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Sample GSM2693506 Query DataSets for GSM2693506
Status Public on Jun 04, 2018
Title Gorilla_Sakura_PMC
Sample type SRA
 
Source name premotor cortex
Organism Gorilla gorilla
Characteristics individual id: Sakura
age (year): 38
Sex: female
rin: 7.1
processing date: 20160401
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 4000
 
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
Street address 38 Nishigonaka Myodaiji
City Okazaki
ZIP/Postal code 4448585
Country Japan
 
Platform ID GPL23656
Series (1)
GSE100796 Human-specific features of special gene expression and regulation in eight brain regions
Relations
BioSample SAMN07315632
SRA SRX2983716

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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