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Sample GSM1855559 Query DataSets for GSM1855559
Status Public on Aug 22, 2019
Title MDA231-LM2 shCntr rep1
Sample type SRA
 
Source name Breast cancer cells
Organism Homo sapiens
Characteristics cell type: Lung metastatic derivative of MDA-MB-231
passage: 5-10
genotype: nontargeting shRNA
Treatment protocol NA
Growth protocol MDA-MB-231 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 2 days.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated using Qiazol (Qiagen, Valencia, CA) followed by chloroform extraction.
Total RNAs were subjected to enrichment of polyA+ RNA using Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). Strand-specific RNA-seq libraries were prepared from the polyA+ RNA. The RNA-seq libraries were sequenced using single-end methodology with a length of 50 nt (SE50) (two replicates each) using an Illumina HiSeq 2500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing RNA-Seq reads were aligned to the human reference genome (NCBI 37, hg19) using the spliced read aligner TopHat version 1.4.0 (1).
The bam files from TopHat were assembled using Cufflinks
The individual transcript assemblies from multiple RNA-Seq libraries are assembled into one master transcriptome using Cuffmerge
using Cuffdiff comparisons of expression levels of genes from the different conditions was performed
Genome_build: hg19
 
Submission date Aug 17, 2015
Last update date Aug 22, 2019
Contact name Mi Young Kim
E-mail(s) miyoungkim@kaist.ac.kr
Organization name KAIST
Street address Biological science
City DaeJeon
ZIP/Postal code 305-701
Country South Korea
 
Platform ID GPL16791
Series (1)
GSE72111 Genome-wide RNA-seq from GALNT14-depleted and GALNT14 overexpressing MDA-MB-231 LM2 and Par cells
Relations
BioSample SAMN03996581
SRA SRX1153664

Supplementary file Size Download File type/resource
GSM1855559_MK4.bw 61.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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