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Sample GSM2693517

Query DataSets for GSM2693517

Status

Public on Jun 04, 2018

Title

Gibbon_DAICHI_STR

Sample type

SRA

Source name

striatum

Organism

Hylobates lar

Characteristics

individual id: DAICHI
age (year): 9
Sex: male
rin: 6.1
processing date: 20130405

Extracted molecule

polyA RNA

Extraction protocol

Brain dissection was performed from either fresh specimens or frozen tissue slabs by the same person to ensure sampling consistency between specimens. About 100 mg of dissected tissues were used and total RNA were extracted using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively, and the RNA Integrity Number (RIN) were determined using Bioanalyzer RNA 6000 Nano Kit (Agilent).
Sequencing libraries were prepared using the NEBNext mRNA Library Prep Kit for non-directional libraries and the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Raw reads of four species were aligned to the reference genomes (human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1) by “STAR” (parameters: outFilterMultimapNmax = 1, outFilterMatchNminOverLread = 0.95, outFilterMismatchNoverLmax = 0.05, outFilterIntronMotifs = RemoveNoncanonical).
PCR duplicates removal was then conducted using SAMtools and only uniquely mapped reads were considered as validity to avoid the estimation ambiguity.
We obtained chimpanzee, gorilla and gibbon orthologs of human genes (GENCODE v19) by reciprocal liftOver requiring the same exon orders and no less than 50% exons preserved.
Based on the annotations, numbers of reads were counted per gene per sample using htseq-count within HTSeq. Only genes with counts greater than 0 in all four species in at least one brain region were used in the following analysis
We took advantage of the median ratio method implemented in DESeq2 to normalize the gene abundance data for further comparisons across species and brain regions.
Genome_build: human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1
Supplementary_files_format_and_content: tab-delimited text files include raw count, normalized count, and RPKM for each sample

Submission date

Jul 05, 2017

Last update date

May 15, 2019

Contact name

Yasuhiro Go

E-mail(s)

yasuhirogo@gmail.com

Organization name

National Institutes of Natural Sciences

Department

Department of Brain Sciences, Center for Novel Science Initiatives