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Sample GSM1892459 Query DataSets for GSM1892459
Status Public on May 03, 2016
Title 920_Sorted_M_Neuro_2
Sample type SRA
 
Source name Mouse Brain Nuclei_Sorted_M_Neuro
Organism Mus musculus
Characteristics mouse line: B6.FVB-Tg(Snap25-EGfp/Rpl10a)JD362Htz/J
age: 6-12 Weeks
Sex: M
tissue: whole Brain
cell type: Neuron
molecule subtype: nuclear RNA
Extracted molecule total RNA
Extraction protocol Trizol, DNAse Treatment, Qiagen RNAeasy minelute
Nugene Ovation RNAseq V2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Single-end 100 bp read ends trimmed using Trimmomatic
Samples mapped to rRNA sequences using Bowtie2
Excluded two samples
Surviving reads mapped to Ensembl v. 75 of genome using STAR
Counting reads performed using BedTools
Removed genes with biotype other than protein_coding, lincRNA, sense_overlapping snoRNA, or snRNA
Differential expression analysis performed using EdgeR
Read counts fit to negative binomial generalized log-linear model
Likelihood ratio test done to determine differential expression
Multiple correction testing done using Benjamini-Hochberg's false discovery rate algorithm
Genome_build: Ensembl 75 (mouse)
Supplementary_files_format_and_content: CSV file with counts for each gene (rows) and sample (columns)
 
Submission date Sep 24, 2015
Last update date May 15, 2019
Contact name Joseph D Dougherty
Organization name Washington University
Department Genetics and Psychiatry
Street address 4566 Scott Ave, box 8232
City St Louis
State/province Missouri
ZIP/Postal code 63110
Country USA
 
Platform ID GPL13112
Series (1)
GSE73391 Nuclear RNA in the nervous system
Relations
BioSample SAMN04110370
SRA SRX1284274

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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