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| Status |
Public on Mar 01, 2015 |
| Title |
582_N |
| Sample type |
SRA |
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| Source name |
Adjacent normal tissue
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| Organism |
Homo sapiens |
| Characteristics |
age (years): 83
Stage: N/A
grade: N/A
tumor size: N/A
recurrence: N/A
lymph node metastasis: N/A
recurrence-free time (years): N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each small RNA library was constructed from total RNA of each sample using the SOLiD Total RNA-Seq Kit (Applied Biosystems, Foster City, CA, USA). Integrity of each small RNA library was examined by using RNA 6000 Nano Chip (Agilent, Santa Clara, CA, USA), Small RNA Chip (Agilent), and Bioanalyzer (Agilent) following the standard protocol.
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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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| Data processing |
All SOLiD small RNA reads generated from ligation sequencing were screened to filter out any reads containing ribosomal RNA, transfer RNA, and adaptor sequences (AB Small RNA Analysis Tool V0.5).
The remaining reads were aligned to human miRNA reference (AB Small RNA Analysis Tool V0.5). The reference databases used for alignment were miRBase (version 17.0) and human genome RefSeq Hg19.
One mismatch was allowed for the first 16 sequences of a SOLiD read and up to 4 maximum mismatches were allowed for a miRNA read count.
Reads that were not uniquely mapped to miRBase reference were disregarded to eliminate ambiguous alignments.
miRNA reads derived from each sample were normalized using the quantile-quantile scaling method. A miRNA mean expression profile obtained from 38 samples was used as the reference for quantile-quantile linear scaling. A scaling factor was determined for each sample dataset to vertically shift all miRNA expression data close to the diagonal line in each log10-scaled quantile-quantile plot.
Genome_build: human genome hg 19
Supplementary_files_format_and_content: tab-delimited text files include miRNA ID, mapped miRNA read counts, RNA strand direction, and genomic coordinates.
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| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
King-Jen Chang |
| Organization name |
National Taiwan University Hospital
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| Department |
Department of Surgery
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| Street address |
No.1, Changde St., Zhongzheng Dist.
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| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE40049 |
Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing |
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| Relations |
| SRA |
SRX176355 |
| BioSample |
SAMN01113053 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM984360_solid_20101214_KuoWH_SmallRNA_F3_582_N.csfasta_extend.counts.35.4.txt.gz |
28.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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