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Series GSE27004 Query DataSets for GSE27004
Status Public on Feb 11, 2011
Title Genome-wide gene expression atlas of maize inbred line B73
Organism Zea mays
Experiment type Expression profiling by genome tiling array
Summary Genome-wide gene expression atlas of maize inbred line B73. Maize inbred B73 was used for constructing the gene atlas. Plants were grown in Plano silt loam soil at the West Madison Agricultural Research Station, Verona, WI during Summer 2008. During field preparation, 200 kg/acre of Urea (46-0-0) was applied. One day after planting, herbicides including Callisto (142 g/acre), Dual II (710 ml/acre), and Simazine (227 g/acre) were applied. For collection of seed tissues, shoots were covered before silk emergence avoiding any injury to the plants. Plants were self-pollinated on the same day to establish a common time initiation point for the harvest timeline. Greenhouse-grown plants were propagated by growing five plants per pot (30 cm top diameter, 28 cm height, 14.5 L volume) containing Metro-Mix 300 (Sun Gro Horticulture, Bellevue, WA, USA) with no additional fertilization. The growing conditions were 27 deg. C day and 24 deg. C night temperature with a 16h light (5:00am to 9:00pm) and 8h dark regime. Germinating seed tissue was generated by soaking seeds in distilled water in a Petri dish for 12h and then placing seeds between layers of moist paper towels for another 12h to allow germination. The field samples were collected between 8:00am and 10:00am, approximately 3 hours after sunrise. The greenhouse samples were collected between 8:00am and 9:00am, three hours after turning on the lights. Three biological replicates were collected for each tissue type. For all the tissues except germinating seeds, a biological replicate was constituted by collecting and pooling samples from three competitive randomly chosen plants. For germinating seed, ten randomly chosen seeds were pooled to form a biological replicate. The harvested tissues were immediately frozen in liquid nitrogen and stored at -80 deg. C. Total RNA was extracted using TRIZOL reagent (Invitrogen, http://www.invitrogen.com) following the manufacturer's protocol, and purified using RNeasy MinElute Cleanup Kit (Qiagen, http://www.qiagen.com) following the manufacturer's instructions.

PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rajandeep S Sekhon. The equivalent experiment is ZM29 at PLEXdb.
 
Overall design organism part name: 24H_Germinating Seed(3-replications); organism part name: 6DAS_GH_Coleoptile(3-replications); organism part name: 6DAS_GH_Primary Root(3-replications); organism part name: V1_GH_Primary Root(3-replications); organism part name: VE_Whole Seedling(3-replications); organism part name: VE_Primary Root(3-replications); organism part name: V1_Pooled Leaves(3-replications); organism part name: V1_Stem and SAM(3-replications); organism part name: V4_Stem and SAM(3-replications); organism part name: V3_Stem and SAM(3-replications); organism part name: V3_First Leaf and Sheath(3-replications); organism part name: V3_Topmost Leaf(3-replications); organism part name: V5_Shoot Tip(3-replications); organism part name: V5_First Internode(3-replications); organism part name: V5_Tip of stage-2 Leaf(3-replications); organism part name: V5_Base of stage-2 Leaf(3-replications); organism part name: V7_First Internode(3-replications); organism part name: V7_Tip of stage-2 Leaf(3-replications); organism part name: V7_Base of stage-2 Leaf(3-replications); organism part name: V9_Fourth Internode(3-replications); organism part name: V9_Eighth Leaf(3-replications); organism part name: V9_Eleventh Leaf(3-replications); organism part name: V9_Thirteenth Leaf(3-replications); organism part name: V9_Immature Leaves(3-replications); organism part name: V13_Immature Tassel(3-replications); organism part name: V18_Meiotic Tassel(3-replications); organism part name: V18_Immature Cob(3-replications); organism part name: VT_Thirteenth Leaf(3-replications); organism part name: R1_Pre-pollination Cob(3-replications); organism part name: R1_Silks(3-replications); organism part name: R1_Anthers(3-replications); organism part name: R1_Innermost Husk(3-replications); organism part name: R2_Thirteenth Leaf(3-replications); organism part name: R2_Outer Husk(3-replications); organism part name: R2_Innermost Husk(3-replications); organism part name: 2DAP_Whole Seed(3-replications); organism part name: 4DAP_Whole Seed(3-replications); organism part name: 6DAP_Whole Seed(3-replications); organism part name: 8DAP_Whole Seed(3-replications); organism part name: 10DAP_Whole Seed(3-replications); organism part name: 12DAP_Whole Seed(3-replications); organism part name: 12DAP_Endosperm(3-replications); organism part name: 14DAP_Whole Seed(3-replications); organism part name: 14DAP_Endosperm(3-replications); organism part name: 16DAP_Whole Seed(3-replications); organism part name: 16DAP_Endosperm(3-replications); organism part name: 16DAP_Embryo(3-replications); organism part name: 18DAP_Whole Seed(3-replications); organism part name: 18DAP_Endosperm(3-replications); organism part name: 18DAP_Embryo(3-replications); organism part name: 18DAP_Pericarp(3-replications); organism part name: 20DAP_Whole Seed(3-replications); organism part name: 20DAP_Endosperm(3-replications); organism part name: 20DAP_Embryo(3-replications); organism part name: 22DAP_Whole Seed(3-replications); organism part name: 22DAP_Endosperm(3-replications); organism part name: 22DAP_Embryo(3-replications); organism part name: 24DAP_Whole Seed(3-replications); organism part name: 24DAP_Endosperm(3-replications); organism part name: 24DAP_Embryo(3-replications)
Web link http://www.plexdb.org/modules/PD_browse/experiment_browser.php?experiment=ZM29
 
Contributor(s) Sekhon RS
Citation(s) 21299659
Submission date Feb 01, 2011
Last update date Mar 23, 2012
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platforms (1)
GPL12620 Nimblegen Maize Whole-Genome Microarray 385K (VersionV1_4a.53)
Samples (180)
GSM665151 organism part name: 24H_Germinating Seed - rep1
GSM665152 organism part name: 24H_Germinating Seed - rep2
GSM665153 organism part name: 24H_Germinating Seed - rep3
Relations
BioProject PRJNA137659

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE27004_RAW.tar 1.1 Gb (http)(custom) TAR (of PAIR)
Processed data included within Sample table
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