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Status |
Public on Jan 14, 2013 |
Title |
brain |
Sample type |
SRA |
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Source name |
brain
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Organism |
Tupaia chinensis |
Characteristics |
tissue: brain
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Treatment protocol |
total RNA is extracted by TRIzol Reagent
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
Sequenced reads were generated from brain in Chinese tree shrew
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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
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Submission date |
Jul 06, 2012 |
Last update date |
May 15, 2019 |
Contact name |
zhiyong huang |
E-mail(s) |
huangzhiyong@genomics.org.cn
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Organization name |
BGI-Shenzhen, Shenzhen 518083, China
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Street address |
F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
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City |
shenzhen |
State/province |
Guangdong |
ZIP/Postal code |
518083 |
Country |
China |
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Platform ID |
GPL15772 |
Series (1) |
GSE39150 |
Transcriptome sequencing of Chinese tree shrew, Tupaia belangeri chinensis |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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