|
Status |
Public on Nov 29, 2022 |
Title |
RNA-Seq Cells USC MP05 |
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 dECM deposited by human urine stem cells (USCs)
|
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
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|
|
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 |
SAMN29615850 |
SRA |
SRX16103088 |