|
| Status |
Public on Mar 17, 2018 |
| Title |
Control_6W_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bronchial epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEAS-2B
cell type: Bronchial epithelial cell
|
| Treatment protocol |
For Ni exposure, various concentrations of NiCl2 (Sigma N6136) was added to the media and the cells were cultured for 6 weeks. Following exposure, the cells were washed and cultured in Ni-free medium for 2 weeks to obtain the Ni-washed-out cells. To obtain homogenous populations of Ni-exposed cells, the cells exposed to 100 mM NiCl2 for 6 weeks were plated in 15 cm plates in Ni-free medium at the rate of 1000, 500, 100 and 50 cells per plate. Nicely separated single colonies were picked and the populations were expanded in Ni-free medium.
|
| Growth protocol |
BEAS-2B cells were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from treated cells using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample and DESeq Differential expression analysis between control and test samples
|
| |
|
| Submission date |
Feb 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Suresh Cuddapah |
| E-mail(s) |
Suresh.Cuddapah@nyumc.org
|
| Organization name |
New York University Langone Medical center
|
| Department |
Environmental Sciecne
|
| Street address |
57 Old Forge Road
|
| City |
Tuxedo |
| State/province |
New York |
| ZIP/Postal code |
10987 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE95180 |
Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1 |
|
| Relations |
| BioSample |
SAMN06368748 |
| SRA |
SRX2581729 |
