Maloof Lab:Resources

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RNAseq data of 4 tomato species.  Data is from seedlings.  This data is unpublished.  By accessing this data you agree not to publish transcriptome-wide analyses of these data before our primary publication.
RNAseq data of 4 tomato species.  Data is from seedlings.  This data is unpublished.  By accessing this data you agree not to publish transcriptome-wide analyses of these data before our primary publication.
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[http://data.iplantcollaborative.org/quickshare/ed6cab6a3d9952b7/SHA.reads.tar.gz S. habrochaites (LA1777)]
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[http://data.iplantcollaborative.org/quickshare/dcef407b369b971b/SHA.reads.tar.gz S. habrochaites (LA1777)]
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[http://data.iplantcollaborative.org/quickshare/b062d8a2ab14a268/SLY.reads.tar.gz S. lycopersicum var. M82 (LA3475)]
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[http://data.iplantcollaborative.org/quickshare/cf74a53e1146d4f0/SLY.reads.tar.gz S. lycopersicum var. M82 (LA3475)]
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[http://data.iplantcollaborative.org/quickshare/21cdae35adeedde7/SPE.reads.tar.gz S. pennellii (LA0716)]
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[http://data.iplantcollaborative.org/quickshare/d0030051e53882b4/SPE.reads.tar.gz S. pennellii (LA0716)]
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[http://data.iplantcollaborative.org/quickshare/6b03632313290d76/SPI.reads.tar.gz S pimpenllifolium (LA1589)]
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[http://data.iplantcollaborative.org/quickshare/fd35a7338e106b97/SPI.reads.tar.gz S pimpenllifolium (LA1589)]
==Microarray Data==
==Microarray Data==

Current revision

Image:logo2_final.jpg

Room 2115
Section of Plant Biology
1002 Life Sciences, One Shields Ave.
University of California Davis
Davis, CA 95616

Contact

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Contents

RIL Data

Col x X

Col x X genotype data

Col x X field phenotype data

RIL genotypic data from MSATs assayed in the Maloof Lab and by Sequenom SNP analysis performed by Cogenics, inc. RIL Phenotypic data from Weinig Lab field grown plants in Minnesota. For RIL construction, Col was crossed to an unknown accession; resulting F2 plants were self-fertilized until the F8 generation and then genotyped. Genotyping revealed a strong bias to Col genotypes and higher heterozygosity than expected. Subsequent flow cytometry analysis by Brian Dilkes revealed that some RILs are tetraploid and that the Col parent was likely tetraploid. Flow cytometry data will be made available when analysis is complete.

B. Rapa RILs

B. rapa field phenotype data

Phenotypic measurements of Brassica rapa RILs grown in high and low density field plantings as described in Dechaine et al., 2007 (PMID 17822398). Data collection from Weinig Lab. RILs developed by Federico Iniguez-Luy and Tom Osborn.

Association Mapping Data

GI

GI association data

Data for GIGANTEA associations as published in Brock et al, 2007 (PMID 17614917)

PHYB

PHYB association data

PHYB association R script

Data and R analysis script for PHYB associations as published in Filiault et al, 2008 (PMID 18287016)

PHYC

PHYC association data

Data for PHYB and PHYC associations reported in Balasubramanian et al, 2006 (PMID 16732287)


Sequence Data

Arabidopsis

Arabidopsis PHYB Sequences reported in Filiault et al, 2008 (PMID 18287016) are available from NCBI here

Arabidospis sequences reported by Brock et al, 2007 (PMID 17614917) are available for PHYB, PIF3, PIF4, NDPK2, PKS1, GI, and ATHB2

Tomato

SNPs derived from the analysis of tomato ESTs described in Jimenez-Gomez and Maloof, 2009 (PMID 19575805) is at Tomato SNPS


RNAseq data of 4 tomato species. Data is from seedlings. This data is unpublished. By accessing this data you agree not to publish transcriptome-wide analyses of these data before our primary publication.

S. habrochaites (LA1777)

S. lycopersicum var. M82 (LA3475)

S. pennellii (LA0716)

S pimpenllifolium (LA1589)

Microarray Data

Microarray expression profiling of genes correlated with elongation, as described in Nozue et al, 2007 (PMID 17589502) is available from the GEO Database as accession GSE6906


Software Tools

LeafJ. This is an ImageJ plugin that allows rapid measurement of Arabidopsis leaf blade and petiole length from scanned images.


LED Controller. This is a LabVIEW virtual instrument that allows control of intensity duration of illumination of Quantum Devices SNAPlite LEDs. Useful for setting up custom incubators. Current configuration is for four incubators with two to three colors of LEDs each. You will need a PC with LabVIEW, a PCI-DAC6703 from Measurement Computing, and suitable connectors. It should be possible to modify the VI to work with other LabVIEW compatible digital-to-analog convertors.


Camera and IR LED controller. This is a LabVIEW virtual instrument that will control a digital camera and a bank of infra-red LEDs for time-lapse photography in the dark. The LEDs are switched on just briefly as the picture is taken. A complete parts list for the system is available here.


Excel macro for data input. An Excel macro for plant measurement input. Allows semi-automated data entry using a barcode reader for plant identification and digital calipers for plant measurement. Runs in Office 2003. Requires a USB barcode reader such as the Metrologic MS5145 USB barcode reader, Mitutoyo digital calipers, Mitutoyo RS-232 data cable, Edgeport serial to USB convertor, and WinWedge.

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