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Sample GSM2068603

Query DataSets for GSM2068603

Status

Public on Jun 01, 2017

Title

Control Day

Sample type

SRA

Source name

Control Day

Organism

Macaca mulatta

Characteristics

time: Day
tissue: mixed (corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, testis and ovary)

Extracted molecule

total RNA

Extraction protocol

Twelve adult rhesus macaques (Macaca mulatta, 3 to 33 years of age, male and female, 4 to 10.3 kg) were obtained through the Veterinary Resources Program Primate Recycle Program of NIH over a period of 11 years. All protocols and handling of the animals conformed to the Guidelines for Care and Use of Laboratory Animals (NIH Publication 80-23; Protocols 99-012 and 11-055 ). Animals were housed under a 12-h light, 12-h dark lighting regimen (lights on at 0600 h) in NIH facilities for at least 6 wk. The light level in the cages was approximately 325 Lux. Animals (three per time point) were sacrificed between 1100 and 1300 (day) , 1700 and 1900 (dusk), 2300 and 0100 (night) and 0500 and 0700 (dawn). Animals were anesthetized (ketamine, 0.1 ml/kg body weight) and a catheter was placed in the saphenous vein prior to transport to the procedure room. Animals were sacrificed using Euthasol (Virbac, Fort Worth, TX) or Beuthanasia D ( Schering Plough, Union, NJ). Animals sampled at night or dusk were anesthesized under dim red light and blindfolded; euthanasia was done under dim white light and the blindfold was removed after decapitation. Removal of tissues, including the pineal gland, retina, and others (corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, testis and ovary) was complete within 45 minutes following euthanasia; immediately following removal, samples of each tissue were obtained and placed on solid CO2. Tissue was store at -80° C. Total RNA was extracted from individual pineal glands or pieces of other tissues ( 2 to 4 mm 3 pieces) with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina Casava1.9 software used for basecalling.
Reads were aligned with the RNA-STAR aligner (v. 2.3.0e) , using a rhesus rheMac3 genome build. STAR aligner parameters used: --runThreadN 8 --outFilterMultimapNmax 1 --outSAMunmapped Within --outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in-house written scripts, and no major artifacts or abnormalities were found
Gene read counts were provided by R subreads package, (featureCounts function) with parameters specifying: paired-end reads, and reverse-complement for the second strand (-p, -S2). Annotation for assigning the reads was derived from Gencode v.19 human annotation. Gene coordinates were lifted over using RheMac3/hg19 liftover chains, and only sequences that shared no less than 95% homology were kept, resulting in total of 50308 genes. Differential expression analysis was performed using DESeq2 software package.
Genome_build: RheMac3
Supplementary_files_format_and_content: retina_pineal_control.xlsx file includes FPKM values for all of the Samples, pineal_DE.xlsx includes the differential expression analysis for pineal gland, Retina_DE.xlsx includes the differential expression analysis for retiina

Submission date

Feb 22, 2016

Last update date

May 15, 2019

Contact name

Marjan Bozinoski

E-mail(s)

mab2092@med.cornell.edu

Organization name

Weill Cornell Medicine

Department

Physiology and Biophysics