PBAF associates with repressed chromatin to enable REST occupancy
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 61 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)
- Samples
- 61 samples: 49 distinct titles, 12 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
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 GSE278549_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 PRJNA1167756 and SRA study SRP521147. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 61 sample titles: 49 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
- GSM8476621 4L_Parental_rep1
- GSM8476622 4L_Parental_rep2
- GSM8476623 4L_sgNTC_rep1
- GSM8476624 4L_sgNTC_rep2
- GSM8476625 4L_ARID2KO_sg1.17_rep1
- GSM8476626 4L_ARID2KO_sg1.17_rep2
- GSM8476627 4L_ARID2KO_sg5.11_rep1
- GSM8476628 4L_ARID2KO_sg5.11_rep2
- GSM8476629 SW11_sgNTC_rep1
- GSM8476630 SW11_sgNTC_rep2
- GSM8476631 SW11_ARID2KO_sg1_rep1
- GSM8476632 SW11_ARID2KO_sg1_rep2
+ 21 more — browse all 61 samples with per-sample file links →
- GSE288701 A pathogenic GATA2 zinc finger mutation restricts chromatin occupancy in human erythroid progenitor cells 36 samples shares rest, chromatin, occupancy
- GSE261846 ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial to mesenchymal transition in cranial neural crest lineage commitment. 74 samples shares rest, occupancy
- GSE235534 BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates 41 samples shares rest, chromatin
- GSE193413 Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth [Hi-C] 28 samples shares rest, chromatin
- GSE290342 Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes [ATAC-Seq] 12 samples shares rest, chromatin
- GSE299017 Basis for Lineage-Determining Pioneer Factors Targeting Distinct Repressed Chromatin States 69 samples shares repressed, chromatin
- GSE263717 Epigenomic profiles of SLE resting and transitional B cells 150 samples shares rest
- GSE242143 DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex 75 samples shares rest
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.