Silkworm, Bombyx mori, reference transcriptome data

2019/10/18

HTTPS Site: https://dbarchive.biosciencedbc.jp/data/kaiko/

The reference transcriptomic data from new reference genome data and RNAseq data of multiple tissues in Bombyx mori P50T strain.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Metadata of reference transcriptomic data
  3. Expression data of each transcript in mutiple tissue
  4. Annotations of each trascript (doing blast against human and Drosophila gene sets)
  5. Predicted amino acid sequences in the reference transcriptomic data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Silkworm, Bombyx mori, reference transcriptome data" data.
File README_e.html (English)
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2.2 Metadata of reference transcriptomic data

Data name Metadata of reference transcriptomic data
Description of data contents

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
File kaiko_transcript_data.zip (3.9 MB)

Data items are the following:
Data itemDescription
seqname Sequence name
source Analysis software
feature Feature of the sequence region
start Start sequence number of the region
end End sequence number of the region
score Confidence score of the region
strand Strand of the region
frame Codon frame of the region
attributes Other attributes
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2.3 Expression data of each transcript in mutiple tissue

Data name Expression data of each transcript in mutiple tissue
Description of data contents

This data file contains values of expressions (tpm value) in multiple tissues of Bombyx mori per each transcript.
File kaiko_transcript_tpm_data.zip (5.8 MB)

Data items are the following:
Data itemDescription
ASG1 Anterior silk gland (biological replicate 1)
ASG2 Anterior silk gland (biological replicate 2)
ASG3 Anterior silk gland (biological replicate 3)
MSG_A1 Anterior part of the middle silk gland (biological replicate 1)
MSG_A2 Anterior part of the middle silk gland (biological replicate 2)
MSG_A3 Anterior part of the middle silk gland (biological replicate 3)
MSG_M1 Middle part of the middle silk gland (biological replicate 1)
MSG_M2 Middle part of the middle silk gland (biological replicate 2)
MSG_M3 Middle part of the middle silk gland (biological replicate 3)
MSG_P1 Posterior part of the middle silk gland (biological replicate 1)
MSG_P2 Posterior part of the middle silk gland (biological replicate 2)
MSG_P3 Posterior part of the middle silk gland (biological replicate 3)
PSG1 Posterior silk gland (biological replicate 1)
PSG2 Posterior silk gland (biological replicate 2)
PSG3 Posterior silk gland (biological replicate 3)
MG1 Midgut (biological replicate 1)
MG2 Midgut (biological replicate 2)
MG3 Midgut (biological replicate 3)
FB1 Fat body (biological replicate 1)
FB2 Fat body (biological replicate 2)
FB3 Fat body (biological replicate 3)
MT1 Malpighian tubules (biological replicate 1)
MT2 Malpighian tubules (biological replicate 2)
MT3 Malpighian tubules (biological replicate 3)
TT1 Testis (biological replicate 1)
TT2 Testis (biological replicate 2)
TT3 Testis (biological replicate 3)
OV1 Ovary (biological replicate 1)
OV2 Ovary (biological replicate 2)
OV3 Ovary (biological replicate 3)
BN_FB1 Fat body from SRA (biological replicate 1)
BN_FB2 Fat body from SRA (biological replicate 2)
BN_FB3 Fat body from SRA (biological replicate 3)
BN_MG1 Midgut from SRA (biological replicate 1)
BN_MG2 Midgut from SRA (biological replicate 2)
BN_MG3 Midgut from SRA (biological replicate 3)
BN_MT1 Malpighian tubules from SRA (biological replicate 1)
BN_MT2 Malpighian tubules from SRA (biological replicate 2)
BN_MT3 Malpighian tubules from SRA (biological replicate 3)
BN_SG1 Silk gland from SRA (biological replicate 1)
BN_SG2 Silk gland from SRA (biological replicate 2)
BN_SG3 Silk gland from SRA (biological replicate 3)
BN_TT1 Testis from SRA (biological replicate 1)
BN_TT2 Testis from SRA (biological replicate 2)
BN_TT3 Testis from SRA (biological replicate 3)
target_id Unique ID allocated to each transcript in reference transcriptomic data
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2.4 Annotations of each trascript (doing blast against human and Drosophila gene sets)

Data name Annotations of each trascript (doing blast against human and Drosophila gene sets)
Description of data contents

Functional annotations of each transcript. These annotations were performed by doing blast against human and Drosophila gene sets.
File kaiko_annotation_human_drosophila_data.zip (391 KB)

Data items are the following:
Data itemDescription
human_gname Symbol of top hit human gene.
fly_gname Symbol of top hit Drosophila gene.
target_id Unique ID allocated to each transcript in reference transcriptomic data
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2.5 Predicted amino acid sequences in the reference transcriptomic data

Data name Predicted amino acid sequences in the reference transcriptomic data
Description of data contents

Multi fasta file of amino acid sequence predicted with Transcoder (v5.5.0) from the reference transcriptomic data.
File kaiko_bm_ref_transcript_TSA.zip (11 MB)
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3. License

Last updated : 2019/10/18

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "Silkworm, Bombyx mori, reference trascriptome data © Kakeru Yokoi licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Kakeru Yokoi email: yokoi123[at]affrc[dot]go[dot]jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2019/10/18 Silkworm, Bombyx mori, reference trascriptome Database English archive site is opened. (Archive V1)
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5. Literature

Kakeru Yokoi, Takuya Tsubota, Jianqiang Sun, Akiya Jouraku, Hideki Sezutsu, Hidemasa Bono
Reference transcriptome data in silkworm, Bombyx mori
bioRxiv https://doi.org/10.1101/805978

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6. Contact address

When you have any question about "Silkworm, Bombyx mori, reference transcriptome data", contact the following:

Kakeru Yokoi email: yokoi123[at]affrc[dot]go[dot]jp

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