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Sample GSM1100314

Query DataSets for GSM1100314

Status

Public on Mar 31, 2014

Title

Chimpanzee_6

Sample type

SRA

Source name

Prefrontal Cortex

Organism

Pan troglodytes

Characteristics

tissue: Prefrontal Cortex
organism: chimpanzee

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.
RNA libraries were prepared for sequencing using Illumina TruSeq protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.
Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.
We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.
Then quantile normalization was applied, and each gene was z-transformed.
Genome_build: hg19, panTro3
Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Submission date

Mar 18, 2013

Last update date

May 15, 2019

Contact name

Liu He

E-mail(s)

heliu@picb.ac.cn

Organization name

PICB

Street address

320 Yue Yang Road