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Sample GSM957061 Query DataSets for GSM957061
Status Public on Jan 14, 2013
Title brain
Sample type SRA
 
Source name brain
Organism Tupaia chinensis
Characteristics tissue: brain
Treatment protocol total RNA is extracted by TRIzol Reagent
Extracted molecule total RNA
Extraction protocol For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sequenced reads were generated from brain in Chinese tree shrew
Data processing use Chinese tree shrew genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except -r 20 --mate-std-dev 10 -I 10000 --segment-mismatches 3 --segment-length 24 --solexa1.3-quals
Genome_build: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession ALAR00000000. The version described in this paper is the first version, ALAR01000000.
Supplementary_files_format_and_content: sequenced reads were aligned onto the corresponding contig
 
Submission date Jul 06, 2012
Last update date May 15, 2019
Contact name zhiyong huang
E-mail(s) huangzhiyong@genomics.org.cn
Organization name BGI-Shenzhen, Shenzhen 518083, China
Street address F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
City shenzhen
State/province Guangdong
ZIP/Postal code 518083
Country China
 
Platform ID GPL15772
Series (1)
GSE39150 Transcriptome sequencing of Chinese tree shrew, Tupaia belangeri chinensis
Relations
SRA SRX157964
BioSample SAMN01085959

Supplementary file Size Download File type/resource
GSM957061_Brain.coverage.bedGraph.gz 170.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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