Comparison of NK cell transcriptomes between C57BL6 and NOD mouse strains
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 4 × C57BL6-Spleen-NK vs 4 × NOD-Spleen-NKGroups 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 GSE342137_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 PRJNA1505654 and SRA study SRP723220. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 2 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9923728 C57BL6-Spleen-NK-2 C57BL6-Spleen-NK
- GSM9923729 C57BL6-Spleen-NK-3 C57BL6-Spleen-NK
- GSM9923730 C57BL6-Spleen-NK-4 C57BL6-Spleen-NK
- GSM9923731 C57BL6-Spleen-NK-6 C57BL6-Spleen-NK
- GSM9923732 NOD-Spleen-NK-2 NOD-Spleen-NK
- GSM9923733 NOD-Spleen-NK-3 NOD-Spleen-NK
- GSM9923734 NOD-Spleen-NK-4 NOD-Spleen-NK
- GSM9923735 NOD-Spleen-NK-5 NOD-Spleen-NK
- GSE275350 Effect of anti-CD3 antibody treatment on islet transcriptomes in the nonobese diabetic (NOD) mouse model 12 samples shares nod, transcriptomes
- GSE155577 Gene expression data from epithelial and mesenchymal tumor cells isolated from E-A14 mouse mammary tumors grown in immunodeficient and immunocompetent mice 26 samples shares nod
- GSE297835 Single Cell RNA Sequencing of C57BL6 mouse whole aortas after 8 weeks of L-NAME treatment 22 samples shares c57bl6
- GSE281117 Small intestinal lymph node identity is defined by medullary stromal cells in mice 50 samples shares nod
- GSE282129 Small intestinal lymph node identity is defined by medullary stromal cells in humans and mice [Sorted_lns_macrophages_RNAseq] 45 samples shares nod
- GSE315893 Characterization of Subchronic Lung and Brain Consequences Caused by Mouse-Adapted SARS-CoV-2 and Influenza A Infection of C57BL6 mice 44 samples shares c57bl6
- GSE285165 Wnt and Nodal asymmetries stratify mouse laterality phenotypes in the absence of node flow 42 samples shares nod
- GSE276797 Gene expression profile at single cell level of immune cells from the deep cervical lymph nodes (dCLNs), superficial cervical lymph nodes (sCLNs), and inguinal lymph nodes (iLNs) of wild-type (WT) and Alzheimer's disease (AD) transgenic animals (5xFAD) 34 samples shares nod
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.