|
| Status |
Public on Dec 30, 2018 |
| Title |
UACC62P_1 |
| Sample type |
SRA |
| |
|
| Source name |
Parental Cancer Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line name: UACC62P
cell type: melanoma
treatment: none
treatment time (h): 0
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS + 1% Anti/Anti. Vemurafenib-resistant variants were selected in 2 uM Vemurafenib for 2 months, and were continuously cultured in 2 uM Vemurafenib.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was harvested from the cell lines using the Qiagen Rneasy Mini Kit (Cat# 74104)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Caliper LabChipGX HS DNA assays. Libraries were pooled and run on two lanes, and sequencing was performed in a 1x50bp single end read format using HiSeq 4000 SBS reagents.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed with Illumina Real Time Analysis, RTA_v2.7.7
Demultiplexing and FastQ conversion with Illumina Bcl2fastq v2.19.0
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample
|
| |
|
| Submission date |
Jun 18, 2018 |
| Last update date |
Jun 08, 2020 |
| Contact name |
Sean Alexander Misek |
| E-mail(s) |
miseksean@gmail.com
|
| Organization name |
Michigan State University
|
| Street address |
1355 Bogue Street
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE115938 |
Treatment of melanoma cell lines with CCG-222740 |
|
| Relations |
| BioSample |
SAMN09439826 |
| SRA |
SRX4230291 |
