Virus Dataset Detail

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Dataset Information
Accession GSE187515
Status 2022/3/21
Title Single-cell multiomics of CD4+ T cell clones in HIV-1 infected individuals
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing;Other
Summary The clonal expansion of HIV-1-infected CD4+ T cells is a major barrier to cure. Using single-cell ECCITE-seq, we examined the transcriptional landscape, upstream immune regulators, HIV-1 RNA expression, and T cell clonal expansion dynamics of 215,458 CD4+ T cells (267 HIV-1 RNA+ cells and 68 expanded HIV-1 RNA+ T cell clones) from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. We found that despite antiretroviral therapy, antigen and TNF responses persisted and shaped T cell clonal expansion. HIV-1 resided in Th1 polarized, antigen-responding T cells expressing Bcl-2 family anti-apoptotic genes. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides a new direction for HIV-1 eradication.
Samples
GSM ID Sample info Characteristics Description
GSM5668800 pooled m3mscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3m_all_contig.fasta;m3m_all_contig_annotations.csv
GSM5668745 2023Rep1Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M1matrix.tar
GSM5668801 pooled hdcmvfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdcmvbarcodes.tsv.gz;hdcmvfeatures.tsv.gz;hdcmvmatrix.mtx.gz
GSM5668746 2023Rep2Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M2matrix.tar
GSM5668802 pooled hdm1featurebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm1barcodes.tsv.gz;hdm1features.tsv.gz;hdm1matrix.mtx.gz
GSM5668747 IV640scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV640filtered_contig_igblast_db-pass_parse-select.tab
GSM5668803 pooled hdm2featurebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm2barcodes.tsv.gz;hdm2features.tsv.gz;hdm2matrix.mtx.gz
GSM5668804 pooled m1cmfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1cmbarcodes.tsv.gz;m1cmfeatures.tsv.gz;m1cmmatrix.mtx.gz
GSM5668805 pooled m1hcafeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hcabarcodes.tsv.gz;m1hcafeatures.tsv.gz;m1hcamatrix.mtx.gz
GSM5668806 pooled m1hcbfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hcbbarcodes.tsv.gz;m1hcbfeatures.tsv.gz;m1hcbmatrix.mtx.gz
GSM5668807 pooled m1hmfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hmbarcodes.tsv.gz;m1hmfeatures.tsv.gz;m1hmmatrix.mtx.gz
GSM5668808 pooled m2cmfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2cmbarcodes.tsv.gz;m2cmfeatures.tsv.gz;m2cmmatrix.mtx.gz
GSM5668809 pooled m2hcfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hcbarcodes.tsv.gz;m2hcfeatures.tsv.gz;m2hcmatrix.mtx.gz
GSM5668748 IS640scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS640filtered_contig_igblast_db-pass_parse-select.tab
GSM5668749 DS739scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS739filtered_contig_igblast_db-pass_parse-select.tab
GSM5668750 DS799scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS799filtered_contig_igblast_db-pass_parse-select.tab
GSM5668751 DV910scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV910filtered_contig_igblast_db-pass_parse-select.tab
GSM5668709 IV236scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV236filtered_contig_igblast_db-pass_parse-select.tab;IV236matrix.tar
GSM5668810 pooled m2hmfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hmbarcodes.tsv.gz;m2hmfeatures.tsv.gz;m2hmmatrix.mtx.gz
GSM5668710 IS236scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS236filtered_contig_igblast_db-pass_parse-select.tab;IS236matrix.tar
GSM5668811 pooled m3hcfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3hcbarcodes.tsv.gz;m3hcfeatures.tsv.gz;m3hcmatrix.mtx.gz
GSM5668711 IV640scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV640filtered_contig_igblast_db-pass_parse-select.tab;IV640matrix.tar
GSM5668712 IS640scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS640filtered_contig_igblast_db-pass_parse-select.tab;IS640matrix.tar
GSM5668752 DS910scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS910filtered_contig_igblast_db-pass_parse-select.tab
GSM5668713 IV829scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV829filtered_contig_igblast_db-pass_parse-select.tab;IV829matrix.tar
GSM5668812 pooled m3mfeaturebarcoding cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3mbarcodes.tsv.gz;m3mfeatures.tsv.gz;m3mmatrix.mtx.gz
GSM5668753 RDS739scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS739filtered_contig_igblast_db-pass_parse-select.tab
