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| Status |
Public on Aug 18, 2013 |
| Title |
Lib5 |
| Sample type |
SRA |
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| Source name |
squamous cell carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE Tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from altogether four 20-micrometer sections from FFPE tissue samples were harvested using the RecoverAll total RNA isolation kit (Ambion)
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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
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| Description |
small RNA
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| 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
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| Submission date |
Nov 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kui Qian |
| E-mail(s) |
kui.qian@helsinki.fi
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| Organization name |
University of Helsinki
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| Lab |
DNA Sequencing and Genomics Laboratory
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| Street address |
Viikinkaari 4
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| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE42380 |
MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples |
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| Relations |
| SRA |
SRX205119 |
| BioSample |
SAMN01816091 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1038619_Lib5.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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