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Browse MaizePLEX Experiment Data

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Genome-wide gene expression atlas of maize inbred line B73 (clone of ZM29 for nimbMaizeV2)
Rajandeep S Sekhon, Great Lakes Bioenergy Research Center 443 Plant Sciences, 1575 Linden Drive University of Wisconsin Madison, WI, U.S.A. (rsekhon@glbrc.wisc.edu)
Experiment design (180 hybridizations)
organism part name
•24H_Germinating Seed •6DAS_GH_Coleoptile •6DAS_GH_Primary Root •V1_GH_Primary Root •VE_Whole Seedling •VE_Primary Root •V1_Pooled Leaves •V1_Stem and SAM •V4_Stem and SAM •V3_Stem and SAM •V3_First Leaf and Sheath •V3_Topmost Leaf •V5_Shoot Tip •V5_First Internode •V5_Tip of stage-2 Leaf •V5_Base of stage-2 Leaf •V7_First Internode •V7_Tip of stage-2 Leaf •V7_Base of stage-2 Leaf •V9_Fourth Internode •V9_Eighth Leaf •V9_Eleventh Leaf •V9_Thirteenth Leaf •V9_Immature Leaves •V13_Immature Tassel •V18_Meiotic Tassel •V18_Immature Cob •VT_Thirteenth Leaf •R1_Pre-pollination Cob •R1_Silks •R1_Anthers •R1_Innermost Husk •R2_Thirteenth Leaf •R2_Outer Husk •R2_Innermost Husk •2DAP_Whole Seed •4DAP_Whole Seed •6DAP_Whole Seed •8DAP_Whole Seed •10DAP_Whole Seed •12DAP_Whole Seed •12DAP_Endosperm •14DAP_Whole Seed •14DAP_Endosperm •16DAP_Whole Seed •16DAP_Endosperm •16DAP_Embryo •18DAP_Whole Seed •18DAP_Endosperm •18DAP_Embryo •18DAP_Pericarp •20DAP_Whole Seed •20DAP_Endosperm •20DAP_Embryo •22DAP_Whole Seed •22DAP_Endosperm •22DAP_Embryo •24DAP_Whole Seed •24DAP_Endosperm •24DAP_Embryo

