|
| Status |
Public on Jan 12, 2022 |
| Title |
HBE FOXA1 KD rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HBE FOXA1 KD rep3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human bronchial epithelial cells
|
| Treatment protocol |
Samples were treated with negative control siRNA (sc-37007, Santa Cruz Biotechnology) or siRNA targetting either FOXA1 (sc-37930), FOXA2 (sc-35569), or a combination of the latter two, each at 30nM using RNAiMax transfection reagent (Life Technologies)
|
| Growth protocol |
HBE ALI cells were cultured according to Fulcher et al. 2005
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Confluent HBE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FOXA1_DEGs.csv
|
| Data processing |
Sequences were mapped to the hg19 human genome with STAR 2.6 (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 gProfiler.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample
|
| |
|
| Submission date |
Jan 16, 2020 |
| Last update date |
Jan 12, 2022 |
| Contact name |
Ann Harris |
| E-mail(s) |
[email protected]
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genome Sciences
|
| Street address |
2109 Adelbert Rd Building
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE143767 |
The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. [RNA-seq] |
| GSE143769 |
The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. |
|
| Relations |
| BioSample |
SAMN13871473 |
| SRA |
SRX7570761 |
