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| Status |
Public on Nov 18, 2017 |
| Title |
Z2013-6992 |
| Sample type |
SRA |
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| Source name |
serum
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 68
disease state (dignity): renal cell carcinoma
t-stage: 2
n-stage: 0
m-stage: 0
grade: 2
uicc: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the miRNeasy serum/plasma Kit (Qiagen) following the manufacturer instructions. The RNA concentration was determined using the Nanodrop UV-Vis Spectrophotometer (Thermo Fisher Scientific).
NEBNext small RNA library prep kit (New England Biolabs) was used according to the manufacturers instructions, followed by Illumina single-end sequencing with read length of 75bp on the NextSeq 500 Sequencing System (Illumina). There were 20 M indexed reads per sample on average.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Processed data files: annex 2_miRNA result tables.xlsx, annex 3_miRNA counts.xlsx, annex 3_piRNA counts.xlsx, annex 4_miRNA expression.xlsx, annex 4_piRNA expression.xlsx, annex 5_isomiR counts.xlsx, annex 5_piRNA result tables.xlsx, annex 6_counts other small RNAs.txt
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| Data processing |
Sequencing reads are processed using Cobra, Biogazelle’s proprietary small RNA sequencing pipeline for read QC, adapter trimming, read mapping and read annotation.
Mapped reads are annotated based on the latest miRBase release. Read QC, read annotation and read length distribution are provided for each sample.
Raw and normalized expression data is reported for each mature miRNA in miRBase. In addition, expression levels for individual isomiRs is provided.
Genome_build: miRBase Release 21 (June 2014)
Supplementary_files_format_and_content: abundance measurements
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| Submission date |
Aug 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jörg Ellinger |
| E-mail(s) |
joerg.ellinger@ukb.uni-bonn.de
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| Organization name |
Universitätsklinikum Bonn
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| Department |
Urologie
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| Street address |
Sigmund-Freud-Straße 25
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| City |
Bonnn |
| State/province |
NRW |
| ZIP/Postal code |
53127 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE85699 |
Serum miR-122-5p and miR-206 expression: Non-invasive prognostic biomarkers for renal cell carcinoma |
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| Relations |
| BioSample |
SAMN05579938 |
| SRA |
SRX2026419 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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