Microarray Hybridization Details
Step 1. Select an experiment
Please choose Species/Platform/Experiment1. TA1: Wheat--Rehybridization of Wheat and Barley cRNAs to the Affymetrix Wheat Genome Ar...2. TA2: Wheat--Wheat GeneChip Test3. OS1: Rice--Rice 57K Affymetrix GeneChip Test4. FG1: Fusarium--Fusarium transcript detection on Morex barley spikes using Fusarium Affy Ge...5. FG2: Fusarium--Expression Profiles in Carbon and Nitrogen Starvation Conditions6. FG4: Fusarium--Fusarium/Barley RNA dilution7. ZM1: CornChip0--Maize Pilot GeneChip Array8. BB1: Barley1--Cross-species Detection in Barley1 GeneChip Array9. BB3: Barley1--Transcription patterns during barley development10. BB4: Barley1--Mla-specified Transcriptional Responses in Barley-Powdery Mildew Interactio...11. BB5: Barley1--A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule de...12. BB7: Barley1--mlo5-mediated resistance responses in barley13. BB8: Barley1--Microarray of barley genes in wheat-barley chromosome addition lines14. BB9: Barley1--Barley cv Morex inoculated with Fusarium graminearum and water as mock cont...15. AT4: ATH1--Arabidopsis thaliana gene expression during floral transition and early fl...16. AT5: ATH1--Arabidopsis gene expression atlas across developmental time17. AT6: ATH1--Loss of a callose synthase results in salicylic acid-dependent disease resi...18. AT8: ATH1--Expression analysis of Arabidopsis suspension cells during sucrose starvati...19. AT10: ATH1--Arabidopsis thaliana gene expression after 6 days in shoot induction medium20. AT11: ATH1--Transcriptome analysis of glyoxylate cycle knock-out mutants in early stage...21. AT12: ATH1--Gene expression and carbohydrate metabolism through the diurnal cycle22. AT13: ATH1--Impact of Type III effectors on plant defense responses23. AT14: ATH1--Genes affected by hog1 alleviation of CHS silencing24. AT15: ATH1--Analysis of anther development by analysing downstream genes controlled by ...25. AT16: ATH1--Carbohydrate- and redox-regulation of gene expression in a TPT mutant26. AT17: ATH1--Indole acetic acid treatment-dose response and time course27. AT18: ATH1--The mechanisms involved in the interplay between dormancy and secondary gro...28. AT19: ATH1--The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress respon...29. AT20: ATH1--The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress respon...30. AT23: ATH1--AtGenExpress: Pseudomonas half leaf injection31. AT26: ATH1--3-week old Arabidopsis Col-0 and pmr4 plants were infected with Erysiphe ci...32. AT27: ATH1--Erysiphe orontii infection, 7 dpi33. AT28: ATH1--Erysiphe orontii infection, 5 dpi34. AT29: ATH1--Comparison of Col wild-type and mutant sid2-2 (eds16) responses to Erysiphe...35. AT30: ATH1--Response to Erysiphe orontii infection, time course experiment36. AT7: AG--The Transcriptional Innate Immune Response to flg22-Interplay and Overlap w...37. FG3: --Cross-species hybridization Step 2. Select a hybridization to view details:
1. TA1_H1: T = 1, REP = 1,genotype=Wheat (BB1-H1/S1)2. TA1_H2: T = 2, REP = 1,genotype=Barley (Mla1-5874-0hai) Details of Hybridization TA1_H2 Hybridization Accession No.:TA1_H2Treatment No.:2Replicate Number:1File Name Prefix:0502-2_0449-35Sample Accession No.:TA1_S2Sample Name:0449-35Factor--genotype:Barley (Mla1-5874-0hai) EXP File for Hybridization Conditions: Affymetrix GeneChip Experiment Information Version 1 [Sample Info] Chip Type wheat Chip Lot Operator jpeng Sample Type barley Description Project 0502 Comments Solution Type Solution Lot [Fluidics] Protocol EukGE-WS2v5_450 Wash A1 Recovery Mixes 0 Wash A1 Temperature (C) 30 Number of Wash A1 Cycles 10 Mixes per Wash A1 Cycle 2 Wash B Recovery Mixes 0 Wash B Temperature (C) 50 Number of Wash B Cycles 6 Mixes per Wash B Cycle 15 Stain Temperature (C) 35 First Stain Time (seconds) 300 Wash A2 Recovery Mixes 0 Wash A2 Temperature (C) 30 Number of Wash A2 Cycles 10 Mixes per Wash A2 Cycle 4 Second Stain Time (seconds) 300 Third Stain Time (seconds) 300 Wash A3 Recovery Mixes 0 Wash A3 Temperature (C) 35 Number of Wash A3 Cycles 15 Mixes per Wash A3 Cycle 4 Holding Temperature (C) 25 Station 2 Module 1 Hybridize Date Jan 06 2005 02:34PM [Scanner] Pixel Size 1.56 Filter 570 Scan Temperature Scan Date Jan 06 2005 02:18PM Scanner ID 50102680 Number of Scans 1 Scanner Type M10 Robust Muti-Array (RMA) Estimation Parameters: Robust Multi-array Average or Robust Mult-chip Average (RMA). It is calculated with affy 1.4 package's rma function from Bioconductor project. ALl hybridizations are normalized together. <br>This function implements RMA in 3 steps: 1. Make background-corrected probe-specific correction of the perfect match (PM) probes, this correction uses a model assuming that observed intensity is the sum of signal and noise. In this step,the base-2 logarithm of each background-corrected PM intensity is obtained. 2. Normalize corrected PM probes using quantile normalization. 3. Calculate expression measure with median polish. The returned expression measure is in the base-2 logarithm, which need be transform to linear scale for some analysis. Further details can be obtained from Bioconductor website ( www.bioconductor.org). All hybridizations are normalized together in RMA of this experiment Affymetrix MAS5.0 Estimation Parameters: Raw Intensity Summary: PM Summary: CEL Name Statistic 1 X0502.2_0449.35.CEL Min. : 35.0 2 X0502.2_0449.35.CEL 1st Qu.: 68.0 3 X0502.2_0449.35.CEL Median : 82.0 4 X0502.2_0449.35.CEL Mean : 181.9 5 X0502.2_0449.35.CEL 3rd Qu.: 119.0 6 X0502.2_0449.35.CEL Max. :34780.0 MM Summary: CEL Name Statistic 1 X0502.2_0449.35.CEL Min. : 34.0 2 X0502.2_0449.35.CEL 1st Qu.: 66.0 3 X0502.2_0449.35.CEL Median : 77.0 4 X0502.2_0449.35.CEL Mean : 111.1 5 X0502.2_0449.35.CEL 3rd Qu.: 100.0 6 X0502.2_0449.35.CEL Max. :26243.0 RMA Estimation Summary: Min. 1st Qu. Median Mean 3rd Qu Max 0.1297 7.754 31.39 251.7 79.81 64440 MAS5.0 Estimation Summary: Min. 1st Qu. Median Mean 3rd Qu Max 0.1297 7.754 31.39 251.7 79.81 64440 Histogram of Raw PM and MM Intensities, red= PM, white = MM: View Image of Perfect Match(PM) Intensity [Back to Top]
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