title: IFN stimulated T0 4

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57534.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 4690; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206703; Parameter Laser Power = 3.85; Parameter Scan Time = 00:57:15; 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 = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425638; Parameter Laser Power = 2.62; Parameter Scan Time = 00:57:15; 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 IFN stimulated T0 4

value: time(absolute) 0 h


title: IL12 stimulated IL12 4 h

status: Public on Mar 22 2010

type: RNA

city: London

first: Simon

last: Waddell

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

country: United Kingdom

institute: University of London Tooting

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57568.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 = 1440, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206902; Parameter Laser Power = 3.44; Parameter Scan Time = 04:16:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425837; Parameter Laser Power = 2.62; Parameter Scan Time = 04:16:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

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

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene 1 Round Amplification 3 ug

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IL12 stimulated IL12 4 h

tag: measurement

value: time(absolute) 4 h

tag: compound based treatment


title: IFN omega stimulated IFNo 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57558.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 3920; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206766; Parameter Laser Power = 3.75; Parameter Scan Time = 01:59:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425701; Parameter Laser Power = 2.62; Parameter Scan Time = 01:59:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN omega stimulated IFNo 12 h

value: time(absolute) 12 h

value: IFNo


title: CD138_selected_plasma_cells_presentation_MM314_nsp

type: genomic

city: Sutton

first: Brian

middle: A

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

institute: The Institute of Cancer Research

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

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

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

label: biotin

molecule: genomic DNA

source_name: pre-treatment bone marrow

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

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

tag: extraction

value: AllPrep


title: IFN omega stimulated IFNo 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57557.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 3920; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206755; Parameter Laser Power = 3.82; Parameter Scan Time = 01:47:55; 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 = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425690; Parameter Laser Power = 2.62; Parameter Scan Time = 01:47:55; 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 IFN omega stimulated IFNo 8 h

value: time(absolute) 8 h


title: CD138_selected_plasma_cells_presentation_MM318_nsp


title: IFN beta stimulated IFNb 1 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57549.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206641; Parameter Laser Power = 3.73; Parameter Scan Time = 23:54:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 425576; Parameter Laser Power = 2.62; Parameter Scan Time = 23:54:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN beta stimulated IFNb 1 h

value: time(absolute) 1 h

value: IFNb


title: CD138_selected_plasma_cells_presentation_MM312_nsp


title: CD138_selected_plasma_cells_presentation_MM315_nsp


title: TNFa stimulated TNFa 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57576.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 207000; Parameter Laser Power = 3.33; Parameter Scan Time = 05:53:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.65; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 425935; Parameter Laser Power = 2.61; Parameter Scan Time = 05:53:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.65; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 12 h

value: TNFa


title: CD138_selected_plasma_cells_presentation_MM316_nsp


title: CD138_selected_plasma_cells_presentation_MM313_nsp


title: ML, replicate 5

status: Public on Mar 21 2010

city: Parkville

first: Jane

middle: E

last: Visvader

state: Victoria

address: 1G Royal Parade

department: Victorian Breast Cancer Research Consortium

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: no additional information

hyb_protocol: Labeled cRNA (1.5 μg) was prepared for hybridization to Illumina mouseWG-6 V2 (R1) BeadChips.

scan_protocol: After washing, we coupled the chips with Cy3 and scanned them in an Illumina BeadArray Reader.

data_processing: Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma packages of the Bioconductor open-source software project (http://www.bioconductor.org). The raw intensities were normalized using the neqc function with offset 16.

organism: Mus musculus

source_name: FACS sorted mammary cell subpopulation

label_protocol: We labeled up to 500 ng with the Total Prep RNA amplification kit (Ambion).

extract_protocol: RNA from sorted cell populations was prepared with the RNeasy Micro kit (Qiagen). RNA quality was ascertained using the Agilent Bioanalyser 2100 with the NanoChip protocol.

