RNA sequencing of PDX-AML samples using prime-seq
RNA-seq (gene expression) · human · 25 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
- 25 samples
- 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.
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 GSE307747_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 PRJNA1327255. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run AML955 … AML959 and carry no group information.
- GSM9230267 AML955
- GSM9230268 AML393
- GSM9230269 AML661
- GSM9230270 AML981
- GSM9230271 AML979
- GSM9230272 AML415
- GSM9230273 AML664
- GSM9230274 AML356
- GSM9230275 AML788
- GSM9230276 AML358
- GSM9230277 AML579
- GSM9230278 AML842
- GSM9230279 AML372
- GSM9230280 AML602
- GSM9230281 AML896
- GSM9230282 AML388
- GSM9230283 AML640
- GSM9230284 AML573
- GSM9230285 AML980
- GSM9230286 AML491
- GSM9230287 AML810
- GSM9230288 AML663
- GSM9230289 AML346
- GSM9230290 AML538
- GSM9230291 AML959
- GSE137851 The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia 387 samples same disease briefing
- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing
- 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
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing
- 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
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.