Pharmacological inhibition of PRKDC-mediated DNA damage response by 3-hydroxyflavone selectively alleviates MLL-rearranged acute myeloid leukemia
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
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- 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.
Read the full summary ↓
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 GSE338690_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 PRJNA1495519 and SRA study SRP739431. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
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.
- GSM9879662 MOLM13, DMSO-1 MOLM13, DMSO
- GSM9879663 MOLM13, DMSO-2 MOLM13, DMSO
- GSM9879664 MOLM13, DMSO-3 MOLM13, DMSO
- GSM9879665 MOLM13, 3-HF-1 MOLM13, 3-HF
- GSM9879666 MOLM13, 3-HF-2 MOLM13, 3-HF
- GSM9879667 MOLM13, 3-HF-3 MOLM13, 3-HF
- GSM9879668 MV411, DMSO-1 MV411, DMSO
- GSM9879669 MV411, DMSO-2 MV411, DMSO
- GSM9879670 MV411, DMSO-3 MV411, DMSO
- GSM9879671 MV411, 3-HF-1 MV411, 3-HF
- GSM9879672 MV411, 3-HF-2 MV411, 3-HF
- GSM9879673 MV411, 3-HF-3 MV411, 3-HF
- GSM9879674 U937, DMSO-1 U937, DMSO
- GSM9879675 U937, DMSO-2 U937, DMSO
- GSM9879676 U937, DMSO-3 U937, DMSO
- GSM9879677 U937, 3-HF-1 U937, 3-HF
- GSM9879678 U937, 3-HF-2 U937, 3-HF
- GSM9879679 U937, 3-HF-3 U937, 3-HF
- GSE137851 The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia 387 samples same disease briefing · shares leukemia
- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing · shares leukemia
- GSE303795 Halofuginone exerts broad-spectrum cytotoxic effects by regulating p-eIF2α-S100A8/A9-calcium signaling, inhibiting global protein synthesis, and reversing the resistance of idarubicin in acute myeloid leukemia 6 samples same disease briefing · shares leukemia
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing · shares leukemia
- GSE129437 Genome-wde mapping of BRD9 binding sites and gene expression changes upon BRD9 knockdown 6 samples same disease briefing
- GSE122515 Bonn Dataset 3 of meta-analysis on AML classification, RNAseq dataset 0 samples same disease briefing
- GSE248265 Genetic or pharmacological inactivation of CREBBP sensitizes B-cell Acute Lymphoblastic Leukemia to Ferroptotic Cell Death upon BCL2 Inhibition 24 samples shares pharmacological, inhibition, leukemia
- GSE289011 Genetic or pharmacological inactivation of CREBBP sensitizes B-cell Acute Lymphoblastic Leukemia to Ferroptotic Cell Death upon BCL2 Inhibition [ChIP-seq] 4 samples shares pharmacological, inhibition, leukemia
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.