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Capturing totipotency in human cells through spliceosomal repression

GSE226231 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 112 samples Submitted 2024/05/30 Platform GPL20795
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 112 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
Homo sapiens (human)
Samples
112 samples: 87 distinct titles, 7 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Paper
Capturing totipotency in human cells through spliceosomal repressionCell · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Capturing totipotency in human cells through spliceosomal repression
Li S, Yang M, Shen H et al. · Cell 2024 · PMID 38843832 · doi:10.1016/j.cell.2024.05.010
This dataset
Open GSE226231 in finder → Find more human microarray 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 GSE226231_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 PRJNA939202 and SRA study SRP424823. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38843832) ↗
Study design
87 distinct titles, 7 of them repeated
WIBR3-E-MYCP-P ×10 WIBR3-N-MYCP-P ×5 EB-hTBLC-D ×5 EB-Primed-D ×5 IPS18-E-MYCP-P ×3 WIBR3-E-MYCP-INTER-P ×2 siSNRPD2 ×2

How we read this: Read from 112 sample titles: 87 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.

Samples in this study

+ 72 more — browse all 112 samples with per-sample file links →

Datasets on a similar topic

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