Transcriptional profiling of AGPS knockout breast cancer cells treated with TGF-B
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 2 × WT parental, untreated, vs 2 × WT parental, TGFB treated, vs 2 × AGPS KO, untreated, vs 2 × AGPS KO, TGFB treated,Groups 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 GSE300281_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 PRJNA1280027 and SRA study SRP593346. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9057373 WT parental, untreated, rep1 WT parental, untreated,
- GSM9057374 WT parental, untreated, rep2 WT parental, untreated,
- GSM9057375 WT parental, TGFB treated, rep1 WT parental, TGFB treat…
- GSM9057376 WT parental, TGFB treated, rep2 WT parental, TGFB treat…
- GSM9057377 AGPS KO, untreated, rep1 AGPS KO, untreated,
- GSM9057378 AGPS KO, untreated, rep2 AGPS KO, untreated,
- GSM9057379 AGPS KO, TGFB treated, rep1 AGPS KO, TGFB treated,
- GSM9057380 AGPS KO, TGFB treated, rep2 AGPS KO, TGFB treated,
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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.