|
| Status |
Public on Jun 26, 2024 |
| Title |
NHBE cells, secretory population, rep C |
| Sample type |
SRA |
| |
|
| Source name |
NormalHumanBronchial/TrachealEpithelialcells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: NormalHumanBronchial/TrachealEpithelialcells
cell type: Secretory cells (SiR-tubulin-/CD271-/CD66c+/TSPAN8-)
|
| Growth protocol |
Normal human bronchial/tracheal epithelial (NHBE) (Lonza Bioscience, CC-2540S) cells, harvested from healthy individuals, were expanded using either Pneumacult-Ex Plus Media (STEMCELL Technologies) and seeded on 6.5mm Transwell 0.4 μm pore polyester inserts (STEMCELL Technologies). Once confluent 2-4 days post-seeding, the ALI cultures were airlifted: apical media was removed to expose cells and basal compartment media was replaced with either Pneumacult-ALI Basal Media (STEMCELL Technologies). Cells were maintained at air-liquid interface (ALI) at 37°C and 5% CO2 in a humidified incubator. Cells were used at 3+ weeks post-ALI.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Library preparation was performed using the SMART-Seq mRNA LP kit (Takara).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
150 bp reads
|
| Data processing |
Reads were trimmed of adapter sequences and low-quality bases with Trimmomatic (version 0.39) and mapped to the human reference genome from Ensembl (GRCh38 release 111) with STAR (version 2.7.8a).
Reads per gene were counted with HTSeq (version 1.99.2). Differential expression testing was performed with DESeq2 (version 1.42).
Assembly: GRCh38 release 111
Supplementary files format and content: Tab-separated gene count files from HTSeq
|
| |
|
| Submission date |
Apr 05, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Frances Shepherd |
| Organization name |
University of Minnesota
|
| Street address |
689 23rd Ave SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE263356 |
Gene expression profiling of sorted primary human bronchial epithelial cell populations |
|
| Relations |
| BioSample |
SAMN40728785 |
| SRA |
SRX24133599 |
