title: IFNg stimulated 0.006 pM IFN 2 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56718.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 3720; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 200461; Parameter Laser Power = 3.57; Parameter Scan Time = 00:15:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.80; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419430; Parameter Laser Power = 2.65; Parameter Scan Time = 00:15:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.80; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.006 pM IFN 2 h


title: IFNg stimulated Mock 4 h

status: Public on Mar 22 2010

type: RNA

city: London

first: Simon

last: Waddell

department: Division of Cellular and Molecular Medicine St. George's

country: United Kingdom

institute: University of London Tooting

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56703.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 5640; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 490; Parameter Laser on time = 200220; Parameter Laser Power = 2.99; Parameter Scan Time = 20:12:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.40; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419188; Parameter Laser Power = 2.63; Parameter Scan Time = 20:12:18; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.40; Performer: Simon,,Waddell

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene 1 Round Amplification 3 ug

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFNg stimulated Mock 4 h

tag: measurement

value: time(absolute) 4 h

tag: compound based treatment

value: Mock


title: CD138_selected_plasma_cells_presentation_MM360_nsp

type: genomic

city: Sutton

first: Brian

middle: A

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

institute: The Institute of Cancer Research

hyb_protocol: 90 ug of fragmented labeled DNA is hybridised to the array for 16 hours at 49C accoring to Affymetrix protocols.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G/4 color early acces scanner and processed using GCOS 1.4.0.

data_processing: SNP genotype calls were generated using Affymetrix Powertools  v1.8.0 (apt-probeset-genotype).  Calls were generated using the default parameters and the brlmm calling algorithm.

label: biotin

molecule: genomic DNA

source_name: pre-treatment bone marrow

label_protocol: 250 ng of DNA is digested with NspI/StyI, and processed accorodng to Affymetrix 500K protocol.  DNA is end-labeled with biotin using TdT.

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, extracted using Qiagen AllPrep as per manufacturer's protocol.

tag: extraction

value: AllPrep


title: IFNg stimulated 0.6 pM IFN 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56729.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 4630; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 200603; Parameter Laser Power = 3.56; Parameter Scan Time = 02:37:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 419571; Parameter Laser Power = 2.66; Parameter Scan Time = 02:37:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.6 pM IFN 12 h

value: time(absolute) 12 h

value: 0.6 pM IFNg


title: IFNg stimulated 0.006 pM IFN 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56716.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 3720; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 200436; Parameter Laser Power = 3.46; Parameter Scan Time = 23:50:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419404; Parameter Laser Power = 2.65; Parameter Scan Time = 23:50:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.006 pM IFN 0.5 h

value: time(absolute) 0.5 h

value: 0.006 pM IFNg


title: IFNg stimulated Mock 2 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56702.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 5640; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 490; Parameter Laser on time = 200206; Parameter Laser Power = 2.73; Parameter Scan Time = 19:58:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.34; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419174; Parameter Laser Power = 2.63; Parameter Scan Time = 19:58:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.34; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated Mock 2 h

value: time(absolute) 2 h


title: IFNg stimulated 60 pM IFN 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56712.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 840, 5000; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 200360; Parameter Laser Power = 3.51; Parameter Scan Time = 22:33:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419328; Parameter Laser Power = 2.65; Parameter Scan Time = 22:33:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 60 pM IFN 8 h

value: time(absolute) 8 h

value: 60 pM IFNg


title: IFNg stimulated Mock 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56704.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 5640; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 200232; Parameter Laser Power = 3.13; Parameter Scan Time = 20:25:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419201; Parameter Laser Power = 2.63; Parameter Scan Time = 20:25:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated Mock 8 h


title: CD138_selected_plasma_cells_presentation_MM357_nsp


title: IFNg stimulated Mock 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56701.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 5640; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 200193; Parameter Laser Power = 3.09; Parameter Scan Time = 19:45:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.31; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 419162; Parameter Laser Power = 2.63; Parameter Scan Time = 19:45:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.31; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated Mock 1 h

value: time(absolute) 1 h


title: CD138_selected_plasma_cells_presentation_MM362_nsp


title: CD138_selected_plasma_cells_presentation_MM364_nsp


title: CD138_selected_plasma_cells_presentation_MM356_nsp


title: IFNg stimulated 0.6 pM IFN 2 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56726.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 4630; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 200564; Parameter Laser Power = 3.60; Parameter Scan Time = 01:58:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 419532; Parameter Laser Power = 2.66; Parameter Scan Time = 01:58:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.6 pM IFN 2 h