tag: gender

value: female

tag: cell subpopulation

value: ML

tag: mouse pool (biological replicate)

tag: hybridization batch

tag: beadchip barcode

tag: beadchip section

value: E


title: IFN stimulated T0 5

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57535.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 3920; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 206792; Parameter Laser Power = 3.66; Parameter Scan Time = 02:25:32; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 425726; Parameter Laser Power = 2.62; Parameter Scan Time = 02:25:32; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN stimulated T0 5

value: Mock


title: CD138_selected_plasma_cells_presentation_MM308_nsp


title: MS, replicate 5

description: no additional information

value: MS

value: D


title: LP, replicate 4

description: no additional information

value: LP

value: B


title: MS, replicate 4

description: no additional information

value: C


title: LP, replicate 5

description: no additional information

value: F


title: CD138_selected_plasma_cells_presentation_MM310_nsp


title: IFN gamma stimulated IFNg 12 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57564.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206853; Parameter Laser Power = 3.55; Parameter Scan Time = 03:27:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425788; Parameter Laser Power = 2.62; Parameter Scan Time = 03:27:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN gamma stimulated IFNg 12 h

value: time(absolute) 12 h

value: IFNg


title: TNFa stimulated TNFa 1h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57573.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206964; Parameter Laser Power = 3.43; Parameter Scan Time = 05:16:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425898; Parameter Laser Power = 2.62; Parameter Scan Time = 05:16:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Simon,,Waddell

source_name: 4ug Amplified TNFa stimulated TNFa 1h


title: CD138_selected_plasma_cells_presentation_MM306_nsp

value: AllPrep


title: IFN gamma stimulated IFNg 4 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57562.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206829; Parameter Laser Power = 3.57; Parameter Scan Time = 03:02:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 425763; Parameter Laser Power = 2.61; Parameter Scan Time = 03:02:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN gamma stimulated IFNg 4 h

value: time(absolute) 4 h


title: CD138_selected_plasma_cells_presentation_MM309_nsp


title: IFN stimulated T0 2

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57532.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206529; Parameter Laser Power = 2.80; Parameter Scan Time = 22:02:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425464; Parameter Laser Power = 2.61; Parameter Scan Time = 22:02:41; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Simon,,Waddell

source_name: 4ug Amplified IFN stimulated T0 2

value: time(absolute) 0 h


title: MS, replicate 3

description: no additional information


title: ML, replicate 4

description: no additional information

value: A


title: IFN alpha stimulated IFNa 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57545.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5880; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206578; Parameter Laser Power = 3.47; Parameter Scan Time = 22:51:15; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.74; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425513; Parameter Laser Power = 2.62; Parameter Scan Time = 22:51:15; 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 IFN alpha stimulated IFNa 8 h

value: time(absolute) 8 h

value: IFNa


title: CD138_selected_plasma_cells_presentation_MM311_nsp


title: CD138_selected_plasma_cells_presentation_MM307_nsp


title: Prkar1a+/-Prkaca+/- caudal vertebral bone lesion, rep1

city: Bethesda

first: Kitman

last: Tsang

state: MD

address: 10 Center Drive, 10-CRC, Rm1E-3216

country: USA

institute: SEGEN/PDEGEN/NICHD/NIH

description: Replicate 1 of 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Z score transformation for normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

source_name: vertebral bone, Prkar1a+/- Prkaca+/-

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: background

value: C57BL/6x129Sv/B6 hybrid

tag: genotype

value: Prkar1a+/- Prkaca+/-

tag: age

value: 9 months

tag: tissue

value: caudal vertebral bone lesion


title: Prkar1a+/- caudal vertebral bone lesion, rep3

description: Replicate 3 of 3.

source_name: vertebral bone, Prkar1a+/-


title: CD138_selected_plasma_cells_presentation_MM304_nsp


title: MS, replicate 2

description: no additional information

value: female

value: MS


title: Prkar1a+/- caudal vertebral bone lesion, rep2

description: Replicate 2 of 3.


title: CD138_selected_plasma_cells_presentation_MM301_nsp


title: ML, replicate 3

description: no additional information

value: ML

value: D


title: IFN gamma stimulated IFNg 8 h

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57563.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 4480; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 206842; Parameter Laser Power = 3.52; Parameter Scan Time = 03:15:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-18; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425777; Parameter Laser Power = 2.61; Parameter Scan Time = 03:15:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Simon,,Waddell

value: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN gamma stimulated IFNg 8 h


title: CD138_selected_plasma_cells_presentation_MM305_nsp


title: Prkar1a+/-Prkaca+/- caudal vertebral bone lesion, rep2

description: Replicate 2 of 2.


