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Sample GSM1821690

Query DataSets for GSM1821690

Status

Public on Aug 24, 2017

Title

AE1_2

Sample type

SRA

Source name

airway epithelial cells

Organism

Homo sapiens

Characteristics

cell line: BEAS-2B
tissue: lung/bronchus
cell type: epithelial
treatment: oil

Treatment protocol

For the oil treatment, we used WAF of crude oil (3%) dilution. For the dispersant treatment, we used Corexit 9500 or Corexit 9527 at 300ppm. For the oil-dispersant mixture treatment, we used WAF-dispersed oil at 300ppm. For controls, we added the equivalent volume of water to the medium, which is the same water solution that was used to dilute the oil or dispersants. For each treatment, including the control, three independent replicate cell samples were used.

Growth protocol

Human bronchial epithelial cells (BEAS-2B cells), purchased from American Type Culture Collection (ATCC, Wiltshire, USA), were cultured following standard guidelines. Thawed cells were initially grew in a pre-coated flask containing fibronectin (0.01g/ml), bovine collagen type 1 (0.03mg/ml), and bovine serum albumin (0.01mg/ml). Following overnight growth in this pre-coated flask, the cells were sub-cultured in Dulbecco's Modified Eagle Medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin and 100U/ml streptomycin (Invitrogen, Carlsbad, CA). Cells were cultured at 37 ºC in a 100% humidified atmosphere of 5% CO2 in air. A single clone of BEAS-2B was grown to homogenize genomic variation between cultured cells. The cells were divided equally into separate flasks and grown under treatment or no treatment conditions (controls) for 22 passages (P22) for ~ 2.5 months.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted at Omega Bio-Tek, Inc (Norcross, GA) using the E.Z.N.A Total RNA kit II produced by the company (Omega Bio-Tek, Inc, Norcross, GA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

For the raw fastq files from each sample, we performed alignment to the Human Reference Genome (hg19) using TopHat to generate the BAM files.
We then used a number of Bioconductor packages to process the BAM files into gene count matrix following the procedures listed under http://www.bioconductor.org/help/workflows/rnaseqGene/.
Specifically, we used “BamFileList” function from the “Rsamtools” package to specify the number of reads (2,000,000 reads in our study) to be processed at a time.
We then used “makeTrascriptDbFromGFF” from the “GenomicFeatures” package to generate a database object that contains annotation information of exons, transcripts and genes from the UCSC Genome Browser. The “summarizeOverlaps” function from the “GenomicAlignments” package was then used to annotate the bam files and generate an object that is the gene count matrix containing the gene count for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes gene count values for each sample

Submission date

Jul 14, 2015

Last update date

May 15, 2019

Contact name

Yao-Zhong Liu

E-mail(s)

yliu8@tulane.edu

Phone

504-988-1888

Organization name

Tulane University School of Public Health and Tropical Medicine