Genome-wide RNAseq of liver tissue derived from DEN-CDA-HFD mice treated with CLDN1 mAb or vehicle Control
RNA-seq (gene expression) · mouse · 17 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
- 17 samples: 6 × Vehicle Control_m vs 6 × CLDN1 mAb_m vs 5 × Regular diet_mGroups 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 GSE174542_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 PRJNA730506 and SRA study SRP320104. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 3 replicated groups read from 17 sample titles; they account for 17 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.
- GSM5319158 Regular diet_m1 Regular diet_m
- GSM5319159 Regular diet_m2 Regular diet_m
- GSM5319160 Regular diet_m3 Regular diet_m
- GSM5319161 Regular diet_m4 Regular diet_m
- GSM5319162 Regular diet_m5 Regular diet_m
- GSM5319163 Vehicle Control_m1 Vehicle Control_m
- GSM5319164 Vehicle Control_m2 Vehicle Control_m
- GSM5319165 Vehicle Control_m3 Vehicle Control_m
- GSM5319166 Vehicle Control_m4 Vehicle Control_m
- GSM5319167 Vehicle Control_m5 Vehicle Control_m
- GSM5319168 Vehicle Control_m6 Vehicle Control_m
- GSM5319169 CLDN1 mAb_m1 CLDN1 mAb_m
- GSM5319170 CLDN1 mAb_m2 CLDN1 mAb_m
- GSM5319171 CLDN1 mAb_m3 CLDN1 mAb_m
- GSM5319172 CLDN1 mAb_m4 CLDN1 mAb_m
- GSM5319173 CLDN1 mAb_m5 CLDN1 mAb_m
- GSM5319174 CLDN1 mAb_m6 CLDN1 mAb_m
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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.