Genetic and Environmental interactions contribute to immune variation in rewilded mice
Single-cell RNA-seq · mouse · 14 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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 GSE236347_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA990675 and SRA study SRP447098. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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.
- GSM7528301 primary cells, lymph nodes [Rewild1_GEX]
- GSM7528302 primary cells, lymph nodes [Rewild2_GEX]
- GSM7528303 primary cells, lymph nodes [Rewild3_GEX]
- GSM7528304 primary cells, lymph nodes [Rewild4_GEX]
- GSM7528305 primary cells, lymph nodes [Rewild5_GEX]
- GSM7528306 primary cells, lymph nodes [Rewild6_GEX]
- GSM7528307 primary cells, lymph nodes [Rewild7_GEX]
- GSM7528308 primary cells, lymph nodes [Rewild8_GEX]
- GSM7528309 primary cells, lymph nodes [Rewild9_GEX]
- GSM7528310 primary cells, lymph nodes [Rewild10_GEX]
- GSM7528311 primary cells, lymph nodes [Rewild11_GEX]
- GSM7528312 primary cells, lymph nodes [Rewild12_GEX]
- GSM7528313 primary cells, lymph nodes [Rewild13_GEX]
- GSM7528314 primary cells, lymph nodes [Rewild14_GEX]
- GSE285231 Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells 186 samples shares variation, genetic
- GSE272206 Natural genetic variation in wild-derived mice controls host survival and transcriptional responses during endotoxic shock 24 samples shares variation, genetic
- GSE267262 Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells. 12 samples shares variation, genetic
- GSE236826 Rapid CRISPR/Cas12a-based dual-crRNA library screening in high fidelity reveals novel genetic interactions during hepatocarcinogenesis [RNA-Seq] 12 samples shares interactions, genetic
- GSE281685 Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [ChIP-seq] 16 samples shares variation, genetic
- GSE274969 Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygeninduced lung injury 77 samples shares variation, genetic
- GSE294258 Intracellular iron homeostasis-regulated epigenetic reprogramming contributes to -7/del(7q) leukemia 71 samples shares contribute, genetic
- GSE312918 Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts 69 samples shares variation, genetic
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.