title: peripheral_white_blood_cells_presentation_PB329_nsp


title: peripheral_white_blood_cells_presentation_PB308_sty

status: Public on Mar 22 2010

type: genomic

city: Sutton

first: Brian

middle: A

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

country: United Kingdom

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

organism: Homo sapiens

source_name: peripheral white blood cell pellets

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: DNA was extracted from peripheral white blood cell pellets using the Qiagen Flexigene kit, as per manufacturer's instructions.

tag: extraction

value: Flexigene


title: peripheral_white_blood_cells_presentation_PB309_sty


title: peripheral_white_blood_cells_presentation_PB328_nsp


title: Monocyte Mock 24 h

type: RNA

city: London

first: Simon

last: Waddell

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

institute: University of London Tooting

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58689.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 = 280, 4950; 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 = 2005-01-11; 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 = 213036; Parameter Laser Power = 3.51; Parameter Scan Time = 18:42:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 432039; Parameter Laser Power = 2.56; Parameter Scan Time = 18:42:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; 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

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 Monocyte Mock 24 h

tag: measurement

value: time(absolute) 24 h

tag: compound based treatment

value: Mock

tag: cell type

value: Monocyte


title: peripheral_white_blood_cells_presentation_PB321_sty


title: peripheral_white_blood_cells_presentation_PB307_sty


title: peripheral_white_blood_cells_presentation_PB305_sty


title: CD8 T01

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58637.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5540; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212050; Parameter Laser Power = 3.81; Parameter Scan Time = 20:12:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431053; Parameter Laser Power = 2.53; Parameter Scan Time = 20:12:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; Performer: Simon,,Waddell

source_name: 4ug Amplified CD8 T01

value: time(absolute) 0 h

value: CD8 Cell


title: peripheral_white_blood_cells_presentation_PB303_sty


title: peripheral_white_blood_cells_presentation_PB304_sty


title: CD8 Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58641.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5540; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212086; Parameter Laser Power = 3.75; Parameter Scan Time = 20:48:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431089; Parameter Laser Power = 2.54; Parameter Scan Time = 20:48:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Simon,,Waddell

source_name: 4ug Amplified CD8 Mock 0.5 h

value: time(absolute) 0.5 h


title: peripheral_white_blood_cells_presentation_PB327_nsp


title: CD8 0.6 pM IFNg 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58647.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212156; Parameter Laser Power = 3.64; Parameter Scan Time = 21:58:50; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431159; Parameter Laser Power = 2.54; Parameter Scan Time = 21:58:50; 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

source_name: 4ug Amplified CD8 0.6 pM IFNg 1 h

value: time(absolute) 1 h

value: 0.6 pM IFNg


title: CD138_selected_plasma_cells_presentation_MM382_sty

source_name: pre-treatment bone marrow

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

value: AllPrep


title: peripheral_white_blood_cells_presentation_PB302_sty


title: Monocyte T03

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58683.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 4950; 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 = 2005-01-11; 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 = 212963; Parameter Laser Power = 3.58; Parameter Scan Time = 17:29:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431966; Parameter Laser Power = 2.55; Parameter Scan Time = 17:29:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Simon,,Waddell

source_name: 4ug Amplified Monocyte T03


title: peripheral_white_blood_cells_presentation_PB306_sty


title: CD8 T02

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58638.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5540; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212061; Parameter Laser Power = 3.79; Parameter Scan Time = 20:24:32; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431064; Parameter Laser Power = 2.54; Parameter Scan Time = 20:24:32; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Simon,,Waddell

source_name: 4ug Amplified CD8 T02


title: CD138_selected_plasma_cells_presentation_MM383_sty


title: CD138_selected_plasma_cells_presentation_MM381_sty


title: peripheral_white_blood_cells_presentation_PB326_nsp


title: peripheral_white_blood_cells_presentation_PB301_sty


title: B Cell Mock 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58659.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, 5800; 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 = 2005-01-10; 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 = 212379; Parameter Laser Power = 3.42; Parameter Scan Time = 01:43:49; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 431382; Parameter Laser Power = 2.57; Parameter Scan Time = 01:43:49; 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 B Cell Mock 24 h

