A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 255 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
- 255 samples: 119 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.
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 GSE262551_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 PRJNA1083571 and SRA study SRP493257. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 238 samples.
How we read this: 119 replicated groups read from 255 sample titles; they account for 238 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.
- GSM8137834 cHiC of wt mouse ESC at the Zfp608 locus_R1 cHiC of wt mouse ESC at…
- GSM8137835 cHiC of wt mouse ESC at the Zfp608 locus_R2 cHiC of wt mouse ESC at…
- GSM8137836 cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R1 cHiC of Zfp608 promoter…
- GSM8137837 cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R2 cHiC of Zfp608 promoter…
- GSM8137838 cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R1 cHiC of polyA insertion…
- GSM8137839 cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R2 cHiC of polyA insertion…
- GSM8137840 cHiC of element A deletion in mouse ESC at the Zfp608 locus_R1 cHiC of element A delet…
- GSM8137841 cHiC of element A deletion in mouse ESC at the Zfp608 locus_R2 cHiC of element A delet…
- GSM8137842 cHiC of element B deletion in mouse ESC at the Zfp608 locus_R1 cHiC of element B delet…
- GSM8137843 cHiC of element B deletion in mouse ESC at the Zfp608 locus_R2 cHiC of element B delet…
- GSM8137844 cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R1 cHiC of element A and B…
- GSM8137845 cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R2 cHiC of element A and B…
- GSM8137846 cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R1 cHiC of CTCF motif dele…
- GSM8137847 cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R2 cHiC of CTCF motif dele…
- GSM8137848 cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R1 cHiC of Pax6 upregulati…
- GSM8137849 cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R2 cHiC of Pax6 upregulati…
- GSM8137850 cHiC of wt mouse NPC at the Zfp608 locus_R1 cHiC of wt mouse NPC at…
- GSM8137851 cHiC of wt mouse NPC at the Zfp608 locus_R2 cHiC of wt mouse NPC at…
- GSM8137852 cHiC of Zfp608 promoter deletion in mouse NPC at the Zfp608 locus_R1 cHiC of Zfp608 promoter…
- GSM8137853 cHiC of Zfp608 promoter deletion in mouse NPC at the Zfp608 locus_R2 cHiC of Zfp608 promoter…
- GSM8137854 cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R1 cHiC of polyA insertion…
- GSM8137855 cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R2 cHiC of polyA insertion…
- GSM8137856 cHiC of element A deletion in mouse NPC at the Zfp608 locus_R1 cHiC of element A delet…
- GSM8137857 cHiC of element A deletion in mouse NPC at the Zfp608 locus_R2 cHiC of element A delet…
- GSM8137858 cHiC of element B deletion in mouse NPC at the Zfp608 locus_R1 cHiC of element B delet…
- GSM8137859 cHiC of element B deletion in mouse NPC at the Zfp608 locus_R2 cHiC of element B delet…
- GSM8137860 cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R1 cHiC of element A and B…
- GSM8137861 cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R2 cHiC of element A and B…
- GSM8137862 cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R1 cHiC of CTCF motif dele…
- GSM8137863 cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R2 cHiC of CTCF motif dele…
- GSM8137864 ChIP-seq of H3K4me3 in wt ESC_R1 ChIP-seq of H3K4me3 in …
- GSM8137865 ChIP-seq of H3K4me3 in wt ESC_R2 ChIP-seq of H3K4me3 in …
- GSM8137866 ChIP-seq of H3K27Ac in wt ESC_R1 ChIP-seq of H3K27Ac in …
- GSM8137867 ChIP-seq of H3K27Ac in wt ESC_R2 ChIP-seq of H3K27Ac in …
- GSM8137868 ChIP-seq of H3K36me3 in wt ESC_R1 ChIP-seq of H3K36me3 in…
- GSM8137869 ChIP-seq of H3K36me3 in wt ESC_R2 ChIP-seq of H3K36me3 in…
- GSM8137870 ChIP-seq of CTCF in wt ESC_R1 ChIP-seq of CTCF in wt …
- GSM8137871 ChIP-seq of CTCF in wt ESC_R2 ChIP-seq of CTCF in wt …
- GSM8137872 ChIP-seq of Rad21 in wt ESC_R1 ChIP-seq of Rad21 in wt…
- GSM8137873 ChIP-seq of Rad21 in wt ESC_R2 ChIP-seq of Rad21 in wt…
+ 215 more — browse all 255 samples with per-sample file links →
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares architecture, scaffolding, element, rewires
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares architecture, chromatin
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares architecture, chromatin
- GSE314917 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture 115 samples shares architecture, chromatin
- GSE279026 cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation 33 samples shares chromatin, element
- GSE307620 Spatial chromatin architecture and accessibility co-profiling of mammalian tissues 2 samples shares architecture, chromatin
- GSE204933 Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice 82 samples shares chromatin
- GSE206011 Stepwise de novo establishment of inactive X chromosome architecture in early development 262 samples shares architecture
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.