Cyclic stretching stimuli promotes HGF and MMP secretion from hESC-derived hepatoblasts and endothelial cells towards liver lobule formation in vitro.
RNA-seq (gene expression) · human · 15 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
- 15 samples: 5 × Day9 mixture, without cMS, vs 5 × Day12 mixture, without cMS, vs 5 × Day12 mixture, with cMS,Groups 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
- Cyclic Stretching Enhances Angiocrine Signals at Liver Bud Stage from Human Pluripotent Stem Cells in Two-Dimensional CultureTissue engineering. Part A · 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 GSE232118_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 PRJNA970861 and SRA study SRP436759. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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.
- GSM7315527 Day9 mixture, without cMS, rep1 Day9 mixture, without c…
- GSM7315528 Day9 mixture, without cMS, rep2 Day9 mixture, without c…
- GSM7315529 Day9 mixture, without cMS, rep3 Day9 mixture, without c…
- GSM7315530 Day9 mixture, without cMS, rep4 Day9 mixture, without c…
- GSM7315531 Day9 mixture, without cMS, rep5 Day9 mixture, without c…
- GSM7315532 Day12 mixture, without cMS, rep1 Day12 mixture, without …
- GSM7315533 Day12 mixture, without cMS, rep2 Day12 mixture, without …
- GSM7315534 Day12 mixture, without cMS, rep3 Day12 mixture, without …
- GSM7315535 Day12 mixture, without cMS, rep4 Day12 mixture, without …
- GSM7315536 Day12 mixture, without cMS, rep5 Day12 mixture, without …
- GSM7315537 Day12 mixture, with cMS, rep1 Day12 mixture, with cMS,
- GSM7315538 Day12 mixture, with cMS, rep2 Day12 mixture, with cMS,
- GSM7315539 Day12 mixture, with cMS, rep3 Day12 mixture, with cMS,
- GSM7315540 Day12 mixture, with cMS, rep4 Day12 mixture, with cMS,
- GSM7315541 Day12 mixture, with cMS, rep5 Day12 mixture, with cMS,
- GSE286069 MMP12-dependent myofibroblast formation contributes to the nucleus pulposus fibrosis and intervertebral disc degeneration 15 samples shares mmp, formation
- GSE64461 Endothelial MMP14 is required for endothelial dependant growth support of human airway basal cells 10 samples shares mmp, endothelial
- GSE249903 Activation of hepatocyte growth factor (HGF)/MET signaling as a mechanism of acquired resistance to a novel YAP1/TEAD small molecule inhibitor. 49 samples shares hgf
- GSE244085 MMPs and NETs are detrimental in CNS-tuberculosis with MMP inhibitor doxycycline improving murine CNS-tuberculosis survival (human) 38 samples shares mmp
- GSE243188 Epithelial barrier function and its underlying mechanical regulation affects the biology of Macro-Metastasis Parenchyma Interface (MMPI). 28 samples shares mmp
- GSE275051 Upregulation of MMP3 promotes cisplatin resistance in ovarian cancer 24 samples shares mmp
- GSE296572 Transcriptomic analysis of therapy-naïve and alectinib-treated H3122 xenograft tumors from NSG and humanized HGF-NSG mice 22 samples shares hgf
- GSE190361 SPOCK2 controls the proliferation and function of immature pancreatic β-cells through MMP2. 10 samples shares mmp
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.