Systemic determination of PRDM16 regulatory genes in the aorta
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 3 × Control, vs 3 × Prdm16SMKO,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
- Vascular smooth muscle cell PRDM16 regulates circadian variation in blood pressureThe Journal of clinical investigation · 2024
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 GSE272891_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 PRJNA1139189 and SRA study SRP521701. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 6 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.
- GSM8414256 Control, rep.1 Control,
- GSM8414257 Control, rep.2 Control,
- GSM8414258 Control, rep.3 Control,
- GSM8414259 Prdm16SMKO, rep.1 Prdm16SMKO,
- GSM8414260 Prdm16SMKO, rep.2 Prdm16SMKO,
- GSM8414261 Prdm16SMKO, rep.3 Prdm16SMKO,
- GSM8414262 Vector, IgG
- GSM8414263 Vector, Flag
- GSM8414264 PRDM16, IgG
- GSM8414265 PRDM16, Flag
- GSE288206 Single-nucleus multiomics of murine gonads reveals gene-regulatory networks underlying sex determination 24 samples shares determination, regulatory
- GSE242882 CPEB2-activated Prdm16 translation promotes brown adipocyte function and prevents obesity 22 samples shares prdm16
- GSE342312 T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics] 40 samples shares regulatory
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares regulatory
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares regulatory
- GSE235598 Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment 12 samples shares systemic
- GSE322558 Physiologic variation in sperm miRNAs tunes embryonic gene regulatory programs and developmental outcomes 622 samples shares regulatory
- GSE292261 A dynamic gene regulatory code drives synaptic development of hippocampal granule cells [SS2] 576 samples shares regulatory
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.