title: Prkaca+/- caudal vertebral bone, rep4

description: Replicate 4 of 4.

source_name: vertebral bone, Prkaca+/-

value: Prkaca+/-

value: caudal vertebral bone


title: stroma, replicate 3

description: no additional information

value: stroma

value: C


title: CD138_selected_plasma_cells_presentation_MM303_nsp

value: AllPrep


title: Prkaca+/- caudal vertebral bone, rep3

description: Replicate 3 of 4.


title: IFN stimulated T0 3

description:
Simple annotation: Stimulation, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57533.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1200, 4970; Software: type: feature extraction; Performer: Simon,,Waddell Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 206616; Parameter Laser Power = 3.72; Parameter Scan Time = 23:29:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-11-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.2; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 425551; Parameter Laser Power = 2.62; Parameter Scan Time = 23:29:22; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [81971]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Simon,,Waddell

source_name: Stratagene 1 Round Amplification 3 ug

source_name: 4ug Amplified IFN stimulated T0 3

value: time(absolute) 0 h

value: Mock


title: LP, replicate 3

description: no additional information

value: LP

value: E


title: LP, replicate 2

description: no additional information

value: A


title: stroma, replicate 2

description: no additional information


title: WT caudal vertebral bone, rep3

description: Replicate 3 of 4.

source_name: vertebral bone, WT

value: C57BL/6x129Sv/B6 hybrid

value: WT

value: 9 months


title: ML, replicate 2

description: no additional information

value: female

value: F


title: CD138_selected_plasma_cells_presentation_MM302_nsp

source_name: pre-treatment bone marrow


title: Prkaca+/- caudal vertebral bone, rep2

description: Replicate 2 of 4.


title: MS, replicate 1

description: no additional information

value: MS

value: D


title: Prkar1a+/- caudal vertebral bone lesion, rep1

description: Replicate 1 of 3.

value: caudal vertebral bone lesion


title: LP, replicate 1

description: no additional information


title: ML, replicate 1

description: no additional information

value: ML

value: B


title: Prkaca+/- caudal vertebral bone, rep1

description: Replicate 1 of 4.

value: Prkaca+/-

value: caudal vertebral bone


title: WT caudal vertebral bone, rep4

description: Replicate 4 of 4.


title: Baseline 1 pct spike

city: Lyngby

first: Aron

middle: C

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Labeled target was fragmented and hybridized to Yeast 2.0 microarrays (Affymetrix) according to the manufacturer's protocol.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 (Affymetrix).

data_processing: Data was processed by the RMA algorithm, using R/Bioconductor.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae, with 1% spike

label_protocol: Double stranded cDNA was synthesized and transcribed in vitro using the MessageAmp II-biotin Enhanced Kit (Ambion), following the manufacturer’s protocol.

growth_protocol: Saccharomyces cerevisiae strain W303, MAT-alpha, with the cdc15–2 mutation was grown at 23 C in minimal media in a fermentor for 340 minutes after release from restrictive temperature, as described (de Lichtenberg et al. (2005) Yeast, Nov;22(15):1191-201).

extract_protocol: Whole RNA was isolated using the FastRNA Pro Red Kit (Qbiogene).

treatment_protocol: None.

tag: sample

value: 99% baseline, 1% spike


title: Baseline 10 pct spike

source_name: S. cerevisiae, with 10% spike

value: 90% baseline, 10% spike


title: stroma, replicate 1

description: no additional information

source_name: FACS sorted mammary cell subpopulation

value: stroma


title: Baseline only

source_name: S. cerevisiae, without spike

value: 100% baseline, 0% spike


title: WT caudal vertebral bone, rep2

description: Replicate 2 of 4.