GSM5668714 IS829scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS829filtered_contig_igblast_db-pass_parse-select.tab;IS829matrix.tar
GSM5668715 DV739scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV739filtered_contig_igblast_db-pass_parse-select.tab;DV739matrix.tar
GSM5668754 RDS799scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS799filtered_contig_igblast_db-pass_parse-select.tab
GSM5668716 DS739scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS739filtered_contig_igblast_db-pass_parse-select.tab;DS739matrix.tar
GSM5668755 RIV236scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic RIV236filtered_contig_igblast_db-pass_parse-select.tab
GSM5668756 RIV829scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic RIV829filtered_contig_igblast_db-pass_parse-select.tab
GSM5668717 DV799scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV799filtered_contig_igblast_db-pass_parse-select.tab;DV799matrix.tar
GSM5668757 2004scTCR cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M3filtered_contig_igblast_db-pass_parse-select.tab
GSM5668718 DS799scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS799filtered_contig_igblast_db-pass_parse-select.tab;DS799matrix.tar
GSM5668758 2023scTCR 1 cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M1filtered_contig_igblast_db-pass_parse-select.tab
GSM5668719 DV910scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV910filtered_contig_igblast_db-pass_parse-select.tab;DV910matrix.tar
GSM5668720 DS910scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS910filtered_contig_igblast_db-pass_parse-select.tab;DS910matrix.tar
GSM5668721 RDS739scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS739filtered_contig_igblast_db-pass_parse-select.tab;RDS739matrix.tar
GSM5668722 RDS799scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS799filtered_contig_igblast_db-pass_parse-select.tab;RDS799matrix.tar
GSM5668759 2023scTCR 2 cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M2filtered_contig_igblast_db-pass_parse-select.tab
GSM5668723 RIV236scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic RIV236filtered_contig_igblast_db-pass_parse-select.tab;RIV236matrix.tar
GSM5668760 IV236Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV236_results.tsv
GSM5668724 RIV829scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic RIV829filtered_contig_igblast_db-pass_parse-select.tab;RIV829matrix.tar
GSM5668761 IS236Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS236_results.tsv
GSM5668762 IV640Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV640_results.tsv
GSM5668763 IS640Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS640_results.tsv
GSM5668764 IV829Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV829_results.tsv
GSM5668765 IS829Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS829_results.tsv
GSM5668766 DV739Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV739_results.tsv
GSM5668767 DS739Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS739_results.tsv
GSM5668768 DV799Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV799_results.tsv
GSM5668725 2004scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M3filtered_contig_igblast_db-pass_parse-select.tab;M3matrix.tar
GSM5668726 2023Rep1scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M1filtered_contig_igblast_db-pass_parse-select.tab;M1matrix.tar
GSM5668727 2023Rep2scRNA-seq cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M2filtered_contig_igblast_db-pass_parse-select.tab;M2matrix.tar
GSM5668728 IV236Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV236matrix.tar
GSM5668729 IS236Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS236matrix.tar
GSM5668730 IV640Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV640matrix.tar
GSM5668731 IS640Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS640matrix.tar
GSM5668769 DS799Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS7999_results.tsv
GSM5668732 IV829Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic IV829matrix.tar
GSM5668770 DV910Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV910_results.tsv
GSM5668733 IS829Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed IS829matrix.tar
GSM5668771 DS910Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS910_results.tsv
GSM5668734 DV739Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV739matrix.tar
GSM5668772 2004BulkTime1 TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected HD2004time1_results.tsv
GSM5668735 DS739Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS739matrix.tar
GSM5668773 2004BulkTime2 TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected HD2004time2_results.tsv
