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Sample GSM1038615 Query DataSets for GSM1038615
Status Public on Aug 18, 2013
Title Lib1
Sample type SRA
 
Source name HPK IA
Organism Homo sapiens
Characteristics tissue: Cell line
Growth protocol HPK IA and HPK II cells established by transfection of primary human foreskin keratinocytes with HPV 16, together with CaSki epidermoid cervical carcinoma cells and SiHa human cervical tumor cells were cultured in DMEM (Sigma-Aldrich Inc., Saint Louis, MO) supplemented with 10% fetal bovine serum and penicillin/streptomycin at 37°C and 5% CO2 in a humidified incubator.
Extracted molecule total RNA
Extraction protocol Total RNA from cultured cells was isolated using the mirVana RNA isolation kit (Ambion, Austin, TX).
Small RNA fragments of ~18–25nt were enriched from total RNA preparations (ca. 6 mg) from HPK IA cells, HPK II cells and ten tissue samples by flashPAGE system (Ambion). All of the enriched small RNA fractions (30-60 ng) was used for preparing the libraries and subsequently ligated to adaptors in the SOLiDTM Total RNA-Seq kit (Ambion). Next, small RNAs were reverse transcribed into cDNA libraries, size selected using PAGE gel, and amplified with PCR primers introducing barcode sequences. The libraries were prepared for emulsion PCR (emPCR) according to SOLiD sequencing instructions followed by sequencing using the SOLiD 4 instrument (Life Technologies, Carlsbad, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB SOLiD 4 System
 
Description small RNA
Data processing The reads in SOLiD colorspace format were mapped to papillomavirus genomes using SOLiD small RNA pipeline (RNA2MAP) with default parameters.
The mapped results were converted to GFF files using MaToGff (Applied Biosystems).
We predicted novel virus-encoded miRNA candidates from the small RNA sequencing data using our recently developed miRSeqNovel software
Genome_build: The reference genome was constructed by concatenating 393 complete papillomavirus genomes retrieved from NCBI, including known subtypes and isolates of HPV and papillomaviruses in other species.
Supplementary_files_format_and_content: wig files were generated using RNA2MAP
 
Submission date Nov 19, 2012
Last update date May 15, 2019
Contact name Kui Qian
E-mail(s) kui.qian@helsinki.fi
Organization name University of Helsinki
Lab DNA Sequencing and Genomics Laboratory
Street address Viikinkaari 4
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL13393
Series (1)
GSE42380 MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples
Relations
SRA SRX205115
BioSample SAMN01816087

Supplementary file Size Download File type/resource
GSM1038615_Lib1.wig.gz 798.0 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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