|
| Status |
Public on Jan 20, 2023 |
| Title |
nanoCAGE-seq_SKMEL2 |
| Sample type |
SRA |
| |
|
| Source name |
SKMEL2 cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SKMEL2
cancer type: A Melanoma cell line established from a metastasis of Thigh skin
|
| Treatment protocol |
No treatment was applied to the cell lines before profile.
|
| Growth protocol |
All cell lines were grown under the optimal condition according to ATCC handling guidelines for each cell line.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To identify transcription start site locations, we generated nanoCAGE-seq libraries following published methods(Jang, Hyo Sik et al. 2019; Salimullah, Md et al. 2011). In brief, we extracted mRNA from cancer cell lines using Dynabeads mRNA DIRECT Purification Kit (ThermoFisherScientific, 61011). 5'-capped mRNA was enriched through Terminator exonuclease digestion (Lucigen, TER51020). Afterwards, we processed 25ng of Terminator-treated mRNA following standard nanoCAGE protocol to capture 5' ends of mRNA via template-switching technology.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
nanoCAGE-seq libraries were sequenced on the Illumina NextSeq platform and aligned to the hg38 reference genome with STAR. All browser tracks are visualized on the WashU Epigenome Browser70.
Assembly: hg38
Supplementary files format and content: reads are aligned to hg38
Library strategy: nanoCAGE
|
| |
|
| Submission date |
Apr 19, 2022 |
| Last update date |
Jan 23, 2023 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
|
| Phone |
(314) 286-0866
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue
|
| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE201021 |
Pan-cancer tumor-specific antigens and membrane targets from transposable elements |
|
| Relations |
| BioSample |
SAMN27629814 |
| SRA |
SRX14906978 |