title: CD138_selected_plasma_cells_presentation_MM363_nsp


title: TNFa stimulated TNFa 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57572.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206951; Parameter Laser Power = 3.44; Parameter Scan Time = 05:04:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425886; Parameter Laser Power = 2.62; Parameter Scan Time = 05:04:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 0.5 h

value: TNFa


title: CD138_selected_plasma_cells_presentation_MM354_nsp


title: IFN stimulated T0 1

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57531.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206353; Parameter Laser Power = 3.95; Parameter Scan Time = 19:06:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425288; Parameter Laser Power = 2.61; Parameter Scan Time = 19:06:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN stimulated T0 1

value: time(absolute) 0 h


title: IFN Mock stimulated Mock 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57541.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206518; Parameter Laser Power = 2.71; Parameter Scan Time = 21:50:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425453; Parameter Laser Power = 2.62; Parameter Scan Time = 21:50:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN Mock stimulated Mock 24 h

value: time(absolute) 24 h


title: CD138_selected_plasma_cells_presentation_MM361_nsp


title: CD138_selected_plasma_cells_presentation_MM359_nsp


title: IFNg stimulated 0.6 pM IFN 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56724.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 3720; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 200539; Parameter Laser Power = 3.66; Parameter Scan Time = 01:33:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 419508; Parameter Laser Power = 2.66; Parameter Scan Time = 01:33:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.6 pM IFN 0.5 h


title: CD138_selected_plasma_cells_presentation_MM353_nsp


title: CD138_selected_plasma_cells_presentation_MM358_nsp


title: CD138_selected_plasma_cells_presentation_MM355_nsp


title: CD138_selected_plasma_cells_presentation_MM351_nsp

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, extracted using Qiagen RNA/DNA kit and nucleic acids extracted as per manufacturer's protocol.

value: RNA/DNA kit


title: CD138_selected_plasma_cells_presentation_MM349_nsp


title: IFNg stimulated 0.006 pM IFN 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56717.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 3720; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 200449; Parameter Laser Power = 3.54; Parameter Scan Time = 00:03:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 419417; Parameter Laser Power = 2.64; Parameter Scan Time = 00:03:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.006 pM IFN 1 h


title: IFN alpha stimulated IFNa 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57542.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206542; Parameter Laser Power = 3.03; Parameter Scan Time = 22:15:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.55; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425476; Parameter Laser Power = 2.61; Parameter Scan Time = 22:15:05; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.55; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN alpha stimulated IFNa 0.5 h

value: IFNa


title: CD138_selected_plasma_cells_presentation_MM350_nsp


title: IFNg stimulated 0.6 pM IFN 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56725.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 4630; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 200552; Parameter Laser Power = 3.61; Parameter Scan Time = 01:46:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419520; Parameter Laser Power = 2.65; Parameter Scan Time = 01:46:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFNg stimulated 0.6 pM IFN 1 h


title: Rat 18, Day 3, 8 mm

status: Public on Mar 25 2010

city: Silver Spring

first: Rasha

last: Hammamieh

state: MD

address: 503 Robert Grant Ave

department: Molecular Pathology

country: USA

institute: Walter Reed Army Institute of Research

description: Gene expression 3 day post 8 mm defect created in calvarial bone

hyb_protocol: The 0.5µg of cRNA extracted from each of the CSD and non-CSD sampels were hybridized onto a microarray slide at 65⁰C for 17 h in a rotisserie chamber at 10 rpm the microarray slides were washed with wash buffer with 0.005% Triton X-102 for 1 min. at RT, followed by wash buffer 2 at 37⁰C for 1 min and drying in the dark for 5 min.

scan_protocol: The slides were scanned with a GenePix 4000B fluorescence scanner (Axon).

data_processing: Data filter and statistical analysis were carried out using GeneSpring(r) 7.3. Local background was subtracted from individual spot intensity and genes that failed 'background check' in any of the experiments were eliminated from further analysis. Each chip was next subjected to intra-chip normalization (LOWESS). Differentially regulated genes were selected using Welch t-test analysis (P < 0.05).

