|
| Status |
Public on Sep 22, 2023 |
| Title |
HCFs, CDCP1 siRNA, 48 hrs, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary HCF
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Primary HCF
cell type: cardiac fibroblast
|
| Growth protocol |
Cryopreserved adult human cardiac fibroblasts (HCFs) were purchased from Cell Applications, Inc. (Cat#:306V-05a, San Diego, CA). Cell culture and subculture were performed following the manufacturer’s Instructions for HCF Culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol® Reagent (ThermoFisher) and the miRNAeasy kit (QIAGEN) per the manufacturer’s instructions.
RNA-seq libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA sequencing quality was determined with FastQC.
Sequencing reads were aligned to human genome using STAR.
Raw counts were generated with featureCounts.
Differential expression analysis was conducted with the EdgeR package using R
Assembly: hg38
Supplementary files format and content: tab-delimited text files which is a matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Jan 11, 2023 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Duan Liu |
| E-mail(s) |
liud25@gmail.com, liu.duan@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
MPET
|
| Street address |
200 1st ST SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55901 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE222695 |
Transcriptomic profiling of CDCP1 knock-down in human cardiac fibroblasts (HCFs) |
|
| Relations |
| BioSample |
SAMN32682700 |
| SRA |
SRX19008315 |
