Bulk RNA sequencing and analysis of sorted Common Lymphoid Progenitor (CLP) cells from WT, Notch1+/-, and Notch1+/ΔTAD adult mouse bone marrow
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 13 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.
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 GSE189370_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 PRJNA782674 and SRA study SRP347315. 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 13 sample titles: 13 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.
- GSM5700165 CLPs, WT (PAJ011719-001)
- GSM5700166 CLPs, WT (PAJ011719-002)
- GSM5700167 CLPs, WT (PAJ011719-003)
- GSM5700168 CLPs, Notch1+/- (PAJ011719-004)
- GSM5700169 CLPs, Notch1+/- (PAJ011719-005)
- GSM5700170 CLPs, Notch1+/- (PAJ011719-006)
- GSM5700171 CLPs, Notch1+/dTAD (PAJ011719-007)
- GSM5700172 CLPs, Notch1+/dTAD (PAJ011719-009)
- GSM5700173 CLPs, WT (PAJ011719-010)
- GSM5700174 CLPs, WT (PAJ011719-011)
- GSM5700175 CLPs, Notch1+/- (PAJ011719-012)
- GSM5700176 CLPs, Notch1+/- (PAJ011719-013)
- GSM5700177 CLPs, Notch1+/dTAD (PAJ011719-014)
- GSE291075 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - ex vivo, Nfil3] 27 samples shares progenitor, lymphoid
- GSE171815 Loss of BAP1 cooperates with TP53 deficiency to transform a common myelo-erythroid progenitor (RNA-seq - mus musculus) 27 samples shares progenitor, common
- GSE294951 GABA produced by multiple bone marrow niche cell types regulate hematopoietic stem and progenitor cells 12 samples shares progenitor, marrow
- GSE291316 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - Tox] 12 samples shares progenitor, lymphoid
- GSE291076 The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors [RNA-seq - Il7rLT] 12 samples shares progenitor, lymphoid
- GSE224160 Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes 12 samples shares progenitor, marrow
- GSE329337 ATAD3A Limits Aortic Dissection via Mito-Lysosome Contacts and Lipoylation 24 samples shares tad
- GSE285263 Mitochondrial unfolding protein CLPX is required for oocyte competence during ovarian aging 14 samples shares clp
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.