Detect IGF1R function in postnatal bone marrow mesenchymal stem cell
RNA-seq (gene expression) · mouse · 11 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
- 11 samples: 3 × sca1-pos-cre-neg vs 3 × sca1-pos-cre-pos vs 3 × neg vs 2 × sca1-negGroups 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 GSE276419_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 PRJNA1157324 and SRA study SRP530540. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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.
- GSM8498320 sca1-neg2 sca1-neg
- GSM8498321 sca1-neg3 sca1-neg
- GSM8498322 sca1-pos-cre-neg1 sca1-pos-cre-neg
- GSM8498323 sca1-pos-cre-neg2 sca1-pos-cre-neg
- GSM8498324 sca1-pos-cre-neg3 sca1-pos-cre-neg
- GSM8498325 sca1-pos-cre-pos1 sca1-pos-cre-pos
- GSM8498326 sca1-pos-cre-pos2 sca1-pos-cre-pos
- GSM8498327 sca1-pos-cre-pos3 sca1-pos-cre-pos
- GSM8498328 neg-1 neg
- GSM8498329 neg-2 neg
- GSM8498330 neg-3 neg
- GSE228749 Novel ex vivo culture of purified mouse mesenchymal stromal cells reveals tissue-dependent niche heterogeneity in bone marrow and functional interaction with macrophages 12 samples shares mesenchymal, marrow, bone
- GSE294362 Aged bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes 80 samples shares mesenchymal, marrow, bone
- GSE252394 Fgf9 promotes adipogenesis and reduces osteogenesis by regulating mesenchymal stromal cells differentiation in adult bone marrow 18 samples shares mesenchymal, marrow, bone
- GSE269006 YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1 mediated reprogramming of bone mesenchymal stem cells [RNA-seq] 15 samples shares mesenchymal, bone, stem
- GSE269007 YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1 mediated reprogramming of bone mesenchymal stem cells 27 samples shares mesenchymal, bone, stem
- GSE123160 Immunomodulatory properties of slowly cycling and mesenchymal-like castration-resistant prostate cancer stem cells 70 samples shares mesenchymal, stem
- GSE273883 CX3CR1+ Synovial Macrophages for Barrier Restore in Rheumatoid Arthritis: A New Target for Mesenchymal Stem Cell-Based Therapy? 35 samples shares mesenchymal, stem
- GSE282285 Aged muscle stem cells epigenetically drive the expansion of mesenchymal progenitors [bulk RNA-Seq] 31 samples shares mesenchymal, stem
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.