|
| Status |
Public on Feb 01, 2015 |
| Title |
Sample_P019 |
| Sample type |
SRA |
| |
|
| Source name |
progressive leukoplakias 009
|
| Organism |
Homo sapiens |
| Characteristics |
histologic diagnosis: hyperkeratosis with focus of mild dysplasia
source tissue: gingival leukoplakia
|
| 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 |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
small RNA (18 to 30nt)
incisional biopsy of an oral leukoplakia that progressed to oral cancer within 5 yrs
|
| 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
|
| |
|
| Submission date |
Oct 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Elizabeth Philipone |
| E-mail(s) |
ep2464@columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Oral & Maxillofacial Pathology
|
| Street address |
630 West 168th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE62809 |
Predictive Value of MicroRNAs in the Progression of Oral Leukoplakias |
|
| Relations |
| BioSample |
SAMN03151517 |
| SRA |
SRX746173 |