organism: Rattus norvegicus

source_name: Rat 18, Day 3, 8 mm

label_protocol: The Cy-3 labeled RNA applied to Agilent rat whole genome oligo microarray kit (G4131F) was performed according to the manufacturer's instructions.

extract_protocol: Tissues from each individual defect were harvested using the trephine for the same size and total RNA was isolated using 1 ml Tri Reagent according to the manufacturer's directions in lysing matrix D tubes and homogenized using the FastPrep24 at 4.0 mls for 30 sec. and stored on ice for 1 min. This sequence was repeated 4x. total RNA was further purified by RNeasy columns according to the manufacturer's specifications, quantified by Nanodrop and its integrity confirmed by Bioanalyzer.

treatment_protocol: Using a drill press and copiou irrigation with saline, a trephine was used to create the 4 or 8 mm defect. The surgical site was then closed in standard fashion using a non-resorpable suture. No additional treatments were applied to either defect and the animals were survived in their home environment for the respective period of time.

tag: tissue

value: Calvarial bone with healing tissue plug

tag: age

value: 12 weeks

tag: gender

value: male

tag: defect size

value: 8 mm


title: IFN Mock stimulated Mock 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57538.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206399; Parameter Laser Power = 3.96; Parameter Scan Time = 19:51:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425333; Parameter Laser Power = 2.62; Parameter Scan Time = 19:51:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Simon,,Waddell

source_name: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN Mock stimulated Mock 4 h

value: time(absolute) 4 h

value: Mock


title: IL12 stimulated IL12 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57566.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206878; Parameter Laser Power = 3.49; Parameter Scan Time = 03:51:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425812; Parameter Laser Power = 2.62; Parameter Scan Time = 03:51:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified IL12 stimulated IL12 0.5 h

value: time(absolute) 0.5 h


title: CD138_selected_plasma_cells_presentation_MM346_nsp

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G/4 color early acces scanner and processed using GCOS 1.4.0.

source_name: pre-treatment bone marrow

value: AllPrep


title: IFN Mock stimulated Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57536.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206367; Parameter Laser Power = 3.91; Parameter Scan Time = 19:19:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425302; Parameter Laser Power = 2.62; Parameter Scan Time = 19:19:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN Mock stimulated Mock 0.5 h


title: CD138_selected_plasma_cells_presentation_MM348_nsp


title: CD138_selected_plasma_cells_presentation_MM345_nsp


title: CD138_selected_plasma_cells_presentation_MM344_nsp


title: CD138_selected_plasma_cells_presentation_MM352_nsp


title: IFN alpha stimulated IFNa 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57543.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206554; Parameter Laser Power = 3.23; Parameter Scan Time = 22:27:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.64; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425489; Parameter Laser Power = 2.61; Parameter Scan Time = 22:27:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.64; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN alpha stimulated IFNa 1 h


title: IFNg stimulated T0 III

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56715.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 3720; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 200421; Parameter Laser Power = 3.48; Parameter Scan Time = 23:35:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.74; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-10-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 419389; Parameter Laser Power = 2.65; Parameter Scan Time = 23:35:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.74; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated T0 III


title: IL12 stimulated IL12 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57570.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 4830; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206927; Parameter Laser Power = 3.44; Parameter Scan Time = 04:40:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425862; Parameter Laser Power = 2.61; Parameter Scan Time = 04:40:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified IL12 stimulated IL12 12 h

value: time(absolute) 12 h


title: IFN Mock stimulated Mock 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57539.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206411; Parameter Laser Power = 3.97; Parameter Scan Time = 20:03:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 425346; Parameter Laser Power = 2.62; Parameter Scan Time = 20:03:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN Mock stimulated Mock 8 h

value: time(absolute) 8 h


title: TNFa stimulated TNFa 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57574.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206975; Parameter Laser Power = 3.39; Parameter Scan Time = 05:28:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425910; Parameter Laser Power = 2.61; Parameter Scan Time = 05:28:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 4 h


title: TNFa stimulated TNFa 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57577.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 207013; Parameter Laser Power = 3.31; Parameter Scan Time = 06:06:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.68; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425948; Parameter Laser Power = 2.61; Parameter Scan Time = 06:06:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.68; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 24 h


