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Sample GSM6822502 Query DataSets for GSM6822502
Status Public on Jun 07, 2023
Title 16HBE14o- CFTRlow #3 rep2 [RNA-seq]
Sample type SRA
 
Source name 16HBE14o-
Organism Homo sapiens
Characteristics cell line: 16HBE14o-
cell type: human bronchial epithelial cells
genotype: CFTRlow
Growth protocol Cells were grown in DMEM + 10% FBS using standard methods
Extracted molecule total RNA
Extraction protocol Confluent 16HBE14o- cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and Bioanalyzer. Samples stored at -80oC under ethanol.
Oligo-dt mRNA directional
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequences were mapped to the hg19 human genome with STAR 2.7 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using DAVID 2021.
Assembly: hg19
Supplementary files format and content: CSV file includes normalized count values for each sample
 
Submission date Dec 13, 2022
Last update date Jun 07, 2023
Contact name Ann Harris
E-mail(s) axh575@case.edu
Organization name Case Western Reserve University
Department Genetics and Genome Sciences
Street address 2109 Adelbert Rd
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL24676
Series (2)
GSE220854 Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts [RNA-seq]
GSE220855 Cellular heterogeneity in the 16HBE14o- airway epithelial line impacts functional readouts.
Relations
BioSample SAMN32192557
SRA SRX18671435

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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