title: dental follicle cells IGF2 1

status: Public on Mar 20 2010

city: Regensburg

first: Christian

last: Morsczeck

address: Franz-Josef Strauss Allee 11

country: Germany

institute: University of Regensburg

description: Gene expression of dental follicle cells after 7 days differentiation in IGF medium

hyb_protocol: Hybridization to Affymetrix oligonucleotide microarray Human Gene 1.0 ST array was carried out overnight with 1biotin-labeled cRNA in a hybridization oven 640

scan_protocol: GeneChip Scanner 3000 (Affymetrix)

data_processing: Affymetrix GeneChip Operating Software (GCOS) 1.4 and the Expression Console 1.1. Software. For the creation of the summarized log-signal the robust multi-chip analysis (RMA) algorithm was used.

source_name: dental follicle cells after differentiation IGF

label_protocol: Double-stranded cDNA was prepared from 5 μg of total cellular RNA (cDNA synthesis kit, Affymetrix Santa Clara, CA, USA), in vitro transcribed using an IVT labeling kit, and the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). All procedures according to the Affymetrix protocol.

growth_protocol: Cell were grown in in MesenchymStem Medium (PAA, Pasching, Austria) at 37°C in 5% CO2

extract_protocol: Total RNAs were extracted using the kit NucleoSpin® RNA II kit (Macherey Nagel, Düren, Germany) and quality-controlled using the RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: Osteogenic differentiation was induced after cultivation in  DMEM (PAA) supplemented with 10% foetal bovine serum (PAA), 100 µmol/L ascorbic acid 2-phosphate, 2.8 mmol/l KH2PO4, 1 × 10−7 mol/l dexamethasone sodium phosphate (Sigma-Aldrich) and HEPES (20 mmol/L). Alternatively for BMP2 or IGF2 (50 ng/mL; Sigma-Aldrich) induction of osteogenic differentiation, DFCs were cultivated in DMEM (PAA) supplemented with 1% fetal bovine serum (PAA), 100 μmol/L ascorbic acid 2-phosphate, 2.8 mmol/L KH 2 PO 4 , and HEPES (20 mmol/L).

tag: medium type

value: IGF

tag: cell type

value: dental progenitor/stem cells


title: dental follicle cells BMP2 2

description: Gene expression of dental follicle cells after 7 days differentiation in BMP medium

source_name: dental follicle cells after differentiation BMP

value: BMP


title: dental follicle cells IGF2 3


title: WT caudal vertebral bone, rep1

description: Replicate 1 of 4.

value: C57BL/6x129Sv/B6 hybrid

value: WT

value: 9 months


title: dental follicle cells BMP2 3


title: dental follicle cells IGF2 2


title: AM8

city: Pittsburgh

first: Monica

last: Panelli

state: PA

address: 5117 Centre Ave

department: Hematology-Oncology

institute: Hillman Cancer Center, University of Pittsburgh

description:
TB09-043B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were  exported  from the Plate Centric View into the ABI TaqMan RQ manager software. Automatic baseline and manual CT  were set to 0.2 for all samples. Statistical analysis of TLDA: The global data set of 666 miRs was used for analysis. Data were normalized using BRB Tools [Simon R and Lam A. BRB-ArrayTools User Guide, version 3.2. Biometric Research Branch, National Cancer Institute. http://linus.nci.nih.gov/brb]. Input data for class comparison, permutations and prediction analysis consisted of the miR expression CT values normalized to the endogenous housekeeping MummU6 [delta][delta] CT = [delta] CT,sample - [delta] CT,reference.

source_name: Nodular melanoma (3% in situ)

