RNA-sequencing data from mouse kidneys to identify candidate players in kidneys responding to VNS and/or macrophage-specific deletion of Notch2.
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 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.
Read the full summary ↓
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 GSE284008_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 PRJNA1196830 and SRA study SRP550946. 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 18 sample titles: 18 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.
- GSM8675864 1N2WTShamSaline
- GSM8675865 2N2WTShamSaline
- GSM8675866 3N2WTShamSaline
- GSM8675867 4N2WTVNSSaline
- GSM8675868 5N2WTVNSSaline
- GSM8675869 6N2WTVNSSaline
- GSM8675870 7N2WTShamLPS
- GSM8675871 8N2WTShamLPS
- GSM8675872 9N2WTShamLPS
- GSM8675873 10N2KOShamLPS
- GSM8675874 11N2KOShamLPS
- GSM8675875 12N2KOShamLPS
- GSM8675876 13N2WTVNSLPS
- GSM8675877 14N2WTVNSLPS
- GSM8675878 15N2WTVNSLPS
- GSM8675879 16N2KOVNSLPS
- GSM8675880 17N2KOVNSLPS
- GSM8675881 18N2KOVNSLPS
- GSE272652 Bulk RNA-sequencing of kidneys from male C57BL/6 mice subacutely exposed to TCDD. 40 samples shares rna-sequencing, kidneys
- GSE94685 RNA-sequencing of lung ECs isolated at P5 from mice with EC-specific deletion of LATS1/2 and LATS1/2;YAP/TAZ 12 samples shares rna-sequencing, deletion
- GSE94673 RNA-sequencing of brain ECs isolated at P8 from mice with EC-specific deletion of YAP/TAZ 8 samples shares rna-sequencing, deletion
- GSE274992 Splenic fibroblasts control marginal zone B-cell movement and function via two distinct Notch2-dependent regulatory programs 119 samples shares notch2
- GSE335245 Forced Notch2 signaling instructs TLR and BCR responsiveness in B cells [RNA-Seq] 45 samples shares notch2
- GSE274990 Marginal zone B cells receive robust Notch2 signals within the B cell follicle in the absense of S1pr1 signaling. 42 samples shares notch2
- GSE297361 Loss of NOTCH2 Creates a TRIM28-Dependent Vulnerability in Small Cell Lung Cancer [bulk_murine_RNA_seq] 36 samples shares notch2
- GSE248790 BCR and TLR-induced IRF1 promotes T cell independent B cell responses by supporting Notch2 dependent Marginal Zone B cell development 24 samples shares notch2
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.