RNA sequencing of bone marrow
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 18 samples: 14 distinct titles, 2 of them repeatedGroups 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 GSE236768_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 PRJNA992398 and SRA study SRP447930. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 14 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
- GSM7575194 eGFPlo _ LT_HSCs, rep1
- GSM7575195 eGFPlo _ LT_HSCs, rep2
- GSM7575196 eGFPlo _ LT_HSCs, rep3
- GSM7575197 eGFPhi _ LT_HSCs, rep1
- GSM7575198 eGFPhi _ LT_HSCs, rep2
- GSM7575199 eGFPhi _ LT_HSCs, rep3
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares marrow, bone
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares marrow, bone
- GSE301127 RNA sequencing of primary bone marrow-derived macrophages from MAPL KO and control mice. 18 samples shares marrow, bone
- GSE293533 Bulk RNA sequencing of bone marrow CD8+ T cells in BMF mice treated with or without baricitinib at different time points 16 samples shares marrow, bone
- GSE264700 RNA sequencing of NPM1cA/SMC+/- mouse myeloid sarcoma and whole bone marrow 16 samples shares marrow, bone
- GSE189370 Bulk RNA sequencing and analysis of sorted Common Lymphoid Progenitor (CLP) cells from WT, Notch1+/-, and Notch1+/ΔTAD adult mouse bone marrow 13 samples shares marrow, bone
- GSE236765 RNA sequencing of LT-HSCs in the bone marrow from WT and Trim47-/- mice untreated or treated with 5-FU for 10 days 12 samples shares marrow, bone
- GSE324139 Short read direct RNA-sequencing of mammalian bone marrow derived macrophages for chimeric RNA discovery 12 samples shares 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.