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Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia

GSE261339 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)
Topic
Myelodysplastic syndromesThis series is part of our curated briefing on it.
Samples
18 samples: 7 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
TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cellsNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cells
Truong P, Shen S, Joshi S et al. · Nature communications 2024 · PMID 39198401 · doi:10.1038/s41467-024-51646-6
This dataset
Open GSE261339 in finder → Find more human RNA-seq datasets → Myelodysplastic syndromes landscape →
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 GSE261339_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 PRJNA1086510 and SRA study SRP494593. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39198401) ↗
Study design
7 conditions, mostly in triplicate
MDSL-Cas9-sgROSA, D4, DMSO, Rp ×3 MDSL-Cas9-sgROSA, D4, AZA , Rp ×3 MDSL-Cas9-sgTOPORS, D4, DMSO, Rp ×3 MDSL-Cas9-sgTOPORS, D4, AZA, Rp ×3 MDSL-Cas9, BRUNELLO, T0, Untreated, Rp ×2 MDSL-Cas9, BRUNELLO, T19, DMSO, Rp ×2 MDSL-Cas9, BRUNELLO, T19, AZA, Rp ×2

Supports a between-group comparison across 18 samples.

How we read this: 7 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
More Myelodysplastic syndromes datasets

Search all human RNA-seq datasets in GEO →

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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.