RED

2015/12/21

Web Site: http://red.dna.affrc.go.jp/RED/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/red/

Comprehensive information around the constitution of the Microarrays on Rice Microarray Project.

README Content

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

1. Database Component

  1. README
  2. Research Groups & Research Subjects
  3. Outline of the experiment
  4. Experimental information
  5. Sample information
  6. Expression data
  7. EST data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "RED" data.
File README_e.html(English)
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2.2 Research Groups & Research Subjects

Data name Research Groups & Research Subjects
Description of data contents Information for each year about research groups and research subjects.
File red_subject_info.zip (5.2 KB)

Data items are the following:
Data itemDescription
Research ID Research ID (Subject number)
Institute Organization
Section Section (Department)
User name User name
Experimental title Experimental title (Research Subject)
Year Year
HP url URL of the site
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2.3 Outline of the experiment

Data name Outline of the experiment
Description of data contents Outline of the experiment including sample combinations of each round.
File red_experiment_outline.zip (7.8 KB)

Data items are the following:
Data itemDescription
Experimental ID String connected by a '_' between "Research ID", "Round", "C", "Group no" of "Control no" data, "Intra no" of "Control no" data, "T", "Group no" of "Target no" data, and "Intra no" of "Target no" data.
Research ID Research ID (Subject number)
Round Round
Combination ID ID of the sample combination
Control no Control data, correspondence to column of "Sample no" on the red_sample table.
Target no Target data, correspondence to column of "Sample no" on the red_sample table.
Method Method
  • "1" : 1-color method
  • "2" : 2-color method
Release Public status of subject
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2.4 Experimental information

Data name Experimental information
Description of data contents Detailed information of the experiment of each array glass.
File red_experiment_info.zip (20.3 KB)

Data items are the following:
Data itemDescription
Info ID ID of the experimental information
Research ID Research ID (Subject number)
Round Round
Control no Control data, correspondence to column of "Sample no" on the red_sample table.
Target no Target data, correspondence to column of "Sample no" on the red_sample table.
Glass position Spotted position on the glass
  • "1" : 1st grass
  • "2" : 2nd grass
Probe type Probe type, f or 3 or G
  • "f" : Rice8987 f_array (Full insert version)
  • "3" : Rice8987 Array (3'UTR version)
  • "g" : Rice8987 g_array (Full insert version)
  • "others" : Other types
  • "blank" : Unknown
glass ID Array glass ID
experiment date Experiment date
glass production date Array glass production date
spotter No Spot number
pen set Pen set
glass batch Array glass batch
Array name Array name
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2.5 Sample information

Data name Sample information
Description of data contents Sample information used as control sample or target sample.
File red_sample.zip (27.5 KB)

Data items are the following:
Data itemDescription
Research ID Research ID (Subject number)
Round Round
Sample no Sample number
Sample name Sample name
Sample type Sample type
  • "C" : Control sample
  • "T" : Target sample
treatment Keyword Treatment keyword
Physiology1 Physiological conditions 1
Physiology2 Physiological conditions 2
Organism Organism
Scientific name Scientific name
Cultivar Cultivar
Tissue stage detail Details of tissue stage
stage Keyword Developmental stage
other stage Keyword Other developmental stage
tissue Keyword Collected organ
other tissue Keyword Other collected organ
mRNA type mRNA type
  • "t" : Total
  • "m" : mRNA
Treatment comment Details of treatment
Group no Group number
Intra no Intra number (Identification ID)
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2.6 Expression data

Data name Expression data
Description of data contents Normalized expression data derived from experiments.
File red_expression.zip (85.5 MB)

Data items are the following:
Data itemDescription
Experimental ID String connected by a '_' between "Research ID", "Round", "C", "Group no" of "Control no" data, "Intra no" of "Control no" data, "T", "Group no" of "Target no" data, and "Intra no" of "Target no" data.
Research ID Research ID (Subject number)
Round Round
Control no Control data, correspondence to column of "Sample no" on the red_sample table.
Target no Target data, correspondence to column of "Sample no" on the red_sample table.
Element No(Glass) Element number (spotted position on the glass)
EST name EST name, correspondence to column of "Clone name" on the red_est.
Expression value Expression value (normalized ratio average)
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2.7 EST data

Data name EST data
Description of data contents Position information of the clone of Rice8987 Array on chromosomes.
File red_est.zip (629 KB)

Data items are the following:
Data itemDescription
Element No(Glass) Element number (spotted position on the glass)
Clone name Clone name
Accession_01 DDBJ accession number (5')
Accession_02 DDBJ accession number (3')
Locus name Locus name
Chr type Chromosome number
EST cluster type Cluster type of EST
  • "D" : Mapping the clone sequences directly into the genome.
  • "G" : Mapping a representative clone sequences of similar sequences group into the genome.
Availability Availability
  • "true" : Available
  • "false" : Not available
3'UTR M /no check PCR products check (3'UTR)
  • "blank" : result match to the prediction
  • "no" : no band
  • "m" : multiband
Full insert M /no check PCR products check (Full inserts)
  • "blank" : Result match to the prediction
  • "no" : no band
  • "m" : multiband
Destination Plate Destination Plate number, which used for PCR check of the clone
Dplate Pos Posision on the Destination Plate used for PCR check of the clone
Mapped 3'UTR Primer seq (Upper) Mapped 3'UTR Primer sequence (Upper)
Mapped 3'UTR Primer seq (Lower) Mapped 3'UTR Primer sequence (Lower)
Unmapped 3'UTR Primer seq (Upper) Unmapped 3'UTR Primer sequence (Upper)
Unmapped 3'UTR Primer seq (Lower) Unmapped 3'UTR Primer sequence (Lower)
Putative Identification Putative Gene Identification
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3. License

Last updated : 2015/12/21

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: "Rice Expression Database © Shoshi Kikuchi (National Institute of Agrobiological Sciences) 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.

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Plant Genome Research Unit
Shoshi Kikuchi
E-mail: skikuchi[at]nias[dot]affrc[dot]go[dot]jp

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4. Update History

DateUpdate contents
2015/12/21 Rice Expression Database English archive site is opened.
2000/10/1 Rice Expression Database (http://red.dna.affrc.go.jp/RED/) is opened.
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5. Literature

Junshi Yazaki, Naoki Kishimoto, Masahiro Ishikawa and Shoshi Kikuchi
Rice Expression Database: the gateway to rice functional genomics
Trends in Plant Science (2002) Dec 7 (12):563-564

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6. Contact address

When you have any question about "RED", contact the following:

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Plant Genome Research Unit
Shoshi Kikuchi
E-mail: skikuchi[at]nias[dot]affrc[dot]go[dot]jp

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