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Protocols

SilkDB specifications

Information


Unique identifier OMICS_03139
Name SilkDB
Restrictions to use None
Database management system MySQL
Data access File download, Browse
Version 2.0
Maintained Yes

Taxon


  • Invertebrates
    • Bombyx mori

Maintainers


  • person_outline Qingyou Xia1
  • person_outline Ze Zhang

Additional information


Guide: http://silkworm.genomics.org.cn/silkdb/doc/help.html

Publications for SilkDB

SilkDB citations

 (77)
call_split

Bombyx mori histone methyltransferase BmAsh2 is essential for silkworm piRNA mediated sex determination

2018
PLoS Genet
PMCID: 5841826
PMID: 29474354
DOI: 10.1371/journal.pgen.1007245
call_split See protocol

[…] g with illumine HiSeq 2500 platform, the generated reads were filtered and small RNA reads from 24 to 30 nt in length were selected for mapping to the silkworm genome (http://silkworm.genomics.org.cn/silkdb/#), 121 annotated transposons and 1668 ReAS clones to identify the piRNAs as reported previously []. […]

library_books

Genome Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori

2018
Int J Mol Sci
PMCID: 5855749
PMID: 29425159
DOI: 10.3390/ijms19020527

[…] orhabditis elegans, Onchocerca volvulus, Brugia malayi, Pristionchus pacificus and Strongyloides ratti.The chromosomal locations, gene lengths, probes and predicted protein lengths were obtained from SilkDB and KAIKObase. Theoretical molecular weights and isoelectric point values were calculated online at http://web.expasy.org/protparam/. Three online programs, CDD (http://www.ncbi.nlm.nih.gov/Str […]

library_books

The pivotal role of aristaless in development and evolution of diverse antennal morphologies in moths and butterflies

2018
BMC Evol Biol
PMCID: 5785806
PMID: 29370752
DOI: 10.1186/s12862-018-1124-2

[…] closion under a stereomicroscope or a compound microscope.We also tried to knock down al function by RNAi. There are at least two al homologs in the B. mori genome (al1/BMgn006008 and al2/BMgn006007, SilkDB/KAIKObase). We designed four different siRNAs for each of al1 and al2, and used them in various combinations. However, we failed to deplete either of al1 or al2 mRNA effectively by unknown reas […]

call_split

Genome wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

2017
Sci Rep
PMCID: 5635003
PMID: 29018289
DOI: 10.1038/s41598-017-13186-6
call_split See protocol

[…] the raw and processed reads was evaluated using FastQC (Version 0.11.1). PolyA tails were filtered by fqtrim (Version 0.93), and reads were aligned to the silkworm tRNA and rRNA database (http://www.silkdb.org/silkdb/doc/download.htm) using bowtie2 software (Version 2.2.9). Low-quality reads were removed using Trimmomatic (Table ). The cleaned short reads were mapped to the silkworm reference gen […]

library_books

Differentially expressed genes in the head of the 2nd instar pre molting larvae of the nm2 mutant of the silkworm, Bombyx mori

2017
PLoS One
PMCID: 5519023
PMID: 28727825
DOI: 10.1371/journal.pone.0180160

[…] C) procedures to determine whether a resequencing step was needed. After QC, the raw reads were filtered into clean reads, which were aligned to reference sequences from the silkworm genome database, SilkDB (http://silkworm.swu.edu.cn/silkdb/). QC of the alignment was performed to determine whether resequencing was needed. The alignment data were utilized to calculate the read distribution and map […]

library_books

Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome

2017
Mol Biol Evol
PMCID: 5850747
PMID: 28957502
DOI: 10.1093/molbev/msx190

[…] there is no linkage information for the genome and to make our analyses comparable to those of . Plodia interpunctella transcripts () were first mapped to the whole set of B. mori protein sequences (SilkDB, genome version 2.0, ; ) using Blast () with an e-value cut-off of e-5. The reverse mapping was then performed (B. mori proteins against P. interpunctella transcripts) with the same parameters […]


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SilkDB institution(s)
The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing, China; The Institute of Agriculture and Life Sciences, Chongqing University, Chongqing, China; Beijing Genomics Institute at Shenzhen, Shenzhen, China; National Institute of Agrobiological Sciences, Tsukuba, Japan
SilkDB funding source(s)
Supported by National Basic Research Program of China (No. 2005CB121000); Program for Changjiang Scholars and innovative Research Team in University of China (No. IRT0750); Programme of Introducing Talents of Discipline to Universities (No. B07045); National Natural Science Foundation of China (No. 30800804) and National Hi-Tech Research and Development Program of China (No. 2006AA10A118).

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