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| Status |
Public on May 03, 2016 |
| Title |
920_Presort_F_Oligo_33 |
| Sample type |
SRA |
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| Source name |
Mouse Brain Nuclei_Presort_F_Oligo
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| Organism |
Mus musculus |
| Characteristics |
mouse line: B6.FVB-Tg(Cnp-EGfp/Rpl10a)JD368Htz/J
age: 6-12 Weeks
Sex: F
tissue: whole Brain
cell type: Mixed
molecule subtype: nuclear RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol, DNAse Treatment, Qiagen RNAeasy minelute
Nugene Ovation RNAseq V2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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)
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| Submission date |
Sep 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph D Dougherty |
| Organization name |
Washington University
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| Department |
Genetics and Psychiatry
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| Street address |
4566 Scott Ave, box 8232
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| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE73391 |
Nuclear RNA in the nervous system |
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| Relations |
| BioSample |
SAMN04110354 |
| SRA |
SRX1284258 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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