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Sample GSM1308330 Query DataSets for GSM1308330
Status Public on Jan 17, 2014
Title MCF-7mRNA
Sample type SRA
 
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell type: Breast cancer
cell line: MCF-7
Growth protocol Human breast cancer cell lines MCF-7 and MDA-MB-435 were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco BRL, Grand island, NY) supplemented with 10 % fetal bovine serum (PAA Laboratories, Linz, Austria), 1% penicillin/streptomycin (Genom, China) at 37°C in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol Standard Trizol protocol
Standard Illumina TruSeq mRNA library prep
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description High quality reads which passed Illumina filter were kept
Data processing Basecalls performed using CASAVA version 1.8
Raw reads were aligned to human mRNA reference sequence (RefSeq) for GRCh37/hg19 downloaded from UCSC Genome browser employing FANSe2 mapping algorithm ((http://bioinformatics.jnu.edu.cn/software/fanse2/intro.html)) along with the options –L80–S10 –E5.
Splice variants were summed. The mRNA abundance was calculated using rpkM (reads per kilobase per million reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each sample
 
Submission date Jan 15, 2014
Last update date May 15, 2019
Contact name Cuihua Wang
E-mail(s) wang_cuihua@gzlab.ac.cn
Organization name Guangzhou Lab
Street address 601 Huangpu Ave, Guangzhou
City Guangzhou
State/province Guangdong
ZIP/Postal code 510632
Country China
 
Platform ID GPL10999
Series (1)
GSE54122 Next Generation Sequencing of MCF-7 and MDA-MB-435 cells
Relations
BioSample SAMN02585261
SRA SRX434441

Supplementary file Size Download File type/resource
GSM1308330_MCF-7.txt.gz 348.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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