Effect of COQ6 D316Y homozygosity on BMDM transcriptome
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 × WT unstim vs 3 × WT 24hr LPS vs 3 × DY unstim vs 3 × DY 24hr LPSGroups 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 GSE226704_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 PRJNA941256 and SRA study SRP425836. 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.
- GSM7082361 WT unstim rep 1 WT unstim
- GSM7082362 WT unstim rep 2 WT unstim
- GSM7082363 WT unstim rep 3 WT unstim
- GSM7082364 WT 24hr LPS rep 1 WT 24hr LPS
- GSM7082365 WT 24hr LPS rep 2 WT 24hr LPS
- GSM7082366 WT 24hr LPS rep 3 WT 24hr LPS
- GSM7082367 DY unstim rep 1 DY unstim
- GSM7082368 DY unstim rep 2 DY unstim
- GSM7082369 DY unstim rep 3 DY unstim
- GSM7082370 DY 24hr LPS rep 1 DY 24hr LPS
- GSM7082371 DY 24hr LPS rep 2 DY 24hr LPS
- GSM7082372 DY 24hr LPS rep 3 DY 24hr LPS
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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.