|
| Status |
Public on Mar 18, 2020 |
| Title |
HBEC_BAP_2 |
| Sample type |
SRA |
| |
|
| Source name |
HBEC_Benzo[a]pyrene
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human 3D bronchial epithelial cells (HBEC)
Stage: differentiated at air-liquid interface
treatment: Benzo[a]pyrene
|
| Treatment protocol |
Inserts were washed with phosphate buffered saline (PBS, pH 7.4) and then treated with PAHs in acetone vehicle on apical surface for up to 48 hrs, BAP (500 ug/ml), DBC (10 ug/ml) .
|
| Growth protocol |
Primary HBEC differentiated on transwell inserts (EpiAirway™ 100, Mattek, Ashland, MA) were transferred to 6-well plates each well containing 1 ml of assay medium and equilibrated for 24 hours at 37°C, 5% CO2 followed by a change of fresh medium before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from HBEC (n=4) using TRizol® reagent and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek). RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
mRNA was poly-A selected, and libraries were prepared with the PrepXTM mRNA and Illumina sequencing workflow (Wafergen Biosystems, Fremont, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
lane1-s010-indexRPI10-TAGCTT-SCT-3B_S10_L001
|
| Data processing |
Cutadapt (version 1.8.1) to trim adapter sequences from the paired-end reads
The human genome assembly GRCh38.84 was indexed using bowtie2-build (version 2.2.3)
TopHat (version 2.1.1.) was used to index the transcriptome and to align the trimmed reads to indexed transcriptome and genome.
Differential expression (q<0.05) was determined in CuffDiff (version 2.2.1) compared to vehicle control.
Genome_build: GRCh38.84
Supplementary_files_format_and_content: abudance measurements
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Mar 20, 2020 |
| Contact name |
Susan C. Tilton |
| E-mail(s) |
[email protected]
|
| Organization name |
Oregon State University
|
| Department |
AG Envr & Molec Toxicology
|
| Street address |
1007 ALS Bldg
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE128471 |
Benzo[a]pyrene and dibenzo[def,p]chrysene in 3D primary human bronchial epithelial cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN11160468 |
| SRA |
SRX5537206 |
