Rapid Disease Progression of Myelodysplastic Syndrome is Reflected in Transcriptomic and Functional Abnormalities of Bone Marrow MSCs
RNA-seq (gene expression) · human · 22 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
- Homo sapiens (human)
- Topic
- Myelodysplastic syndromesThis series is part of our curated briefing on it.
- Samples
- 22 samples: 18 × BM vs 4 × HDGroups 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.
Read the full summary ↓
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 GSE280881_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 PRJNA1180964 and SRA study SRP542638. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 2 replicated groups read from 22 sample titles; they account for 22 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.
- GSM8606918 BM378 BM
- GSM8606919 BM768 BM
- GSM8606920 BM775 BM
- GSM8606921 BM808 BM
- GSM8606922 BM819 BM
- GSM8606923 BM290 BM
- GSM8606924 BM305 BM
- GSM8606925 BM630 BM
- GSM8606926 BM455 BM
- GSM8606927 BM613 BM
- GSM8606928 BM625 BM
- GSM8606929 BM659 BM
- GSM8606930 BM797 BM
- GSM8606931 BM1254 BM
- GSM8606932 BM2565 BM
- GSM8606933 BM2589 BM
- GSM8606934 BM2598 BM
- GSM8606935 BM2651 BM
- GSM8606936 HD01 HD
- GSM8606937 HD02 HD
- GSM8606938 HD03 HD
- GSM8606939 HD04 HD
- GSE278230 Single-cell sequencing identifies characteristics of disease and bone marrow in concurrent multiple myeloma and myelodysplastic syndrome 4 samples same disease briefing · shares myelodysplastic, marrow, bone
- GSE284647 The genotype-integrated gene expression profile at the single-cell level of bone marrow CD34-positive hematopoietic stem and progenitor cells (HSPCs) from a patient with myelodysplastic neoplasms (MDS) harboring germline and somatic DDX41 variants. 1 samples same disease briefing · shares myelodysplastic, marrow, bone
- GSE279914 Molecular fingerprints for bone marrow cells, myelodysplastic syndrome and aplastic anemia 14 samples same disease briefing · shares myelodysplastic, marrow, bone
- GSE290183 Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes 15 samples same disease briefing · shares myelodysplastic, progression
- GSE316081 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [RNA-seq] 6 samples same disease briefing · shares marrow, bone
- GSE288862 ScRNA-Seq of Human MDS and AML Bone Marrow Marrow Microenvironment. 3 samples same disease briefing · shares marrow, bone
- GSE326589 Bone marrow immunosuppressive states associate with survival after guadecitabine and atezolizumab therapy in HMA-R/R MDS 58 samples same disease briefing · shares marrow, bone
- GSE316079 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [ATAC-seq] 6 samples same disease briefing · 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.