|
| Status |
Public on Jan 31, 2024 |
| Title |
C_24hr_2: Charcoal-exposure 24 hours-replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
BEAS-2B bronchial epithelial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEAS-2B
cell type: bronchial epithelial
treatment: Charcoal
time: 24 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
| |
|
| Description |
Charcoal, exposure 24 hours, replicate 2
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters -p 8 --mm --dta
Fragments Per Kilobase of transcript per Million (FPKM) were calculated using stringtie v1.3.4d with parameter -e -B -p 8
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
|
| |
|
| Submission date |
Dec 01, 2020 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Sing-Hang Huang |
| E-mail(s) |
gb921.tw@gmail.com
|
| Organization name |
National Chiao Tung University
|
| Department |
Institute of Bioinformatics and Systems Biology
|
| Lab |
Prof. Jinn-Moon Yang
|
| Street address |
Rm. 304, No.75, Bo’ai St., East Dist.
|
| City |
Hsinchu City |
| ZIP/Postal code |
300 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE162386 |
Characterizing hookah smoking-induced transcriptional regulations in the human bronchial epithelial cell |
|
| Relations |
| BioSample |
SAMN16968355 |
| SRA |
SRX9610378 |
