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. ZM1: CornChip0--Maize Pilot GeneChip Array5. BB1: Barley1--Cross-species Detection in Barley1 GeneChip Array6. BB4: Barley1--Mla-specified Transcriptional Responses in Barley-Powdery Mildew Interactio...7. BB5: Barley1--A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule de...8. BB7: Barley1--mlo5-mediated resistance responses in barley9. BB8: Barley1--Microarray of barley genes in wheat-barley chromosome addition lines10. AT4: ATH1--Arabidopsis thaliana gene expression during floral transition and early fl...11. AT5: ATH1--Arabidopsis gene expression atlas across developmental time12. AT6: ATH1--Loss of a callose synthase results in salicylic acid-dependent disease resi...13. AT8: ATH1--Expression analysis of Arabidopsis suspension cells during sucrose starvati...14. AT10: ATH1--Arabidopsis thaliana gene expression after 6 days in shoot induction medium15. AT11: ATH1--Transcriptome analysis of glyoxylate cycle knock-out mutants in early stage...16. AT12: ATH1--Gene expression and carbohydrate metabolism through the diurnal cycle17. AT13: ATH1--Impact of Type III effectors on plant defense responses18. AT14: ATH1--Genes affected by hog1 alleviation of CHS silencing19. AT15: ATH1--Analysis of anther development by analysing downstream genes controlled by ...20. AT16: ATH1--Carbohydrate- and redox-regulation of gene expression in a TPT mutant21. AT17: ATH1--Indole acetic acid treatment-dose response and time course22. AT18: ATH1--The mechanisms involved in the interplay between dormancy and secondary gro...23. AT19: ATH1--The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress respon...24. AT20: ATH1--The effects of the sfr2, sfr3 and sfr6 mutations on lyotropic stress respon...25. AT23: ATH1--AtGenExpress: Pseudomonas half leaf injection26. AT7: AG--The Transcriptional Innate Immune Response to flg22-Interplay and Overlap w... Step 2. Select a hybridization to view details:
1. BB1_H1: T = 1, REP = 1,species=Barley2. BB1_H2: T = 1, REP = 2,species=Barley3. BB1_H3: T = 2, REP = 1,species=Wheat4. BB1_H4: T = 2, REP = 2,species=Wheat5. BB1_H5: T = 3, REP = 1,species=Oat6. BB1_H6: T = 3, REP = 2,species=Oat7. BB1_H7: T = 4, REP = 1,species=Sorghum8. BB1_H8: T = 4, REP = 2,species=Sorghum9. BB1_H9: T = 5, REP = 1,species=Corn10. BB1_H10: T = 5, REP = 2,species=Corn11. BB1_H11: T = 6, REP = 1,species=Rice12. BB1_H12: T = 6, REP = 2,species=Rice Details of Hybridization BB1_H12 Hybridization Accession No.:BB1_H12Treatment No.:6Replicate Number:2File Name Prefix:0315-1Sample Accession No.:BB1_S12Sample Name:Expt # 11771-1Factor--species:Rice EXP File for Hybridization Conditions: Affymetrix GeneChip Experiment Information Version 1 [Sample Info] Chip Type Barley1 Chip Lot 3000644 Operator Jiqing Peng Sample Type Description Project Comments Solution Type Solution Lot [Fluidics] Protocol EukGE-WS2v4 Wash A1 Recovery Mixes 0 Wash A1 Temperature (C) 25 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 4 Mixes per Wash B Cycle 15 Stain Temperature (C) 25 First Stain Time (seconds) 600 Wash A2 Recovery Mixes 0 Wash A2 Temperature (C) 25 Number of Wash A2 Cycles 10 Mixes per Wash A2 Cycle 4 Second Stain Time (seconds) 600 Third