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Sample GSM1557608 Query DataSets for GSM1557608
Status Public on Oct 15, 2015
Title Control
Sample type SRA
Source name Control
Organism Homo sapiens
Characteristics cell type: macrophage
treatment: Control
time: Control
concentration sample (ng/ul): 626.7
ratio 260/280: 2.08
ratio 260/230: 2.25
rin number: 10.0
Treatment protocol 1 mM Staurosporine (STS) treatment samples for 4h and 6h
Extracted molecule total RNA
Extraction protocol RNA extraction with Trizol
1.5 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 110 nt to 150 nt on a 8% acrylamide gel. Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB 5500 Genetic Analyzer
Description Sample name: 20121015_21
SOLiD5500, Life Technology. Sequencing of 35b. with 10b. barcoding sequences.
Small-RNA seq
Processed data file: norm1Msignal_human.txt
Data processing Lifescope v2.5 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then merged per samples with keeping read group per lane.
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 18), tRNAs from UCSC web server (UCSC tables), yRNAs and ncRNAs from ensembl ncRNAs release 69 and piRNAs from fRNAdb.
Genome_build: hg19
Supplementary_files_format_and_content: [norm1Msignal_human.txt] Tabulated text file of raw data counts normalized to 1000000 count in each sample.
Submission date Dec 03, 2014
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 GPL16558
Series (2)
GSE63799 High-throughput small RNA sequencing of human primary macrophages stimulated with staurosporine
GSE63802 Small RNA-sequencing in apoptotic macrophages
BioSample SAMN03249356
SRA SRX794041

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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