Transcriptional profiling of intestinal tissue from mice with Apc and additional mutations.
RNA-seq (gene expression) · mouse · 47 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
- 47 samples: 21 conditions, mostly with about 4 replicates eachGroups 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 GSE272639_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 PRJNA1137873 and SRA study SRP520992. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 13 samples read as cases, 14 as controls.
How we read this: 21 replicated groups read from 98 sample titles; they account for 98 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.
- GSM8408141 SI Apc Rep1 SI Apc
- GSM8408142 SI Apc Rep2 SI Apc
- GSM8408143 SI Apc Rep3 SI Apc
- GSM8408144 SI Apc Kras/+ Rep1 SI Apc Kras/+
- GSM8408145 SI Apc Kras/+ Rep2 SI Apc Kras/+
- GSM8408146 SI Apc Kras/+ Rep3 SI Apc Kras/+
- GSM8408147 SI Apc Kras/+ Rep4 SI Apc Kras/+
- GSM8408148 SI Apc Kras/+ Pik3ca/+ Rep1 SI Apc Kras/+ Pik3ca/+
- GSM8408149 SI Apc Kras/+ Pik3ca/+ Rep2 SI Apc Kras/+ Pik3ca/+
- GSM8408150 SI Apc Kras/+ Pik3ca/+ Rep3 SI Apc Kras/+ Pik3ca/+
- GSM8408151 SI Apc Kras/+ Pik3ca/+ Rep4 SI Apc Kras/+ Pik3ca/+
- GSM8408152 SI Apc Kras/+ Pten Rep1 SI Apc Kras/+ Pten
- GSM8408153 SI Apc Kras/+ Pten Rep2 SI Apc Kras/+ Pten
- GSM8408154 SI Apc Kras/+ Pten Rep3 SI Apc Kras/+ Pten
- GSM8408155 SI Apc Kras/+ Pten Rep4 SI Apc Kras/+ Pten
- GSM8408156 SI Apc Pik3ca/+ Rep1 SI Apc Pik3ca/+
- GSM8408157 SI Apc Pik3ca/+ Rep2 SI Apc Pik3ca/+
- GSM8408158 SI Apc Pik3ca/+ Rep3 SI Apc Pik3ca/+
- GSM8408159 SI Apc Pik3ca/+ Rep4 SI Apc Pik3ca/+
- GSM8408160 SI Apc Pten Rep1 SI Apc Pten
- GSM8408161 SI Apc Pten Rep2 SI Apc Pten
- GSM8408162 SI Apc Pten Rep3 SI Apc Pten
- GSM8408163 SI Apc Pten Rep4 SI Apc Pten
- GSM8408164 SI Apc Pik3ca Rep1 SI Apc Pik3ca
- GSM8408165 SI Apc Pik3ca Rep2 SI Apc Pik3ca
- GSM8408166 SI Apc Pik3ca Rep3 SI Apc Pik3ca
- GSM8408167 SI Apc Pik3ca Rep4 SI Apc Pik3ca
- GSM8408168 SI Apc Pik3ca Rep5 SI Apc Pik3ca
- GSM8408169 SI Apc Pik3ca Rep6 SI Apc Pik3ca
- GSM8408170 SI Apc Kras/+ Pik3ca Rep1 SI Apc Kras/+ Pik3ca
- GSM8408171 SI Apc Kras/+ Pik3ca Rep2 SI Apc Kras/+ Pik3ca
- GSM8408172 SI Apc Kras/+ Pik3ca Rep3 SI Apc Kras/+ Pik3ca
- GSM8408173 SI Apc Kras/+ Pik3ca Rep4 SI Apc Kras/+ Pik3ca
- GSM8408174 SI Apc Kras/+ Pik3ca Rep5 SI Apc Kras/+ Pik3ca
- GSM8408175 SI Apc Kras/+ Pik3ca Rep6 SI Apc Kras/+ Pik3ca
- GSM8408176 SI Apc Pik3ca Slc7a5 Rep1 SI Apc Pik3ca Slc7a5
- GSM8408177 SI Apc Pik3ca Slc7a5 Rep2 SI Apc Pik3ca Slc7a5
- GSM8408178 SI Apc Pik3ca Slc7a5 Rep3 SI Apc Pik3ca Slc7a5
- GSM8408179 SI Apc Pik3ca Slc7a5 Rep4 SI Apc Pik3ca Slc7a5
- GSM8408180 SI Apc Pik3ca Slc7a5 Rep5 SI Apc Pik3ca Slc7a5
+ 7 more — browse all 47 samples with per-sample file links →
- GSE333820 Transcriptome profiling of ovaries in aged mice administered additional Samul-tang-associated compounds 96 samples shares additional
- GSE188361 RNA sequencing data of intestinal tissue from wild-type C57BL/6 mice and ITGB6-overexpressing transgenic mice 10 samples shares intestinal
- GSE279074 Comparative characterization of AHC associated mutations in ATP1A3 reveals diverse neurological alterations in mice. 48 samples shares mutations
- GSE282129 Small intestinal lymph node identity is defined by medullary stromal cells in humans and mice [Sorted_lns_macrophages_RNAseq] 45 samples shares intestinal
- GSE328885 Liver transcriptomic response to partial hepatectomy in intestinal-specific SIRT1 knockout mice 34 samples shares intestinal
- GSE244320 RNA-sequencing analysis of colon RNA from mice with compound mutations of XBP1, caspase-8, TNFR1 and MLKL. 30 samples shares mutations
- GSE276312 Two mutations associated with leukemia that change a single tyrosine residue in the STAT5B SH2 domain have opposite effects on the transcriptional programs controlling hematopoiesis [scRNA-seq] 23 samples shares mutations
- GSE247149 Type III interferons induce pyroptosis in gut epithelial cells and delay tissue restitution upon acute intestinal injury. 16 samples shares intestinal
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.