title: IFN alpha stimulated IFNa 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57544.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206566; Parameter Laser Power = 3.39; Parameter Scan Time = 22:39:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.71; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425501; Parameter Laser Power = 2.62; Parameter Scan Time = 22:39:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.71; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN alpha stimulated IFNa 4 h


title: CD138_selected_plasma_cells_presentation_MM337_nsp


title: CD138_selected_plasma_cells_presentation_MM338_nsp


title: IFN beta stimulated IFNb 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57550.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206653; Parameter Laser Power = 3.79; Parameter Scan Time = 00:06:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425588; Parameter Laser Power = 2.62; Parameter Scan Time = 00:06:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 4 h

value: IFNb


title: IL12 stimulated IL12 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57569.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206914; Parameter Laser Power = 3.48; Parameter Scan Time = 04:28:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425849; Parameter Laser Power = 2.62; Parameter Scan Time = 04:28:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

source_name: 4ug Amplified IL12 stimulated IL12 8 h


title: CD138_selected_plasma_cells_presentation_MM342_nsp


title: CD138_selected_plasma_cells_presentation_MM341_nsp


title: CD138_selected_plasma_cells_presentation_MM340_nsp


title: CD138_selected_plasma_cells_presentation_MM335_nsp


title: CD138_selected_plasma_cells_presentation_MM343_nsp


title: CD138_selected_plasma_cells_presentation_MM339_nsp


title: CD138_selected_plasma_cells_presentation_MM333_nsp


title: IFN Mock stimulated Mock 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57537.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206380; Parameter Laser Power = 3.95; Parameter Scan Time = 19:33:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425314; Parameter Laser Power = 2.62; Parameter Scan Time = 19:33:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN Mock stimulated Mock 1 h

value: time(absolute) 1 h


title: IFN gamma stimulated IFNg 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57560.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 4550; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206805; Parameter Laser Power = 3.69; Parameter Scan Time = 02:38:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425740; Parameter Laser Power = 2.61; Parameter Scan Time = 02:38:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN gamma stimulated IFNg 0.5 h

value: IFNg


title: IL12 stimulated IL12 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57571.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206939; Parameter Laser Power = 3.43; Parameter Scan Time = 04:52:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425874; Parameter Laser Power = 2.61; Parameter Scan Time = 04:52:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified IL12 stimulated IL12 24 h

value: time(absolute) 24 h


title: IFN alpha stimulated IFNa 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57547.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206604; Parameter Laser Power = 3.65; Parameter Scan Time = 23:16:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.89; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425539; Parameter Laser Power = 2.62; Parameter Scan Time = 23:16:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.89; Performer: Simon,,Waddell

source_name: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN alpha stimulated IFNa 24 h


title: CD138_selected_plasma_cells_presentation_MM334_nsp


title: CD138_selected_plasma_cells_presentation_MM336_nsp


title: IFN alpha stimulated IFNa 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57546.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206591; Parameter Laser Power = 3.54; Parameter Scan Time = 23:04:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.83; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425525; Parameter Laser Power = 2.62; Parameter Scan Time = 23:04:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.83; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN alpha stimulated IFNa 12 h


title: CD138_selected_plasma_cells_presentation_MM332_nsp

source_name: pre-treatment bone marrow


title: IFN beta stimulated IFNb 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57551.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206665; Parameter Laser Power = 3.80; Parameter Scan Time = 00:18:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425600; Parameter Laser Power = 2.62; Parameter Scan Time = 00:18:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 8 h


title: Vungu R ER2 (2) swap

city: Pretoria

first: Dave

middle: K

last: Berger

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

description:
Cowpea_drought_reverse library_rep2_dye swap (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: R library clone data extracted and SSHscreen used to calculate invER2 values for R library.

