DESPRAD/TEMBLOR Partner

University of CambridgeDept of Genetics

FLYCHIP Group

cDNA spotted slides

Affymetrix

Genomic Solutions and ArrayWorx

Data generated from Drosophila melanogaster

Generating ADF file for FlyChip 2.0

v_array : Generates ADF style files from various input data such as plate rearraying information, geneIDs, PCR

results

UniqueID tool_x tool_y sgrid_x sgrid_y CloneID Pred_Gene EST5 EST3 cDNA Vector marker pcr_score not_DGC norm_ignore show FlyBase_gene FlyBaseID

1000005124 1 1 1 4 LD06393 CG6084 AA263299 AW941617 BT003280 pBS SK- amp Y 0

0 1 CG6084 FBgn0036182

1000004548 1 1 1 5 GH15861 CG1358 AI292851 AW940603 AY069142 pOT2 cam D 0

1 0 CG1358 FBgn0033196

1000003996 1 1 1 6 GH01501 CG3427 AI062330 AW940048 AY058255 pOT2 cam N 0

1 0 CG3427 FBgn0033102

1000003444 1 1 1 7 GH28796 CG8001 AI517742 AW941103 AY094738 pOT2 cam Y 0

0 1 CG8001 FBgn0035268

1000002988 1 1 1 8 LP04941 CG12118 AI293381 AW944034 AY052039 pOT2 cam Y 0

0 1 CG12118 FBgn0030101

1000002412 1 1 1 9 LD27537 CG6854 AA948865 AW942761 AY058581 pOT2 cam Y 0

0 1 CG6854 FBgn0036478

1000001860 1 1 1 10 GH01093 CG31374 AI062049 AW940095 pOT2 cam Y 0 0

1 CG31374 FBgn0051374

1000001308 1 1 1 11 GM14292 CG11444 AA803795 AW941385 AY060986 pOT2 cam Y 0

0 1 CG11444 FBgn0029715

1000000732 1 1 1 12 GH06781 CG15093 AI108060 AI402055 AY069057 pOT2 cam Y 0

0 1 CG15093 FBgn0034390

1000007164 1 1 1 13 LANDMARK 1 1 1

:

Cleanup_adf: This script converts the file from above into ADF file

Date of Submission 04/06/2003

Submitter Name FlyChip, University of Cambridge

Organisation Name University of Cambridge

Array Design Name FlyChip D. melanogaster version FC002

Array Design Version 2.0

Technology Type Spotted PCR products

Substrate Type Glass

Surface Type Non-adsorptive

Strandedness Double

Attachment Non-covalent

MetaColumn MetaRow Column Row Reporter Identifier Reporter Name Reporter BioSequence Database Entry[flybase] Reporter BioSequence Database Entry[embl] Reporter BioSequence Type Reporter BioSequence Polymer Type Reporter Group Role Reporter Control Type Reporter Fail Type Reporter Comment

1 1 1 1 1000007164 LANDMARK genomic_DNA DNA CONTROL control_label Sonica

ted Salmon Sperm DNA

1 1 1 2 1000006036 LD14383 FBgn0051522 AA439743;AW942311 cDNA_clone DNA EXPERIMENTAL

1 1 1 3 1000005460 LD04815 FBgn0010173 AY069331;AA201663;AW941561 cDNA_clone DNA EXPERIMENTAL

MetaColumn MetaRow Column Row Reporter Identifier Reporter Name Reporter BioSequence Database Entry[Flybase] Reporter BioSequence Database Entry[GenBank] Reporter BioSequence Database Entry[GenBank] Reporter BioSequence Type Reporter BioSequence Polymer Type Reporter Group Role Reporter Control Type Reporter Fail Type Reporter Comment

1 1 1 1 1000007164 LANDMARK genomic_DNA DNA CONTROL control_label Sonicated Salmon Sperm DNA

1 1 1 2 1000006036 LD14383 FBgn0051522 AA439743;AW942311 cDNA_clone DNA EXPERIMENTAL

1 1 1 3 1000005460 LD04815 FBgn0010173 AY069331;AA201663;AW941561 cDNA_clone DNA EXPERIMENTAL

1 1 1 4 1000005124 LD06393 FBgn0036182 BT003280;AA263299;AW941617 cDNA_clone DNA EXPERIMENTAL

1 1 1 5 1000004548 GH15861 FBgn0033196 AY069142;AI292851;AW940603 cDNA_clone DNA EXPERIMENTAL FAIL Doublet generated by PCR

1 1 1 6 1000003996 GH01501 FBgn0033102 AY058255;AI062330;AW940048 cDNA_clone DNA EXPERIMENTAL FAIL PCR failed

Processing the data files

Currently three replicates are scanned one after another and Put into one file

Not all the quantitation types are actually present in the data file

Formatting is not right

Clean_data.pl: Generates individual files from the single output

Data Submission:

We have installed MIAMExpress locallyWe are populating it with experimental data

We are using the ArrayExpress schema as a starting point in Flymine

Submitted ADF file and waiting for the implementation of The multiple file loading utility of the MIAMExpress

The project is funded by the European Commission as theTEMBLOR, contract-no. QLRI-CT-2001-00015 under the RTD programme “Quality of Life and management of LivingResources”

Acknowledgements

Gos MicklemHelen ParkinsonPhilippe Rocca-SerraNiran AbeygunawardenaMohammadreza ShojatalabMembers of FlyMine Group