NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE166120 Query DataSets for GSE166120
Status Public on Oct 28, 2021
Title Spatial transcriptomics of healing and non-healing diabetic foot ulcers
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Diabetic foot ulcers (DFUs) are a devastating complication of diabetes. To better understand the molecular mechanisms and cell types implicated in DFU healing, we used NanoString’s GeoMx Digital Spatial profiling platform on DFU tissue sections and compared gene expression of areas within the same ulcer as well as between patients who in 12 weeks following surgery healed their DFU (Healers, N=2) vs those who did not (Non-Healers, N=2).
 
Overall design The spatial transcriptome profiling was performed using NanoString’s GeoMx Digital Spatial profiling platform on unfixed frozen 5 μm tissue sections. Samples were processed as follows: 1) 10% neutral buffered formalin fixation overnight, 2) target retrieval (1X Tris EDTA, pH 9.0 for 20 min), 3) proteinase K digestion (1 µg/mL for 15 min), 4) post-fixation (10% NBF, Tris-glycine stop buffer), 5) in-situ hybridization overnight with the GeoMx Cancer Transcriptome Atlas probe panel (1800-plex), 6) stringent washes (50:50 formamide/4X SSC), and 7) fluorescent antibody/marker (aSMA, Clone: 1A4, Abcam; CD45, Clone: 2B11+PD7/26, Novus; PanCK, Clone: AE1/AE3, Novus) incubation, 1 hour at room temperature. Sections were then loaded onto the GeoMx® Digital Spatial Profiler. For profiling, circular regions of interest (ROIs), approximately 500 μm in diameter, located within the ulcers or in neighboring non-ulcerated tissue were selected to include high concentrations of CD45+ immune cells in close proximity to vessels (aSMA+ structures). After ROI selection, the GeoMx instrument illuminated each ROI separately with UV light to cleave, aspirate, and deposit the oligonucleotides from the hybridized ISH probes for downstream sequencing into a 96-well plate.
 
Contributor(s) Theocharidis G, Veves A
Citation(s) 35013299
Submission date Feb 03, 2021
Last update date Jan 12, 2022
Contact name Aristidis Veves
E-mail(s) aveves@bidmc.harvard.edu
Phone 6176627075
Organization name Beth Israel Deaconess Medical Center
Lab Rongxiang Xu, MD, Center for Regenerative Therapeutics
Street address 330 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (23)
GSM5061969 A02
GSM5061970 A03
GSM5061971 A04
Relations
BioProject PRJNA699294
SRA SRP304590

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
GSE166120_Alpha_CTA_v2.0.pkc.txt.gz 676.0 Kb (ftp)(http) TXT
GSE166120_RAW.tar 730.0 Kb (http)(custom) TAR (of DCC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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