Effect of RXRα agonist bexarotene on gene expression in hepatocytes of hepatic RXRα knockout mice
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × Flox_Con vs 3 × Flox_Bex vs 3 × LKO_Con vs 3 × LKO_BexGroups 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 GSE317638_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 PRJNA1414579 and SRA study SRP666551. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9475703 Flox_Con_rep1 Flox_Con
- GSM9475704 Flox_Con_rep2 Flox_Con
- GSM9475705 Flox_Con_rep3 Flox_Con
- GSM9475706 Flox_Bex_rep1 Flox_Bex
- GSM9475707 Flox_Bex_rep2 Flox_Bex
- GSM9475708 Flox_Bex_rep3 Flox_Bex
- GSM9475709 LKO_Con_rep1 LKO_Con
- GSM9475710 LKO_Con_rep2 LKO_Con
- GSM9475711 LKO_Con_rep3 LKO_Con
- GSM9475712 LKO_Bex_rep1 LKO_Bex
- GSM9475713 LKO_Bex_rep2 LKO_Bex
- GSM9475714 LKO_Bex_rep3 LKO_Bex
- GSE319754 RXRα Suppression Drives Hepatic Metabolic and Immune Dysfunction in Sepsis: Gene induction by BEX in Sham & CLP (8h) 12 samples shares rxr, hepatic
- GSE319852 RXRα Suppression Drives Hepatic Metabolic and Immune Dysfunction in Sepsis: RXRα KO in CLP/SHAM 12 samples shares rxr, hepatic
- GSE330380 The effects of adiponectin knockout on hepatic gene expression in male and female C57BL/6NCrl mice fed ad libitum or undergoing caloric restriction 22 samples shares knockout, hepatic
- GSE243160 Transcriptomic differences in RXRαβ-deficient and WT alveolar macrophages using the CD11c-Cre+ mouse model (RNA-Seq) 11 samples shares rxr
- GSE309637 Effects of TCDD on gene expression in hepatocytes isolated from WT and PkmΔDRE mice. 144 samples shares hepatocytes
- GSE255762 ChIP-seq for PPARg, RXRa, and H3K27Ac in inflammation-associated unsaturated fatty acid-supplemented Th2 cells 25 samples shares rxr
- GSE284373 The effect of STING knockout on gene expression in cholestatic mice 20 samples shares knockout
- GSE290328 A Study of Allostery Within Liganded RARα:RXR Heterodimers at the Genome Scale [CUT&Run] 14 samples shares rxr
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.