value: B Cell


title: CD138_selected_plasma_cells_presentation_MM384_sty


title: CD138_selected_plasma_cells_presentation_MM380_sty


title: peripheral_white_blood_cells_presentation_PB324_nsp


title: CD138_selected_plasma_cells_presentation_MM378_sty


title: CD4 0.6 pM IFNg 8 h A

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58634.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 5720; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212014; Parameter Laser Power = 3.83; Parameter Scan Time = 19:37:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431017; Parameter Laser Power = 2.52; Parameter Scan Time = 19:37:00; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 0.6 pM IFNg 8 h A

value: time(absolute) 8 h

value: CD4 Cell


title: peripheral_white_blood_cells_presentation_PB323_nsp


title: peripheral_white_blood_cells_presentation_PB325_nsp


title: peripheral_white_blood_cells_presentation_PB322_nsp


title: peripheral_white_blood_cells_presentation_PB320_nsp


title: CD138_selected_plasma_cells_presentation_MM379_sty


title: peripheral_white_blood_cells_presentation_PB318_nsp


title: peripheral_white_blood_cells_presentation_PB321_nsp


title: CD138_selected_plasma_cells_presentation_MM372_sty


title: CD138_selected_plasma_cells_presentation_MM370_sty


title: CD4 Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58625.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 211794; Parameter Laser Power = 2.90; Parameter Scan Time = 15:56:33; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.61; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 430797; Parameter Laser Power = 2.49; Parameter Scan Time = 15:56:33; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.61; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 Mock 0.5 h


title: CD138_selected_plasma_cells_presentation_MM373_sty


title: NK Cell Mock 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58672.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5200; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212806; Parameter Laser Power = 3.38; Parameter Scan Time = 14:52:01; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431809; Parameter Laser Power = 2.52; Parameter Scan Time = 14:52:01; 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 NK Cell Mock 8 h

value: NK Cell


title: NK Cell T01 Repeat

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58809.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, 5800; 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 = 2005-01-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 214184; Parameter Laser Power = 2.52; Parameter Scan Time = 14:41:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; 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 = 2005-01-21; 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 = 433190; Parameter Laser Power = 2.50; Parameter Scan Time = 14:41:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.61; Performer: Simon,,Waddell

source_name: 4ug Amplified NK Cell T01 Repeat


title: CD138_selected_plasma_cells_presentation_MM367_sty


title: CD138_selected_plasma_cells_presentation_MM377_sty


title: peripheral_white_blood_cells_presentation_PB317_nsp


title: peripheral_white_blood_cells_presentation_PB316_nsp


title: CD138_selected_plasma_cells_presentation_MM369_sty


title: B Cell T03

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58653.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212230; Parameter Laser Power = 3.53; Parameter Scan Time = 23:13:31; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431233; Parameter Laser Power = 2.55; Parameter Scan Time = 23:13:31; 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 B Cell T03


title: CD138_selected_plasma_cells_presentation_MM375_sty


title: CD138_selected_plasma_cells_presentation_MM374_sty


title: CD138_selected_plasma_cells_presentation_MM368_sty


title: CD138_selected_plasma_cells_presentation_MM366_sty


title: CD138_selected_plasma_cells_presentation_MM364_sty


title: CD138_selected_plasma_cells_presentation_MM365_sty


title: CD138_selected_plasma_cells_presentation_MM376_sty


title: B Cell Mock 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58656.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212267; Parameter Laser Power = 3.52; Parameter Scan Time = 23:50:54; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431270; Parameter Laser Power = 2.56; Parameter Scan Time = 23:50:54; 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 B Cell Mock 4 h

