“Bench-to-Bedside and Back” analysis of NAFLD model reveals common transcriptomic shifts between mouse and human during disease progression
RNA-seq (gene expression) · mouse · 152 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
- 152 samples: 14 conditions, mostly with about 8 replicates eachGroups 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 GSE159911_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 PRJNA670860 and SRA study SRP288278. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 152 samples.
How we read this: 14 replicated groups read from 152 sample titles; they account for 152 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.
- GSM4850133 Week 1 control 1 Week 1 control
- GSM4850134 Week 1 control 2 Week 1 control
- GSM4850135 Week 1 control 3 Week 1 control
- GSM4850136 Week 1 control 4 Week 1 control
- GSM4850137 Week 1 control 5 Week 1 control
- GSM4850138 Week 1 control 6 Week 1 control
- GSM4850139 Week 1 control 7 Week 1 control
- GSM4850140 Week 1 control 8 Week 1 control
- GSM4850141 Week 1 LIDPAD 1 Week 1 LIDPAD
- GSM4850142 Week 1 LIDPAD 2 Week 1 LIDPAD
- GSM4850143 Week 1 LIDPAD 3 Week 1 LIDPAD
- GSM4850144 Week 1 LIDPAD 4 Week 1 LIDPAD
- GSM4850145 Week 1 LIDPAD 5 Week 1 LIDPAD
- GSM4850146 Week 1 LIDPAD 6 Week 1 LIDPAD
- GSM4850147 Week 1 LIDPAD 7 Week 1 LIDPAD
- GSM4850148 Week 1 LIDPAD 8 Week 1 LIDPAD
- GSM4850149 Week 4 control 1 Week 4 control
- GSM4850150 Week 4 control 2 Week 4 control
- GSM4850151 Week 4 control 3 Week 4 control
- GSM4850152 Week 4 control 4 Week 4 control
- GSM4850153 Week 4 control 5 Week 4 control
- GSM4850154 Week 4 control 6 Week 4 control
- GSM4850155 Week 4 control 7 Week 4 control
- GSM4850156 Week 4 control 8 Week 4 control
- GSM4850157 Week 4 LIDPAD 1 Week 4 LIDPAD
- GSM4850158 Week 4 LIDPAD 2 Week 4 LIDPAD
- GSM4850159 Week 4 LIDPAD 3 Week 4 LIDPAD
- GSM4850160 Week 4 LIDPAD 4 Week 4 LIDPAD
- GSM4850161 Week 4 LIDPAD 5 Week 4 LIDPAD
- GSM4850162 Week 4 LIDPAD 6 Week 4 LIDPAD
- GSM4850163 Week 4 LIDPAD 7 Week 4 LIDPAD
- GSM4850164 Week 4 LIDPAD 8 Week 4 LIDPAD
- GSM4850165 Week 8 control 1 Week 8 control
- GSM4850166 Week 8 control 2 Week 8 control
- GSM4850167 Week 8 control 3 Week 8 control
- GSM4850168 Week 8 control 4 Week 8 control
- GSM4850169 Week 8 control 5 Week 8 control
- GSM4850170 Week 8 control 6 Week 8 control
- GSM4850171 Week 8 control 7 Week 8 control
- GSM4850172 Week 8 control 8 Week 8 control
+ 112 more — browse all 152 samples with per-sample file links →
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares nafld
- GSE305214 Transcriptomic profiling of liver tissue from control, DHT-induced PCOS-NAFLD model, and baicalin-treated mice using RNA-seq 12 samples shares nafld
- GSE245519 Inter-individual variations in circadian misalignment-induced NAFLD pathophysiology in mice 41 samples shares nafld
- GSE247323 Maternal indole supplementation protects offspring from NAFLD through altered microbiota- and AHR-mediated ceramide metabolism 40 samples shares nafld
- GSE252928 Berberine directly targets AKR1B10 protein to modulate lipid and glucose metabolism disorders in NAFLD 16 samples shares nafld
- GSE225560 Divergent roles for caspase-8 and MLKL in high-fat diet induced obesity and NAFLD in mice 12 samples shares nafld
- GSE275176 Transcriptomic alterations associated with the progression of metabolic dysfunction-associated steatotic liver disease in CC042 Collaborative Cross mice. 60 samples shares progression
- GSE299709 Longitudinal monitoring of Type 1 Diabetes progression to disease onset 120 samples shares progression
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.