|
| Status |
Public on Oct 21, 2014 |
| Title |
Oral Cancer Poor 5-year survival Y014 |
| Sample type |
SRA |
| |
|
| Source name |
Oral cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: oral mucosa
survival: Poor 5-year survival
disease state: oral cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ten 10-mm sections were obtained from archived FFPE tumor tissue samples for all subjects. Total RNA was isolated from tissues using RNeasy FFPE kit (Qiagen Inc., Valencia, CA) following the manufacturer’s protocol and yield was quantitated by Nanodrop, and stored at -80o C.
Total RNA (minimum of 2 mg) ranging from 18 to 30 nt were gel-purified and ligated to 3’ adaptor and 5’adaptor. Ligation products were reverse transcribed, then amplified for 16 cycles using the adaptor primers, and the fragments around 150 bp were isolated from PAGE-gel using TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Oral Cancer Poor 5-year survival Y014
|
| Data processing |
3'end adapters were clipped with fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
Clipped reads were processed with miraligner (Pantano. NAR 2010)
Genome_build: miRBase v20
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Nov 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Angela Yoon |
| E-mail(s) |
ajk55@columbia.edu
|
| Organization name |
Columbia University Medical Center
|
| Street address |
630 West 168th Street, PH15W-1562
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE52633 |
MicroRNA Marker Based Prognostication of Oral Squamous Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN02419041 |
| SRA |
SRX381517 |
