 5.6 Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048478 ATAC-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 536;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 2004;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/10/11;mtb challenged: no;average tagmented library size: 964;fragments in clean bam: 14984310;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048479 ATAC-Seq Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 56;medical.history: HIV (2002);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 536;prescription drugs: Truvada, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Raltegravir;art start year: 2004;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/10/11;mtb challenged: yes;average tagmented library size: 1029;fragments in clean bam: 20240580;sequencing run: 1;lane: 1,2,3,4 Person living with HIV sample 9, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048453 ATAC-Seq Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Hispanic;Sex: M;age: 36;medical.history: None;sexually transmitted infections: chlamydia PCR+ and gonorrhea PCR+;quantiferon tb reagent: no;cd4 count: 961;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2014;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/11/21;mtb challenged: yes;average tagmented library size: 1371;fragments in clean bam: 16535209;sequencing run: 5;lane: 5.6 Pre-exposure prophylaxis sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048480 ATAC-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (1992);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 269;prescription drugs: Intelence, Prezista, Tivicay, Norvir;active ingredient: Etravirine, Darunavir, Dolutegravir, Ritonavir;art start year: 1996;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/11/01;mtb challenged: no;average tagmented library size: 553;fragments in clean bam: 9528148;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048481 ATAC-Seq Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (1992);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 269;prescription drugs: Intelence, Prezista, Tivicay, Norvir;active ingredient: Etravirine, Darunavir, Dolutegravir, Ritonavir;art start year: 1996;recreational drugs: no;cigarette smoker: no;bal sampling date: 2017/11/01;mtb challenged: yes;average tagmented library size: 752;fragments in clean bam: 9612499;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 10, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048482 ATAC-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: Complera;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine;art start year: 1999;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/11/29;mtb challenged: no;average tagmented library size: 1452;fragments in clean bam: 41369033;sequencing run: 2;lane: 1,2 Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048454 ATAC-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: hypertension, diabetes, attention.deficit.hyperactivity.disorder;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1254;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2018/11/21;mtb challenged: no;average tagmented library size: 1679;fragments in clean bam: 23044555;sequencing run: 4,5;lane: 7,8 Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048483 ATAC-Seq Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 439;prescription drugs: Complera;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine;art start year: 1999;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2017/11/29;mtb challenged: yes;average tagmented library size: 1245;fragments in clean bam: 34123694;sequencing run: 2;lane: 1,2 Person living with HIV sample 11, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048484 ATAC-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: F;age: 54;medical.history: HIV (1994);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 716;prescription drugs: Complera, Reyataz, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir;art start year: 1994;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: no;average tagmented library size: 1094;fragments in clean bam: 18877151;sequencing run: 2;lane: 1,2 Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048455 ATAC-Seq Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: hypertension, diabetes, attention.deficit.hyperactivity.disorder;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1254;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: yes;bal sampling date: 2018/11/21;mtb challenged: yes;average tagmented library size: 1602;fragments in clean bam: 40104333;sequencing run: 4,5;lane: 7,8 Pre-exposure prophylaxis sample 28, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048485 ATAC-Seq Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: F;age: 54;medical.history: HIV (1994);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 716;prescription drugs: Complera, Reyataz, Isentress;active ingredient: Emtricitabine, Tenofovir_DF, Rilpivirine, Atazanavir, Raltegravir;art start year: 1994;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: yes;average tagmented library size: 1181;fragments in clean bam: 21021524;sequencing run: 2;lane: 1,2 Person living with HIV sample 13, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048456 ATAC-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: North african;Sex: M;age: 37;medical.history: None;sexually transmitted infections: chlamydia PCR+;quantiferon tb reagent: yes;cd4 count: 981;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2013;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/12/03;mtb challenged: no;average tagmented library size: 1293;fragments in clean bam: 27557230;sequencing run: 5;lane: 5.6 Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048457 ATAC-Seq Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: North african;Sex: M;age: 37;medical.history: None;sexually transmitted infections: chlamydia PCR+;quantiferon tb reagent: yes;cd4 count: 981;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2013;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/12/03;mtb challenged: yes;average tagmented library size: 1553;fragments in clean bam: 23654474;sequencing run: 5;lane: 5.6 Pre-exposure prophylaxis sample 29, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048486 ATAC-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 983;prescription drugs: Kivexa, Reyataz, Norvir;active ingredient: Abacavir, Lamivudine, Atazanavir, Ritonavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: no;average tagmented library size: 1149;fragments in clean bam: 11573443;sequencing run: 2;lane: 1,2 Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048458 ATAC-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 