PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 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
- 11 samples: 6 × ATAC lungs, Control, vs 5 × ATAC lungs, Prdm3/16KO,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.
- Paper
- PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and FunctionbioRxiv : the preprint server for biology · 2023
Read the full summary ↓
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 GSE250359_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 PRJNA1053412 and SRA study SRP478323. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 2 replicated groups read from 11 sample titles; they account for 11 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.
- GSM7977941 ATAC lungs, Control, rep1 ATAC lungs, Control,
- GSM7977942 ATAC lungs, Control, rep2 ATAC lungs, Control,
- GSM7977943 ATAC lungs, Control, rep3 ATAC lungs, Control,
- GSM7977944 ATAC lungs, Control, rep4 ATAC lungs, Control,
- GSM7977945 ATAC lungs, Control, rep5 ATAC lungs, Control,
- GSM7977946 ATAC lungs, Control, rep6 ATAC lungs, Control,
- GSM7977947 ATAC lungs, Prdm3/16KO, rep1 ATAC lungs, Prdm3/16KO,
- GSM7977948 ATAC lungs, Prdm3/16KO, rep2 ATAC lungs, Prdm3/16KO,
- GSM7977949 ATAC lungs, Prdm3/16KO, rep3 ATAC lungs, Prdm3/16KO,
- GSM7977950 ATAC lungs, Prdm3/16KO, rep4 ATAC lungs, Prdm3/16KO,
- GSM7977951 ATAC lungs, Prdm3/16KO, rep5 ATAC lungs, Prdm3/16KO,
- GSE250360 PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [Cut&Run] 12 samples shares nkx2-1, prdm3, differentiations, accessibility, epithelial, chromatin, regulate, required
- GSE250366 PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function 46 samples shares nkx2-1, prdm3, differentiations, accessibility, epithelial, chromatin, regulate, required
- GSE253187 Ca2+ influx through ORAI1 and ORAI2 channels regulates chromatin accessibility in CD4+ T cells 13 samples shares accessibility, chromatin, regulate
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares accessibility, chromatin, regulate
- GSE242945 Nuclear actin structure regulates chromatin accessibility. 48 samples shares accessibility, chromatin, regulate
- GSE246707 Liver-specific matrin-3 knockout regulates hepatic transcriptome and chromatin accessibility in mice 42 samples shares accessibility, chromatin, regulate
- GSE269683 CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development 26 samples shares accessibility, chromatin, regulate
- GSE242943 Nuclear actin structure regulates chromatin accessibility [RNA-seq] 18 samples shares accessibility, chromatin, regulate
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.