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Series GSE133140 Query DataSets for GSE133140
Status Public on Apr 16, 2020
Title CARD9-associated Dectin-1 and Dectin-2 are Required for Protective Immunity of a Multivalent Vaccine Against Coccidioides posadasii Infection
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module) were conducted at the Genomics Core of UT Health San Antonio. Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench. To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010). Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).
Overall design BMMs were incubated with GCP-rCpa1 at a ratio of 50:1 for 12 hours with 5% CO2. BMMs incubated with PBS served as controls. Total RNA was isolated from BMMs cells using the Qiagen RNeasy kit.
Web link
Contributor(s) Hung C, Zhang H, Campuzano A
Citation(s) 32358020
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AI135005 Development of a multivalent vaccine against Coccidioides infection THE UNIVERSITY OF TEXAS AT SAN ANTONIO Chiung Yu Hung
Submission date Jun 21, 2019
Last update date Jul 16, 2020
Contact name Chiung-Yu Hung
Organization name The University of Texas at San Antonio
Department Biology
Lab MBT 1.308
Street address One UTSA Circle
City San Antonio
State/province Texas
ZIP/Postal code 78249
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (6)
GSM3900865 PBS_1
GSM3900866 PBS_2
GSM3900867 PBS_3
BioProject PRJNA550079
SRA SRP202204

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133140_edgeR.output.csv.gz 423.4 Kb (ftp)(http) CSV
GSE133140_raw.counts.txt.gz 329.8 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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