extract_protocol: Total RNA was isolated from FFPE-tissue utilizing a modified RecoverALL (Recover All Ambion #AM1975) protocol for isolation of RNA from paraffin slide sections. In brief, using a scalpel blade (#15) wetted in xylene, areas containing >70% tumor were excised from thirty 5 um paraffin tissue sections and placed in an microcentrifuge tube containing 1ml of xylene, vortexed and incubated at 50˚C for 3 minutes to melt the paraffin. The material was then centrifuged at 14,000rpm for 5-10min at room temperature. The xylene was then removed using a 1ml pipette and the pellet was washed 3 times with 1ml of 100% room temperature-ethanol. The pellet was then air-dried at room temperature for 15 minutes. Following deparaffinization, tissue was protease digested by incubating the pellet in 400ul digestion buffer and 4ul protease at 50˚C for 3 hours. For RNA isolation, 480ul of isolation additive was added to the sample, followed by vortexing and addition of 1.1ml of 100% ethanol. The mixture was then loaded onto a prepared filter and collection tube according to the manufacturer-supplied procedure. Flow through was discarded and filter washed with wash buffer. Nuclease digestion and final RNA purification was carried over as follows. Sixty ul DNase master mix (containing 6ul10x DNase buffer ,4ul DNase, 50ul nuclease free water) was added to the center of the filter and incubated for 30 minutes at room temperature. The filter was subsequently washed according to the manufacturer’s protocol, and RNA was eluted twice with 30ul preheated nuclease-free water. RNA quality and quantity was measured by Nanodrop technology. RNA was further purified and concentrated by precipitation for 1 hour at -70˚C using 1/10 volume ammonium acetate, 1ul glycogen (5ug/ul) and 2.5 volume 100% ethanol. RNA was then washed, dried and resuspended in 12-15 ul nuclease-free water. RNA reverse transcription was accomplished according to the ABI microRNA TLDA Reverse Transcription Reaction protocol. In brief, the Megaplex RT Primers, TaqMan® MicroRNA Reverse Transcription Kit components and MgCl2 were thawed on ice. Two master mixes per specimen, one for each TLDA panel ( panel A and panel B) consisting of 0.80 ul MegaPlex RT primers (10x), 0.20 ul dNTPs with dTTP (100 mM), 1.50 ul MultiScribe™ ReverseTranscriptase (50 U/μL), 0.80 ul 10✕ RT Buffer, 0.90 ul MgCl2 (25 mM), 0.10 ul RNase Inhibitor, 0.20 ul nuclease-free water (20 U/μL) were prepared. Three μL (30 ng) total RNA (or 3uL of water for the No Template Control reactions) were loaded into each tube containing  4.5uL RT reaction mix  and incubated on ice for 5 min. The following thermal cycling conditions were used in the ABI 9700 thermal cycler: standard or max ramp speed, 16°C 2 min, 42°C 1  min 40 cycles, 50°C 1 sec, hold 85°C 5 min, hold 4°C. The cDNA product (2.5 ul per specimen) was preamplified according to the ABI TLDA preamplification protocol. A total of 22.5ul of pre-amplification reaction mix consisting of 12.5 ul TaqMan® PreAmp Master Mix (2x); 2.5 ul Megaplex™ PreAmp Primers (10x); 7.5 ul nuclease-free water was prepared and added to the cDNA product in a 96-well optical plate sealed with MicroAmp® Clear Adhesive Film (ABI PN #4306311).The plate was spun briefly and incubated on ice for 5 min. The preamplifcation  was conducted in the ABI 9700 thermal cycler using standard ramp speed and the following thermal cycling conditions: hold 95°C10 min; hold 55°C 2 min; hold 72°C 2 min; 12 cycle at 95°C 15 sec and 60°C 4 min; hold 4°C forever. The preamplified product was diluted with 75uL of 0.1x TE pH 8.0 mixed, briefly centrifuged  and stored at -25°C before TaqMan Real Time assay. TLDA TaqMan Real Time Assay was set up for each sample as follows: 450μl of TaqMan® Universal PCR Master Mix-No AmpErase® UNG (2x) were added to 9μl of diluted PreAmp product in a 1.5-mL microcentrifuge tube containing 441 ul of nuclease-free water. The reaction was mixed six times by inverting the tube and then briefly centrifuged. One hundred ul of the PCR reaction mix were loaded into each port of the TLDA array. B36The TLDA plate was centrifuged with 9 up and down ramp rates at 1200rpm for 1 min and loaded into the 7900 HT Sequence Detection System using the 384-well TaqMan Low Density Array default thermal-cycling conditions.

value: Mel 60

tag: histology

value: Mel

tag: percentage tumor or nevus

tag: sex

value: M

tag: site

value: Flank

tag: tstage

tag: nstage

tag: mstage


title: PM6

description:
TB09-044B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

scan_protocol: The TLDA plate was centrifuged with 9 up and down ramp rates at 1200rpm for 1 min and loaded into the 7900 HT Sequence Detection System using the 384-well TaqMan Low Density Array default thermal-cycling conditions.

