The transcriptional factor ONECUT3 is a driver and therapeutic target for complex karyotype MDS
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 3 × ONECUT3-OE, ONECUT3-FLAG, vs 3 × Control, vs 3 × ONECUT3-OE,Groups 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 GSE202694_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 PRJNA837004 and SRA study SRP374619. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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.
- GSM6128373 Control, ONECUT3-FLAG, rep1
- GSM6128374 ONECUT3-OE, Input, rep1
- GSM6128375 ONECUT3-OE, IgG, rep1
- GSM6128376 ONECUT3-OE, ONECUT3-FLAG, rep1 ONECUT3-OE, ONECUT3-FLA…
- GSM6128377 ONECUT3-OE, ONECUT3-FLAG, rep2 ONECUT3-OE, ONECUT3-FLA…
- GSM6128378 ONECUT3-OE, ONECUT3-FLAG, rep3 ONECUT3-OE, ONECUT3-FLA…
- GSM6128533 Control, rep1 Control,
- GSM6128534 Control, rep2 Control,
- GSM6128535 Control, rep3 Control,
- GSM6128536 ONECUT3-OE, rep1 ONECUT3-OE,
- GSM6128537 ONECUT3-OE, rep2 ONECUT3-OE,
- GSM6128538 ONECUT3-OE, rep3 ONECUT3-OE,
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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.