Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases [RNA-seq]
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 3 × U2OS, untreated control, vs 3 × U2OS, treated with doxorubicin, vs 3 × Raji, untreated, vs 3 × Raji, treated with doxorubicin,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.
- Paper
- Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseasesHuman molecular genetics · 2024
Read the full summary ↓
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 GSE235999_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 PRJNA988153 and SRA study SRP446179. 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.
- GSM7516606 U2OS, untreated control, rep1 U2OS, untreated control,
- GSM7516607 U2OS, untreated control, rep2 U2OS, untreated control,
- GSM7516608 U2OS, untreated control, rep3 U2OS, untreated control,
- GSM7516609 U2OS, treated with doxorubicin, rep1 U2OS, treated with doxo…
- GSM7516610 U2OS, treated with doxorubicin, rep2 U2OS, treated with doxo…
- GSM7516611 U2OS, treated with doxorubicin, rep3 U2OS, treated with doxo…
- GSM7516612 Raji, untreated, rep1 Raji, untreated,
- GSM7516613 Raji, untreated, rep2 Raji, untreated,
- GSM7516614 Raji, untreated, rep3 Raji, untreated,
- GSM7516615 Raji, treated with doxorubicin, rep1 Raji, treated with doxo…
- GSM7516616 Raji, treated with doxorubicin, rep2 Raji, treated with doxo…
- GSM7516617 Raji, treated with doxorubicin, rep3 Raji, treated with doxo…
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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.