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List of Data Metadata
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Data name Database name DOI Description of data contents Data file Simple search URL Data acquisition method Data analysis method Number of data entries Data detail
Protein Basic Information SAHG 10.18908/lsdba.nbdc01193-001

Basic information of the target protein. Amino acid sequence, RefSeq ID, etc.

sahg_protein.zip
(8.1 MB)
http://togodb.biosciencedbc.jp/togodb/view/sahg_protein#en

Retrieved from RefSeq (NCBI Reference Sequence Database). Protein sequence search on EzCatDB (A Database of Enzyme Catalytic Mechanisms), Human Protein Reference Database (HPRD), UniProtKB/Swiss-Prot.

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24,878 entries
Data detail open_in_full
Annotations of each trascript (doing blast against human and Drosophila gene sets) Silkworm, Bombyx mori, reference transcriptome data 10.18908/lsdba.nbdc02443-003

Functional annotations of each transcript. These annotations were performed by doing blast against human and Drosophila gene sets.

kaiko_annotation_human_drosophila_data.zip
(391 KB)
https://togodb.biosciencedbc.jp/togodb/view/kaiko_annotation_human_drosophila_data#en

Blast Search of each transcript was done against human (version GRCh38)and Drosophila melanogaster (version BDGP6.22) protein data set in Ensemble database. Top hit gene in the results was converted to symbol description by Biomart.

Blast search

51,926 entries
Data detail open_in_full
Expression data of each transcript in mutiple tissue Silkworm, Bombyx mori, reference transcriptome data 10.18908/lsdba.nbdc02443-002

This data file contains values of expressions (tpm value) in multiple tissues of Bombyx mori per each transcript.

kaiko_transcript_tpm_data.zip
(5.8 MB)
https://togodb.biosciencedbc.jp/togodb/view/kaiko_transcript_tpm_data#en

Reference transcriptomic data and raw RNAseq data constructed with the method described in "Metadata of reference transcriptomic data"
Other RNAseq data was downloaded from Sequence Read Archive(SRA): DRA005094, DRA005878, DRA005094.

Using the above data, estimation of tpm values of each transcript was performed by Kallisto ver0.44.0.

51,926 entries
Data detail open_in_full
Metadata of reference transcriptomic data Silkworm, Bombyx mori, reference transcriptome data 10.18908/lsdba.nbdc02443-001

Metadata of Bombyx mori reference transcriptomic data is described in GFT2 file format.
About GFT2 format, see the following site:
http://mblab.wustl.edu/GTF22.html

kaiko_transcript_data.zip
(3.9 MB)
https://togodb.biosciencedbc.jp/togodb/view/kaiko_transcript_data#en

Tissues of silk gland, fat body, midgut, Malpighian tubules, testis and ovary were dissected on the 3rd day of fifth instar larva which is Silkworm P50T (daizo) strain. The silk gland was further subdivided into anterior silk gland, anterior part of the middle silk gland, middle part of the middle silk gland, posterior part of the middle silk gland and posterior silk gland . Each tissue was dissected from one individual and totally three biological replicates were obtained and analyzed separately. The tissues were homogenized using ISOGEN (NIPPON GENE, Tokyo, Japan) and SV Total RNA Isolation System (Promega, Madison, WI) was used for RNA extraction. The extract total RNA samples were sequenced by Illumina Novaseq6000 (Macrogen Japan Corp., Kyoto, Japan) .

The raw RNA-seq data of the samples were trimmed by Trimmomatic-version 0.36. The trimmed RNA-seq data of each tissue was mapping to the new reference genome with new gene model by Hisat2 version 2.1.0. The each mapped data was assembled to transcript data by stringtie version 1.3.3. The transcript data was merged to one transcript data set we refer as “reference transcriptome” by the stringtie, and gtf file of the reference transcriptome had been gotten.

421,949 entries
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Predicted amino acid sequences in the reference transcriptomic data Silkworm, Bombyx mori, reference transcriptome data 10.18908/lsdba.nbdc02443-004

Multi fasta file of amino acid sequence predicted with Transcoder (v5.5.0) from the reference transcriptomic data.

kaiko_bm_ref_transcript_TSA.zip
(11 MB)
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Reference transcriptomic data

Transcoder (v5.5.0)

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Data detail open_in_full
Data name Database name DOI Description of data contents Data file Simple search URL Data acquisition method Data analysis method Number of data entries Data detail