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Sample GSM1899422 Query DataSets for GSM1899422
Status Public on Mar 03, 2016
Title A673
Sample type SRA
 
Source name EWS
Organism Homo sapiens
Characteristics cell line: A673
cell type: Ewing's sarcoma cell line
Growth protocol All Ewing’s sarcoma cell lines were kept in RPMI1640 medium supplemented with 10% FCS. The MSC lines 4+v and 5H [PMID:20466760] were grown in MesenCult MSC basal medium supplemented with 10% MesencCult stimulatory supplements (Stemcell Technologies)
Extracted molecule polyA RNA
Extraction protocol total RNA was extracted from each cell line using Trizol RNA extraction reagent (Life Technologies), according to manufacturer’s recommendations and 75 µg was used in two rounds of polyA selection to purify the mRNA.
The mRNA was reverse transcribed into cDNA and made into dsDNA using Just cDNA Double Stranded cDNA Synthesis Kit (Stratagene). The double stranded products were fragmented using Covaris S2 System, size selected using Ampure XP beads (Beckman Coulter), then sequencing libraries prepared before single end deep sequencing was carried out with an Illumina GA IIx to obtain 80bp reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description a673
Data processing Read trimming with Trim Galore, default settings
Alignment and transcript abundance estimation with Sailfish, default settings
Differential expression with DESeq2, default settings
Genome_build: human cDNA, Ensembl version 75
Supplementary_files_format_and_content: CSV, estimated transcripts per million (Sailfish estimate), cell type mean, standard deviation and log fold change (estimated by DESeq2)
 
Submission date Sep 30, 2015
Last update date May 15, 2019
Contact name Helio Pais
E-mail(s) helio.pais@imm.ox.ac.uk
Organization name University of Oxford
Department Weatherall Institute of Molecular Medicine
Street address Jonh Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL10999
Series (1)
GSE73610 RNA-Seq profiling of Ewing's sarcoma and MSC cell lines
Relations
BioSample SAMN04123613
SRA SRX1297097

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

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