RED II INAHO
2016/01/14Web Site: http://red.dna.affrc.go.jp/INAHO/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/redii-inaho/
RED II INAHO is the database that analyzed the gene expression of rice using a 60-mer oligonucleotide microarray.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "RED II INAHO" data. |
| File | README_e.html(English) |
2.2 Probe data
| Data name | Probe data |
| Description of data contents | Probe information |
| File | redii_inaho_probe.zip (3.1 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Probe no | Probe number |
| Probe ID | Probe ID |
| TU ID | ID of the TU (Transcriptional Unit) |
| Microarray | Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database |
| Accession | Gene Accession number of probe |
| 5'end Accession | Gene Accession number of probe 5'end |
| 3'end Accession | Gene Accession number of probe 3'end |
| Gene name | Gene name |
| Probe name | Probe name |
| Annotation | Probe Annotation |
| 5'probe sequence | Sequence of probe 5'end |
| 3'probe sequence | Sequence of probe 3'end |
2.3 Experimental information
| Data name | Experimental information |
| Description of data contents | Outline of the experiment including sample combinations of each round. |
| File | redii_inaho_experiment.zip (22.7 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Experiment no | Experiment number |
| Experiment ID | String connected by a '_' between "Research ID", "Round", "Group no" of "Control ID" data and "Group no" of "Target ID" data. |
| Microarray | Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database |
| Control ID | Control Data, correspondence to column of "Sample ID" on the redii_inaho_sample table. |
| Target ID | Target Data, correspondence to column of "Sample ID" on the redii_inaho_sample table. |
| Control dye | Control dye |
| Target dye | Target dye |
| Experimenter | User name |
| Institute | Organization |
| Experimental category1 | Experimental category 1 |
| Experimental category2 | Experimental category 2 |
| Experimental category3 | Experimental category 3 |
| Experimental category4 | Experimental category 4 |
| Keyword | Experimental keyword |
| Method | Method |
| Experiment Date 1 | Experiment date 1 |
| Glass ID 1 | Array glass ID 1 |
| Glass Production Date 1 | Array glass production date 1 |
| Spotter No 1 | Spot number 1 |
| Pen Set ID 1 | Pen set ID 1 |
| Glass Batch ID 1 | Array glass batch 1 |
| Experiment Date 2 | Experiment date 2 |
| Glass ID 2 | Array glass ID 2 |
| Glass Production Date 2 | Array glass production date 2 |
| Spotter No 2 | Spot number 2 |
| Pen Set ID 2 | Pen set ID 2 |
| Glass Batch ID 2 | Array glass batch 2 |
2.4 Sample information
| Data name | Sample information |
| Description of data contents | Sample information used as control sample or target sample. |
| File | redii_inaho_sample.zip (11.4 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sample ID | Sample ID |
| Microarray | Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database |
| Experiment ID | Original experimental ID. String connected by a '_' between "Research ID", "Round" and "Group no". |
| Organism | Organism |
| Subspecies | Subspecies |
| Cultivar | Cultivar, Line |
| Developmental Stage | Developmental stage |
| Tissue | Tissue |
| Mutant | Mutant |
| Transgenic | Transgenic |
2.5 Expression data
| Data name | Expression data |
| Description of data contents | Normalized expression data derived from experiments. |
| File | redii_inaho_expression.zip (101 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Microarray | Microarray name RED : Rice 9k Array used in the RMOS database ARRAY22K : Rice 22k Array used in the KOME database |
| Experiment no | Experiment number |
| Spot ID | Spot ID |
| Probe no | Probe number |
| Probe name | Probe name |
| Expression value | Expression value (log ratio) |
3. License
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.
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 II INAHO © 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:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- 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:
- 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.
- 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).
- 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
4. Update History
| Date | Update contents |
|---|---|
| 2016/01/14 | Rice Expression Database II INAHO English archive site is opened. |
| 2009/04/01 | Rice Expression Database II INAHO (http://red.dna.affrc.go.jp/INAHO/) is opened. |
5. Literature
-6. Contact address
When you have any question about "RED II INAHO", 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