GSM5668736 DV799Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV799matrix.tar
GSM5668737 DS799Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS799matrix.tar
GSM5668738 DV910Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic DV910matrix.tar
GSM5668739 DS910Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed DS910matrix.tar
GSM5668740 RDS739Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS739matrix.tar
GSM5668741 RDS799Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Suppressed RDS799matrix.tar
GSM5668742 RIV236Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Viremic RIV236matrix.tar
GSM5668774 2022BulkTime1 TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected HD2022time1_results.tsv
GSM5668743 RIV829Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Virmeic RIV829matrix.tar
GSM5668775 2022BulkTime2 TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected HD2022time2_results.tsv
GSM5668744 2004Feature Barcoding cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected M3matrix.tar
GSM5668776 2023Bulk TCR sequencing cell state:Isolated unstimulated CD4+ T cells by negative selection; hiv-1 infection status:Uninfected HD2023time1_results.tsv
GSM5668777 pooled hdcmvscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdcmvbarcodes.tsv.gz;hdcmvfeatures.tsv.gz;hdcmvmatrix.mtx.gz
GSM5668778 pooled hdm1scRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm1barcodes.tsv.gz;hdm1features.tsv.gz;hdm1matrix.mtx.gz
GSM5668779 pooled hdm2scRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm2barcodes.tsv.gz;hdm2features.tsv.gz;hdm2matrix.mtx.gz
GSM5668780 pooled m1cmscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1cmbarcodes.tsv.gz;m1cmfeatures.tsv.gz;m1cmmatrix.mtx.gz
GSM5668781 pooled m1hcascRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hcabarcodes.tsv.gz;m1hcafeatures.tsv.gz;m1hcamatrix.mtx.gz
GSM5668782 pooled m1hcbscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hcbbarcodes.tsv.gz;m1hcbfeatures.tsv.gz;m1hcbmatrix.mtx.gz
GSM5668783 pooled m1hmscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hmbarcodes.tsv.gz;m1hmfeatures.tsv.gz;m1hmmatrix.mtx.gz
GSM5668784 pooled m2cmscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2cmbarcodes.tsv.gz;m2cmfeatures.tsv.gz;m2cmmatrix.mtx.gz
GSM5668785 pooled m2hcscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hcbarcodes.tsv.gz;m2hcfeatures.tsv.gz;m2hcmatrix.mtx.gz
GSM5668786 pooled m2hmscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hmbarcodes.tsv.gz;m2hmfeatures.tsv.gz;m2hmmatrix.mtx.gz
GSM5668787 pooled m3hcscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3hcbarcodes.tsv.gz;m3hcfeatures.tsv.gz;m3hcmatrix.mtx.gz
GSM5668788 pooled m3mscRNAseq cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3mbarcodes.tsv.gz;m3mfeatures.tsv.gz;m3mmatrix.mtx.gz
GSM5668789 pooled hdcmvscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdcmv_all_contig.fasta;hdcmv_all_contig_annotations.csv
GSM5668790 pooled hdm1scTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm1_all_contig.fasta;hdm1_all_contig_annotations.csv
GSM5668791 pooled hdm2scTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:Uninfected hdm2_all_contig.fasta;hdm2_all_contig_annotations.csv
GSM5668792 pooled m1cmscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1cm_all_contig.fasta;m1cm_all_contig_annotations.csv
GSM5668793 pooled m1hcascTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hca_all_contig.fasta;m1hca_all_contig_annotations.csv
GSM5668794 pooled m1hcbscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hcb_all_contig.fasta;m1hcb_all_contig_annotations.csv
GSM5668795 pooled m1hmscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m1hm_all_contig.fasta;m1hm_all_contig_annotations.csv
GSM5668796 pooled m2cmscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2cm_all_contig.fasta;m2cm_all_contig_annotations.csv
GSM5668797 pooled m2hcscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hc_all_contig.fasta;m2hc_all_contig_annotations.csv
GSM5668798 pooled m2hmscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m2hm_all_contig.fasta;m2hm_all_contig_annotations.csv
GSM5668799 pooled m3hcscTCR cell state:antigen stimulated CD4+ T cells; hiv-1 infection status:HIV-1-infected m3hc_all_contig.fasta;m3hc_all_contig_annotations.csv
Platform GPL15520  GPL20301  GPL24676  : Illumina MiSeq (Homo sapiens);Illumina HiSeq 4000 (Homo sapiens);Illumina NovaSeq 6000 (Homo sapiens)
Literature 35320704  
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