value: time(absolute) 4 h


title: peripheral_white_blood_cells_presentation_PB319_nsp


title: peripheral_white_blood_cells_presentation_PB315_nsp


title: CD138_selected_plasma_cells_presentation_MM371_sty


title: CD138_selected_plasma_cells_presentation_MM363_sty


title: B Cell Mock 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58657.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212279; Parameter Laser Power = 3.50; Parameter Scan Time = 00:02:46; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431282; Parameter Laser Power = 2.56; Parameter Scan Time = 00:02:46; 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 B Cell Mock 8 h


title: NK Cell Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58669.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 720, 5760; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212760; Parameter Laser Power = 2.86; Parameter Scan Time = 14:06:18; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431763; Parameter Laser Power = 2.51; Parameter Scan Time = 14:06:18; 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 NK Cell Mock 0.5 h


title: peripheral_white_blood_cells_presentation_PB314_nsp

source_name: peripheral white blood cell pellets


title: CD138_selected_plasma_cells_presentation_MM362_sty


title: CD138_selected_plasma_cells_presentation_MM361_sty


title: peripheral_white_blood_cells_presentation_PB313_nsp


title: NK Cell 0.6 pM IFNg 12 h Repeat

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58834.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 5800; 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 = 2005-01-21; 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 = 214280; Parameter Laser Power = 3.09; Parameter Scan Time = 16:18:08; 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 = 2005-01-21; 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 = 433286; Parameter Laser Power = 2.49; Parameter Scan Time = 16:18:08; 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: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified NK Cell 0.6 pM IFNg 12 h Repeat

value: time(absolute) 12 h


title: B Cell Mock 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58658.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212291; Parameter Laser Power = 3.45; Parameter Scan Time = 00:15:33; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 431294; Parameter Laser Power = 2.56; Parameter Scan Time = 00:15:33; 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 B Cell Mock 12 h


title: CD138_selected_plasma_cells_presentation_MM357_sty

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


title: Monocyte Mock 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58686.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 4950; 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 = 2005-01-11; 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 = 212998; Parameter Laser Power = 3.57; Parameter Scan Time = 18:04:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.35; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 432001; Parameter Laser Power = 2.56; Parameter Scan Time = 18:04:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.35; Performer: Simon,,Waddell

source_name: 4ug Amplified Monocyte Mock 4 h


title: peripheral_white_blood_cells_presentation_PB312_nsp

value: Flexigene


title: CD138_selected_plasma_cells_presentation_MM358_sty

source_name: pre-treatment bone marrow


title: CD138_selected_plasma_cells_presentation_MM356_sty


title: Monocyte Mock 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58688.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 4950; 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 = 2005-01-11; 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 = 213024; Parameter Laser Power = 3.51; Parameter Scan Time = 18:29:56; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 432027; Parameter Laser Power = 2.56; Parameter Scan Time = 18:29:56; 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

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified Monocyte Mock 12 h


title: peripheral_white_blood_cells_presentation_PB311_nsp


title: CD8 0.6 pM IFNg 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58649.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212181; Parameter Laser Power = 3.63; Parameter Scan Time = 22:23:08; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431184; Parameter Laser Power = 2.55; Parameter Scan Time = 22:23:08; 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

source_name: 4ug Amplified CD8 0.6 pM IFNg 8 h


title: peripheral_white_blood_cells_presentation_PB310_nsp


title: CD138_selected_plasma_cells_presentation_MM353_sty


title: CD138_selected_plasma_cells_presentation_MM355_sty


title: CD138_selected_plasma_cells_presentation_MM352_sty


title: CD138_selected_plasma_cells_presentation_MM359_sty


title: CD138_selected_plasma_cells_presentation_MM354_sty


title: Monocyte T01

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58681.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 4950; 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 = 2005-01-11; 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 = 212939; Parameter Laser Power = 3.55; Parameter Scan Time = 17:05:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431942; Parameter Laser Power = 2.55; Parameter Scan Time = 17:05:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Simon,,Waddell

