VSMC phenotypic transition
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 6 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.
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 GSE229130_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 PRJNA953005 and SRA study SRP431362. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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.
- GSM7152979 primary mouse VSMCs,shNT,rep1 primary mouse VSMCs,shN…
- GSM7152980 primary mouse VSMCs,shNT,rep2 primary mouse VSMCs,shN…
- GSM7152981 primary mouse VSMCs,shNT,rep3 primary mouse VSMCs,shN…
- GSM7152982 primary mouse VSMCs,shH3.3,rep1 primary mouse VSMCs,shH…
- GSM7152983 primary mouse VSMCs,shH3.3,rep2 primary mouse VSMCs,shH…
- GSM7152984 primary mouse VSMCs,shH3.3,rep3 primary mouse VSMCs,shH…
- GSM7152987 shNT_H3.3_1 shNT_H3.3
- GSM7152988 shNT_H3.3_2 shNT_H3.3
- GSM7152989 shH3f3b_H3.3_1 shH3f3b_H3.3
- GSM7152990 shH3f3b_H3.3_2 shH3f3b_H3.3
- GSM7152991 shNT_input_1 shNT_input
- GSM7152992 shNT_input_2 shNT_input
- GSM7152993 shH3f3b_input_1 shH3f3b_input
- GSM7152994 shH3f3b_input_2 shH3f3b_input
- GSE329653 Flow induced-endothelial phenotypic transition contributes to Intracranial Aneurysm 9 samples shares phenotypic, transition
- GSE294868 Loss of EGFR prevents the synergistic early-phase impact of obesity-associated metabolic and humoral stress on primary VSMC – stressor synergy, sex-dependence 69 samples shares vsmc
- GSE294678 Dietary restriction mitigates vascular aging, modulates the cGAS-STING pathway and reverses macrophage-like VSMC phenotypes in progeroid DNA-repair-deficient Ercc1Δ/- mice 29 samples shares vsmc
- GSE276417 Data Mining of IFNgamma-induced macrophage and Atherosclerotic Plaque Transcriptomes predicts a macrophage-specific role of STAT1 in human atherosclerosis [VSMC] 18 samples shares vsmc
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares phenotypic
- GSE233057 A gene regulatory network of the endothelial-to-hematopoietic transition 63 samples shares transition
- GSE253147 Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition 33 samples shares transition
- GSE333887 Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [transplantations_OneCell_multiome] 14 samples shares transition
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.