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Status |
Public on Apr 09, 2010 |
Title |
Dazao strain p50_biological_Replicate1 DGE analysis |
Sample type |
SRA |
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Source name |
the silkgland of female larva of fifth instar of silkworm P50 strain
|
Organism |
Bombyx mori |
Characteristics |
strain: silkworm Dazao strain gender: female age: fifth instar larva tissue: the silkgland
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Extracted molecule |
total RNA |
Extraction protocol |
Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Total RNAs extract were extracted using RNeasy Mini Kit (Qiagen). DGE-tag libraries were constructed using DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina). Libraries were sequenced using the Illumina Genetic Analyzer (GA2) according to the manufacturer’s instruction.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
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Description |
DGE-tag libraries were constructed using DGE-Tag Profiling NlaIII Sample Prep Kit (Illumina). Libraries were sequenced using the Illumina Genetic Analyzer (GA2) according to the manufacturer’s instruction.
|
Data processing |
Gene annotation information was downloaded from the SilkDB (ftp://silkworm.swu.edu.cn/pub/Glean_genes/silkworm_glean.gff.gz). Because annotated genes were mainly predicted using prediction software, only ORF positions were available. We created putative full-length cDNA sequences for each gene by adding 1kb downstream sequences of ORF to coding sequences. Then all possible CATG + 17nt tag sequences were created from putative full-length cDNAs and used as reference tag database. Unique tag sequences and their numbers were extracted from our raw DGE tags and these tags were aligned against the reference tag database using SOAP 4. Only perfect matches were kept for further analysis, and no mismatches were allowed. Expression level of one gene was represented by the total number of tags which uniquely aligned to this gene.
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Submission date |
Sep 29, 2009 |
Last update date |
May 15, 2019 |
Contact name |
Hui Xiang |
E-mail(s) |
xiangh@mail.kiz.ac.cn
|
Organization name |
Kunming Insititute of Zoology
|
Street address |
32 East Jiaochang Road
|
City |
Kunming |
State/province |
Yunnan Province |
ZIP/Postal code |
650223 |
Country |
China |
|
|
Platform ID |
GPL9151 |
Series (1) |
GSE18315 |
Single-Base Resolution Methylomes of Silkworms and Functional Importance of Gene Methylation in Insects Revealed by Ultra-High-Throughput Sequencing |
|
Relations |
SRA |
SRX018972 |
BioSample |
SAMN00011076 |