|
| Status |
Public on Sep 14, 2023 |
| Title |
PVNS4 |
| Sample type |
SRA |
| |
|
| Source name |
synovium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Synovium
diagnosis: PVNS
|
| Treatment protocol |
Sample of osteoarthritis or PVNS synovium receive no treatment before harvest during surgery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PVNS4.cellBarcode.txt
5Sample.NormalizedCounts.txt
3Sample.NormalizedCounts.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8.
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
o MT% < 20%;
o Cell Gene Number < Median Gene Number * 2;
o Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include normalized counts for each cell.
|
| |
|
| Submission date |
Aug 01, 2020 |
| Last update date |
Sep 14, 2023 |
| Contact name |
fei wu |
| E-mail(s) |
wufeipku2020@126.com
|
| Organization name |
Peking university 3rd hospital
|
| Lab |
Sports Medicine Institute
|
| Street address |
49 North Garden Rd
|
| City |
beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE155527 |
Single cell analysis of PVNS synovium from human |
|
| Relations |
| BioSample |
SAMN15693631 |
| SRA |
SRX8863955 |
