|
| Status |
Public on Jul 16, 2019 |
| Title |
SKMel147_0h_N2 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: melanoma cell line SKMel147
treatment: control
treatment time: 0 hr
|
| Treatment protocol |
Cells were treated with 10 uM CCG-222740 or vehicle control for either 0, 2, 6, or 24 h.
|
| Growth protocol |
Cells were grown in DMEM + 10% FBS + 1% Anti/Anti and were passaged in 10-cm cell culture plates. To generate experimental samples the cells were seeded into 6-cm plates.
|
| 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 |
Jul 15, 2019 |
| Last update date |
Jul 17, 2019 |
| 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) |
| GSE134320 |
Treatment of melanoma cell lines with CCG-222740 |
|
| Relations |
| BioSample |
SAMN12280564 |
| SRA |
SRX6449278 |
