RNA-seq of endothelial cells in wild-type and Shb iECKO mice
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 8 conditions, mostly in triplicateGroups 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 GSE293931_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 PRJNA1247456 and SRA study SRP577063. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 8 replicated groups read from 21 sample titles; they account for 21 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.
- GSM8894717 Experiment1_KO1 Experiment1_KO
- GSM8894718 Experiment1_KO2 Experiment1_KO
- GSM8894719 Experiment1_WT1 Experiment1_WT
- GSM8894720 Experiment1_WT2 Experiment1_WT
- GSM8894721 Experiment1_WT3 Experiment1_WT
- GSM8894722 Experiment2_KO1 Experiment2_KO
- GSM8894723 Experiment2_KO2 Experiment2_KO
- GSM8894724 Experiment2_KO3 Experiment2_KO
- GSM8894725 Experiment2_WT1 Experiment2_WT
- GSM8894726 Experiment2_WT2 Experiment2_WT
- GSM8894727 Experiment2_WT3 Experiment2_WT
- GSM8894728 Experiment3_KO1 Experiment3_KO
- GSM8894729 Experiment3_KO2 Experiment3_KO
- GSM8894730 Experiment3_WT1 Experiment3_WT
- GSM8894731 Experiment3_WT2 Experiment3_WT
- GSM8894732 Experiment4_KO1 Experiment4_KO
- GSM8894733 Experiment4_KO2 Experiment4_KO
- GSM8894734 Experiment4_KO3 Experiment4_KO
- GSM8894735 Experiment4_WT1 Experiment4_WT
- GSM8894736 Experiment4_WT2 Experiment4_WT
- GSM8894737 Experiment4_WT3 Experiment4_WT
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares endothelial, rna-seq
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares wild-type, rna-seq
- GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares endothelial
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares rna-seq
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq
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.