Comprehensive analysis of mesenchymal cells reveals a deregulated TGF-B/Wnt/HOXB7 axis in patients with myelofibrosis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Myeloproliferative neoplasmsThis series is part of our curated briefing on it.
- Samples
- 17 samples: 17 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.
- Paper
- Comprehensive analysis of mesenchymal cells reveals a dysregulated TGF-β/WNT/HOXB7 axis in patients with myelofibrosisJCI insight · 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 GSE234390_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA981171. 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 17 sample titles: 17 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.
- GSM7466604 nMSC1_S1_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466605 nMSC2_S2_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466606 nMSC3_S3_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466607 nMSC4_S4_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466608 MPN10_S14_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466609 MPN11_S15_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466610 MPN12_S16_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466611 MPN1_S5_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466612 MPN2_S6_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466613 MPN3_S7_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466614 MPN6_S10_STARAligned.sortedByCoord.out.bam [RNA-seq]
- GSM7466615 nMSC1 [ATAC-seq]
- GSM7466616 nMSC2 [ATAC-seq]
- GSM7466617 nMSC3 [ATAC-seq]
- GSM7466618 fMPN1 [ATAC-seq]
- GSM7466619 fMPN2 [ATAC-seq]
- GSM7466620 fMPN3 [ATAC-seq]
- GSE241825 Mesenchymal stromal cell reprogramming and aberrant inflammatory signalling in myelofibrosis: insights from single-cell RNA sequencing 21 samples same disease briefing · shares myelofibrosis, mesenchymal
- GSE221946 Single-Cell ATAC+RNAseq from CD34+ cells of a Primary Myelofibrosis patient evolved to secondary Acute Myeloid Leukemia 4 samples same disease briefing · shares myelofibrosis
- GSE300470 A Stem and Progenitor Cell-Derived Gene Expression Signature is Prognostic for Survival in Myelofibrosis [RNA-Seq] 358 samples same disease briefing · shares myelofibrosis
- GSE332562 Comprehensive spatial profiling of the spleen in human myelofibrosis [snRNAseq] 1 samples same disease briefing · shares myelofibrosis
- GSE288706 Mesenchymal stromal cells from JAK2V617F myeloproliferative neoplasms support healthy and malignant haematopoiesis in a humanised scaffold model in vivo 12 samples same disease briefing · shares mesenchymal
- GSE242730 Comparision of bone marrow cells between trisomy 8+ myelofibrosis vs. normal cells. 4 samples same disease briefing · shares myelofibrosis
- GSE240407 Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A 28 samples same disease briefing
- GSE277354 Genetic charcterization of myeloproliferative neoplasms (MPN) 402 samples same disease briefing
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.