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Sample GSM8076161 Query DataSets for GSM8076161
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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