source_name: 4ug Amplified Monocyte T01


title: peripheral_white_blood_cells_presentation_PB309_nsp


title: peripheral_white_blood_cells_presentation_PB308_nsp


title: CD138_selected_plasma_cells_presentation_MM350_sty


title: CD4 0.6 pM IFNg 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58633.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 5720; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212001; Parameter Laser Power = 3.84; Parameter Scan Time = 19:23:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431004; Parameter Laser Power = 2.53; Parameter Scan Time = 19:23:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 0.6 pM IFNg 4 h


title: CD138_selected_plasma_cells_presentation_MM351_sty

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_MM348_sty


title: CD138_selected_plasma_cells_presentation_MM347_sty


title: CD4 0.6 pM IFNg 24 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58636.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5540; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212039; Parameter Laser Power = 3.81; Parameter Scan Time = 20:01:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431042; Parameter Laser Power = 2.53; Parameter Scan Time = 20:01:13; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.44; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 0.6 pM IFNg 24 h

value: time(absolute) 24 h


title: CD138_selected_plasma_cells_presentation_MM349_sty


title: CD4 T03

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58624.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 211775; Parameter Laser Power = 2.47; Parameter Scan Time = 15:37:29; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 430778; Parameter Laser Power = 2.49; Parameter Scan Time = 15:37:29; 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

source_name: 4ug Amplified CD4 T03

value: Mock


title: CD138_selected_plasma_cells_presentation_MM346_sty


title: CD138_selected_plasma_cells_presentation_MM345_sty


title: CD138_selected_plasma_cells_presentation_MM344_sty


title: CD138_selected_plasma_cells_presentation_MM360_sty


title: peripheral_white_blood_cells_presentation_PB307_nsp


title: CD138_selected_plasma_cells_presentation_MM343_sty


title: NK Cell Mock 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58670.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 720, 5760; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212779; Parameter Laser Power = 3.01; Parameter Scan Time = 14:26:02; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431782; Parameter Laser Power = 2.52; Parameter Scan Time = 14:26:02; 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 NK Cell Mock 1 h


title: CD138_selected_plasma_cells_presentation_MM342_sty


title: peripheral_white_blood_cells_presentation_PB305_nsp


title: NK Cell Mock 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58673.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 5200; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212834; Parameter Laser Power = 3.55; Parameter Scan Time = 15:20:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431837; Parameter Laser Power = 2.53; Parameter Scan Time = 15:20:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Simon,,Waddell

source_name: 4ug Amplified NK Cell Mock 12 h


title: erStress_60grandparents_GM12750_4_ug_ml_tunicamycin_8_hours_rep1

status: Public on Mar 30 2010

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

country: USA

institute: HHMI, University of Pennsylvania

description: Gene expression data under ER stress from lymphoblastoid cells of individual GM12750 treated with 4 ug/ml tunicamycin 8 hours.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Lymphoblastoid cell lines derived from GM12750

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

growth_protocol: The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

treatment_protocol: 4 ug/ml tunicamycin 8 hours

tag: cell line

value: lymphoblastoid cell line

tag: coriell cell line repository identifier

tag: agent

value: tunicamycin

tag: dose

value: 4 ug/ml

tag: time

value: 8 hours


title: CD138_selected_plasma_cells_presentation_MM339_sty


title: peripheral_white_blood_cells_presentation_PB303_nsp


title: peripheral_white_blood_cells_presentation_PB304_nsp


title: CD138_selected_plasma_cells_presentation_MM338_sty


title: peripheral_white_blood_cells_presentation_PB302_nsp


title: peripheral_white_blood_cells_presentation_PB306_nsp


title: CD138_selected_plasma_cells_presentation_MM383_nsp


title: CD138_selected_plasma_cells_presentation_MM336_sty


title: B Cell 0.6 pM IFNg 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58663.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212341; Parameter Laser Power = 3.43; Parameter Scan Time = 01:05:13; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431344; Parameter Laser Power = 2.56; Parameter Scan Time = 01:05:13; 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 B Cell 0.6 pM IFNg 8 h

