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Effect of depletion of IMPDH1 and IMPDH2 on gene expression after DNA damage in HeLa cells

GSE265772 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/07/24 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 6 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.
Summary (written by the submitters)
Guanosine nucleotide (GTP) serves as a pivotal purine nucleoside triphosphate, essential for DNA and RNA structure and function. Additionally, it acts as an activator for the guanine-binding protein family (G protein), participating in crucial cellular processes such as cytoskeleton rearrangement, membrane transport, protein synthesis, and signal transduction.
Read the full summary ↓
IMPDH1 and IMPDH2 are key enzymes in the de novo synthesis of guanine nucleotides. Our research shows that they exhibit differential activities under DNA damage conditions. Specifically, IMPDH1 predominantly maintains enzymatic activity during DNA damage, facilitating GTP synthesis and cell survival. Our data indicate that following DNA damage, IMPDH1 and IMPDH2 affect distinct pathways in cells, with IMPDH1 potentially promoting the expression of homologous recombination repair proteins.
This dataset
Open GSE265772 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 GSE265772_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 PRJNA1104179 and SRA study SRP503773. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
HeLa, WT, NT ×3 HeLa, WT, TMZ ×3 HeLa, IMPDH1 knockout, NT ×3 HeLa, IMPDH1 knockout, TMZ ×3 HeLa, IMPDH2 knockout, NT ×3 HeLa, IMPDH2 knockout, TMZ ×3

Supports a case/control comparison: 12 samples read as cases, 6 as controls.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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