Cross-Talk between Haematopoietic Cells and Stromal cells Subsets Drives the Remodelling of the Bone Marrow Microenvironment in Myeloproliferative Neoplasms
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 22 samples: 22 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
- A proinflammatory stem cell niche drives myelofibrosis through a targetable galectin-1 axisScience translational medicine · 2024
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 GSE228995_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 PRJNA952518 and SRA study SRP431014. 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 22 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.
- GSM7147187 Batch1_Sample1_GFP_MNC
- GSM7147188 Batch1_Sample2_MPL_MNC
- GSM7147189 Batch1_Sample3_GFP_Stroma
- GSM7147190 Batch1_Sample4_MPL_Stroma
- GSM7147191 Batch1_Sample5_MPL_CD41
- GSM7147192 Batch1_Sample6_MPL_LK
- GSM7147193 Batch1_Sample7_GFP_LK
- GSM7147194 Batch2_Sample8_GFP_LK
- GSM7147195 Batch2_Sample9_MPL_LK
- GSM7147196 Batch2_Sample10_GFP_MNC
- GSM7147197 Batch2_Sample11_MPL_MNC
- GSM7147198 Batch2_Sample15_MPL_Stroma
- GSM7147199 Batch3_Sample16_GFP_MNC
- GSM7147200 Batch3_Sample17_GFP_MNC
- GSM7147201 Batch3_Sample18_MPL_MNC
- GSM7147202 Batch3_Sample19_GFP_LK
- GSM7147203 Batch3_Sample20_MPL_LK
- GSM7147204 Batch3_Sample21_MPL_CD41
- GSM7147205 Batch3_Sample22_GFP_CD41
- GSM7147206 Batch3_Sample23_GFP_Stroma
- GSM7147207 Batch3_Sample24_GFP_Stroma
- GSM7147208 Batch3_Sample25_MPL_Stroma
- GSE306986 Synergistic Stromal Remodeling and Dual Chemo-Immunotherapy in Pancreatic Cancer: A Two-Stage Losartan-Primed followed Nanocarrier Strategy for Tumor Microenvironment Reprogramming 24 samples shares microenvironment, stromal
- GSE308233 JAK2V617F Myeloproliferative Neoplasms Support Parallel Evolution of Independent Leukemic Clones 16 samples shares myeloproliferative, neoplasms
- GSE266091 Asxl1 mutation enhances differentiation in CSF3R-mutated myeloproliferative neoplasms [RNA-Seq] 12 samples shares myeloproliferative, neoplasms
- GSE269888 Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [scRNA-seq] 11 samples shares microenvironment, stromal
- GSE266087 Asxl1 mutation enhances differentiation in CSF3R-mutated myeloproliferative neoplasms [ATAC-Seq] 12 samples shares myeloproliferative, neoplasms
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment
- GSE218173 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid] 150 samples shares microenvironment
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares microenvironment
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.