source_name: Superficial spreading melanoma, invasive

value: Mel 30

value: F

value: Thigh


title: dental follicle cells dexamethasone 2

description: Gene expression of dental follicle cells after 7 days differentiation in dexamethasone medium

source_name: dental follicle cells after differentiation dexamethasone

value: dexamethasone


title: dental follicle cells control 3

description: Gene expression of dental follicle cells after 7 days  in standard medium

source_name: dental follicle cells in control medium

value: control medium


title: AM3

description:
TB08-217 1D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Desmoplastic melanoma, invasive

value: Forehead


title: dental follicle cells dexamethasone 3


title: LEC_AdNICD_24h

city: los angeles

first: Young Kwon

last: Hong

state: CA

address: 1441 Eastlake Ave NOR6336

institute: Norris Cancer Center

description: Gene expression data from normal human primary lymphatic endothelial cells that were infected with a NICD-expressing adenovirus for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U1333A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: LECs, infected with NICD-expressing adenovirus for 24 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Standard Endothelial Basal Media (Lonza, Inc), 5% CO2 incubator at 37C

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Primary cells were treated with adenovirus between 1~10 MOI

value: Primary lymphatic endothelial cells


title: dental follicle cells BMP2 1


title: LEC_No_Treatment

description: Gene expression data from normal human primary lymphatic endothelial cells

source_name: LECs, uninfected


title: dental follicle cells control 1


title: dental follicle cells control 2


title: LEC_AdNICD_10h

description: Gene expression data from normal human primary lymphatic endothelial cells that were infected with a NICD-expressing adenovirus for 10 hours

source_name: LECs, infected with NICD-expressing adenovirus for 10 hours


title: PM4

description:
TB08-231 A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

value: Shin


title: PM5

description:
TB08-195 2A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma in situ (arising in compound melanocytic nevus)

value: Abdomen

value: pTis


title: AM2

description:
TB08-180(P) 1H
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading (outside path) and Nevoid Melanoma, invasive at WLE

value: Ear


title: AM5

description:
TB08-211 1J
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, insitu and invasive

value: Foot


title: dental follicle cells dexamethasone 1

value: dental progenitor/stem cells


title: LEC_AdCTR_24h

description: Gene expression data from normal human primary lymphatic endothelial cells that were infected with a GFP-expressing adenovirus for 24 hours

source_name: LECs, infected with GFP-expressing adenovirus for 24 hours


title: LCO-48h-rep3

city: Ste-Anne-de-Bellevue

last: Wang

state: Quebec

address: 21111 Lakeshore Road

department: Dept. of Plant Science

country: Canada

institute: McGill University/MacDonald Campus

description: Gene expression profile from soybean trifoliates at 15 °C

hyb_protocol: The cRNA quality was determined using a 2100 BioAnalyzer (Agilent) equipped with an RNA Nano LabChip, overnight hybridization of the chip utilized 15 µg of fragmented cRNA and the staining and washes were performed using an Affymetrix GeneChip Fluidics Station 450 robot, following the manufacturer's protocols.

scan_protocol: The microarray chips were scanned with an Affymetrix GeneChip Scanner 3000 7G, following the manufacturer's protocols.  Description All steps followed Affymetrix guidelines and protocols.

data_processing: All calculations were performed by FlexArray software (Blazejczyk, Miron et al. 2007), version 1.4.1, provided and developed by the McGill University and the Génome Québec Innovation Centre, using Bioconductor libraries.  The robust multi-array average (RMA) algorithm (Bolstad, Irizarry et al. 2003) was utilized to normalize the microarray raw data.  Three separate algorithms were used to calculate p-values: Cyber-T, Local Pooled Error (LPE) and Empirical Bayes (EB; Rocke).

organism: Glycine max

source_name: Soybean trifoliates harvested 48 h after foliar spray with LCO

label_protocol: A total of 3.5 µg extracted RNA was used to synthesize labeled target cRNA using the GeneChip HT One-Cycle Target Labeling and Controls kit (Affymetrix). cRNA were labelled with biotin, stained with Streptavidin-phycoerythrin (SAPE) and detected with Biotinylated anti-streptavidin antibody.

