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Sample GSM3192123 Query DataSets for GSM3192123
Status Public on Jun 23, 2018
Title RV_21
Sample type SRA
 
Source name Brain neuron
Organism Mus musculus
Characteristics strain: Ai9 (B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J
age: 5 weeks
injected virus: the recombinant glycoprotein (G)-deleted rabies virus(rRV-deltaG-GFP)
injection site: Different nuclei of mouse brain including hypothalamus, thalamus, hippocampus and amygdala
sequeneced tissue name: RV-deltaG-EGFP retrograde labeled neurons in different nuclei
Treatment protocol For the tissue mRNA-seq mice were anesthetized using isoflurane, immediately following which the brains were dissected and sectioned to a thickness of 300 μm in ice-cold ACSF, tissue were micro-dissected under a fluorescence microscope.For the single cell RNA-seq the Fluorescence-labeled neuron were isolated using the papain-based dissociation protocol.
Growth protocol For the tissue mRNA-seq C57BL/6 mice of 8 weeks were injected with 200 nL RV-ΔG-EGFP or rAAV2-retro-YFP and housed for 2 weeks. For the single cell RNA sequenece of neuron labeled by virus 4 weeks Ai9 reporter mice were used for RV-ΔG-EGFP injections, and 3 weeks mice were used for rAAV2-retro-cre-tagBFP injection.
Extracted molecule total RNA
Extraction protocol Total RNA of the dissected tissue was extracted using TRIzol  Reagent.
The RNA-seq library was constructed in accordance with the manufacturer's protocol using the VAHTSTM Stranded mRNA-seq Library Preparation Kit for Illumina® . For single-cell RNA-seq library construction, cDNA was generated in accordance with the Smart-seq2 method
mRNA-seq and scRNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description single cell RNA-Seq( The number represent different group of neuron in different circuit )
single_cell_expression.xls
Data processing All the raw sequencing data from different samples were taken for quality check by FastQC and the samples with high-quality reads were collected for downstream analysis.
Library construction adapters in reads were trimmed by Trimmomatic and the clean reads were aligned to the mouse genome GRCm38(mm10) with HISAT2.
The expression level of all genes were counted and normalized to FPKM (Fragments Per Kilobase of transcript per Million) by StringTie
Differential gene expression analysis for RNA-Seq data were performed using edgeR R pakage and KEGG enrichment analysis were performed using clusterProfiler package . And for single cell RNA-Seq ,We designed a differential analysis step.
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jun 15, 2018
Last update date Jun 23, 2018
Contact name Gang Cao
E-mail(s) gcao@mail.hzau.edu.cn
Organization name Huazhong Agricultural University
Lab State Key Laboratory of Agricultural Microbiology
Street address Lion Rock One
City wuhan
State/province hubei
ZIP/Postal code 430070
Country China
 
Platform ID GPL21273
Series (1)
GSE115865 Neurotropism and Neurotoxicity Comparison among Retrograde Viral Tracers and Their Combinational Application in High-order Circuit Tracing
Relations
BioSample SAMN09430281
SRA SRX4221527

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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