Virus Dataset Detail

> Detail information for each sample

Dataset Information

Accession

GSE147406

Status

2021/1/1

Title

Polyomavirus and neuroendocrine regulomes converge to establish tumor dependencies

Organism

Homo sapiens

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer often driven by Merkel cell polyomavirus T antigens. The epigenomic mechanisms driving MCC are poorly understood. We show that virus positive MCC (VP-MCC) super enhancer networks are committed to and controlled by lineage-specific neuroendocrine transcription factors (TFs) including LHX3, ISL1, ATOH1, INSM1, SOX2 and POU4F3. These VP-MCC TFs are central to core regulatory (CR) transcriptional circuitry, essential for growth, and co-bind enhancers with polyomavirus small T antigen. We establish that T antigen expression is directly regulated by LHX3 and ISL1, establishing a positive feedback autoregulatory circuitry for a neuroendocrine state.

Samples

GSM ID	Sample info	Characteristics	Description
GSM4430120	MCC13 DNase rep1	cell line:MCC13; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430121	MCC26 DNase rep1	cell line:MCC26; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430122	UISO DNase rep1	cell line:UISO; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430123	MCC26 DNase rep2	cell line:MCC26; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430124	UISO DNase rep2	cell line:UISO; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430125	MKL1 DNase rep1	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430126	MKL1 DNase rep2	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430127	MKL2 DNase rep1	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430128	MKL2 DNase rep2	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430129	MS1 DNase rep1	cell line:MS1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430130	MS1 DNase rep2	cell line:MS1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430131	Waga DNase rep1	cell line:Waga; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430132	Waga DNase rep2	cell line:Waga; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:DNase; enrichment target:DNase; target function:Open Chromatin	DNA (ChIP-enriched)
GSM4430133	MKL1 ATOH1	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-MATH1 (pAb, rabbit, ThermoFisher, cat#PA5-29392); enrichment target:ATOH1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430134	MKL1 INSM1	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-INSM1 (A-8) X (mAb., mouse, SantaCruz, cat#sc-271408 X); enrichment target:INSM1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430135	MKL1 ISL1	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-Islet 1 (mAb, rabbit, abcam cat#ab109517); enrichment target:ISL1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430136	MKL1 LXH3	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-LHX3/LIM (pAb, rabbit, abcam cat#ab14555); enrichment target:LXH3; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430137	MKL1 POU4F3	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-POU4F3 (mAb, mouse, abcam cat#ab58128); enrichment target:POU4F3; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430138	MKL1 SOX2	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-human/mouse/Rat SOX2 (pAb, goat, R&D systems cat@#AF2018); enrichment target:SOX2; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430139	MKL2 ATOH1	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-MATH1 (pAb, rabbit, ThermoFisher, cat#PA5-29392); enrichment target:ATOH1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430140	MKL2 INSM1	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-INSM1 (A-8) X (mAb., mouse, SantaCruz, cat#sc-271408 X); enrichment target:INSM1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430141	MKL2 ISL1	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-Islet 1 (mAb, rabbit, abcam cat#ab109517); enrichment target:ISL1; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430142	MKL2 LXH3	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-LHX3/LIM (pAb, rabbit, abcam cat#ab14555); enrichment target:LXH3; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430143	MKL2 POU4F3	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-POU4F3 (mAb, mouse, abcam cat#ab58128); enrichment target:POU4F3; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430144	MKL2 SOX2	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-human/mouse/Rat SOX2 (pAb, goat, R&D systems cat@#AF2018); enrichment target:SOX2; target function:Transcription Factor	DNA (ChIP-enriched)
GSM4430106	MKL1 input	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430107	MKL2 input	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430108	MS1 input	cell line:MS1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430109	Waga input	cell line:Waga; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430110	MCC13 input	cell line:MCC13; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430111	MCC26 input	cell line:MCC26; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430112	UISO input	cell line:UISO; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:none (input); enrichment target:input; target function:control	DNA (input control)
GSM4430113	MKL1 H3K27ac	cell line:MKL1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430114	MKL2 H3K27ac	cell line:MKL2; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430115	MS1 H3K27ac	cell line:MS1; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430116	Waga H3K27ac	cell line:Waga; virus status:positive; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430117	MCC13 H3K27ac	cell line:MCC13; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430118	MCC26 H3K27ac	cell line:MCC26; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)
GSM4430119	UISO H3K27ac	cell line:UISO; virus status:negative; cell type:Merkel Cell carcinoma (MCC); antibody/treatment:anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133); enrichment target:H3K27ac; target function:Active enhancers	DNA (ChIP-enriched)