value: 0.6 pM IFNg


title: CD138_selected_plasma_cells_presentation_MM337_sty

value: AllPrep


title: CD138_selected_plasma_cells_presentation_MM335_sty


title: CD4 T02

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58623.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 211763; Parameter Laser Power = 2.97; Parameter Scan Time = 15:25:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.28; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 430766; Parameter Laser Power = 2.49; Parameter Scan Time = 15:25:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.28; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 T02

value: time(absolute) 0 h


title: CD138_selected_plasma_cells_presentation_MM382_nsp


title: CD138_selected_plasma_cells_presentation_MM384_nsp


title: CD138_selected_plasma_cells_presentation_MM381_nsp


title: peripheral_white_blood_cells_presentation_PB301_nsp

source_name: peripheral white blood cell pellets


title: CD138_selected_plasma_cells_presentation_MM334_sty


title: CD138_selected_plasma_cells_presentation_MM380_nsp


title: B Cell 0.6 pM IFNg 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58660.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 212305; Parameter Laser Power = 3.48; Parameter Scan Time = 00:28:55; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 431308; Parameter Laser Power = 2.56; Parameter Scan Time = 00:28:55; 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

source_name: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified B Cell 0.6 pM IFNg 0.5 h

value: time(absolute) 0.5 h

value: B Cell


title: CD138_selected_plasma_cells_presentation_MM330_sty


title: CD138_selected_plasma_cells_presentation_MM341_sty


title: CD4 0.6 pM IFNg 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58635.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 5720; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212027; Parameter Laser Power = 3.82; Parameter Scan Time = 19:49:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; 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 = 2005-01-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431029; Parameter Laser Power = 2.53; Parameter Scan Time = 19:49:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Simon,,Waddell

source_name: 4ug Amplified CD4 0.6 pM IFNg 12 h

value: CD4 Cell


title: NK Cell Mock 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58671.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 700, 5980; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212792; Parameter Laser Power = 3.16; Parameter Scan Time = 14:38:33; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 431794; Parameter Laser Power = 2.52; Parameter Scan Time = 14:38:33; 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 NK Cell Mock 4 h

value: time(absolute) 4 h

value: NK Cell


title: CD138_selected_plasma_cells_presentation_MM333_sty

source_name: pre-treatment bone marrow


title: CD138_selected_plasma_cells_presentation_MM340_sty


title: B Cell 0.6 pM IFNg 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58664.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 580, 4750; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 212353; Parameter Laser Power = 3.43; Parameter Scan Time = 01:17:19; 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 = 2005-01-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 431356; Parameter Laser Power = 2.57; Parameter Scan Time = 01:17:19; 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

source_name: 4ug Amplified B Cell 0.6 pM IFNg 12 h

value: time(absolute) 12 h


title: IFNg stimulated 0.006 pM IFN 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56719.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 = 520; Parameter Laser on time = 200474; Parameter Laser Power = 3.64; Parameter Scan Time = 00:27:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; 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 = 640; Parameter Scan Power = 100; Parameter Laser on time = 419442; Parameter Laser Power = 2.65; Parameter Scan Time = 00:27:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Simon,,Waddell

value: Stratagene 1 Round Amplification 3 ug

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

value: 0.006 pM IFNg


title: CD138_selected_plasma_cells_presentation_MM329_sty

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


title: Monocyte Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58684.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 4950; 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 = 2005-01-11; 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 = 212975; Parameter Laser Power = 3.61; Parameter Scan Time = 17:41:20; 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 = 2005-01-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 431978; Parameter Laser Power = 2.55; Parameter Scan Time = 17:41:20; 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 Monocyte Mock 0.5 h

