Combinatorial Extracellular Matrix Tissue Chips for Optimizing Mesenchymal Stromal Cell Microenvironment and Manufacturing
RNA-seq (gene expression) · human · 24 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)
- Samples
- 24 samples: 21 distinct titles, 1 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
- Combinatorial extracellular matrix tissue chips for optimizing mesenchymal stromal cell microenvironment and manufacturingNPJ Regenerative medicine · 2025
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 GSE288678_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 PRJNA1219056 and SRA study SRP561433. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 24 sample titles: 21 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.
- GSM8772943 A1_1_4_1
- GSM8772944 A2_1_4_2
- GSM8772945 A3_1_4_3
- GSM8772946 A4_1_4_4
- GSM8772947 A5_1_234_1
- GSM8772948 A6_1_23_2
- GSM8772949 A7_1_23_3
- GSM8772950 A8_1_23_4
- GSM8772951 A9_1_234F_1
- GSM8772952 A10_1_234F_2
- GSM8772953 A11_1_234F_3
- GSM8772954 A12_1_234F_4
- GSM8772955 A13_9_4_1
- GSM8772956 A14_9_4_2
- GSM8772957 A15_9_4_3
- GSM8772958 A16_9_4_4
- GSM8772959 A17_9_234_1
- GSM8772960 A18_9_234_2
- GSM8772961 A19_9_234_3
- GSM8772962 A20_9_234_4
- GSM8772963 A21_9_234F_1
- GSM8772964 A21_9_234F_2
- GSM8772965 A21_9_234F_3
- GSM8772966 A21_9_234F_4
- GSE289930 Proteogenomic Characterization of Primary Oral Cancer Unveils Extracellular Matrix Remodeling and Immunosuppressive Microenvironment Linked to Lymph Node Metastasis [RNA-seq] 33 samples shares microenvironment, extracellular, matrix
- GSE298139 Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [snRNA-seq] 16 samples shares extracellular, mesenchymal, matrix
- GSE208732 Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer [RNA-seq] 102 samples shares extracellular, matrix
- GSE309392 Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [scRNA-Seq] 23 samples shares extracellular, matrix
- GSE306800 Extracellular matrix-myCAF signatures correlate with resistance to neoadjuvant aPD-L1 immune checkpoint inhibition with durvalumab + metformin in HPV+ HNSCC 18 samples shares extracellular, matrix
- GSE285234 KLF9-GRK5-HDAC6 axis aggravates osteoarthritis pathogenesis by promoting chondrocyte extracellular matrix degradation and apoptosis 12 samples shares extracellular, matrix
- GSE226347 Extracellular matrix derived from dental pulp stem cells promotes osteogenic differentiation of gingival fibroblasts via Wnt and Hippo signaling pathway 12 samples shares extracellular, matrix
- GSE341139 A conserved HAND2-BMP5-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies 10 samples shares extracellular, matrix
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.