Transcriptomic profiles of intestinal stem cells cultured in natural and synthetic three-dimensional matrices
RNA-seq (gene expression) · mouse · 9 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
- 9 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.
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 GSE85391_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 PRJNA338315 and SRA study SRP081167. 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.
+ 9 more — browse all 9 samples with per-sample file links →
- GSE294512 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [RNA-seq] 92 samples shares intestinal, stem
- GSE275418 Weaning-Driven Gut Microbiome Shapes Intestinal Stem Cell Epigenetics to Train Immunological Memory (RNA-seq) 18 samples shares intestinal, stem
- GSE278384 Colonic Epithelial-derived FGF1 Protects against Inflammatory Bowel Disease via Driving Intestinal Stem Cells Differentiation toward Goblet Cells 12 samples shares intestinal, stem
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares intestinal, stem
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares intestinal, stem
- GSE318068 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [Multiome] 16 samples shares intestinal, stem
- GSE288156 Progressive intestinal tumor cell plasticity, Myc activation and loss of Lgr5+ tumor stem cell lineage commitment upon Wnt depletion 14 samples shares intestinal, stem
- GSE230307 NAC regulates metabolism and cell fate in intestinal stem cells 12 samples shares intestinal, stem
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.