Stain Time (seconds) 600 Wash A3 Recovery Mixes 0 Wash A3 Temperature (C) 30 Number of Wash A3 Cycles 15 Mixes per Wash A3 Cycle 4 Holding Temperature (C) 25 Station 1 Module 1 Hybridize Date [Scanner] Pixel Size 3 Filter 570 Scan Temperature Scan Date Jun 24 2003 12:16PM Scanner ID Number of Scans 2 Scanner Type HP Robust Muti-Array (RMA) Estimation Parameters: Robust Multi-array Average or Robust Mult-chip Average (RMA). It is calculated with affy 1.2.8 packages rma function from Bioconductor project. This function implements RMA in 3 steps: First step, 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. Second step, normalize corrected PM probes using quantile normalization, and finally expression measure is calculated with median polish. Further details can be obtained from Bioconductor website ( www.bioconductor.org) Affymetrix MAS5.0 Estimation Parameters: Report Type: Expression Report Date: 05:05PM 09/08/2003 ______________________________________________________________________ Filename: 0315-1.CHP Probe Array Type: Barley1 Algorithm: Statistical Probe Pair Thr: 8 Controls: Antisense ______________________________________________________________________ Alpha1: 0.05 Alpha2: 0.065 Tau: 0.015 Noise (RawQ): 2.080 Scale Factor (SF): 3.418 Norm Factor (NF): 1.000 ______________________________________________________________________ Background: Avg: 46.87 Std: 1.06 Min: 45.70 Max: 50.60 Noise: Avg: 2.06 Std: 0.12 Min: 1.90 Max: 2.50 Corner+ Avg: 107 Count: 32 Corner- Avg: 11361 Count: 32 Central- Avg: 9577 Count: 9 ______________________________________________________________________ The following data represents probe sets that exceed the probe pair threshold and are not called "No Call". Total Probe Sets: 22840 Number Present: 2145 9.4% Number Absent: 20336 89.0% Number Marginal: 359 1.6% Average Signal (P): 439.4 Average Signal (A): 46.7 Average Signal (M): 127.4 Average Signal (All): 84.9 ______________________________________________________________________ Spike Controls: Probe Set Sig(5') Det(5') Sig(M') Det(M') Sig(3') Det(3') Sig(all) Sig(3'/5') BIOB 489.9 P 507.6 P 469.9 P 489.16 0.96 BIOC 1154.3 P 648.5 P 901.40 0.56 BIODN 993.2 P 5909.1 P 3451.11 5.95 CREX 11617.9 P 16887.6 P 14252.78 1.45 DAPX 14.7 A 43.4 M 6.7 A 21.60 0.46 LYSX 15.0 A 39.2 A 10.7 A 21.66 0.71 PHEX 2.7 A 7.7 A 11.1 A 7.17 4.04 THRX 6.3 A 22.7 A 10.4 A 13.15 1.66 TRPNX 40.7 A 4.0 A 5.2 A 16.66 0.13 ______________________________________________________________________ Raw Intensity Summary: PM Summary: CEL Name Statistic 1 X0315.1.CEL Min. : 37.0 2 X0315.1.CEL 1st Qu.: 73.0 3 X0315.1.CEL Median : 104.3 4 X0315.1.CEL Mean : 193.1 5 X0315.1.CEL 3rd Qu.: 177.0 6 X0315.1.CEL Max. :22147.5 MM Summary: CEL Name Statistic 1 X0315.1.CEL Min. : 36.3 2 X0315.1.CEL 1st Qu.: 69.3 3 X0315.1.CEL Median : 97.0 4 X0315.1.CEL Mean : 169.0 5 X0315.1.CEL 3rd Qu.: 161.8 6 X0315.1.CEL Max. :16433.8 RMA Estimation Summary: Min. 1st Qu. Median Mean 3rd Qu Max 2.259 4.313 5.276 5.251 6.142 13.830 MAS5.0 Estimation Summary: Min. 1st Qu. Median Mean 3rd Qu Max 6.724e-02 1.102e+01 3.453e+01 8.488e+01 7.812e+01 3.102e+04 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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