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Sample GSM1273056 Query DataSets for GSM1273056
Status Public on Oct 21, 2014
Title Oral Cancer Favorable 5-year survival Y003
Sample type SRA
Source name Oral cancer tissue
Organism Homo sapiens
Characteristics tissue: oral mucosa
survival: Favorable 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 Favorable 5-year survival Y003
Data processing 3'end adapters were clipped with 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
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
BioSample SAMN02419030
SRA SRX381506

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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