|
| Status |
Public on May 22, 2023 |
| Title |
MCC-3 |
| Sample type |
SRA |
| |
|
| Source name |
MCC-3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCC-3
cell type: Merkel cell carcinoma cell line
genotype: MCPyV negative
treatment: none
time: Day 0
|
| Treatment protocol |
none
|
| Growth protocol |
Suspension cultures were maintained in RPMI-1640 media supplemented with 10% Fetal bovine serum, penicillin-streptomycin (100 U/ml) and L-glutamine (4mM), at 37C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). >1.0 ug of total RNA was evaluated for quality using Agilent Bioanalyzer Nano RNA chip prior to library construction
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Rsubread for alignment
Sequence reads were mapped to GRCh38 reference human genome
Read count extraction was carried out using featureCounts() function
Differential analysis on raw data and sample distance calculations on normalized data performed using DESeq2
Assembly: hg38
Supplementary files format and content: consolidated tab-delimited text file represents raw counts for each sample
|
| |
|
| Submission date |
Jan 19, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Ling Gao |
| E-mail(s) |
ling.gao@va.gov, lingg3@hs.uci.edu
|
| Organization name |
Department of Veterans Affairs
|
| Street address |
5901 E.7th Street
|
| City |
Long Beach |
| State/province |
California |
| ZIP/Postal code |
90822 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE223275 |
Bulk RNA sequencing of MCPyV positive and negative patient derived Merkel cell carcinoma cell lines |
|
| Relations |
| BioSample |
SAMN32798280 |
| SRA |
SRX19076922 |