value: Monocyte


title: CD138_selected_plasma_cells_presentation_MM332_sty


title: CD138_selected_plasma_cells_presentation_MM327_sty


title: CD138_selected_plasma_cells_presentation_MM324_sty


title: CD138_selected_plasma_cells_presentation_MM325_sty


title: CD138_selected_plasma_cells_presentation_MM323_sty


title: CD138_selected_plasma_cells_presentation_MM326_sty


title: CD138_selected_plasma_cells_presentation_MM328_sty


title: IFNg stimulated 60 pM IFN 2 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56710.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 = 530; Parameter Laser on time = 200335; Parameter Laser Power = 3.44; Parameter Scan Time = 22:09:18; 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 = 640; Parameter Scan Power = 100; Parameter Laser on time = 419303; Parameter Laser Power = 2.64; Parameter Scan Time = 22:09:18; 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 2 h

value: time(absolute) 2 h

value: 60 pM IFNg


title: CD138_selected_plasma_cells_presentation_MM379_nsp


title: CD138_selected_plasma_cells_presentation_MM378_nsp


title: IFNg stimulated 0.6 pM IFN 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56727.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 = 200577; Parameter Laser Power = 3.58; Parameter Scan Time = 02:11:32; 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 = 419546; Parameter Laser Power = 2.65; Parameter Scan Time = 02:11:32; 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 4 h


title: CD138_selected_plasma_cells_presentation_MM319_sty


title: CD138_selected_plasma_cells_presentation_MM331_sty


title: IFNg stimulated 60 pM IFN 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56708.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 = 200284; Parameter Laser Power = 3.51; Parameter Scan Time = 21:16:51; 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 = 2004-10-22; 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 = 419252; Parameter Laser Power = 2.64; Parameter Scan Time = 21:16:51; 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 IFNg stimulated 60 pM IFN 0.5 h


title: CD138_selected_plasma_cells_presentation_MM321_sty


title: IFNg stimulated T0 I

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56707.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 = 200273; Parameter Laser Power = 3.46; Parameter Scan Time = 21:05:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.67; 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 = 419241; Parameter Laser Power = 2.64; Parameter Scan Time = 21:05:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.67; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated T0 I

value: Mock


title: CD138_selected_plasma_cells_presentation_MM322_sty


title: CD138_selected_plasma_cells_presentation_MM318_sty


title: CD138_selected_plasma_cells_presentation_MM320_sty


title: CD138_selected_plasma_cells_presentation_MM315_sty


title: CD138_selected_plasma_cells_presentation_MM316_sty


title: CD138_selected_plasma_cells_presentation_MM376_nsp


title: CD138_selected_plasma_cells_presentation_MM377_nsp


title: CD138_selected_plasma_cells_presentation_MM374_nsp


title: CD138_selected_plasma_cells_presentation_MM313_sty


title: CD138_selected_plasma_cells_presentation_MM375_nsp


title: IFNg stimulated 60 pM IFN 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56711.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 = 200347; Parameter Laser Power = 3.46; Parameter Scan Time = 22:21:26; 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 = 419316; Parameter Laser Power = 2.64; Parameter Scan Time = 22:21:26; 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 4 h


title: IFNg stimulated 60 pM IFN 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56709.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 = 520; Parameter Laser on time = 200323; Parameter Laser Power = 3.47; Parameter Scan Time = 21:56:49; 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 = 419291; Parameter Laser Power = 2.64; Parameter Scan Time = 21:56:49; 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 1 h

value: time(absolute) 1 h


title: CD138_selected_plasma_cells_presentation_MM311_sty


title: CD138_selected_plasma_cells_presentation_MM317_sty


title: CD138_selected_plasma_cells_presentation_MM312_sty


title: IFNg stimulated T0 II

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56723.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 = 520; Parameter Laser on time = 200526; Parameter Laser Power = 3.68; Parameter Scan Time = 01:20:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; 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 = 419494; Parameter Laser Power = 2.65; Parameter Scan Time = 01:20:11; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated T0 II


