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Sample GSM457286 Query DataSets for GSM457286
Status Public on Apr 09, 2010
Title Dazao strain p50_biological_Replicate1 DGE analysis
Sample type SRA
 
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
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
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.
 
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

Data table header descriptions
SEQUENCE TAG
COUNT
TPM(Transcript Per Million)

Data table
SEQUENCE COUNT TPM(Transcript Per Million)
CATGTTACCATAATATCTTAG 1 1
CATGTCTTATTTTGTAAGCCA 1 1
CATGGCCTGCCAGGGCGATTG 1 1
CATGAGAACGACTGCCACGTA 1 1
CATGGCCTGGGGCTACAAAGG 1 1
CATGTGGTCGGCCCTCGGATG 1 1
CATGAGAATAAAACAGGTAGC 1 1
CATGTTCTTCAAGAAGTTCAT 1 1
CATGACGCTTACGAACTGTGT 1 1
CATGGCGAGAATGCAAAGGGA 1 1
CATGTGTCAGCCCTATTACGC 1 1
CATGTGACGGCATTGAGGACT 1 1
CATGGGCCTATGGGCTTCTAT 1 1
CATGGAGTACATCCACAGAAA 1 1
CATGGTCTACTGATGGGCTTA 1 1
CATGAATCAGCTCGTTGAGTT 1 1
CATGCGAATTTGATGGTGGAG 1 1
CATGTTACTATGGAAAGCCTA 1 1
CATGAACTATAAGCCTAAGTG 1 1
CATGAGTCCTACTAACTAAGA 1 1

Total number of rows: 165367

Table truncated, full table size 4224 Kbytes.




Supplementary data files not provided
SRA Run SelectorHelp
Processed data included within Sample table
Raw data are available in SRA

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