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Sample GSM1354442 Query DataSets for GSM1354442
Status Public on Sep 24, 2014
Title RNASeq_Control
Sample type SRA
 
Source name BEAS-2B cells
Organism Homo sapiens
Characteristics treatment: none
time point (hours): 0
Treatment protocol For exposing cells to nickel, NiCl2 (Sigma N6136) was added to the media at a concentration of 500 mM and the cells were cultured for 72 hours.
Growth protocol Immortalized human Bronchial Epithelial Cells (Beas-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (Atlanta Biologicals) at 37° C and 5 % CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from untreated and nickel treated cells using RNeasy kit (Qiagen, 74104) according to manufacturer’s instructions.
RNA-Seq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample 1
Data processing basecalling have been done by CASAVA-1.8.2
RNA-seq raw sequence data have been aligned to human hg19 by tophat (version 2.0.8 beta default parameters) with known reference annotation gtf file download from GENCODE website (v16). The gtf file have been modified to be compatible to tophat that only records denoted as “CDS,exon,start_codon,stop_codon,UTR” have been kept. Records annotated as "miRNA,misc_RNA,Mt_rRNA,Mt_tRNA,rRNA" have been export to another mask gtf file for further usage.
To estimate the FPKM values, cuffdiff from cufflinks package (version 2.1.1 default parameters with --multi-read-correct and --frag-bias-correct) have been used with mask gtf file that 15836 genes have been estimated as expressed in control( Fragments Per Kilobase of exon per Million fragments mapped (FPKM) > 1).
Genome_build: hg19
 
Submission date Mar 20, 2014
Last update date May 15, 2019
Contact name Dustin E Schones
E-mail(s) schoneslab@gmail.com
Phone +1-626-471-9319
Organization name City of Hope
Department Cancer Biology
Lab Schones
Street address 1500 Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL16791
Series (2)
GSE56052 Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [RNA-Seq]
GSE56053 Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption
Relations
BioSample SAMN02692748
SRA SRX497259

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

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