RNA-seq profiling transcriptome of liver endothelial cells of conventionally raised (CONV-R) and germ-free (GF) mice.
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 7 × LECs, CONV-R sample vs 6 × LECs, GF sampleGroups 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 GSE295338_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 PRJNA1254225 and SRA study SRP580539. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 2 replicated groups read from 13 sample titles; they account for 13 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.
- GSM8945943 LECs, CONV-R sample1 LECs, CONV-R sample
- GSM8945944 LECs, CONV-R sample2 LECs, CONV-R sample
- GSM8945945 LECs, CONV-R sample3 LECs, CONV-R sample
- GSM8945946 LECs, CONV-R sample4 LECs, CONV-R sample
- GSM8945947 LECs, CONV-R sample5 LECs, CONV-R sample
- GSM8945948 LECs, CONV-R sample6 LECs, CONV-R sample
- GSM8945949 LECs, CONV-R sample7 LECs, CONV-R sample
- GSM8945950 LECs, GF sample 8 LECs, GF sample
- GSM8945951 LECs, GF sample 9 LECs, GF sample
- GSM8945952 LECs, GF sample 10 LECs, GF sample
- GSM8945953 LECs, GF sample 11 LECs, GF sample
- GSM8945954 LECs, GF sample 12 LECs, GF sample
- GSM8945955 LECs, GF sample 13 LECs, GF sample
- GSE31115 Transcriptional profiling of 53 tissue samples from germ-free and conventionally raised mice 53 samples shares conventionally, germ-free, raised
- GSE274544 Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [scRNA-Seq] 1494 samples shares endothelial, rna-seq
- GSE309071 Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [RNA-seq] 221 samples shares endothelial, rna-seq
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares endothelial, rna-seq
- GSE233056 A gene regulatory network of the endothelial-to-hematopoietic transition [RNA-seq] 28 samples shares endothelial, rna-seq
- GSE287115 Emergence of Endothelial Cell Subtypes and Role of Cell Cycle Control in Arterial-Venous Specification During Embryonic Vascular Development [bulk RNA-seq] 27 samples shares endothelial, rna-seq
- GSE327619 Murine Endothelial Chromatin Remodeling Enzymes Modulate Plasmin Activity and Sterile Inflammation to Prevent Lethal Embryonic Liver Deterioration 24 samples shares endothelial, liver
- GSE330229 Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex [RNA-seq] 24 samples shares endothelial, 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.