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Sample GSM1293429

Query DataSets for GSM1293429

Status

Public on Dec 31, 2016

Title

B-Liver

Sample type

SRA

Source name

Liver

Organism

Macaca mulatta

Characteristics

gender: male
tissue: Liver

Extracted molecule

total RNA

Extraction protocol

All kinds of tissue from the two aborted male rhesus monkeys were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 Off-Line Basecaller(OLB) 1.9.4 software used for basecalling.
Sequenced reads mapped to rhesus whole genome(MMUL_1.73) using Tophat(vision 1.3.2) with default parameters and max-multihits=10 ,min-anchor-length=5
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using Cufflinks (version 2.0.2). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MMUL_1.73
Supplementary_files_format_and_content: The "fpkm" file includes FPKM values for each Sample
Supplementary_files_format_and_content: The "cvrg" file contain transcript coverage calculated by Cufflinks.

Submission date

Dec 18, 2013

Last update date

May 15, 2019

Contact name

hygine lin

E-mail(s)

haijunlin@163.com

Phone

+8615026869194

Organization name

tongji unversity