|
|
| Status |
Public on Jun 10, 2019 |
| Title |
Parent_IFN_B_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BEAS-2B_Parent_IFN_B
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEAS-2B
cell type: respiratory epithelial cells
genotype/variation: Wild type
treated with: 0.2 ng/ml IFNβ for 24h
|
| Treatment protocol |
Cells were treated with IFNβ (0.2 ng/ml) and IFNλ1 (5ng/ml) for 24h.
|
| Growth protocol |
Cells were grown in Lonza's bronchial epithelial cell growth medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy mini kit (Qiagen).
To obtain the final sequencing library, 14 cycles of PCR were performed using Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes, Espoo, Finland). Three biological replicates were used and for each sample replicate we obtained ~50 million paired 50-mer reads (using Illumina HiSeq 2500 platform).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
p_ifn_b_rep2
|
| Data processing |
Data were examined using Tuxedo pipeline for differential gene expression analysis. We used default parameters for these software programs and used a cutoff of 0.05 False Discovery Rate (FDR) by Benjamin-Hochberg method to determine differentially expressed genes with statistical significance.
We aligned to hg38 reference genome using HISAT2, version 2.0.5.
FPKM values were obtained using Cufflinks, patched version of 2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM abundance measurements
|
| |
|
| Submission date |
May 10, 2018 |
| Last update date |
Jun 10, 2019 |
| Contact name |
Sijung Yun |
| Organization name |
NIH/JHU
|
| Street address |
8908 Ewing Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20817 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE114284 |
IRF1 regulates IFN dependent and independent gene expression |
|
| Relations |
| BioSample |
SAMN09104956 |
| SRA |
SRX4063209 |
