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Sample GSM4292918 Query DataSets for GSM4292918
Status Public on Jan 20, 2023
Title WT BEAS-2B 0hr Replicate 3
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: 0hr
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 W3_S9
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 SAMN13973077
SRA SRX7664269

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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