hyb_protocol: Labelled SSH targets were combined in pairs using equal amounts of Cy3 and Cy5 dye incorporation for each target in each pair required for SSHscreen analysis. Each labelled target DNA mix was dried down in a vacuum centrifuge at 45°C and resuspended in 50μl hybridisation solution (50% formamide, 25% 4X Microarray hybridisation buffer (Amersham Biosciences), 25% SDW). Labelled targets in hybridisation solution were denatured at 95°C for 2 min and placed on ice. Glass slides arrayed with the SSH cDNA libraries were pre-treated in 1% bovine serum albumin (BSA; Roche Diagnostics), 3.5X SSC (525mM sodium chloride and 52.5mM sodium citrate) and 0.2% sodium dodecyl sulphate (SDS) at 60°C for 20 min. After rinsing in SDW at room temperature, the slide was dried by centrifugation in a 50ml tube at 1000×g for 4 min at room temperature in a swing-out rotor (Eppendorf 5810R centrifuge). The slide was placed in a locally manufactured hybridisation chamber (HybUP, NB Engineering, Pretoria, South Africa) with 20μl SDW in the reservoirs on either side. Labelled and denatured target was applied to the slide and gently overlaid with a cover slip. The chamber was sealed and incubated in a water bath at 42°C for 16h. Slides were washed for 4 min at 42°C with 1× SSC (150mM NaCl, 15mM sodium citrate)/ 0.2% SDS, twice with 0.1× SSC (15mM NaCl, 1.5mM sodium citrate)/ 0.2% SDS and three washes of 0.1× SSC for 1 min at room temperature. After dipping the slide in SDW at room temperature and centrifuged to dry, it was immediately scanned using a GenePix 4000B scanner (Axon Instruments, Foster City, CA).

scan_protocol: GenePix Pro 5.1 software (Axon Instruments) was used to automatically locate all the spot positions from the scanner-generated TIFF images and associate them with each specific clone in a GenePix Array List (GAL file). The GAL file links the information from the arraying process to the analysis, since it provides identification information for each spot printed on the slide. Bad quality spots (irregularly shaped or with hybridisation artefacts; signal/noise ratio < 3) were flagged for exclusion during data analysis and the array of circles were manually adjusted for a better fit. GenePix Pro 5.1 was used to extract the dye intensity data of each spot and save the data for each slide in a GenePix Results file (.gpr).

data_processing:
Pre-processing of fluorescence data was carried out using the SSHscreen software, which implements functions of limma (Smyth (2004) Stat Appl Genet Mol Biol 3:Article 3). Pre-processing was carried out using unflagged spots for transformation calculations: background correction - normexp method from limma; within-slide normalization - spike-in control spot normalization; between-slide normalization - Aquantile method from limma. Spike-in controls are labelled in the data matrix as control_GFP, control_Globin, control_ITS, control_NPTII. Data presented in the matrix are the log 2 ratios after normalization. Further analysis using SSHscreen was required to calculate ER3 and ER2 values.

ER2 and ER3 values for the forward and reverse libraries are available as supplementary files on the Series record.

organism: Vigna unguiculata

source_name: cDNA before subtraction from CONTROL Cowpea, unstressed

label_protocol: Targets were labelled by direct Cy-dUTP incorporation by Klenow enzyme (Fermentas, Vilnius, Lithuania). Each SSH fragment sample was labelled with both dyes (Cy3 and Cy5) for a dye-swap experiment of each slide. The protocols and data analysis techniques described in Berger et al. (2007) were followed, with some modifications. DNA to be labelled, in a volume of 12μl, was denatured at 95°C for 5 min and placed on ice. The following were added to the pairs of denatured DNA samples to yield a total reaction volume of 20μl: 2μl of 10x Klenow buffer (Fermentas); 2μl 10x Hexanucleotide mix (Roche Diagnostics); 2μl Klenow enzyme (5U/μl; Fermentas); 2μl of a dNTP mix containing 1nmol each of dATP, dCTP and dGTP, 0.74nmol dTTP and 0.27nmol of either Cy3-dUTP or Cy5-dUTP (Amersham Biosciences). The labelling reaction was incubated overnight (17-20h) at 37°C. The labelled DNA was cleaned up from unincorporated dye using the Qiaquick PCR purification kit (Qiagen). Dye incorporation was measured using a NanoDrop ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Wilmington, DE).

growth_protocol: Cowpea seeds were germinated and plants were grown in a glasshouse under 11h day length, 28°C and 18°C day and night temperatures, respectively, and watered three times weekly.