36;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1163;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/12/21;mtb challenged: no;average tagmented library size: 1483;fragments in clean bam: 19365351;sequencing run: 5;lane: 7,8 Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048487 ATAC-Seq Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (1996);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 983;prescription drugs: Kivexa, Reyataz, Norvir;active ingredient: Abacavir, Lamivudine, Atazanavir, Ritonavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2017/12/06;mtb challenged: yes;average tagmented library size: 942;fragments in clean bam: 12660069;sequencing run: 2;lane: 3,4 Person living with HIV sample 14, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048488 ATAC-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 51;medical.history: HIV x 2003;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 468;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2004;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/24;mtb challenged: no;average tagmented library size: 1603;fragments in clean bam: 26304176;sequencing run: 3,4;lane: 4,4 Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048459 ATAC-Seq Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 36;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1163;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/12/21;mtb challenged: yes;average tagmented library size: 1674;fragments in clean bam: 14087008;sequencing run: 5;lane: 7,8 Pre-exposure prophylaxis sample 31, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048489 ATAC-Seq Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 51;medical.history: HIV x 2003;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 468;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2004;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/01/24;mtb challenged: yes;average tagmented library size: 1345;fragments in clean bam: 22515120;sequencing run: 3,4;lane: 4,4 Person living with HIV sample 15, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048490 ATAC-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 41;medical.history: HIV (2014);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1267;prescription drugs: Viread, Tivicay, Edurant;active ingredient: Tenofovir_DF, Dolutegravir, Rilpivirine;art start year: 2015;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: no;average tagmented library size: 1250;fragments in clean bam: 21698134;sequencing run: 5;lane: 5,6 Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048460 ATAC-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 36;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1069;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2017;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/12/21;mtb challenged: no;average tagmented library size: 1765;fragments in clean bam: 12492089;sequencing run: 5;lane: 3,4 Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048491 ATAC-Seq Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 41;medical.history: HIV (2014);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1267;prescription drugs: Viread, Tivicay, Edurant;active ingredient: Tenofovir_DF, Dolutegravir, Rilpivirine;art start year: 2015;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/02/07;mtb challenged: yes;average tagmented library size: 1375;fragments in clean bam: 16725440;sequencing run: 5;lane: 5,6 Person living with HIV sample 17, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048461 ATAC-Seq Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 36;medical.history: None;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 1069;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2017;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/12/21;mtb challenged: yes;average tagmented library size: 1888;fragments in clean bam: 15051625;sequencing run: 5;lane: 3,4 Pre-exposure prophylaxis sample 32, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048492 ATAC-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (2005);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 565;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2006;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2018/02/14;mtb challenged: no;average tagmented library size: 892;fragments in clean bam: 14385521;sequencing run: 3,4;lane: 3,3 Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048493 ATAC-Seq Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 57;medical.history: HIV (2005);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 565;prescription drugs: Triumeq;active ingredient: Abacavir, Dolutegravir, Lamivudine;art start year: 2006;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2018/02/14;mtb challenged: yes;average tagmented library size: 1188;fragments in clean bam: 16015184;sequencing run: 3,4;lane: 3,3 Person living with HIV sample 19, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048462 ATAC-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 28;medical.history: depression;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 691;prescription drugs: Truvada, Remeron;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2019;recreational drugs: speed;cigarette smoker: no;bal sampling date: 2019/10/31;mtb challenged: no;average tagmented library size: 807;fragments in clean bam: 38923323;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048494 ATAC-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 58;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 727;prescription drugs: Truvada, Tybost, Prezista;active ingredient: Emtricitabine, Tenofovir_DF, Cobiscistat, Darunavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2018/05/30;mtb challenged: no;average tagmented library size: 1479;fragments in clean bam: 39900855;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048495 ATAC-Seq Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 58;medical.history: HIV (1997);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 727;prescription drugs: Truvada, Tybost, Prezista;active ingredient: Emtricitabine, Tenofovir_DF, Cobiscistat, Darunavir;art start year: 1997;recreational drugs: cannabis;cigarette smoker: no;bal sampling date: 2018/05/30;mtb challenged: yes;average tagmented library size: 1400;fragments in clean bam: 37031839;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 20, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048463 ATAC-Seq Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 28;medical.history: depression;sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 691;prescription drugs: Truvada, Remeron;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2019;recreational drugs: speed;cigarette