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Transcriptomic Analysis Reveals Co-Regulation by PRMT5 and WDR77 in HSC-5 Cells

GSE272319 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2024/09/19 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 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
PRMT5/WDR77 Enhances the Proliferation of Squamous Cell Carcinoma via the ΔNp63α-p21 AxisCancers · 2024
Summary (written by the submitters)
CRISPR was utilized to deplete either PRMT5 or WDR77 in HSC-5 cells. Subsequently, RNA-seq was performed to identify changes in the transcriptome following the loss of PRMT5 or WDR77 in these cells. Critically, Gene Set Enrichment Analysis (GSEA) was conducted to screen and identify a list of genes co-regulated by PRMT5 and WDR77.
Published in
PRMT5/WDR77 Enhances the Proliferation of Squamous Cell Carcinoma via the ΔNp63α-p21 Axis
Liang H, Fisher ML, Wu C et al. · Cancers 2024 · PMID 39594744 · doi:10.3390/cancers16223789
This dataset
Open GSE272319 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 GSE272319_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 PRJNA1136436 and SRA study SRP520129. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39594744) ↗
Study design
5 conditions, mostly in triplicate
HSC5 cells, sgNeg, biol ×3 HSC5 cells, sgPRMT5#1, biol ×3 HSC5 cells, sgPRMT5#2, biol ×3 HSC5 cells, sgWDR77#1, biol ×3 HSC5 cells, sgWDR77#2, biol ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.

Samples in this study
Datasets on a similar topic

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