scramble control and Hif-1a knockdown mESCs cultured under normoxia and two-day hypoxia
RNA-seq (gene expression) · mouse · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples
- 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
- The stage-specific roles of HIF-1α in regulating mESC pluripotency during oxygen transitionThe Journal of biological chemistry · 2025
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 GSE268827_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1118804 and SRA study SRP511099. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 12 more — browse all 12 samples with per-sample file links →
- GSE200739 mesendoderm differentiation with Hif-1a knockdown 12 samples shares hif-1a, knockdown
- GSE299422 Transcriptomic profiling of co-cultured cancer-host cells identifies hypoxia as a driver of the skeletal muscle cell’s antiproliferative effect on cancer cells 28 samples shares cultured, hypoxia
- GSE243700 Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain Type-2 immunity [RNA-seq: cultured cells] 14 samples shares cultured, control
- GSE272936 Transcriptomes of UFMylation gene knockdown in mouse embryonic fibroblast cell (MEF) treated with hypoxia for 24 hours [mouse] 6 samples shares knockdown, hypoxia
- GSE230527 Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq] 18 samples shares cultured, hypoxia
- GSE228365 Effect of depletion of HIF-1a on gene expression during B cell IgA class switching [RNA-seq] 6 samples shares hif-1a
- GSE228366 Chromatin remodeling in HIF-1a deficient B cell during IgA class switching [ChIP-seq] 12 samples shares hif-1a
- GSE311286 Analysis of murine normal pancreatic organoids, pancreatitis-derived organoids, and PDAC organoids in complete media and of pancreatitis-derived organoids, and PDAC organoids cultured alone or cocultured with pancreatic stellate cells in reduced media 75 samples shares cultured
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.