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Sample GSM1241414

Query DataSets for GSM1241414

Status

Public on May 14, 2014

Title

rhesus_27_M

Sample type

SRA

Source name

prefrontal cortex (PFC)

Organism

Macaca mulatta

Characteristics

Sex: male
age (year): 6
age (day): 165

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted by a Trizol (Invitrogen) procedure according to the manufacturer’s instructions. All RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the Truseq RNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
Polyadenylated RNA was isolated using a poly-dT bead procedure and then chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3′-end adenylation of these products, Illumina Single-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were then PCR-amplified (15 cycles). The RNA-seq libraries were sequenced (100 cycles) on the Illumina Hiseq 2000 platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

For transcript assembly, TopHat2 was used with default parameters to align all sequenced reads to the human genome (hg19).
Using the GENCODE v16 annotation, all sequeced transcripts overlapping annotated transcripts were removed.
To estimate gene expression including both protein-coding genes and lincRNAs in human and macaque, a human-macaque consensus genome based on a pairwise whole-genome alignment of the human (hg19) and the rhesus macaque (rheMac3) genomes was constructed.
Reads in both, human and macaque samples were mapped to the consensus genome using STAR with default parameters.
Gene expression was quantified using RPKM = n*1000*100/L/N, where n is the number of reads aligned to exon regions, and L is the length of exons regions, N is the total number of reads in the sample.
Genome_build: GENCODE 16; hg19; GCA_000230795.1; consensus genome
Supplementary_files_format_and_content: rpkm_human.tsv is a table showing gene expression (in RPKM) of each gene in each human PFC sample. rpkm_macaque.tsv is a similar table but showing information in macaque PFC samples.
Supplementary_files_format_and_content: All the ENSG* IDs in the GENE_ID column are correspond to GENCODE v16 gene IDs (not transcript IDs). The "CUFF.*" IDs are novel lincRNAs we identified. Please see the file named "novel_lincrna.gtf", which involves the information of them.

Submission date

Sep 30, 2013

Last update date

May 15, 2019

Contact name

Zhisong He

Organization name

Max Planck Institute for Evolutionary Anthropology

Lab

Single Cell Genomics

Street address

Deutscher Platz 6