smoker: no;bal sampling date: 2019/10/31;mtb challenged: yes;average tagmented library size: 830;fragments in clean bam: 37160360;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 33, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048496 ATAC-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 62;medical.history: HIV (2012);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 650;prescription drugs: Truvada, Tivicay;active ingredient: Emtricitabine, Tenofovir_DF, Dolutegravir;art start year: 2012;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/06/20;mtb challenged: no;average tagmented library size: 1048;fragments in clean bam: 21764135;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048497 ATAC-Seq Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 62;medical.history: HIV (2012);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 650;prescription drugs: Truvada, Tivicay;active ingredient: Emtricitabine, Tenofovir_DF, Dolutegravir;art start year: 2012;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/06/20;mtb challenged: yes;average tagmented library size: 1007;fragments in clean bam: 22505435;sequencing run: 3,4;lane: 1,1 Person living with HIV sample 21, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048464 ATAC-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Asian;Sex: M;age: 42;medical.history: None;sexually transmitted infections: Chlamydia 2017;quantiferon tb reagent: no;cd4 count: 208;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: no;bal sampling date: 2019/10/31;mtb challenged: no;average tagmented library size: 1138;fragments in clean bam: 34508747;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048498 ATAC-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 33;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 633;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2017;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/07/11;mtb challenged: no;average tagmented library size: 1197;fragments in clean bam: 18159762;sequencing run: 3,4;lane: 3,3 Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048499 ATAC-Seq Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 33;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 633;prescription drugs: Genvoya;active ingredient: Emtricitabine, Tenofovir_AF, Cobicistat, Elvitegravir;art start year: 2017;recreational drugs: cannabis;cigarette smoker: yes;bal sampling date: 2018/07/11;mtb challenged: yes;average tagmented library size: 1078;fragments in clean bam: 15055848;sequencing run: 3,4;lane: 3,3 Person living with HIV sample 23, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048500 ATAC-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (2006);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 906;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2007;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: no;average tagmented library size: 1260;fragments in clean bam: 18538072;sequencing run: 3,4;lane: 2,2 Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048465 ATAC-Seq Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Asian;Sex: M;age: 42;medical.history: None;sexually transmitted infections: Chlamydia 2017;quantiferon tb reagent: no;cd4 count: 208;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2016;recreational drugs: no;cigarette smoker: no;bal sampling date: 2019/10/31;mtb challenged: yes;average tagmented library size: 992;fragments in clean bam: 38937371;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 34, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048501 ATAC-Seq Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 60;medical.history: HIV (2006);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 906;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2007;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: yes;average tagmented library size: 1195;fragments in clean bam: 19577519;sequencing run: 3,4;lane: 2,2 Person living with HIV sample 25, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048502 ATAC-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (2000);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 471;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2010;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: no;average tagmented library size: 1095;fragments in clean bam: 22858216;sequencing run: 3,4;lane: 2,2 Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048466 ATAC-Seq Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 25;medical.history: None;sexually transmitted infections: Chlamydia 2018;quantiferon tb reagent: no;cd4 count: 832;prescription drugs: Truvada;active ingredient: Emtricitabine, Tenofovir_DF;art start year: 2018;recreational drugs: cocaine;cigarette smoker: yes;bal sampling date: 2019/11/06;mtb challenged: no;average tagmented library size: 1055;fragments in clean bam: 41284773;sequencing run: 6;lane: 1,2 Pre-exposure prophylaxis sample 35, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048503 ATAC-Seq Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 50;medical.history: HIV (2000);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 471;prescription drugs: Atripla;active ingredient: Emtricitabine, Tenofovir_DF, Efavirenz;art start year: 2010;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/07/04;mtb challenged: yes;average tagmented library size: 994;fragments in clean bam: 21212891;sequencing run: 3,4;lane: 2,2 Person living with HIV sample 26, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
GSM5048504 ATAC-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 501;prescription drugs: Descovy, Isentress;active ingredient: Emtricitabine, Tenofovir_AF, Raltegravir;art start year: 2017;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/09/19;mtb challenged: no;average tagmented library size: 1013;fragments in clean bam: 15598775;sequencing run: 6;lane: 3,4 Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis non-challenged library;Tn5 transposase
GSM5048505 ATAC-Seq Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library ethnicity: Caucasian;Sex: M;age: 59;medical.history: HIV (2017);sexually transmitted infections: no;quantiferon tb reagent: no;cd4 count: 501;prescription drugs: Descovy, Isentress;active ingredient: Emtricitabine, Tenofovir_AF, Raltegravir;art start year: 2017;recreational drugs: no;cigarette smoker: no;bal sampling date: 2018/09/19;mtb challenged: yes;average tagmented library size: 968;fragments in clean bam: 19972864;sequencing run: 6;lane: 3,4 Person living with HIV sample 27, Alveolar macrophage, Mycobacterium tuberculosis challenged library;Tn5 transposase
Platform GPL20301  : Illumina HiSeq 4000 (Homo sapiens)
Literature 34473646  
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