GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE179983 Query DataSets for GSE179983
Status Public on Apr 30, 2023
Title A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Intratumor heterogeneity associates with poor patient outcome. Stromal stiffening also accompanies cancer. Whether cancers demonstrate stiffness heterogeneity, and if this is linked to tumor cell heterogeneity remains unclear. We developed a method to measure the stiffness heterogeneity in human breast tumors that quantifies the stromal stiffness each cell experiences and permits visual registration with biomarkers of tumor progression. We present Spatially Transformed Inferential Force Map (STIFMap) which exploits computer vision to precisely automate atomic force microscopy (AFM) indentation combined with a trained convolutional neural network to predict stromal elasticity with micron-resolution using collagen morphological features and ground truth AFM data. We registered high-elasticity regions within human breast tumors colocalizing with markers of mechanical activation and an epithelial-to-mesenchymal transition (EMT). The findings highlight the utility of STIFMaps to assess mechanical heterogeneity of human tumors across length scales from single cells to whole tissues and implicates stromal stiffness in tumor cell heterogeneity.
Overall design RNAseq of soft and stiff patient-derived xenograft tumors from three different patients. Each patient-stiffness combination has three replicates for 18 samples total.
Web link
Contributor(s) Northey J, Stashko C, Weaver V
Citation(s) 37322009
Submission date Jul 13, 2021
Last update date Aug 02, 2023
Contact name Valerie M Weaver
Organization name UCSF
Department Surgery
Lab Weaver Lab
Street address 513 Parnassus Avenue, HSE 560
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (18)
GSM5444448 Breast tumor 1, soft gel, rep1 [B63703]
GSM5444449 Breast tumor 1, soft gel, rep2 [B63704]
GSM5444450 Breast tumor 1, soft gel, rep3 [B63705]
BioProject PRJNA746133
SRA SRP328119

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE179983_GO_MSigDB_allpdx_human_greater_in_soft.txt.gz 706.4 Kb (ftp)(http) TXT
GSE179983_GO_MSigDB_allpdx_human_greater_in_stiff.txt.gz 714.8 Kb (ftp)(http) TXT
GSE179983_pdx_hs33_counts.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap