|
| Status |
Public on Apr 20, 2021 |
| Title |
CB1-YDJ-2 |
| Sample type |
SRA |
| |
|
| Source name |
Psoas Major
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Landrace
Sex: female
tissue: muscle
isolation_location: Chengdu, China
reference assembly: ensembl-Sscrofa11.1-release100
10x_visiumslide_no.: V19N11-075
10x_visiumslide_area: C1
|
| Treatment protocol |
The representative oxidative slow psoas major muscle (PM) were collected from two pigs for ST experiments. Fresh porcine PM tissue were cut into about 6.5mm*6.5mm*1cm size and snap-frozen in liquid nitrogen to avoid crystal formation. Then tissue samples were embedded in Optimal Cutting Temperature (OCT) and stored at -80℃. For ST analysis, the samples were sectioned on a cryostat at a thickness of 15μm and place the section within a capture area on the Visium Spatial slide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA capture: The tissue sections on Visium Spatial slide were permeabilized according to the protocol provided by 10x Genomics
Fragmented and barcoded porcine RNA were used as the carrier material. The spike-in constituted around 25% of the libraries. ST cDNA libraries were diluted to 4nM and sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing. Sequenced at a mean depth of 50 million paired-end reads depth which resulted in an average library saturation at above 90%.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Spatial transcriptome data of Psoas muscle sample from Landrace pig
|
| Data processing |
Library strategy: Spatial transcriptomic sequencing
Sample demultiplexing, image alignment, barcode processing, and gene counting were performed by using Space Ranger (version 1.1) according to the 10× GENOMICS Spatial Gene Expression analysis pipelines (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome).
Annotation information of MYH2 and MYH4 genes (from old Sscrofa11.1 release-90, representative gene of muscle fiber type IIA and IIB) were added in the GTF file, because of annotation information of MYH2 and MYH4 genes are lacking in ensembl release-100.
We used the "spaceranger counts" command for reads mapping and gene counting. The H&E stained photos of tissue sections, slide serials and capture area information of each sequencing sample were provided in this counting step for automatic fiducial alignment and tissue detection.
The Loupe Browser software (10X) was used to quickly visualize the spatial results. We evaluated the biological reliability of all spots in each sample and unreliable spots were filter out by using the Manual Alignment function
Genome_build: ensembl-Sscrofa11.1-release100
Supplementary_files_format_and_content: H5 Matrix table with clean gene counts for every gene and every spots
|
| |
|
| Submission date |
Nov 20, 2020 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Bo Zeng |
| E-mail(s) |
14044@sicau.edu.cn
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
211 Huimin road, Wenjiang district
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE161882 |
A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [Spatial transcriptomic] |
|
| Relations |
| BioSample |
SAMN15733084 |
| SRA |
SRX8889436 |
