RMOS

2015/10/27

Web Site: -
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rmos/

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. RMOS Contents
  3. Array patterns and clones
  4. Rice1265 Array: PCR check
  5. Rice8987 Array: PCR check
  6. Rice8987 Array: Gel images
  7. Rice8987 g_array: cDNA information
  8. 8987Array-Chromosome
  9. Rice8987Corresponding Table(f_g_primer)
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "RMOS" data.
File README_e.html(English)
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2.2 RMOS Contents

Data name RMOS Contents
Description of data contents Static files of all RMOS site.
 - General Information
 - Application Guide Microarray System
 - Microarray Center Protocol
 - Microarray / Clone List
 - Search
 - Data Results
 - Publications
File rmos_contents.zip (22.2 MB)
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2.3 Array patterns and clones

Data name Array patterns and clones
Description of data contents Static files of array patterns and cDNA clones.
File rmos_array1265_clone_list.zip (27.3 KB)
rmos_f_array8987_clone_list.zip (321 KB)
rmos_g_array8987_clone_list.zip (827 KB)
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2.4 Rice1265 Array: PCR check

Data name Rice1265 Array: PCR check
Description of data contents List of the PCR check results about clones used in Rice1265 Microarray (Full insert version) / (3'UTR version)
File rmos_1265PCRcheck.zip (11.7 KB)

Data items are the following:
Data itemDescription
Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones')
Clone id Clone ID
96 Plate Identification number of the 96 Plate used for PCR check of the clone
Position Position in the 96 plate used for PCR check of the clone
PCR products check (3'UTR) PCR products check (3'UTR): "blank"; result match to the prediction, "no"; no band, "m"; multiband.
PCR products check (Full inserts) PCR products check (Full inserts): "blank"; result match to the prediction, "no"; no band, "m"; multiband.
Accession id 1 DDBJ accession number 1
Accession id 2 DDBJ accession number 2
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2.5 Rice8987 Array: PCR check

Data name Rice8987 Array: PCR check
Description of data contents List of the PCR check results about clones used in Rice8987 Microarray (f_array/Full insert version)
File rmos_8987pcrcheck.csv.zip (96.3 KB)

Data items are the following:
Data itemDescription
Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones')
Clone name Clone name
Dplate Destination Plate name, which used for PCR check of the clone
Dplate Pos. Position on the Destination Plate used for PCR check of the clone
PCR products check (Full inserts) PCR products check (Full inserts): "blank"; result match to the prediction, "no"; no band, "m"; multiband.
Accession (5') DDBJ accession number (5')
Accession (3') DDBJ accession number (3')
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2.6 Rice8987 Array: Gel images

Data name Rice8987 Array: Gel images
Description of data contents Images of Gel Electrophoresis of 8979 cDNA clones used in Rice8987 Array (f_array/Full insert version).
File rmos_eidou_pict.zip (1.25 MB)
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2.7 Rice8987 g_array: cDNA information

Data name Rice8987 g_array: cDNA information
Description of data contents cDNA information of Rice8987 Array (Rice9000 g_array/Full insert version).
* For all microarray experiments on and after July 1, 2002, second version of our rice microarray (called “g_array”) is used. The “g_array” carries the same 8987 cDNAs (with the full inserts) that the Rice8987 Array carries. However the location of each cDNA clone on “g_array” is different from that on the Rice8987 Array.
File rmos_rice9000array_g.csv.zip (453 KB)

Data items are the following:
Data itemDescription
Element No. (Glass) Element No. (Spotted Position on the Glass: refer to the 'Array patterns and clones')
Spot No. Spot No.
Clone name Clone name
Putative Gene Identification Putative Gene Identification
Destination Plate (96) Destination Plate number, which used for PCR check of the clone
Dplate Pos. Position on the Destination Plate used for PCR check of the clone
Source Plate Name Source Plate Name
*No available data
Clone Pos. in STAFFDWP Clone Pos. in STAFFDWP (STAFF Deep Well Plate)
*No available data
Accession No. (A) DDBJ accession number, which clone neme include A
Accession No. (Z) DDBJ accession number, which clone neme include Z
Primer No. Primer number
*No available data
to Full Spot No. to Full Spot number
*No available data
384Plate Identification number of 384Plate used for spotting cDNA on the Glass
384Plate Pos. Position on the 384Plate
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2.8 8987Array-Chromosome

Data name 8987Array-Chromosome
Description of data contents Position information of the clone of Rice8987 Array (f_array) on chromosomes
File rmos_8987array_chromosome.csv.zip (96.5 KB)

Data items are the following:
Data itemDescription
f_array_element f_array element number (spotted position on the glass: refer to the 'Array patterns and clones')
Accession1 DDBJ accession number 1
Accession2 DDBJ accession number 2
Clone name Clone name
DDBJ name Name in the definition of DDBJ
Multi Similarity between sequences of cDNA clones and those of rice genome.
(high to low ; A, B, C….)
Mapping D : Sequence of the clone was directly used for mapping.
G : Sequence of the representative clone in the group consisting of clones with similar sequences was used for mapping.
Chr. Chromosome number
Clone name (group) Representative clone name in the group
Multi (group) Similarity between sequences of the representative clone and rice genome in the group.
(high to low ; A, B, C….)
Chr. (group) Chromosome number of the genome sequence similar to that of the representative clone in the group
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2.9 Rice8987Corresponding Table(f_g_primer)

Data name Rice8987Corresponding Table(f_g_primer)
Description of data contents List of primer information of Rice8987Array (f_g_primer).
File rmos_f_g_primer_table.csv.zip (636 KB)

Data items are the following:
Data itemDescription
g_Element No. g_Element number on the Rice8987 g_array, which indicates the spotting position on the glass
f_Element No. f_Element number on the Rice8987 f_array, which indicates the spotting position on the glass
3UTR Element No. 3UTR Element number on the Rice8987 Array (3'UTR version), which indicates the spotting position on the glass
Clone name Clone name
Accession 01 DDBJ accession number 01
Accession 02 DDBJ accession number 02
Putative Identification Putative Gene Identification
Destination Plate (96) Destination Plate number, which used for PCR check of the clone
Dplate Pos. Position on the Destination Plate used for PCR check of the clone
Full insert M /no check PCR products check (Full inserts) using the M13 RV primer and the M4 primer (TAKARA) : "blank"; result match to the prediction, "no"; no band, "m"; multiband.
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)
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3. License

Last updated : 2015/10/27

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 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "RMOS © Shoshi Kikuchi (National Institute of Agrobiological Sciences) licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan 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 derivative works 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 derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  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
2015/10/27 RMOS English archive site is opened.
2015/09/17 The original website (http://cdna01.dna.affrc.go.jp/RMOS/) was terminated.
2001/01/12 RMOS (http://cdna01.dna.affrc.go.jp/RMOS/) is opened.
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5. Literature

S.Kikuchi J. Yazaki N. Kishimoto M. ishikawa D. Endo
Chapter 2 Comprehensive Analysis of Rice Gene Expression Using the Microarray System: What We have Learned from the Microarray Project
Rice Improvement in the Genomics Era, edited by Swapan K. Datta, CRC Press NY, 2009, pp.15-58, ISBN 978-1-56022-952-0

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6. Contact address

When you have any question about "RMOS", 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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