Targeting IL-1b–mediated inflammatory signaling overcomes transfusion dependence in early-stage myelodysplastic syndromes
RNA-seq (gene expression) · human · 26 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
- 26 samples: 22 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
- IL-1β-mediated inflammatory signaling drives ineffective erythropoiesis in early-stage myelodysplastic syndromesbioRxiv : the preprint server for biology · 2023
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 GSE237148_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 PRJNA994068 and SRA study SRP448864. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 26 sample titles: 22 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.
- GSM7596072 CK-42-BM
- GSM7596073 CK-42-CD34pos
- GSM7596074 CK-51-BM
- GSM7596075 CK-51-CD34pos
- GSM7596076 CK-58-BM
- GSM7596077 CK-58-CD34pos
- GSM7596078 CK-70-BM
- GSM7596079 CK-70-CD34pos
- GSM7596080 CK-82-BM
- GSM7596081 CK-82-CD34pos
- GSM7596082 CK-C8-BM
- GSM7596083 CK-C8-CD34pos
- GSM7596084 CK-PRE-BM
- GSM7596085 CK-PRE-CD34pos
- GSM7974026 BM-13
- GSM7974027 BM-4
- GSM7974028 BM-8
- GSM7974029 BM-Y
- GSM7974030 CD34-13
- GSM7974031 CD34-4
- GSM7974032 CD34-8
- GSM7974033 CD34-Y
- GSM8409439 CK-30-BM
- GSM8409440 CK-33-BM
- GSM8409441 CK-38-BM
- GSM8409442 CK-43-BM
- GSE289476 Natural killer cells’ functional impairment drives the immune escape of pre-malignant clones in early-stage myelodysplastic syndromes 16 samples same disease briefing · shares myelodysplastic, early-stage, syndromes
- GSE211032 Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls 45 samples same disease briefing · shares myelodysplastic, syndromes
- GSE292039 Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes 27 samples same disease briefing · shares myelodysplastic, syndromes
- GSE290183 Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes 15 samples same disease briefing · shares myelodysplastic, syndromes
- GSE293014 Identifying clones in myelodysplastic syndromes by using single-cell RNA sequencing 11 samples same disease briefing · shares myelodysplastic, syndromes
- GSE245452 Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) Myelodysplastic Syndromes and impact of lenalidomide 7 samples same disease briefing · shares myelodysplastic, syndromes
- GSE256396 Somatic mutations and DNA methylation identify a subgroup of poor prognosis within lower risk myelodysplastic syndromes 374 samples same disease briefing · shares myelodysplastic, syndromes
- GSE129828 DNA Methylation Identifies Genetically and Prognostically Distinct Subtypes of Myelodysplastic Syndromes 141 samples same disease briefing · shares myelodysplastic, syndromes
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.