NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 171 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
- 171 samples: 49 conditions, mostly in triplicateGroups 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 GSE312302_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 PRJNA1372805 and SRA study SRP645486. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 134 samples.
How we read this: 49 replicated groups read from 171 sample titles; they account for 134 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.
- GSM8315416 Control_0h_biol rep1 Control_0h_biol
- GSM8315417 Control_0h_biol rep2 Control_0h_biol
- GSM8315418 Control_0h_biol rep3 Control_0h_biol
- GSM8315419 Control_24h_biol rep1 Control_24h_biol
- GSM8315420 Control_24h_biol rep2 Control_24h_biol
- GSM8315421 Control_24h_biol rep3 Control_24h_biol
- GSM8315422 Control_48h_biol rep1 Control_48h_biol
- GSM8315423 Control_48h_biol rep2 Control_48h_biol
- GSM8315424 Control_48h_biol rep3 Control_48h_biol
- GSM8315425 Control_72h_biol rep1 Control_72h_biol
- GSM8315426 Control_72h_biol rep2 Control_72h_biol
- GSM8315427 Control_72h_biol rep3 Control_72h_biol
- GSM8315428 PBRM1 KO_0h_biol rep1 PBRM1 KO_0h_biol
- GSM8315429 PBRM1 KO_0h_biol rep2 PBRM1 KO_0h_biol
- GSM8315430 PBRM1 KO_0h_biol rep3 PBRM1 KO_0h_biol
- GSM8315431 PBRM1 KO_24h_biol rep1 PBRM1 KO_24h_biol
- GSM8315432 PBRM1 KO_24h_biol rep2 PBRM1 KO_24h_biol
- GSM8315433 PBRM1 KO_24h_biol rep3 PBRM1 KO_24h_biol
- GSM8315434 PBRM1 KO_48h_biol rep1 PBRM1 KO_48h_biol
- GSM8315435 PBRM1 KO_48h_biol rep2 PBRM1 KO_48h_biol
- GSM8315436 PBRM1 KO_48h_biol rep3 PBRM1 KO_48h_biol
- GSM8315437 PBRM1 KO_72h_biol rep1 PBRM1 KO_72h_biol
- GSM8315438 PBRM1 KO_72h_biol rep2 PBRM1 KO_72h_biol
- GSM8315439 PBRM1 KO_72h_biol rep3 PBRM1 KO_72h_biol
- GSM8315440 pLKO_0h_biol rep1 pLKO_0h_biol
- GSM8315441 pLKO_0h_biol rep2 pLKO_0h_biol
- GSM8315442 pLKO_0h_biol rep3 pLKO_0h_biol
- GSM8315443 pLKO_24h_biol rep1 pLKO_24h_biol
- GSM8315444 pLKO_24h_biol rep2 pLKO_24h_biol
- GSM8315445 pLKO_24h_biol rep3 pLKO_24h_biol
- GSM8315446 pLKO_48h_biol rep1 pLKO_48h_biol
- GSM8315447 pLKO_48h_biol rep2 pLKO_48h_biol
- GSM8315448 pLKO_48h_biol rep3 pLKO_48h_biol
- GSM8315449 pLKO_72h_biol rep1 pLKO_72h_biol
- GSM8315450 pLKO_72h_biol rep2 pLKO_72h_biol
- GSM8315451 pLKO_72h_biol rep3 pLKO_72h_biol
- GSM8315452 shATF3_0h_biol rep1 shATF3_0h_biol
- GSM8315453 shATF3_0h_biol rep2 shATF3_0h_biol
- GSM8315454 shATF3_0h_biol rep3 shATF3_0h_biol
- GSM8315455 shATF3_24h_biol rep1 shATF3_24h_biol
+ 131 more — browse all 171 samples with per-sample file links →
- GSE292377 Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq] 41 samples shares atac-seq, rna-seq
- GSE327645 BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq] 28 samples shares atac-seq, rna-seq
- GSE266317 RNA-seq and ChIP-seq analysis of H3K27ac, H3K27me3, H3K9me2, and JMJD1A in 3T3-L1 cells and ChIP-seq analysis of NFIC in imSVF cells. 14 samples shares chip-seq, rna-seq
- GSE222656 RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited 40 samples shares rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq
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.