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| Status |
Public on Apr 19, 2016 |
| Title |
Group 8. LN-PCa |
| Sample type |
SRA |
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| Source name |
lymph node
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| Organism |
Homo sapiens |
| Characteristics |
organ: lymph node
status: tumor
source: metastatic lesion
storage: fresh-frozen
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| Treatment protocol |
n.a.
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| Growth protocol |
Samples obtained by radical prostatectomy
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Bee total RNA extraction
Illumina Small RNA Sample Preparation Guide, Part #1004239
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
metastatic lesion
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| Data processing |
CLC-Bio Genomics Workbench (v. 4.9)
Data Import using Illumina Genome Analyzer Single Read importer. Parameters: Quality score = Illumina Pipeline 1.3 and 1.4 Discard sequence names = Yes Discard quality scores = No
“Small RNA Analysis” workflow
Read-summarizing and adapter-removal parameters from the “Extract and Count” tool: Minimum sampling count: 4; Minimum and maximum number of nucleotides in reads: 15 and 35 nt, respectively; no 3’- or 5’- terminal nucleotide removal
Each read was screened with “no fixed adapter length” for the (partial) presence of Illumina small RNA adapter: CAAGCAGAAGACGGCATACGA on the minus strand with alignment mismatches and gaps allowance at a mismatch cost of 3, and a gap cost of 5, minimum score: ns, minimum score end: 3. If adapter was not found reads were discarded from further analysis
Filtered sequence reads were mapped to sncRNAdb with a maximum of 2 mismatches allowed using the “Annotate and Merge” tool
Boundaries of sdRNAs, tRFs and other sncRNA-derived RNAs (sncdRNAs) and specific location on the precursor sequence were done using Fragment Location Annotation and Identification Mapper (Hoogstrate Y et al., Bioinformatics. 2015; 31:665-673)
Genome_build: Custom sncRNAdb based on hg 19 (Hoogstrate Y et al., Bioinformatics. 2015; 31:665-673)
Supplementary_files_format_and_content: tab-delimited text file including raw and RPM values for each small RNA-derived RNA in each sample
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| Submission date |
Apr 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Elena Martens-Uzunova |
| E-mail(s) |
e.martens@erasmusmc.nl
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| Organization name |
Erasmus MC
|
| Department |
Urology
|
| Street address |
Wytemaweg 80
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| City |
Rotterdam |
| ZIP/Postal code |
3000CA |
| Country |
Netherlands |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE80400 |
Small RNA sequencing of human prostate cancer samples |
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| Relations |
| BioSample |
SAMN04867797 |
| SRA |
SRX1711825 |
| 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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