|
| Status |
Public on Nov 29, 2022 |
| Title |
RNA-Seq Cells PL MP01 |
| Sample type |
SRA |
| |
|
| Source name |
rabbit infrapatellar fat pad derived stem cells (IPFSCs)
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
strain: New Zealand White (NZW)
cell type: infrapatellar fat pad derived stem cells (IPFSCs)
treatment: IPFSCs grown on tissue culture plastic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated by using Trizol (Invitrogen) and purified by using an RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instructions.
RNA-Seq library were prepared by using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to Oryctolagus cuniculus (rabbit) genome (oryCun2 ) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against gene transcripts annotated by Ensembl (OryCun2.0.98)
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: oryCun2
Supplementary files format and content: Text; First colum: Gene ID; columns thereafter: expresion values (log2(RPKM+1)+0.0001) for each sample
|
| |
|
| Submission date |
Jul 08, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
|
| Organization name |
West Virginia University
|
| Department |
MicroBiology, Immunology, and Cell Biology
|
| Lab |
2072A, HSC North, Floor 2
|
| Street address |
64 Medical Center Drive
|
| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
| |
|
| Platform ID |
GPL21255 |
| Series (1) |
| GSE207804 |
Matrix from Urine Stem Cells Boosts Tissue-Specific Stem Cell Mediated Functional Cartilage Reconstruction |
|
| Relations |
| BioSample |
SAMN29615854 |
| SRA |
SRX16103084 |
