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Sample GSM1964910 Query DataSets for GSM1964910
Status Public on Dec 31, 2017
Title HPTB-treated
Sample type SRA
 
Source name MDA-MB-231
Organism Homo sapiens
Characteristics cell line: breast cancer cell line MDA-MB-231
treatment: 5µM HPTB for 4 hours at 37°C
Treatment protocol MDA-MB-231 cells were treated with 5µM DMSO or 5µM HPTB for 4 hours at 37°C
Growth protocol The human breast cancer cell line, MDA-MB-231 was obtained from ATCC and cultured in Dulbecco’s modified essential medium (DMEM) containing 10% fetal bovine serum (FBS) and passaged one or two times a week.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNEasy kit (Qiagen) and treated with RNAse free Dnase-I (Qiagen)
RNA-seq libraries were prepared from RNEasy extracted RNA samples from which rRNA was removed using Ribo-ZeroTM and following the TruSeq Stranded Total RNA Sample Prep kit protocol (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Data processing After filtering contaminant (aligned) reads, the reads with good quality were aligned to several human reference databases including hg19 genome, RefSeq exons, splicing junctions using BWA alignment algorithm.
The filtered reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were then counted as expression level for a corresponding transcript
and was further subjected to log2 transformation and global median normalization, to compare transcripts levels among distinct samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each transcript in each sample
 
Submission date Dec 07, 2015
Last update date May 15, 2019
Contact name Martin J. Walsh
E-mail(s) martin.walsh@mssm.edu
Organization name Mount Sinai School of Medicine
Department Structural and Chemical Biology
Street address One Gustave L. Levy Pl.
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL9052
Series (2)
GSE75742 The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq_HPTB]
GSE75743 The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis
Relations
BioSample SAMN04321296
SRA SRX1466538

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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