ricearray.org
Rice Oligonucleotide Array Database
http://www.ricearray.org/nsfarray/faq_geo.shtml
Array Handling Printing FAQ. Gene Expression Omnibus (GEO) Data Submission FAQ. 1 I would like to publish my microarray results, how do I deposit my array data into a public database such as the NCBI Gene Expression Omnibus (GEO) and obtain an accession for publication? The easiest way is for you to deposit your data to our database and we will deposit it to GEO for you upon your request. Here are the steps:. Deposit your data into the ROMA rice oligo array database. Create a new GEO account.
thellungiella.org
T. parvula genome
http://thellungiella.org/data
Genomic data and gene models. Use right-click and choose "Save Link As." to download files.). Genome version 2.0. Predicted gene models - cDNA version 2.0. Predicted gene models - CDS version 2.0. Predicted gene models - protein version 2.0. Genome version 1.0. Predicted gene models - CDS version 1.0. Predicted gene models - GFF format version 2.0.
ricephylogenomics.ucdavis.edu
Rice Transporter Database
http://ricephylogenomics.ucdavis.edu/transporter
The Voltage-gated Ion Channel (VIC) Superfamily. The Major Intrinsic Protein (MIP) Family. The Glutamate-gated Ion Channel (GIC) Family of Neurotransmitter Receptors. The Ammonia Transporter Channel (Amt) Family. The Non-selective Cation Channel-2 (NSCC2) Family. The Chloroplast Envelope Anion Channel-forming Tic110 (Tic110) Family. The Small Conductance Mechanosensitive Ion Channel (MscS) Family. The Annexin (Annexin) Family. The CorA Metal Ion Transporter (MIT) Family. The Anion Exchanger (AE) Family.
ricephylogenomics.ucdavis.edu
Rice TF Database
http://ricephylogenomics.ucdavis.edu/tf
Last modified: Friday, 17-Apr-2015 10:09:24 PDT. Last Update: June 2015. Go to Another Database -.
ricephylogenomics.ucdavis.edu
Rice Phylogenomics Database
http://ricephylogenomics.ucdavis.edu/description.shtml
Rice Cyt P450 DB. MPSS Small RNA Data. For each family with more than three members, the full protein sequences or domain sequences (Kinase) were aligned using ClustalW Version 2.0 with default options. Then maximum likelihood trees were bulit using PhyML 2.4.4 with JTT model (Kinase, GT, Transporter) or PhyML 3.0 with LG model (GH, TF, Cyt P450). Family assignment for each gene. The chromosome on which each gene is located. Position of 5' end of coding sequence. Position of 3' end of coding sequence.
ricephylogenomics.ucdavis.edu
Rice Phylogenomics Database
http://ricephylogenomics.ucdavis.edu/index.shtml
Rice Cyt P450 DB. And 769 glycosyltransferases ( Rice Glycosyltransferase Database, RGTD. Dardick et al, 2007 Plant Physiology; Cao et al., 2008 Molecular plant; Cao et al, Bioenergy Research, in press). We have also constructed the following databases:. The latter three databases are protected for only internal use now. If you want to access them, please try to contact Peijian Cao to request an account via PeijianCao at gmail dot com. This work was funded by the U.S. Department of Energy.
ricearray.org
Rice Oligonucleotide Array Database
http://www.ricearray.org/nsfarray/validation.shtml
Array Handling Printing FAQ. NSF Rice Oligonucleotide Array Validation. The 45K array was validated using RNA harvested from light/dark grown rice plants. For a detailed description of the experiment used to validate the 45K array design, download the Validation of NSF supported rice 45k array with light vs. dark experiment. The 20K array was validated using RNA harvested from light/dark grown rice plants. Example 1. Positive control; NH1ox transgenic plants vs wild-type. Number of hph spots 2 fold.
ricearray.org
Rice Oligonucleotide Array Database
http://www.ricearray.org/expression/expression.php
Array Handling Printing FAQ. Search Rice Affymetrix Expression Data. Number of experiments in database: 62. Number of samples/hybridizations in database: 1155. A list of all experiments in the database. Upload file (max 1000 identifiers, one per line):. Identifier terms (max 1000 identifiers, one per line):. Select an experiment -. GSE4438 - Expression data from rice under salinity stre. GSE4471 - Rice varieties Azucena and Bala grown in 0 an. GSE5167 - Rice seedling hormone treatment. GSE14275 - Express...
ricearray.org
Rice Oligonucleotide Array Database
http://www.ricearray.org/expression/overview.shtml
Array Handling Printing FAQ. All the raw data were downloaded from public databases, including NCBI GEO, ArrayExpress and PLEXdb. MAS 50 method provided by R package affy was used to convert Affymetrix probe level data to expression values. The trimmed mean target intensity of each array was arbitrarily set to 500. The data were log2 transformed. Whole Affymetrix normalized data (zip, 187M). Whole Agilent 22K normalized data (zip, 6M). Whole Agilent 44K normalized data (zip, 9M).
ricearray.org
Rice Oligonucleotide Array Database
http://www.ricearray.org/expression/meta_analysis.shtml
Array Handling Printing FAQ. Meta-Analysis is an approach to assemble expression data into context-related profiles (metaprofiles). We reclassified all the Affymetrix samples (1,155 hybridations) into anatomies and developmental stages, and provide easy online access to this data. The information for number of Affymetrix samples assigned for each metaprofile is provided here. Based on Agilent 44K platform, was also integrated into our meta-analysis tool. Upload file (max 1000 identifiers, one per line):.
