Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 6 conditions, mostly in duplicateGroups 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.
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 GSE295748_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 PRJNA1256306 and SRA study SRP581724. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 of them. 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.
- GSM8956536 WT ESC ULI-MNase-seq_r1 WT ESC ULI-MNase-seq
- GSM8956537 WT ESC ULI-MNase-seq_r2 WT ESC ULI-MNase-seq
- GSM8956538 KO ESC ULI-MNase-seq_r1 KO ESC ULI-MNase-seq
- GSM8956539 KO ESC ULI-MNase-seq_r2 KO ESC ULI-MNase-seq
- GSM8956540 WT ESC RNA-seq_r1 WT ESC RNA-seq
- GSM8956541 WT ESC RNA-seq_r2 WT ESC RNA-seq
- GSM8956542 KO ESC RNA-seq_r1 KO ESC RNA-seq
- GSM8956543 KO ESC RNA-seq_r2 KO ESC RNA-seq
- GSM8956544 WT ESC ATAC-seq_r1 WT ESC ATAC-seq
- GSM8956545 WT ESC ATAC-seq_r2 WT ESC ATAC-seq
- GSM8956546 KO ESC ATAC-seq_r1 KO ESC ATAC-seq
- GSM8956547 KO ESC ATAC-seq_r2 KO ESC ATAC-seq
- GSE300734 Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis [RNA-seq] 25 samples shares brg1, embryogenesis, pluripotency, totipotency, nucleosome, aberrent, affects, factors
- GSE297843 Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis [MNase-Seq] 16 samples shares brg1, embryogenesis, pluripotency, totipotency, nucleosome, aberrent, affects, factors
- GSE253480 FoxO transcription factors actuate the formative pluripotency specific gene expression programme 66 samples shares pluripotency, factors
- GSE253479 FoxO transcription factors actuate the formative pluripotency specific gene expression programme [ChIP-Seq] 32 samples shares pluripotency, factors
- GSE270036 Investigate the functions of core pluripotency transcription factors in embryonic stem cells 30 samples shares pluripotency, factors
- GSE253473 FoxO transcription factors actuate the formative pluripotency specific gene expression programme [RNA-Seq] 26 samples shares pluripotency, factors
- GSE279674 Regulation of ILC2s by Brg1 30 samples shares brg1
- GSE156569 BRG1 contributes to the global chromatin accessibility revealed by its acute depletion 102 samples shares brg1
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.