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Sample GSM1531202

Query DataSets for GSM1531202

Status

Public on Dec 01, 2014

Title

RNA110714RH_5

Sample type

SRA

Source name

Dissected Tissue - Striatum (Brain)

Organism

Mus musculus

Characteristics

behavioral phenotype: Catalepsy: Non-Responder
Sex: Female

Extracted molecule

total RNA

Extraction protocol

Brain striatum region was hand-dissected and frozen. Total RNA was harvested by using manual homogenization using Trizol reagent (Invitrogen), mortar and pestle. It was then precipitated using sodium acetate after isolation.
RNA libraries were prepared for sequencing using TruSeq PolyA Illumina protocol: PolyA(+) RNA was recovered from 1 ug of total RNA using oligo-dT attached to magnetic beads. PolyA(+) RNA was chemically fragmented. Double stranded DNA was made from the fragmented RNA using random hexamers. All ends were repaired. A single A was added to each of the 3’ ends of each fragment. Illumina adaptors were ligated to the fragments. Concentration was determined by real time PCR. Samples were mixed for multiplexing. Samples were diluted to target 180 million templates per lane on the flow cell

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection; Trimmed 10 base-pairs from 5' end and 5 base-pairs for 3' end from read sequences.
Bowtie 0.12.7 was used for read alignment with the following parameters: v=2 (2 mismatches allowed), trim3=10, trim5=5, k=1, m=1 (report only unique alignments), p=5
Normalization: Gene and exon expression data were imported into the R (version 3.0.2 - Linux) application environment and samples were normalized using the upper-quartile normalization factor generated for each sample by the edgeR (version 3.4.2) Bioconductor package. Following normalization, genes which had zero expression in more than half of the samples were filtered from the analysis and exons with zero expression in more than half of the samples were set to 0.
Genome_build: mm9
Supplementary_files_format_and_content: RNA110714RH_normalizedGeneCounts.txt: first column has the ENSEMBL Gene ID, subsequent 60 columns provide the normalized reads for each sample for each gene
Supplementary_files_format_and_content: RNA110714RH_normalizedExonCounts.txt: first column has the ENSEMBL 'Gene ID_start location' (i.e. the ensemble gene id has the exon start location after the "underscore --> "_"), subsequent 60 columns provide the normalized reads for each sample for each gene exon;

Submission date

Oct 23, 2014

Last update date

May 15, 2019

Contact name

Priscila Darakjian

E-mail(s)

darakjia@ohsu.edu

Organization name

Oregon Health and Science University

Department

Behavioral Neuroscience