SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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
- SWI/SNF-dependent genes are defined by their chromatin landscapeCell reports · 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 GSE249211_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 PRJNA1047897 and SRA study SRP475449. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 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.
- GSM7928368 NmuMG, BRD9, rep1, ChIP
- GSM7928369 NmuMG, BRD9, rep2, ChIP
- GSM7928370 NmuMG, DPF2, rep1, ChIP
- GSM7928371 NmuMG, DPF2, rep2, ChIP
- GSM7928372 NmuMG, H3K27ac, BRM014-30h, rep1, ChIP
- GSM7928373 NmuMG, H3K27ac, BRM014-30h, rep2, ChIP
- GSM7928374 NmuMG, H3K27ac, BRM014-6h, rep1, ChIP
- GSM7928375 NmuMG, H3K27ac, BRM014-6h, rep2, ChIP
- GSM7928376 NmuMG, H3K27ac, DMSO-30h, rep1, ChIP
- GSM7928377 NmuMG, H3K27ac, DMSO-30h, rep2, ChIP
- GSM7928378 NmuMG, H3K27ac, DMSO-6h, rep1, ChIP
- GSM7928379 NmuMG, H3K27ac, DMSO-6h, rep2, ChIP
- GSM7928380 NmuMG, BRM014-30h, rep1, input
- GSM7928381 NmuMG, BRM014-30h, rep2, input
- GSM7928382 NmuMG, BRM014-6h, rep1, input
- GSM7928383 NmuMG, BRM014-6h, rep2, input
- GSM7928384 NmuMG, DMSO-30h, rep1, input
- GSM7928385 NmuMG, DMSO-30h, rep2, input
- GSM7928386 NmuMG, DMSO-6h, rep1, input
- GSM7928387 NmuMG, DMSO-6h, rep2, input
- GSM7928388 NmuMG, rep1, input
- GSM7928389 NmuMG, rep2, input
- GSM7928390 NmuMG, PBRM1, rep1, ChIP
- GSM7928391 NmuMG, PBRM1, rep2, ChIP
- GSE248369 The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo 10 samples shares swi, chromatin
- GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares chromatin, chip-seq
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples shares chromatin, chip-seq
- GSE294085 SIRT6 Overexpression Counteracts Chromatin Aging [ChIP-Seq] 74 samples shares chromatin, chip-seq
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples shares chromatin, chip-seq
- GSE292285 Depletion of lamin-associated polypeptide 2 alpha leads to chromatin reorganization and redistribution of A-type lamins to open genomic regions [ChIP-seq] 22 samples shares chromatin, chip-seq
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares chromatin, defined
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chromatin, chip-seq
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.