|
| Status |
Public on Apr 29, 2016 |
| Title |
siCT-1 |
| Sample type |
SRA |
| |
|
| Source name |
H3A cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human melanocytes
sirna: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tumors was extracted using TRIzol (Ambion, CA, USA). Total RNA from cell lines was extracted using a total RNA miniprep kit (Sigma-Aldrich)
Protocol outlined in Ion AmpliSeq Transcriptome Human Gene Expression Kit from ThermoFisher Scientific
Ampliseq RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
basecalling from AmpliSeq Platform
data pre-processing (5' trimming or low qulaity filter?)
two step alignment integrated with Tophat2 and Bowtie2
count reads (HT-Seq v0.6.0)
read count normalization by edgeR v3.8.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM and raw count values for each Sample.
|
| |
|
| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
brian james |
| E-mail(s) |
bjames@sanfordburnham.org
|
| Organization name |
Sanford Burnham
|
| Street address |
10901 North Torrey Pines Road
|
| City |
San Diego |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE79917 |
Transcriptionally inactive ATF2 variant drives melanomagenesis [Seq] |
| GSE81014 |
Transcriptionally inactive ATF2 variant drives melanomagenesis |
|
| Relations |
| BioSample |
SAMN04606400 |
| SRA |
SRX1678603 |
