DDX41 heterozygosity impairs hematopoietic progenitor cell fitness and cooperates with p53 mutation to drive malignancy
RNA-seq (gene expression) · mouse · 26 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
- Mus musculus (mouse)
- Samples
- 26 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.
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 GSE247409_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 PRJNA1037498 and SRA study SRP471122. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 6 replicated groups read from 26 sample titles; they account for 17 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.
- GSM7889060 Ddx41-WT;p53-WT, WTWT10 Ddx41-WT;p53-WT, WTWT
- GSM7889061 Ddx41-WT;p53-WT, WTWT12 Ddx41-WT;p53-WT, WTWT
- GSM7889062 Ddx41-WT;p53-WT, WTWT11 Ddx41-WT;p53-WT, WTWT
- GSM7889063 Ddx41-HET;p53-WT, HETWT34 Ddx41-HET;p53-WT, HETWT
- GSM7889064 Ddx41-HET;p53-WT, HETWT32 Ddx41-HET;p53-WT, HETWT
- GSM7889065 Ddx41-WT;p53-HET, WTHET24 Ddx41-WT;p53-HET, WTHET
- GSM7889066 Ddx41-WT;p53-HET, WTHET23 Ddx41-WT;p53-HET, WTHET
- GSM7889067 Ddx41-WT;p53-HET, WTHET22 Ddx41-WT;p53-HET, WTHET
- GSM7889068 Ddx41-HET;p53-HET, HETHET46 Ddx41-HET;p53-HET, HETH…
- GSM7889069 Ddx41-HET;p53-HET, HETHET47 Ddx41-HET;p53-HET, HETH…
- GSM7889070 Ddx41-HET-8 Ddx41-HET
- GSM7889071 Ddx41-HET-7 Ddx41-HET
- GSM7889072 Ddx41-HET-6 Ddx41-HET
- GSM7889073 Ddx41-WT-4 Ddx41-WT
- GSM7889074 Ddx41-WT-3 Ddx41-WT
- GSM7889075 Ddx41-WT-2 Ddx41-WT
- GSM7889076 Ddx41-WT-1 Ddx41-WT
- GSM7889134 Sh-Control_38A
- GSM7889135 sh-Control_38B
- GSM7889136 sh-Control_38D
- GSM7889137 Sh-DDX41_1_409A
- GSM7889138 Sh-DDX41_1_409B
- GSM7889139 Sh-DDX41_1_409D
- GSM7889140 Sh-DDX41_2_411A
- GSM7889141 Sh-DDX41_2_411B
- GSM7889142 Sh-DDX41_2_411D
- GSE277684 Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans 52 samples shares hematopoietic, impairs
- GSE100041 Reduced representation bisulfite-sequencing of human leukemia cells and mouse hematopoietic progenitors 34 samples shares hematopoietic, progenitor
- GSE65000 Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion 36 samples shares progenitor
- GSE270069 Species-specific progenitor domain extends neurogenesis and increases motor neuron production 3 samples shares progenitor
- GSE260779 Spatial transcriptomic sequencing of repaired lung transplanted with human P63+ progenitor [STOmics-seq] 1 samples shares progenitor
- GSE240030 ATRX guards against aberrant differentiation in mesenchymal progenitor cells 165 samples shares progenitor
- GSE270148 Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours 85 samples shares progenitor
- GSE296761 Elucidating the impact of chemotherapy on skeletal progenitors 43 samples shares progenitor
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.