|
| Status |
Public on Jun 07, 2023 |
| Title |
16HBE14o- CFTRlow #3 rep3 [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 |
SAMN32192556 |
| SRA |
SRX18671436 |
