|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|