 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2024 |
| Title |
Control vein, canine 3, ST |
| Sample type |
SRA |
| |
|
| Source name |
Cephalic vein
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Cephalic vein
cell type: Endothelial cells, smooth muscle cells, fibroblasts, myeloid cells
Sex: Male
treatment: Control
|
| Treatment protocol |
Bilateral upper limb cephalic vein harvest was performed on 25 kg male (n=3) or female (n=1) mongrel dogs (Marshall Bioresources). General anesthesia was established and maintained with an initial sodium pentothal injection and subsequent 1% isofluorane inhalation after orotracheal intubation. Vein harvest was performed in conventional fashion. The cephalic vein was identified and exposed along the anterior surface from the wrist to the upper forearm. The distal portion of the vein was then ligated and transected. The end of the transected vein was cannulated with a metal cannula and secured with a silk suture. The vein was then sequentially distended by injecting a saline solution (0.9% sodium chloride, papaverine hydrochloride 60 mg, and 43 mg of bivalirudin) while occluding the outflow. Intervening tributaries were identified and ligated with silk sutures. A total length of 15 cm of vein was harvested. Total vein distension and harvest time was approximately 30 minutes. The cephalic vein following distention, along with a separate segment of the undistended cephalic vein, which served as the experimental control, were excised. Samples were collected and immediately snap-frozen in cryovials using liquid nitrogen for single-nuclei analysis or embedded in OCT blocks and flash-frozen in an isopentane and liquid nitrogen bath for spatial transcriptomics analysis. Systemic bivalirudin was then infused before the creation of the anastomoses. Bilateral end-to-side anastomoses were created on the vein with 7-0 Prolene sutures. The intervening segment of the carotid artery was then ligated, creating preferential flow through the graft. After hemostasis was achieved, the wounds were closed in three layers with 3-0 vicryl sutures. The patency of the graft was confirmed through direct palpation and ultrasound imaging. At 24 hours, harvest was performed with the dog under general anesthesia. Vein graft samples were then collected and processed as previously described for cryopreservation and OCT embedding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For spatial transcriptomic analysis, Frozen samples embedded in O.C.T. (TissueTek Sakura) were cryosectioned (10 mm sections) at −20 ºC and transferred onto pre-chilled Visium Tissue Optimization Slides (10x Genomics, 3000394) and Visium Spatial Gene Expression Slides (10x Genomics, 2000233). H&E staining was performed according to the Visium Spatial Gene Expression User Guide (10x Genomics, CG000239 rev. F). For the Visium spatial transcriptomics gene expression assay, tissue was permeabilized for the optimal time (9 minutes).
For spatial transcriptomics, following tissue permeablization, reverse transcription, second strand synthesis and denaturation, cDNA amplification and QC, and gene expression library construction according to 10x Genomics user guide (CG000239 rev. F) was performed.The gene expression libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) and checked for quality using DNA HS bioanalyzer chips (Agilent).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
C3-ST1, 10x Genomics, Visium
GVV10_C3-ST1
|
| Data processing |
*library strategy: Spatial transcriptomics
For spatial transcriptomics samples, demultiplexing, barcoded processing, gene counting, aggregation, and spatial alignment were performed using the 10x SpaceRanger software (v.2.0.0).
Assembly: Dog10K_Boxer_Tasha_1.0
Supplementary files format and content: Tab-separated value files for barcodes and genes with matrix files
Supplementary files format and content: Spatial alignment output files for spatial transcriptomics
|
| |
|
| Submission date |
Apr 05, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Marina Michaud |
| E-mail(s) |
marina.michaud@emory.edu
|
| Phone |
4043078082
|
| Organization name |
Emory University
|
| Department |
School of Medicine
|
| Lab |
Bhasin Lab
|
| Street address |
28 Cass Station Dr NW
|
| City |
Cartersville |
| State/province |
GA |
| ZIP/Postal code |
30120 |
| Country |
USA |
| |
|
| Platform ID |
GPL25760 |
| Series (1) |
| GSE263281 |
Spatial gene expression of canine veins during carotid-cartoid vein bypass implantation |
|
| Relations |
| BioSample |
SAMN40759510 |
| SRA |
SRX24164712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8189154_C3-ST1_Spatial.tar.gz |
3.3 Mb |
(ftp)(http) |
TAR |
| GSM8189154_C3-ST1_barcodes.tsv.gz |
1.9 Kb |
(ftp)(http) |
TSV |
| GSM8189154_C3-ST1_features.tsv.gz |
300.3 Kb |
(ftp)(http) |
TSV |
| GSM8189154_C3-ST1_matrix.mtx.gz |
712.4 Kb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
