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Sample GSM4277372 Query DataSets for GSM4277372
Status Public on Jan 20, 2023
Title WT BMDCs 6hrs post challenge Replicate 3
Sample type SRA
 
Source name BMDCs challenged with viable Aspergillus fumigatus conidia
Organism Mus musculus
Characteristics cell type: Mouse bone marrow derived dendritic cells
time: 6hrs post challenge
genotype: WT
Treatment protocol Cells were challenged with 5 X 10^5 viable Aspergillus fumigatus conidia (AF29) and incubated for various times at 37C in the presense of 5% CO2.
Growth protocol Bone marrow was extracted from the tibia and femur of wildtype and nlrx1 deficient mice. Cells were differentiated using GM-CSF. Cells were grown for 6 days with a medium exchange on day 3. On day 6 cells were harvested and plated at a density of 5 X10^5 cells per well (24-well format)
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 WT9
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 alligned to mouse reference genome (GRCm38.94) using HiSAT2
Transcript Assemble and quantification of RNA-Seq was done via Stringtie, with output specific for DESeq2
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: GRCm38.94
 
Submission date Jan 20, 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 GPL19057
Series (1)
GSE143964 Time course RNA-Seq analysis of wildtype and Nlrx1 deficient bone marrow derived monocytoid dendritic cells indicate decision tree in response to A. fumigatus viable conidia
Relations
BioSample SAMN13893285
SRA SRX7584842

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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