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Sample GSM1701300 Query DataSets for GSM1701300
Status Public on Oct 15, 2015
Title STS_6h_2
Sample type SRA
 
Source name STS 6h
Organism Homo sapiens
Characteristics cell type: macrophage
treatment: Staurosporine
time: 6h
concentration sample (ng/ul): 152.4
ratio 260/280: 1.97
ratio 260/230: 2.28
rin number: 8.7
Treatment protocol 1 mM Staurosporine (STS) treatment samples for 4h and 6h
Extracted molecule total RNA
Extraction protocol RNA extraction with Trizol
50 ng of RNA were treated with the trilink library kit (TriLink Biotechnologies). 17 cycles of PCR were performed. Libraries were size-selected for the 130 to 155 nt fraction on a caliper 300 XT chip. Libraries were sequenced on the Ion Proton, 10 libraries were loaded on one P1 Chip.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Ion Torrent Proton
 
Description Sample name: STS6H_2.010
Staurosporine 6h replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: hg19_tableCount.txt
Data processing Adaptor trimming with cutadapt-1.2.1, then bowtie2 v2.2.4 mapping versus hg19 build with " --local --very-sensitive-local -k 10" parameters.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 20), tRNAs from UCSC web server (UCSC tables), yRNAs and ncRNAs from Ensembl ncRNAs release 75 and piRNAs from fRNAdb.
Genome_build: hg19
Supplementary_files_format_and_content: [hg19_tableCount.txt] Tabulated text file containing raw data of small RNAs, including miRNA from miRBase v20, tRNAs for tRFs identification from UCSC table browser and Ensembl non-coding RNAs r75, no normalisation.
 
Submission date Jun 01, 2015
Last update date May 15, 2019
Contact name Kevin Lebrigand
Organization name IPMC/CNRS
Lab Functional Genomics Platform of Nice-Sophia-Antipolis, France.
Street address 660 route des lucioles
City Valbonne - Sophia-Antipolis
ZIP/Postal code 06560
Country France
 
Platform ID GPL17303
Series (2)
GSE63799 High-throughput small RNA sequencing of human primary macrophages stimulated with staurosporine
GSE63802 Small RNA-sequencing in apoptotic macrophages
Relations
BioSample SAMN03754539
SRA SRX1045287

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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