RNA-seq of chondrogenesis following siRNA depletion of SERPINA3
RNA-seq (gene expression) · human · 18 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
- Homo sapiens (human)
- Samples
- 18 samples: 6 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.
- Paper
- SERPINA3 is a marker of cartilage differentiation and is essential for the expression of extracellular matrix genes during early chondrogenesisMatrix biology : journal of the International Society for Matrix Biology · 2024
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 GSE247491_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 PRJNA1038778 and SRA study SRP471260. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM7890688 Day0_Control_1 Day0_Control
- GSM7890689 Day3_Control_1 Day3_Control
- GSM7890690 Day7_Control_1 Day7_Control
- GSM7890691 Day0_KD_2 Day0_KD
- GSM7890692 Day3_KD_2 Day3_KD
- GSM7890693 Day7_KD_2 Day7_KD
- GSM7890694 Day0_KD_1 Day0_KD
- GSM7890695 Day3_KD_1 Day3_KD
- GSM7890696 Day7_KD_1 Day7_KD
- GSM7890697 Day0_Control_3 Day0_Control
- GSM7890698 Day3_Control_3 Day3_Control
- GSM7890699 Day7_Control_3 Day7_Control
- GSM7890700 Day0_Control_2 Day0_Control
- GSM7890701 Day3_Control_2 Day3_Control
- GSM7890702 Day7_Control_2 Day7_Control
- GSM7890703 Day0_KD_3 Day0_KD
- GSM7890704 Day3_KD_3 Day3_KD
- GSM7890705 Day7_KD_3 Day7_KD
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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.