|
| Status |
Public on Mar 01, 2022 |
| Title |
WTBE ALI rep3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
culture condition: Air-liquid interface
cell line: WTBE (CFBE41o- cells stably expressing wild-type CFTR)
cell type: Cystic fibrosis (CF) bronchial epithelial cells
|
| Treatment protocol |
For transwell-cultured (ALI) condition, cells were seeded on Millicell cell culture insert (Millipore) placed in 24-well plates. Media on the apical surface was removed daily until complete confluency (dry membrane) and basolateral media were replaced every other two days. Confluent cells were cultured for at least another 10days for polarization. For submerged cells, cells were also cultured in 24well plates and cultured till fully confluent.
|
| Growth protocol |
Human bronchial epithelial CFBE41o- cells stably expressing F508del-CFTR (CFBE) or wild-type CFTR (WTBE) were cultured in MEM medium, supplemented with 10% fetal bovine serum (Hyclone), 0.5% Penicillin/Streptomycin and 2mM L-glutamine. 0.5µg/mL puromycin (InvivoGen) were added for WTBE while 25µg/mL puromycin for CFBE cells to select stably transfected cells. Cells were maintained in a humidified chamber with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and quantified by Qubit RNA HS Assay Kit (ThermoFisher).
The library was prepared using illumina TruSeq Stranded mRNA sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
S9_0
|
| Data processing |
Paired raw reads were trimmed and mapped on Banana Slug Analytics Platform (http://sluganalysis.ucsc.edu).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with FPKM values for each sample
|
| |
|
| Submission date |
Nov 01, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Jay Kolls |
| Organization name |
Tulane University
|
| Department |
Medicine
|
| Lab |
Center for Translational Research in Infection and Inflammation
|
| Street address |
1430 Tulane Ave
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE186919 |
mRNA-Seq of WTBE and CFBE cells |
| GSE186920 |
Multi-omics comparisons between CFBE41o- cells stably expressing wide-type CFTR and F508del-mutant CFTR |
|
| Relations |
| BioSample |
SAMN22818369 |
| SRA |
SRX12877076 |