title: CD138_selected_plasma_cells_presentation_MM310_sty


title: IFNg stimulated T0 IV

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56699.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 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 = 200161; Parameter Laser Power = 2.95; Parameter Scan Time = 19:13:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; 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 = 680; Parameter Scan Power = 100; Parameter Laser on time = 419129; Parameter Laser Power = 2.64; Parameter Scan Time = 19:13:59; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated T0 IV


title: CD138_selected_plasma_cells_presentation_MM372_nsp


title: CD138_selected_plasma_cells_presentation_MM308_sty


title: CD138_selected_plasma_cells_presentation_MM370_nsp


title: CD138_selected_plasma_cells_presentation_MM314_sty


title: CD138_selected_plasma_cells_presentation_MM309_sty


title: CD138_selected_plasma_cells_presentation_MM306_sty


title: IFNg stimulated Mock 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56705.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 = 200245; Parameter Laser Power = 3.31; Parameter Scan Time = 20:37:12; 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 = 2004-10-22; 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 = 419213; Parameter Laser Power = 2.64; Parameter Scan Time = 20:37:12; 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 IFNg stimulated Mock 12 h


title: IFNg stimulated 0.6 pM IFN 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56728.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 = 200591; Parameter Laser Power = 3.58; Parameter Scan Time = 02:24:28; 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 = 620; Parameter Scan Power = 100; Parameter Laser on time = 419559; Parameter Laser Power = 2.65; Parameter Scan Time = 02:24:28; 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: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFNg stimulated 0.6 pM IFN 8 h

value: time(absolute) 8 h


title: CD138_selected_plasma_cells_presentation_MM371_nsp


title: CD138_selected_plasma_cells_presentation_MM304_sty


title: CD138_selected_plasma_cells_presentation_MM373_nsp


title: CD138_selected_plasma_cells_presentation_MM307_sty


title: CD138_selected_plasma_cells_presentation_MM305_sty


title: CD138_selected_plasma_cells_presentation_MM302_sty


title: IFNg stimulated 0.006 pM IFN 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56721.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 = 200499; Parameter Laser Power = 3.67; Parameter Scan Time = 00:53:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; 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 = 419468; Parameter Laser Power = 2.66; Parameter Scan Time = 00:53:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.006 pM IFN 12 h


title: CD138_selected_plasma_cells_presentation_MM369_nsp


title: IFNg stimulated 0.006 pM IFN 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56720.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 = 200486; Parameter Laser Power = 3.67; Parameter Scan Time = 00:40:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; 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 = 419454; Parameter Laser Power = 2.65; Parameter Scan Time = 00:40:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated 0.006 pM IFN 8 h


title: CD138_selected_plasma_cells_presentation_MM303_sty

source_name: pre-treatment bone marrow


title: CD138_selected_plasma_cells_presentation_MM366_nsp


title: CD138_selected_plasma_cells_presentation_MM301_sty


title: CD138_selected_plasma_cells_presentation_MM368_nsp


title: CD138_selected_plasma_cells_presentation_MM367_nsp


title: Rat 13, Day 14, 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

institute: Walter Reed Army Institute of Research

description: Gene expression 14 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 13, Day 14, 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: IFNg stimulated Mock 0.5 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56700.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 = 500; Parameter Laser on time = 200180; Parameter Laser Power = 2.98; Parameter Scan Time = 19:32:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.22; 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 = 419148; Parameter Laser Power = 2.64; Parameter Scan Time = 19:32:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.22; Performer: Simon,,Waddell

source_name: 4ug Amplified IFNg stimulated Mock 0.5 h

value: time(absolute) 0.5 h


title: IFNg stimulated 60 pM IFN 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56713.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 4750; 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 = 200372; Parameter Laser Power = 3.54; Parameter Scan Time = 22:46:20; 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 = 2004-10-22; 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 = 419340; Parameter Laser Power = 2.64; Parameter Scan Time = 22:46:20; 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 60 pM IFN 12 h


title: CD138_selected_plasma_cells_presentation_MM365_nsp

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

value: AllPrep