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Analysis of time-resolved immunological phases in the NIF mouse model for liver fibrosis.

GSE255261 Mus musculus (mouse) RNA-seq (gene expression) 31 samples Submitted 2024/03/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 31 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
31 samples: 12 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.
Summary (written by the submitters)
A time-course, bulk RNA-sequencing analysis of liver and kidney tissue from NIF mice was performed to identify the dynamics of key processes contributing to the pathogenesis. Transcriptomics profiling of the NIF mouse revealed a gradual transition from an initially reactive inflammatory response to a regenerative, pro-fibrotic inflammatory response suggesting new avenues for treatment strategies that focus on immunological targets.
Read the full summary ↓
Despite the lack of metabolic stress induced liver phenotype, a large similarity between the NIF mouse and the immunological phase of human MASH was detected. The translational value was further confirmed through comparative analyses with MASH patients and additional animal models.
This dataset
Open GSE255261 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE255261_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1074293 and SRA study SRP488684. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
NIF female, 3 weeks old, total liver RNA, sam… ×3 24abNOD female, 3 weeks old, total liver RNA,… ×3 NIF female, 6 weeks old, total liver RNA, sam… ×3 24abNOD female, 6 weeks old, total liver RNA,… ×3 NIF female, 4 weeks old, total kidney RNA, sa… ×3 24abNOD female, 18 weeks old, total kidney RN… ×3 NIF female, 18 weeks old, total liver RNA, sa… ×2 24abNOD female, 18 weeks old, total liver RNA… ×2 +5 more

Supports a between-group comparison across 30 samples.

How we read this: 12 replicated groups read from 31 sample titles; they account for 30 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.

Samples in this study
Datasets on a similar topic

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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.