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Col2a1-Cre;Idh1LSL/+ embryonic growth plate chondrocytes

GSE201606 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/06/28 Platform GPL19057Platform GPL24247
At a glance

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 × Growth plate cartilage, control vs 3 × Growth plate cartilage, Idh1 mutant vs 2 × Growth plate chondrocytes, control con116, vs 2 × Growth plate chondrocytes, Idh1 mutant 119Groups 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.
Paper
Single-cell transcriptomic analyses of mouse idh1 mutant growth plate chondrocytes reveal distinct cell populations responsible for longitudinal growth and enchondroma formationResearch square · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Single-cell transcriptomic analyses of mouse idh1 mutant growth plate chondrocytes reveal distinct cell populations responsible for longitudinal growth and enchondroma formation
Puviindran V, Shimada E, Huang Z et al. · Research square 2024 · PMID 38883785 · doi:10.21203/rs.3.rs-4451086/v1
This dataset
Open GSE201606 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 GSE201606_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 PRJNA832294 and SRA study SRP372360. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38883785) ↗
Study design
3 × Growth plate cartilage, control vs 3 × Growth plate cartilage, Idh1 mutant vs 2 × Growth plate chondrocytes, control con116, vs 2 × Growth plate chondrocytes, Idh1 mutant 119

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 4 replicated groups read from 12 sample titles; they account for 10 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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