PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 46 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
- 46 samples: 14 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.
- Paper
- PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and FunctionbioRxiv : the preprint server for biology · 2023
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 GSE250366_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 PRJNA1053415 and SRA study SRP478314. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 44 samples.
How we read this: 14 replicated groups read from 46 sample titles; they account for 44 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,
- GSM7977952 lungs, Wild Type C57Bl6, PRDM16, rep1 lungs, Wild Type C57Bl6…
- GSM7977953 lungs, Wild Type C57Bl6, PRDM16, rep2 lungs, Wild Type C57Bl6…
- GSM7977954 lungs, Wild Type C57Bl6, PRDM3, rep1
- GSM7977955 lungs, Wild Type C57Bl6, Rabbit IgG, rep1 lungs, Wild Type C57Bl6…
- GSM7977956 lungs, Wild Type C57Bl6, Sheep IgG, rep1
- GSM7977957 lungs, Wild Type C57Bl6, H3K4me3, rep1 lungs, Wild Type C57Bl6…
- GSM7977958 lungs, Wild Type C57Bl6, NKX2-1, rep1 lungs, Wild Type C57Bl6…
- GSM7977959 lungs, Wild Type C57Bl6, H3K4me3, rep2 lungs, Wild Type C57Bl6…
- GSM7977960 lungs, Wild Type C57Bl6, H3K4me3, rep3 lungs, Wild Type C57Bl6…
- GSM7977961 lungs, Wild Type C57Bl6, NKX2-1, rep2 lungs, Wild Type C57Bl6…
- GSM7977962 lungs, Wild Type C57Bl6, NKX2-1, rep3 lungs, Wild Type C57Bl6…
- GSM7977963 lungs, Wild Type C57Bl6, Rabbit IgG, rep2 lungs, Wild Type C57Bl6…
- GSM7977974 RNA lungs, Control, rep1 RNA lungs, Control,
- GSM7977975 RNA lungs, Control, rep2 RNA lungs, Control,
- GSM7977976 RNA lungs, Control, rep3 RNA lungs, Control,
- GSM7977977 RNA lungs, Control, rep4 RNA lungs, Control,
- GSM7977978 RNA lungs, Control, rep5 RNA lungs, Control,
- GSM7977979 RNA lungs, Control, rep6 RNA lungs, Control,
- GSM7977980 RNA lungs, PRDM3/16KO, rep1 RNA lungs, PRDM3/16KO,
- GSM7977981 RNA lungs, PRDM3/16KO, rep2 RNA lungs, PRDM3/16KO,
- GSM7977982 RNA lungs, PRDM3/16KO, rep3 RNA lungs, PRDM3/16KO,
- GSM7977983 RNA lungs, PRDM3/16KO, rep4 RNA lungs, PRDM3/16KO,
- GSM7977984 RNA lungs, PRDM3/16KO, rep5 RNA lungs, PRDM3/16KO,
- GSM7977985 scRNA lungs, Control, rep1 scRNA lungs, Control,
- GSM7977986 scRNA lungs, Control, rep2 scRNA lungs, Control,
- GSM7977987 scRNA lungs, PRDM3/16KO, Rep1 scRNA lungs, PRDM3/16KO,
- GSM7977988 scRNA lungs, PRDM3/16KO, Rep2 scRNA lungs, PRDM3/16KO,
- GSM8447828 lungs, Control, rep1 lungs, Control,
- GSM8447829 lungs, Control IgG, rep1 lungs, Control IgG,
+ 6 more — browse all 46 samples with per-sample file links →
- 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
- GSE250359 PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [ATAC-seq] 11 samples shares nkx2-1, prdm3, differentiations, accessibility, epithelial, chromatin, regulate, required
- GSE242945 Nuclear actin structure regulates chromatin accessibility. 48 samples shares accessibility, chromatin, regulate
- GSE186632 Microglia and Fn14 regulate transcription and chromatin accessibility in developing neurons 10 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
- GSE253187 Ca2+ influx through ORAI1 and ORAI2 channels regulates chromatin accessibility in CD4+ T cells 13 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.