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| Status |
Public on Jun 30, 2020 |
| Title |
Lib6 |
| Sample type |
SRA |
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| Source name |
adenocarcinoma in situ
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| Organism |
Homo sapiens |
| Characteristics |
tissue: FFPE Tissue from HPV-infected cervical epithelium (adenocarcinoma in situ)
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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 |
miRNA-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 human genome(GRC37) using SOLiD small RNA pipeline (RNA2MAP) with default parameters.
Genome_build: GRCh37, miRBase v17
Supplementary_files_format_and_content: csv files report miRNA normalized counts
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| Submission date |
Oct 10, 2014 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Petri Auvinen |
| Organization name |
University of Helsinki
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| Lab |
DNA Sequencing and Genomics
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| Street address |
Viikinkaari 5
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| City |
Helsinki |
| ZIP/Postal code |
00790 |
| Country |
Finland |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE62239 |
HPV cell lines and HPV tissue MicroRNA SOLiD sequencing |
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| Relations |
| BioSample |
SAMN03103889 |
| SRA |
SRX730589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1523458_Lib6_miRNA.csv.gz |
16.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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