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| Status |
Public on Sep 24, 2014 |
| Title |
RNASeq_Nickel |
| Sample type |
SRA |
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| Source name |
BEAS-2B cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: NiCl2
time point (hours): 72
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 2
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| 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
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| Submission date |
Mar 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
schoneslab@gmail.com
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| Phone |
+1-626-471-9319
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| Organization name |
City of Hope
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| Department |
Cancer Biology
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| Lab |
Schones
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| Street address |
1500 Duarte Rd
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02692743 |
| SRA |
SRX497260 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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