|
Status |
Public on Feb 19, 2024 |
Title |
Untreated_2 |
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: Untreated
|
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 |
SRX23598391 |
BioSample |
SAMN39917544 |