Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 88 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
- 88 samples: 21 conditions, mostly in triplicateGroups 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
- Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and developmentbioRxiv : 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 GSE271760_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 PRJNA1133039 and SRA study SRP517346. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 74 samples.
How we read this: 21 replicated groups read from 88 sample titles; they account for 74 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.
- GSM8372162 es_wt_rep1 es_wt
- GSM8372163 es_wt_rep2 es_wt
- GSM8372164 es_wt_rep3 es_wt
- GSM8372165 es_wt_rep4 es_wt
- GSM8372166 es_wt_rep5 es_wt
- GSM8372167 es_wt_rep6 es_wt
- GSM8372168 es_wt_rep7 es_wt
- GSM8372169 es_c5-c6d_rep1 es_c5-c6d
- GSM8372170 es_c5-c6d_rep2 es_c5-c6d
- GSM8372171 es_c5-c6d_rep3 es_c5-c6d
- GSM8372172 es_c5-c6d_rep4 es_c5-c6d
- GSM8372173 es_c7-c10d_rep1 es_c7-c10d
- GSM8372174 es_c7-c10d_rep2 es_c7-c10d
- GSM8372175 es_c7-c10d_rep3 es_c7-c10d
- GSM8372176 xen_wt_rep1 xen_wt
- GSM8372177 xen_wt_rep2 xen_wt
- GSM8372178 xen_wt_rep3 xen_wt
- GSM8372179 xen_wt_rep4 xen_wt
- GSM8372180 xen_wt_rep5 xen_wt
- GSM8372181 xen_c5-c6d_rep1 xen_c5-c6d
- GSM8372182 xen_c5-c6d_rep2 xen_c5-c6d
- GSM8372183 xen_c5-c6d_rep3 xen_c5-c6d
- GSM8372184 C1-C4flxflx_rep1 C1-C4flxflx
- GSM8372185 C1-C4flxflx_rep2 C1-C4flxflx
- GSM8372186 C1-C4flxflx_rep3 C1-C4flxflx
- GSM8372187 C1-C4flxflx_rep4 C1-C4flxflx
- GSM8372188 C1-C4flxflx_rep5 C1-C4flxflx
- GSM8372189 C1-C4flxflx;CRE_rep1 C1-C4flxflx;CRE
- GSM8372190 C1-C4flxflx;CRE_rep2 C1-C4flxflx;CRE
- GSM8372191 C1-C4flxflx;CRE_rep3 C1-C4flxflx;CRE
- GSM8372192 C1-C4flxflx;CRE_rep4 C1-C4flxflx;CRE
- GSM8372193 C1-C4flxflx;CRE_rep5 C1-C4flxflx;CRE
- GSM8372194 C1-C4flxflx;CRE_rep6 C1-C4flxflx;CRE
- GSM8372195 C1-C4flxflx;CRE_rep7 C1-C4flxflx;CRE
- GSM8384292 ES cells_h3k27ac_wt_rep1 ES cells_h3k27ac_wt
- GSM8384293 ES cells_h3k27ac_wt_rep2 ES cells_h3k27ac_wt
- GSM8384294 ES cells_h3k27ac_c7-c10d_rep1 ES cells_h3k27ac_c7-c10d
- GSM8384295 ES cells_h3k27ac_c7-c10d_rep2 ES cells_h3k27ac_c7-c10d
- GSM8384296 ES cells_h3k27ac_c5-c6d_rep1 ES cells_h3k27ac_c5-c6d
- GSM8384297 ES cells_h3k27ac_c5-c6d_rep2 ES cells_h3k27ac_c5-c6d
+ 48 more — browse all 88 samples with per-sample file links →
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares regulators, chromatin
- GSE249834 Impact of Chromatin Immunoprecipitation Crosslinking Conditions on Selective Genomic Interactions by NF‐κB Family Members 21 samples shares chromatin, impact
- GSE312105 Assessing the impact of epigenetic inhibitors on reversion of the chromatin landscape from metastatic to non-metastatic organoids 18 samples shares chromatin, impact
- GSE314045 Rotational settings quantize nucleosome movement by chromatin regulators 15 samples shares regulators, chromatin
- GSE263333 Spatial-Mux-seq: Multiplexed spatial mapping of chromatin features, transcriptome, and proteins at tissue scale 12 samples shares chromatin, multiple
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chromatin
- GSE295530 MeCP2 stabilizes the glucocorticoid system in active chromatin regions [RNA-seq] 723 samples shares chromatin
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares chromatin
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.