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Status |
Public on Apr 19, 2016 |
Title |
Group 6. PCa 8 recurrent |
Sample type |
SRA |
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Source name |
prostate
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Organism |
Homo sapiens |
Characteristics |
organ: prostate status: tumor source: primary tumor 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 |
carcinoma of the prostate
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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
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Department |
Urology
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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 |
SAMN04867795 |
SRA |
SRX1711823 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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