Mutant NPM1 marginally impacts ribosome footprint in acute myeloid leukemia cells
RNA-seq (gene expression) · human · 12 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
- 12 samples: 2 × IMS-M2 cells, DMSO, RNA-seq, vs 2 × IMS-M2 cells, DMSO, Ribo-seq, vs 2 × IMS-M2 cells, dTAG, RNA-seq, vs 2 × IMS-M2 cells, dTAG, Ribo-seq,Groups 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
- Mutant NPM1 marginally impacts ribosome footprint in acute myeloid leukemia cellsEJHaem · 2024
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 GSE251919_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 PRJNA1055925 and SRA study SRP479687. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 8 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.
- GSM7989984 IMS-M2 cells, DMSO, RNA-seq, replicate 1 IMS-M2 cells, DMSO, RNA…
- GSM7989985 IMS-M2 cells, DMSO, RNA-seq, replicate 2 IMS-M2 cells, DMSO, RNA…
- GSM7989986 IMS-M2 cells, DMSO, Ribo-seq, replicate 1 IMS-M2 cells, DMSO, Rib…
- GSM7989987 IMS-M2 cells, DMSO, Ribo-seq, replicate 2 IMS-M2 cells, DMSO, Rib…
- GSM7989988 IMS-M2 cells, dTAG, RNA-seq, replicate 1 IMS-M2 cells, dTAG, RNA…
- GSM7989989 IMS-M2 cells, dTAG, RNA-seq, replicate 2 IMS-M2 cells, dTAG, RNA…
- GSM7989990 IMS-M2 cells, dTAG, Ribo-seq, replicate 1 IMS-M2 cells, dTAG, Rib…
- GSM7989991 IMS-M2 cells, dTAG, Ribo-seq, replicate 2 IMS-M2 cells, dTAG, Rib…
- GSM7989992 OCI-AML3 cells, DMSO, RNA-seq, replicate 2
- GSM7989993 OCI-AML3 cells, DMSO, Ribo-seq, replicate 2
- GSM7989994 OCI-AML3 cells, dTAG, RNA-seq, replicate 2
- GSM7989995 OCI-AML3 cells, dTAG, Ribo-seq, replicate 2
- GSE137851 The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia 387 samples same disease briefing · shares npm1, leukemia, myeloid
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing · shares leukemia, myeloid, mutant
- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing · shares leukemia, myeloid
- 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, myeloid
- 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
- GSE264084 Depletion of ribosome biogenesis factors in NPM1-mutant acute myeloid leukemia: Insights into direct consequences of the mutation and implications for treatment 12 samples shares npm1, ribosome, leukemia, myeloid, mutant
- GSE307716 Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [CUT&Tag] 52 samples shares npm1, leukemia, myeloid, mutant
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.