extract_protocol: RNA was isolated from cowpea leaves using Tri-reagent (Sigma) and Polyvinyl pyrrolidone (PVP) (Ambion’s Plant RNA isolation aid). Contaminating genomic DNA was removed with the Turbo DNA-free kit (Ambion) and the RNA cleaned up with the Plant RNeasy kit (Qiagen, Hilden, Germany). Messenger RNA (mRNA) was isolated from 50μg pools of stressed IT96D-602 RNA (9 and 12 days without water) (treated) and unstressed Tvu7778 RNA (9 and 12 days) (control) using an Oligotex mRNA purification kit (Qiagen). cDNA was synthesised from each mRNA using the cDNA synthesis system (Roche Diagnostics, Basel, Switzerland) to be used as unsubtracted testers and unsubtracted drivers in SSH as described (BioTechniques (2004): 37 (5):818-824). Subtractive hybridisation was performed on RsaI (Roche Diagnostics) -digested tester and driver cDNA fragments using the PCR-Select cDNA subtraction kit (BD Biosciences Clontech, Palo Alto, CA). A forward subtraction was performed by using the treated sample as tester (and control as driver), and a separate reverse subtraction was performed by using the control cDNA as tester (and treated cDNA as driver). After subtraction the products were amplified by a primary PCR and a nested secondary suppression PCR to generate differentially expressed cDNA fragments (termed ST (subtracted treated) and SC (subtracted control) for the forward and reverse libraries, respectively). In addition, unsubtracted PCR products from the treated cDNA (drought stressed IT96D-602) (termed UT) and control cDNA (control Tvu7778) (termed UC) were also prepared to be used for SSHscreen analysis as described in Berger et al. (2007): Microarrays, Second Edition, Volume II, Applications and Data Analysis, edited by J. Brampal, Totowa, New Jersey, USA: Humana press, p. 177-203.

treatment_protocol: At six weeks, five replicate plants of each variety were divided into two groups. One group was subjected to drought stress by withholding water, and the other group was kept to the control watering scheme.

tag: cowpea line

source_name: cDNA after subtraction from CONTROL Cowpea, unstressed


title: Vungu R ER2 (2)

description:
Cowpea_drought_reverse library_rep2 (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: R library clone data extracted and SSHscreen used to calculate invER2 values for R library.


title: CD138_selected_plasma_cells_presentation_MM329_nsp

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G/4 color early acces scanner and processed using GCOS 1.4.0.


title: CD138_selected_plasma_cells_presentation_MM326_nsp


title: Vungu R ER2 (1) swap

description:
Cowpea_drought_reverse library_rep1_dye swap (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: R library clone data extracted and SSHscreen used to calculate invER2 values for R library.


title: IFN Mock stimulated Mock 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57540.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206504; Parameter Laser Power = 2.68; Parameter Scan Time = 21:36:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425438; Parameter Laser Power = 2.61; Parameter Scan Time = 21:36:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN Mock stimulated Mock 12 h


title: IFN beta stimulated IFNb 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57548.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206629; Parameter Laser Power = 3.72; Parameter Scan Time = 23:42:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425563; Parameter Laser Power = 2.62; Parameter Scan Time = 23:42:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 0.5 h


title: CD138_selected_plasma_cells_presentation_MM328_nsp


title: Vungu F ER2 (2) swap

description:
Cowpea_drought_forward library_rep2_dye swap (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: F library clone data extracted and SSHscreen used to calculate invER2 values for F library.

source_name: cDNA before subtraction from TREATED Cowpea, drought stressed

source_name: cDNA after subtraction from TREATED Cowpea, drought stressed


title: TNFa stimulated TNFa 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57575.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206987; Parameter Laser Power = 3.37; Parameter Scan Time = 05:40:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425922; Parameter Laser Power = 2.61; Parameter Scan Time = 05:40:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 8 h

value: TNFa


title: IFN gamma stimulated IFNg 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57561.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 4550; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206816; Parameter Laser Power = 3.68; Parameter Scan Time = 02:50:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.56; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425751; Parameter Laser Power = 2.62; Parameter Scan Time = 02:50:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.56; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN gamma stimulated IFNg 1 h


title: IFN beta stimulated IFNb 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57553.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206691; Parameter Laser Power = 3.86; Parameter Scan Time = 00:44:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.25; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425626; Parameter Laser Power = 2.62; Parameter Scan Time = 00:44:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.25; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 24 h


title: IFN omega stimulated IFNo 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57554.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 4690; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206717; Parameter Laser Power = 3.85; Parameter Scan Time = 01:09:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425652; Parameter Laser Power = 2.62; Parameter Scan Time = 01:09:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN omega stimulated IFNo 0.5 h

value: IFNo


title: Vungu F ER2 (1) swap

description:
Cowpea_drought_forward library_rep1_dye_swap (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: F library clone data extracted and SSHscreen used to calculate invER2 values for F library.


