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Series GSE104127 Query DataSets for GSE104127
Status Public on Jun 15, 2018
Title Next Generation Sequencing Analysis of WT and Hectd3–/– BMDMs during F. novicida infection
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to compare NGS-derived WT and Hectd3–/– transcrip profiling (RNA-seq) in the absence and presence of F. novicida infection
Methods: Bone marrow derived macrophages (BMDMs) from WT and Hectd3–/– mice were infected with F .novicida for 8 and 12 hours. mRNA profiles were generated by deep sequencing using Illumina GAIIx.
Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample (around 95% clean reads were successfully mapped) to the mouse genome and identified 22,589 transcripts in the WT and Hectd3–/– BMDMs with or without F. novicida infection.
Conclusions: Our study represents the first detailed analysis of HECTD3 deficiency regulated gene expression in response to F. novicida infection generated by RNA-seq technology. Our results demonstrated that the type I IFN signaling induced by F. novicida infection was impaired in the absence of HECTD3.
Overall design mRNA profiles of WT and Hectd3–/– BMDMs with or without F. novicida infection for 8 and 12 h were generated by deep sequencing, using Illumina Hiseq platform.
Contributor(s) Xiaopeng Q, Ceshi C
Citation(s) 29920190
Submission date Sep 22, 2017
Last update date Jul 25, 2021
Contact name Xiaopeng Qi
Phone 15398395819
Organization name Kunming Institute of Zoology, CAS
Street address 32 East Jiaochang Rd
City Kunm,ing
ZIP/Postal code 650223
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (6)
GSM2790362 WT_0
GSM2790363 Hectd3–/–_0
GSM2790364 WT_8
BioProject PRJNA411777
SRA SRP118600

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104127_RAW.tar 2.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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