|
| Status |
Public on Feb 19, 2024 |
| Title |
PSA34_3 |
| Sample type |
SRA |
| |
|
| Source name |
Bronchial epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bronchial epithelium
cell line: CFBE41o-
cell type: Bronchial epithelial cells
genotype: CFTR deltaF508/deltaF508
treatment: PSA34
|
| Treatment protocol |
CFBE41o- cells were apically treated with fluorescently labeled phages OMKO1, LPS-5, PSA04, and PSA34 at a concentration of 1 x 109 PFU/ml in MEM pH-adjusted to 6.5 for 24 h.
|
| Growth protocol |
CFBE41o- cells were cultured in Minimal Essential Media supplemented with 10% of heat-inactivated fetal bovine serum, 2 mM L-glutamine, and 5 U/ml penicillin-5 mg/ml streptomycin in adherent cell culture conditions at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was conducted using the Quick-RNA Miniprep kit (Zymo Research), followed by RNA clean-up using the RNA Clean & Concentrator-5 kit (Zymo Research).
Library preparation was done using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research).
Libraries were sequenced on an Illumina NovaSeq 6000 instrument with a sequencing depth of 30 million read pairs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads quality was first confirmed using FastQC v.0.11.9. Reads were trimmed for adapters and low-quality sequences using Trim Galore! v0.6.6 and aligned to the reference human genome GRCh38/hg38 using STAR v2.6.1d.
Assembly: Reads mapping to exons were assigned using featureCounts v2.0.1. Quality control was tracked using MultiQC v1.9.
Supplementary files format and content: Csv files, raw transcript counts for each treatment
|
| |
|
| Submission date |
Feb 12, 2024 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Paula F. Zamora |
| E-mail(s) |
paula.zamora@dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Street address |
74 College st
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE255619 |
Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells |
|
| Relations |
| SRA |
SRX23598393 |
| BioSample |
SAMN39917554 |
