|
| Status |
Public on Jan 20, 2023 |
| Title |
WT BEAS-2B 3hr Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
BEAS-2B Airway Epithelial Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEAS-2B Airway Epithelial Cells
genotype: WT
challenge: Aspergillus fumigatus conidia
time: 3hr
|
| Treatment protocol |
Cells were challenged with 5 X 10^5 viable Aspergillus fumigatus conidia (AF29) and incubated for various times at 37C in the presence of 5% CO2.
|
| Growth protocol |
BEAS-2B airway epithelial cells were cultures according to standard protocols in RPMI1640 in 10% FBS plus Pen/Strep at 37C in the presence of 5% carbon dioxide. Cells were plated at a density of 5 X10^5 cells per well (24-well format) and allowed to equilibrate for 24 hours prior to challenge.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Buffer RLT containing BME. RNA was immediately extracted following the RNeasy Mini Kit Protocol. DNAase digestion was performed. Samples were eluted in 30ul twice.
Total RNA with RIN ≥ 8.0, was converted into a strand-specific library using Illumina’s TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, RS-122-2103), for subsequent cluster generation and sequencing on Illumina's NextSeq. The library was enriched by 13 cycles of PCR, validated using Agilent TapeStation and quantitated by qPCR. Individually indexed cDNA libraries were pooled and sequenced on NextSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
W6_S11
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequences were trimmed for residual adaptors and poor quality bases (sliding window 4, phred score 25) and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
Filtered paired end reads were aligned and counted to the human reference genome (GRCh38.96) using STAR’s GeneCounts quantitation mode.
DESeq2 analysis was conducted to determine normalized gene counts and differential expression (Padj < 0.05, log2-fold change > 0.5). Differential expression was conducted in a pair-wise manner between genotypes or treatments
Genome_build: GRCh38.96
|
| |
|
| Submission date |
Feb 03, 2020 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Shiv D. Kale |
| E-mail(s) |
sdkale@vt.edu
|
| Phone |
540-231-3784
|
| Organization name |
Virginia Tech
|
| Department |
Biocomplexity Institute
|
| Street address |
1015 Steger Hall, Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE144652 |
RNA-Seq analysis of gene expression changes by wildtype and Nlrx1 deficient BEAS-2B airway epithelial cells in response to A. fumigatus viable conidia |
|
| Relations |
| BioSample |
SAMN13973075 |
| SRA |
SRX7664271 |
