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Series GSE67374 Query DataSets for GSE67374
Status Public on Oct 01, 2015
Title Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, 4L;C* and Isofagamine treated 4L;C* region specifics mouse brain Transcriptomes (RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) in neuropathic region specific Gaucher mouse brain compared with WT and Isofagamine treated mice of the same age and background and secondly to identify the DEmiRNA associated with the DEmRNA before and after treatment This will give us some insights to see if miRNA is also involved in the the regulation of the expression of the genes involved in the disease process before and after treatment.
Methods: 42-45 days old 4L;C*, wild-type (WT) and Isofagamine treated 4L;C* mouse brain were generated by deep sequencing, in triplicate, using IlluminaHiseq. The sequence reads that passed quality filters were analyzed at the gene level with two methods: Burrows–Wheeler Aligner (BWA) followed and TopHat followed by DESeq. qRT–PCR validation was performed using TaqMan and SYBR Green assays
 
Overall design Regional brain mRNA profiles of ~42 -days old wild type (WT) and 4L;C* an d Isofagamine treated mice were generated by deep sequencing, in triplicate, using IlluminaHi Seq.
 
Contributor(s) Dasgupta N, Xu Y, Li R, Peng Y, Pandey M, Tinch S, Liou B, Inskeep V, Zhang W, Keddache M, Grabowski GA, Sun Y
Citation(s) 26430163
Submission date Mar 27, 2015
Last update date May 15, 2019
Contact name Nupur dasgupta
E-mail(s) nupur.dasgupta@cchmc.org
Phone 513-803-1768
Organization name CCHMC
Department human Genetics
Lab Gregory Grabowski
Street address 3333, Burnet Avenue
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (35)
GSM1645630 4L;C* run0140_lane1_index10=5754BS~mouse_align
GSM1645631 4L;C* run0140_lane1_index11=5755BS~mouse_align
GSM1645632 WT run0140_lane1_index1=5186BS~mouse_align
This SubSeries is part of SuperSeries:
GSE67375 Neuropathic Gaucher mouse brain
Relations
BioProject PRJNA279604
SRA SRP056636

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Supplementary file Size Download File type/resource
GSE67374_nupurdasgupta_GEO_file_normlised_mRNA_seq_032415.xlsx 18.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record
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