Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus [ATAC-Seq and Hi-C]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 2 × ATAC-seq in wt NPC vs 2 × ATAC-seq in CTCF motif deletion at element A NPC vs 2 × cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus vs 2 × cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locusGroups 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 GSE308227_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 8 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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.
- GSM9240611 ATAC-seq in wt NPC R1 ATAC-seq in wt NPC
- GSM9240612 ATAC-seq in wt NPC R2 ATAC-seq in wt NPC
- GSM9240613 ATAC-seq in CTCF motif deletion at element A NPC R1 ATAC-seq in CTCF motif …
- GSM9240614 ATAC-seq in CTCF motif deletion at element A NPC R2 ATAC-seq in CTCF motif …
- GSM9240615 cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R1 cHiC of element C2 and …
- GSM9240616 cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R2 cHiC of element C2 and …
- GSM9240617 cHiC of element C2 and C3 deletion in mouse NPC at the Zfp608 locus R2re
- GSM9240618 cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R1 cHiC of element C2,C3, …
- GSM9240619 cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R1re
- GSM9240620 cHiC of element C2,C3, and A deletion in mouse NPC at the Zfp608 locus R2 cHiC of element C2,C3, …
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares zfp608, architecture, scaffolding, element, rewires, locus
- GSE206011 Stepwise de novo establishment of inactive X chromosome architecture in early development 262 samples shares architecture
- GSE341480 Spatiotemporal Clonal Architecture of the Newborn Mouse Forebrain 186 samples shares architecture
- GSE312302 NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq 171 samples shares atac-seq
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares architecture
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares atac-seq
- GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares architecture
- 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
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.