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Effect of treatment with 5uM of the type I PRMT inhibitor MS023 dissolved in DMSO for 3 days and of a stably transduced PRMT1 specific dox-inducible knockdown over 4 days in ccRCC cell line models RCC243 and 786-0

GSE229357 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2024/08/16 Platform GPL24676Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples
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
PRMT1 inhibition perturbs RNA metabolism and induces DNA damage in clear cell renal cell carcinomaNature communications · 2024
Summary (written by the submitters)
To investigate the effect of pharmacological inhibition of the type I PRMTs in ccRCC cell lines. We treated one patient derived cell line (RCC243) and one commercially available line (786-0) in duplicate with 5uM MS023 for 3 days vs. 0.1% DMSO alone. We then performed gene expression profiling analysis using data obtained from RNA-seq.
Read the full summary ↓
Each cell line was treated as a biological replicate. Similarly, to investigate the genetic knockdown of PRMT1 using the same cell lines, stably transduced dox-inducible PRMT1 targeting shRNA's. Cell lines were treated with or with out 1ug/mL dox for 4 days in triplicate. Gene expression profiling analysis was then performed using data obtained from RNA-seq.
Published in
PRMT1 inhibition perturbs RNA metabolism and induces DNA damage in clear cell renal cell carcinoma
Walton J, Ng ASN, Arevalo K et al. · Nature communications 2024 · PMID 39300069 · doi:10.1038/s41467-024-52507-y
This dataset
Open GSE229357 in finder → Find more human 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 GSE229357_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 PRJNA954060 and SRA study SRP431867. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39300069) ↗
Samples in this study

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