RNA-seq analysis of the transcriptomic profiles of ATO+DAC-treated THP-1 cell lines expressing p53-R282W, vector control, or p53-R282W with IRF7 knockdown
RNA-seq (gene expression) · human · 11 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
- 11 samples: 11 samples, each with a distinct title — no replicated groupsGroups 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 GSE269126_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 PRJNA1120356 and SRA study SRP511933. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 4 as controls.
How we read this: Read from 11 sample titles: 11 distinct titles with little repetition. 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.
- GSM8306712 p53 R282W THP-1 cells treated with DMSO for 24 h
- GSM8306713 p53 R282W THP-1 cells treated with 5 μM DAC for 24 h
- GSM8306714 p53 R282W THP-1 cells treated with 1 μg/ml ATO for 24 h
- GSM8306715 p53 R282W THP-1 cells treated with ATO (1 μg/ml )+DAC (5 μM) for 24 h
- GSM8306716 p53 wild-type THP-1 cells
- GSM9159942 p53-R282W + IRF7 KD (#1), DMSO, 24 h
- GSM9159943 p53-R282W + IRF7 KD (#1), ATO (1 μg/ml )+DAC (5 μM), 24 h
- GSM9159944 p53-R282W + IRF7 KD (#2), DMSO, 24 h
- GSM9159945 p53-R282W + IRF7 KD (#2), ATO (1 μg/ml )+DAC (5 μM), 24 h
- GSM9159946 vec, DMSO, 24 h
- GSM9159947 vec, ATO (1 μg/ml )+DAC (5 μM), 24 h
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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.