RNA sequencing of LT-HSCs in the bone marrow from WT and Trim47-/- mice untreated or treated with 5-FU for 10 days
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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
- Trim47 prevents hematopoietic stem cell exhaustion during stress by regulating MAVS-mediated innate immune pathwayNature communications · 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 GSE236765_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 PRJNA992402 and SRA study SRP447930. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM7575158 Wild type-1 LT-HSCs, rep1
- GSM7575159 Wild type-2 LT-HSCs, rep2
- GSM7575160 Wild type-3 LT-HSCs, rep3
- GSM7575161 Trim47-/- -1, LT-HSCs, rep1
- GSM7575162 Trim47-/- -2, LT-HSCs, rep2
- GSM7575163 Trim47-/- -3, LT-HSCs, rep3
- GSM7575164 WT-5-FU-1 LT-HSCs, rep1
- GSM7575165 WT-5-FU-2 LT-HSCs, rep2
- GSM7575166 WT-5-FU-3 LT-HSCs, rep3
- GSM7575167 Trim47-/--5-FU -1 LT-HSCs, rep1
- GSM7575168 Trim47-/--5-FU -2 LT-HSCs, rep2
- GSM7575169 Trim47-/--5-FU -3 LT-HSCs, rep3
- GSE236767 RNA sequencing of eGFPlo and eGFPhi LT-HSCs in the bone marrow from Trim47+/eGFP mice 6 samples shares trim47, lt-hscs, marrow, bone
- GSE268240 Gene expression profiling of neutrophils isolated from bone marrow, spleen and tumor of H16sc-IS1-tumor-bearing mice treated with anti-IL1RAP or untreated. 24 samples shares untreated, treated, marrow, bone
- GSE288474 Gene expression profiles of genes extracted from the hearts of untreated FRDA mice (FA+FA), FRDA mice transplanted with total bone marrow (DP+FA), and WT mice transplanted with total bone marrow (DP+WT) 8 samples shares untreated, treated, marrow, bone
- GSE252894 RNA sequencing of LT-HSCs from the bone marrow of irradiated mice after treated with saline or carnosine 6 samples shares lt-hscs, treated, marrow, bone
- GSE281040 RNA sequencing of LT-HSCs from the bone marrow of unirradiated mice after treated with saline or carnosine 6 samples shares lt-hscs, treated, marrow, bone
- GSE241877 Gene expression profile at the single cell level of CD45+ CD11b+ cells isolated from the brain and bone marrow of mice either untreated or conditioned and transplanted with total bone marrow. 4 samples shares untreated, treated, marrow, bone
- GSE261246 Gene expression profile at the single cell level of CD45+ CD11b+ cells isolated from the brain and bone marrow of mice either untreated or conditioned and transplanted with mouse hematopoietic stem and progenitor cells (HSPCs) expanded in culture. 4 samples shares untreated, treated, marrow, bone
- GSE233828 RNA sequencing of Mmrn1-high LT-HSCs and Mmrn1-low LT-HSCs from murine bone marrow 6 samples shares lt-hscs, marrow, bone
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.