NOTES: ZM37 is the cloned version of ZM29 for the virtual array nimbMaizeV2, corresponding to release 5a (RefGen_v2) gene models. ...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Genome-wide gene expression atlas of maize inbred line B73 (clone of ZM29 for nimbMaizeV2)
Accession No: ZM37
Microarray: nimbMaizeV2
Visibility: public
Experiment Type:
Experiment Factor(s):
organism part name
•24H_Germinating Seed  •6DAS_GH_Coleoptile  •6DAS_GH_Primary Root  •V1_GH_Primary Root  •VE_Whole Seedling  •VE_Primary Root  •V1_Pooled Leaves  •V1_Stem and SAM  •V4_Stem and SAM  •V3_Stem and SAM  •V3_First Leaf and Sheath  •V3_Topmost Leaf  •V5_Shoot Tip  •V5_First Internode  •V5_Tip of stage-2 Leaf  •V5_Base of stage-2 Leaf  •V7_First Internode  •V7_Tip of stage-2 Leaf  •V7_Base of stage-2 Leaf  •V9_Fourth Internode  •V9_Eighth Leaf  •V9_Eleventh Leaf  •V9_Thirteenth Leaf  •V9_Immature Leaves  •V13_Immature Tassel  •V18_Meiotic Tassel  •V18_Immature Cob  •VT_Thirteenth Leaf  •R1_Pre-pollination Cob  •R1_Silks  •R1_Anthers  •R1_Innermost Husk  •R2_Thirteenth Leaf  •R2_Outer Husk  •R2_Innermost Husk  •2DAP_Whole Seed  •4DAP_Whole Seed  •6DAP_Whole Seed  •8DAP_Whole Seed  •10DAP_Whole Seed  •12DAP_Whole Seed  •12DAP_Endosperm  •14DAP_Whole Seed  •14DAP_Endosperm  •16DAP_Whole Seed  •16DAP_Endosperm  •16DAP_Embryo  •18DAP_Whole Seed  •18DAP_Endosperm  •18DAP_Embryo  •18DAP_Pericarp  •20DAP_Whole Seed  •20DAP_Endosperm  •20DAP_Embryo  •22DAP_Whole Seed  •22DAP_Endosperm  •22DAP_Embryo  •24DAP_Whole Seed  •24DAP_Endosperm  •24DAP_Embryo
Quality Control: biological replicates
Treatment summary:
 organism part name  # replicates
 24H_Germinating Seed  3
 6DAS_GH_Coleoptile  3
 6DAS_GH_Primary Root  3
 V1_GH_Primary Root  3
 VE_Whole Seedling  3
 VE_Primary Root  3
 V1_Pooled Leaves  3
 V1_Stem and SAM  3
 V4_Stem and SAM  3
 V3_Stem and SAM  3
 V3_First Leaf and Sheath  3
 V3_Topmost Leaf  3
 V5_Shoot Tip  3
 V5_First Internode  3
 V5_Tip of stage-2 Leaf  3
 V5_Base of stage-2 Leaf  3
 V7_First Internode  3
 V7_Tip of stage-2 Leaf  3
 V7_Base of stage-2 Leaf  3
 V9_Fourth Internode  3
 V9_Eighth Leaf  3
 V9_Eleventh Leaf  3
 V9_Thirteenth Leaf  3
 V9_Immature Leaves  3
 V13_Immature Tassel  3
 V18_Meiotic Tassel  3
 V18_Immature Cob  3
 VT_Thirteenth Leaf  3
 R1_Pre-pollination Cob  3
 R1_Silks  3
 R1_Anthers  3
 R1_Innermost Husk  3
 R2_Thirteenth Leaf  3
 R2_Outer Husk  3
 R2_Innermost Husk  3
 2DAP_Whole Seed  3
 4DAP_Whole Seed  3
 6DAP_Whole Seed  3
 8DAP_Whole Seed  3
 10DAP_Whole Seed  3
 12DAP_Whole Seed  3
 12DAP_Endosperm  3
 14DAP_Whole Seed  3
 14DAP_Endosperm  3
 16DAP_Whole Seed  3
 16DAP_Endosperm  3
 16DAP_Embryo  3
 18DAP_Whole Seed  3
 18DAP_Endosperm  3
 18DAP_Embryo  3
 18DAP_Pericarp  3
 20DAP_Whole Seed  3
 20DAP_Endosperm  3
 20DAP_Embryo  3
 22DAP_Whole Seed  3
 22DAP_Endosperm  3
 22DAP_Embryo  3
 24DAP_Whole Seed  3
 24DAP_Endosperm  3
 24DAP_Embryo  3
Total hybridizations: 180
Description: NOTES:
ZM37 is the cloned version of ZM29 for the virtual array nimbMaizeV2, corresponding to release 5a (RefGen_v2) gene models.

Cloned version:
The microarray experiment is exactly the same as the original ZM29 and includes simply the duplication of raw data files, samples and the treatment factors to ZM37.

Virtual Array nimbMaizeV2 (Nimblegen Maize Whole-Genome Microarray 385K, VersionV2_5a.59):
The probes from the original array NimbMaize (Nimblegen Maize Whole-Genome Microarray 385K) have been mapped by MaizeGDB to the 5a Working Gene Set transcripts (WGS, release 5a.59, corresponding to B73 RefGen_v2). This PLEXdb virtual version of the array contains 70062 gene transcripts (probe sets) of the 136770 transcripts in the WGS, representing 219,816 of the 330,778 total probes which passed the mapping criteria. The criteria are: 1) complete matches of probe sequence with up to two mismatched base pairs with no gap penalty, and 2) probes must map to two or fewer gene models or locations on the assembly. 27% of the probes did not map to B73 RefGen_v2 and 9% were repetitive. This left 64% of the probes which were incorporated into probe sets.

Microarray data analysis invoved summerization of the probe expression values over the corresponding 5a WGS transcripts as probe sets.

The original accession Zm29 used the V1 gene models (release 4b, Filtered Gene Set, corresponding to RefGen_v1) as the basis for probe mapping.
--------

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.

Sekhon RS, Lin H, Childs KL, Hansey CN, Robin Buell C, de Leon N, Kaeppler SM.
Genome-wide atlas of transcription through maize development. Plant J. 2011 Feb
7. doi: 10.1111/j.1365-313X.2011.04527.x. [Epub ahead of print] PubMed PMID:
21299659.
Publication: none
Created: 2011-04-11 00:00:00
Last Update: 2011-04-11 00:00:00
Released: 2011-04-20
Submitter: PLEXdb Curator
Name: Rajandeep S Sekhon
Institution: Great Lakes Bioenergy Research Center 443 Plant Sciences, 1575 Linden Drive University of Wisconsin Madison, WI, U.S.A.
Head of Laboratory: Shawn Kaeppler
email(s):
Homepage:

 
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