Transcript rifgp microarray database demo - The Rice Functional Genomics

RIFGP cDNA Microarray Database
The Rice Functional Genomics Program of China cDNA microarray database
(RIFGP-CDMD) consists of complete datasets, including the probe
sequences, microarray images, raw data, and experiment description.
The main goal of this database is to provide different users to download
the microarray datasets and search the expression profiling for some
interest genes. Also, this database makes available for people to do some
sequence analysis for the genes presented in the cDNA microarray.
RIFGP-CDMD homepage includes four parts of information:
1.
Microarray experiment explorer: list the rice cDNA microarray data by projects and
experiment information;
2.
Analysis of cDNA clones: search the cDNA information by clone ID and blast
sequences against local cDNA database and other databases;
3.
Search data by sample information: download the data for specific experimental
conditions;
4.
Experiment data submission: submit the sample information and raw data for the
new experiments
Download expression
data (tif, gpr, exp files)
Experiment
explorer
Project name and
PI
Table of experiments for
project
cDNA
information
by Clone Id
Analysis of cDNA clone
Blast sequences
against the local
cDNA database
and other database
Search Data by
Sample information
Search by sample
keywords
Advanced search by
multiple keywords
Data Submission
Single experiment
submission
Group experiment
submission
1. cDNA sequence:
link to the NCBI
database
2. Full-length
cDNA: link to
Japanese KOME
database and TIGR
OSA1 sequence
database
3. Annotation
4. GO information
search
Advance search for the
expression profiling for
selected probes and
experiments
Click here to database
structure and demo
Download slides for
the instruction
Login or register here
Please login here
If you are new user, please
click here for asking login
name and password
Click here to explore
the microarray data
Four parts of
content in the
database
Introduction of the cDNA
microarray database
The table lists the project name and
PI. Click here for the experiment
data of the project about the gene
expression profiling in the normal
developmental stages.
Click here to show
the microarray image
Red: higher expression in Cy5-f635;
Green: higher expression in Cy3-f532;
Yellow: equally expression in both sample
ratio image (JPG
file): 5DAP (f635)
vs. 10EM (f532)
Zoom
Array ID
Click here to show
the microarray data
These rows provide the basic
information about the microarray
data generation.
Microarray raw data
Click here to show the microarray
experiment information
Experiment information for the microarray
Click here to explore
the microarray data
Advance search: expression profiling for selected experiments and clones
Click here to get
the advanced
search results
Advance search result:
Click here to search
and analyze the
cDNA clones in the
mcroarray
Click here to get the sequencing results
Click here to get the NCBI information for the clone sequence
The clone information
available in NCBI web
Click here to get the possible full-length cDNA sequence information
Click here to get the cDNA sequence
Note: this research result was based on the annotation table for the cDNA clones
in the microarray. The cDNA clones were blasted against two sequence
databases, TIGR OSA1 and KOME rice full-length cDNA database.
Click here to get the information in KOME
KOME information for the cDNA
Click here to get the sequence annotation
Click here to get the GO information
GO information for sequence p747d07p3; the other two sequences with no GO information
Search the clone ID for sequences
Click here to do
blast against
cDNA clone
database
Click here to get the detail blast result
Note: this page shows the top hit for the blast result
Click here to search
microarray data based
on key words of
sample information
Enter the key words of
sample information
Click here to search
Enter the key words of
sample information
Click here to search
Click here to submit
microarray data in the
web
Enter the general
information for a
microarray
Enter the information
for the microarray
experiment design
Enter the sample
information and target
preparation protocols
used
Put the software information here
Browse the microarray
image and raw data
Briefly add the
information about the
microarray design
Click here to submit the
microarray data information
To submit a group of microarray experments’
information here. For the image and raw data,
the FTP will be used for transferring data.
Development stage
experiment PI
Expermenter
materials
description
ybxue
lefu lan
root
7 days old
ybxue
lefu lan
shoot
7 days old
ybxue
lefu lan
anther
mature
ybxue
ying lai
UP
pistil in the stage of 1-2 days before anthesis
ybxue
ying lai
5hP
pistil in the stage of 0-5 hours after anthesis
ybxue
lefu lan
5DAP
seed of 5 days old
ybxue
lefu lan
10EM
embyro of 10-day old seed
ybxue
lefu lan
10EN
emdosperm of 10-day old seed
Note: ying lai' work include the UP vs. 5hP,UP vs. shoot,5hP vs.shoot hybridization (the materials ,that is ,UP and 5hP are collected by lefu lan and wei chen in hangzhou)
5DAP, 10EM and 10EN ar e col l ect ed by xi ansheng zhang
Hormone treament
experiment PI
Expermenter
materials
description
kang chong
kang chong
kang chong
zheng wang
zheng wang
zheng wang
GA
JA
ck
rice callus cell suspension culture under GA treated
rice callus cell suspension culture under JA treated
r i ce cal l us cel l suspensi on cul t ur e
Mutant
experiment PI
Expermenter
materials
description
ybxue
ybxue
ying lai
ying lai
S6
CK
rice spikes derived from development stage 6 (meiotic division of pollen mother cells) in a floral mutant-1
rice spikes derived from development stage 6 in wild type
ybxue
ybxue
ying lai
ying lai
S7
CK
rice spikes derived from development stage 7 (filling stage of pollen) in the mutant-1
rice spikes derived from development stage 7 in wild type
ybxue
ybxue
ying lai
ying lai
PM
CK
rice spikes derived from development stage 5 (formation of the pollen mother cells) in a floral mutant-2
rice spikes derived from development stage 5 in wild type
Expermenter
materials
description
Stress treamnet
experiment PI
ybxue
lefu lan
w
wounding
ybxue
lefu lan(2hr,6hr(one slidedrdone by meina li),12hr)dehydration
and meina li(ck vs ck,30min,ck vs. 24hr)
ybxue
meina li
re
rehydration
ybxue
meina li
treated
Drought treated with no rehydration
Note: all the materials used in wounding and dehydration are derived from 14-day old shoot of rice