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Sample GSM2794443 Query DataSets for GSM2794443
Status Public on Dec 05, 2017
Title LD3_1 Chemotherapeutic Model Day 3 Post Infection
Sample type SRA
 
Source name whole mouse lungs
Organisms Mus musculus; Aspergillus fumigatus
Characteristics mouse strain: CD1
a. fumigatus strain: CEA10
model: Chemotherapeutic
time point: day 3
Extracted molecule total RNA
Extraction protocol Whole mouse lung tissue was lyophilized and processed through triazol extraction followed by Qiagen clean-up
Library preparation was performed using the TruSeq RNA preparation kit (Illumina, FC-122-1001/1002) from purified RNA (100 ng-1 mg of total RNA with RIN ≥ 8.0).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Adaptor sequences were trimmed and filtered based on phred score (>33) and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
A master GTF was created using the GRCm38 mouse genome build and the Af1163 genome scaffolds
Filtered pair-ended RNA-Seq reads were mapped to the merged reference genome using the splice-aware short read mapping tool TopHat 2.1.0 with Bowtie2 2.2.7118
Abundance estimation and differential expression analysis for the reference genes and transcripts were performed using Cufflinks 2.2.1 and visualized in part via CummRbund120
Abundance estimation and differential expression analysis for fungal genes and transcripts were performed using HTSeq-DeSeq2 1.12.4
Genome_build: GRCm38, EnsembleFungi: Aspergillus fumigatus A1163
Supplementary_files_format_and_content: tab-delimited text containing standard Cufflinks and DeSeq2 output for abundance measurement and differential expression
 
Submission date Sep 26, 2017
Last update date May 15, 2019
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 GPL24049
Series (1)
GSE104290 Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis
Relations
BioSample SAMN07703392
SRA SRX3218155

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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