PBAF associates with repressed chromatin to enable REST occupancy (ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 31 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 31 samples: 29 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- The SWI/SNF PBAF complex facilitates REST occupancy at repressive chromatinbioRxiv : the preprint server for biology · 2024
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE272705_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1138230 and SRA study SRP521147. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 31 sample titles: 29 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8409470 4L_Input_ChIP
- GSM8409471 4L_ARID2_ChIP
- GSM8409472 4L_SS18_ChIP
- GSM8409473 4L_BRG1_ChIP
- GSM8409474 4L_EZH2_ChIC
- GSM8409475 4L_PBRM1_ChIP
- GSM8409476 4L_H3K4me3_ChIP
- GSM8409477 4L_H3K27ac_ChIP
- GSM8409478 4L_H3K27me3_ChIC
- GSM8409479 4L_H3K4me1_ChIC
- GSM8409480 4L_H3K9me3_ChIC
- GSM8409481 4L_REST_ChIP
- GSM8409482 4L_REST_ChIP_NTC
- GSM8409483 4L_REST_ChIP_ARID2_KO1-17
- GSM8409484 NHEM_Input_ChIP
- GSM8409485 NHEM_ARID2_ChIP
- GSM8409486 NHEM_SS18_ChIP
- GSM8409487 NHEM_H3K27ac_ChIP
- GSM8409488 HHEM_H3K9me3_ChIP
- GSM8409489 NHEM_H3K27me3_ChIP
- GSM8409490 NHEM_H3K4me3_ChIP
- GSM8409491 NHEM_H3K4me1_ChIC
- GSM8409492 NHEM_REST_ChIP
- GSM8409493 NHEM_REST_ChIP_NTC1
- GSM8409494 NHEM_REST_ChIP_NTC2
- GSM8409495 NHEM_REST_ChIP_ARID2_KO1
- GSM8409496 NHEM_REST_ChIP_ARID2_KO5
- GSM8409497 NHEM_CTCF_ChIP
- GSM8837078 4L_SMARCB1_ChIP
- GSM8837079 4L_H2AK119ub_ChIP
- GSM8837080 NHEM_H2AK119ub_ChIP
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing · shares chromatin
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares rest
- GSE317605 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer [CITE-Seq] 168 samples same disease briefing
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.