GEO series

Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq)

GSE261221 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 189 samples Submitted 2024/05/23 Platform GPL28457

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 189 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: 189 samples: 87 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.

Summary (written by the submitters)

Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. This study investigates the cis genetic elements as well as trans elements that drive this process in order to better understand how differentiation rewiring occurs.

This dataset

Open GSE261221 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261221_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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.

NCBI GEO page ↗

Study design

87 conditions, mostly in duplicate

ChIP-seq of H3K4me3 in wt ESC ×2 ChIP-seq of H3K27Ac in wt ESC ×2 ChIP-seq of H3K36me3 in wt ESC ×2 ChIP-seq of CTCF in wt ESC ×2 ChIP-seq of Rad21 in wt ESC ×2 ChIP-seq of Pol2 in wt ESC ×2 ChIP-seq of H3K4me3 in wt NPC ×2 ChIP-seq of H3K27Ac in wt NPC ×2 +94 more

Supports a between-group comparison across 174 samples.

How we read this: 87 replicated groups read from 189 sample titles; they account for 174 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.

Samples in this study

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…
GSM8137874 ChIP-seq of Pol2 in wt ESC_R1 ChIP-seq of Pol2 in wt …
GSM8137875 ChIP-seq of Pol2 in wt ESC_R2 ChIP-seq of Pol2 in wt …
GSM8137876 ChIP-seq INPUT in wt ESC
GSM8137877 ChIP-seq of H3K4me3 in wt NPC_R2 ChIP-seq of H3K4me3 in …
GSM8137878 ChIP-seq of H3K4me3 in wt NPC_R1 ChIP-seq of H3K4me3 in …
GSM8137879 ChIP-seq of H3K27Ac in wt NPC_R2 ChIP-seq of H3K27Ac in …
GSM8137880 ChIP-seq of H3K27Ac in wt NPC_R1 ChIP-seq of H3K27Ac in …
GSM8137881 ChIP-seq of H3K36me3 in wt NPC_R2 ChIP-seq of H3K36me3 in…
GSM8137882 ChIP-seq of H3K36me3 in wt NPC_R1 ChIP-seq of H3K36me3 in…
GSM8137883 ChIP-seq of CTCF in wt NPC_R2 ChIP-seq of CTCF in wt …
GSM8137884 ChIP-seq of CTCF in wt NPC_R1 ChIP-seq of CTCF in wt …
GSM8137885 ChIP-seq of Rad21 in wt NPC_R2 ChIP-seq of Rad21 in wt…
GSM8137886 ChIP-seq of Rad21 in wt NPC_R1 ChIP-seq of Rad21 in wt…
GSM8137887 ChIP-seq of Pol2 in wt NPC_R2 ChIP-seq of Pol2 in wt …
GSM8137888 ChIP-seq of Pol2 in wt NPC_R1 ChIP-seq of Pol2 in wt …
GSM8137889 ChIP-seq of Pax6 in wt NPC_R2 ChIP-seq of Pax6 in wt …
GSM8137890 ChIP-seq of Pax6 in wt NPC_R1 ChIP-seq of Pax6 in wt …
GSM8137891 ChIP-seq INPUT in wt NPC
GSM8137892 ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R1 ChIP-seq of H3K4me3 in …
GSM8137893 ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R2 ChIP-seq of H3K4me3 in …
GSM8137894 ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R1 ChIP-seq of H3K27Ac in …
GSM8137895 ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R2 ChIP-seq of H3K27Ac in …
GSM8137896 ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R1 ChIP-seq of H3K36me3 in…
GSM8137897 ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R2 ChIP-seq of H3K36me3 in…
GSM8137898 ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R1 ChIP-seq of CTCF in Zfp…
GSM8137899 ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R2 ChIP-seq of CTCF in Zfp…
GSM8137900 ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R1 ChIP-seq of Rad21 in Zf…
GSM8137901 ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R2 ChIP-seq of Rad21 in Zf…
GSM8137902 ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R1 ChIP-seq of Pol2 in Zfp…
GSM8137903 ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R2 ChIP-seq of Pol2 in Zfp…

+ 149 more — browse all 189 samples with per-sample file links →

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