title: CD138_selected_plasma_cells_presentation_MM327_nsp


title: IFN omega stimulated IFNo 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57559.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 3920; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206779; Parameter Laser Power = 3.68; Parameter Scan Time = 02:12:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.53; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425714; Parameter Laser Power = 2.62; Parameter Scan Time = 02:12:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.53; Performer: Simon,,Waddell

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN omega stimulated IFNo 24 h


title: CD138_selected_plasma_cells_presentation_MM331_nsp


title: Vungu F ER2 (2)

description:
Cowpea_drought_forward library_rep2 (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: F library clone data extracted and SSHscreen used to calculate invER2 values for F library.


title: CD138_selected_plasma_cells_presentation_MM323_nsp


title: CD138_selected_plasma_cells_presentation_MM347_nsp


title: CD138_selected_plasma_cells_presentation_MM324_nsp


title: Vungu F&R ER3 (1) swap

description:
Cowpea_drought_forward & reverse library_rep1_dye swap (for ER3)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: SSHscreen used to calculate ER3 values separately for F and R library clones.


title: Vungu F&R ER3 (2) swap

description:
Cowpea_drought_forward & reverse library_rep2_dye swap (for ER3)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: SSHscreen used to calculate ER3 values separately for F and R library clones.


title: IFN beta stimulated IFNb 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57552.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206678; Parameter Laser Power = 3.86; Parameter Scan Time = 00:31:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.10; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425613; Parameter Laser Power = 2.62; Parameter Scan Time = 00:31:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.10; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 12 h


title: Vungu F ER2 (1)

description:
Cowpea_drought_forward library_rep1 (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: F library clone data extracted and SSHscreen used to calculate invER2 values for F library.


title: CD138_selected_plasma_cells_presentation_MM319_nsp


title: CD138_selected_plasma_cells_presentation_MM330_nsp


title: CD138_selected_plasma_cells_presentation_MM321_nsp


title: IL12 stimulated IL12 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57567.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206890; Parameter Laser Power = 3.47; Parameter Scan Time = 04:03:42; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425825; Parameter Laser Power = 2.61; Parameter Scan Time = 04:03:42; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IL12 stimulated IL12 1 h


title: CD138_selected_plasma_cells_presentation_MM325_nsp


title: Vungu R ER2 (1)

description:
Cowpea_drought_reverse library_rep1 (for ER2)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: R library clone data extracted and SSHscreen used to calculate invER2 values for R library.


title: Vungu F&R ER3 (2)

description:
Cowpea_drought_forward & reverse library_rep2 (for ER3)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: SSHscreen used to calculate ER3 values separately for F and R library clones.


title: CD138_selected_plasma_cells_presentation_MM320_nsp


title: IFN omega stimulated IFNo 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57555.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206729; Parameter Laser Power = 3.85; Parameter Scan Time = 01:22:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425664; Parameter Laser Power = 2.61; Parameter Scan Time = 01:22:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN omega stimulated IFNo 1 h


title: Vungu F&R ER3 (1)

description:
Cowpea_drought_forward & reverse library_rep1 (for ER3)
log2(ch2/ch1) given in data matrix (after normalization). Subsequent analysis: SSHscreen used to calculate ER3 values separately for F and R library clones.


title: CD138_selected_plasma_cells_presentation_MM322_nsp

source_name: pre-treatment bone marrow


title: CD138_selected_plasma_cells_presentation_MM317_nsp


title: IFN omega stimulated IFNo 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57556.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 3920; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206741; Parameter Laser Power = 3.84; Parameter Scan Time = 01:35:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425676; Parameter Laser Power = 2.62; Parameter Scan Time = 01:35:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN omega stimulated IFNo 4 h


title: IFN gamma stimulated IFNg 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57565.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206865; Parameter Laser Power = 3.49; Parameter Scan Time = 03:39:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425800; Parameter Laser Power = 2.62; Parameter Scan Time = 03:39:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN gamma stimulated IFNg 24 h