growth_protocol: Soybean seeds were first surface-sterilized with 25% v/v sodium hypochlorite (Javex) for 2 min. and then rinsed five times with distilled water (dH2O).  Sterilized seeds were scattered evenly on a 5 cm thick layer of autoclaved vermiculite in a large plastic tray (54 × 28 × 6.5 cm) with holes at the bottom for drainage of excess water, and then covered with a 1 cm layer of vermiculite. The tray with seeds was watered thoroughly with dH2O and placed in a growth chamber.  The chamber temperature was maintained at a constant 25 ºC with a 16 h photoperiod and an 8 h period of darkness.  The tray was watered daily with dH2O to allow even germination and emergence.  On the 7th day after sowing (DAS), the seedlings reached the V1 growth stage, manifested by the emergence and separation of the cotyledons (Fehr, Caviness et al. 1971).  Uniform seedlings were selected and transferred to 10 cm pots containing a 1:1 v/v mixture of autoclaved sand and turface as growth media.  Each seedling was transferred to an individual pot and put back into the growth chamber under the conditions described above.  On the 12th DAS, seedlings reached the V2 growth stage in which the first trifoliates had fully expanded (Fehr, Caviness et al. 1971).  The seedlings were then transferred to a different growth chamber and kept at 15 ºC, with a 16 h photoperiod and a dark period of 8 h.  After acclimatizing at 15 ºC for 5 days, plants were ready for treatment and harvest.  The plants were watered with ½ strength Hoagland’s solution (Hoagland and Arnon 1950) at same time every day from transplant to harvest.

extract_protocol: Frozen leaf tissue was rapidly ground in liquid N2 with a mortar and pestle, which had been baked at 230 ºC for 4 h to deactivate RNase, and then chilled with liquid N2 prior to RNA extraction.  All tools and surfaces were sprayed with 70% ethanol at the beginning of RNA extraction to inhibit RNase activity.  Total RNA was extracted from ~80 mg of finely-ground, frozen tissue using the Qiagen RNeasy® Plant Mini Kit for total RNA isolation, following the protocol provided by the manufacturer.

treatment_protocol: On the 17th DAS, the soybean plants had reached the V3 stage of development, marked by the full expansion of the second trifoliates (Fehr, Caviness et al. 1971).  The plants were then divided into groups, each group representing a treatment and sampling time.  The first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O containing one of the following treatments:   1. Control: 0.02 % Tween® 20  2. 10-7 M LCO: 10-7 M LCO and 0.02 % Tween® 20  The first trifoliolate leaves of each plant were harvested at 0 and 48 h after the spray application.  The leaves were quickly cut off from the stem with a scalpel, wrapped individually in aluminum foil and immediately submerged in liquid N2.  All samples were stored at -80 ºC until extraction.

tag: time point

tag: agent

value: Lipo-chitooligosaccharides (LCO)

value: Soybean first trifoliolate leaves

tag: cultivar

value: OAC Bayfield

tag: treatment protocol

value: Transferrd to low temperature at V2 stage; foliar spray performed at V3 stage


title: PM3

description:
TB08-239 B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, superficial spreading in radial growth phase & in vertical, epithelioid, nevoid and balloon cell

value: Mel 30

value: Mel

value: Scapula


title: AN2

description:
TB08-233D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound predominantly intradermal melanocytic nevus with architectural features of congenital onset

value: Nevus 60

value: Nevus

value: M

value: Flank


title: LCO-48h-rep2


title: AM4

description:
TB08-181 B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Nodular melanoma, invasive and insitu

value: Mel 60

value: Calf


title: PN2

description:
TB08-232 2A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

value: Nevus 30

value: Scalp


title: AM1

description:
TB08-236 1L
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, invasive, nevoid type.

value: F

value: Leg


title: AM6

description:
TB08-216 F
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Lentingo malignant melanoma in situ with focus invasive melanoma

value: Back


title: LCO-0h-rep3

source_name: Soybean trifoliates harvested immediately after foliar spray with LCO

value: 0 h

value: Lipo-chitooligosaccharides (LCO)

value: Soybean first trifoliolate leaves


title: AN3

description:
TB08-234A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound melanocytic nevus with moderate cytological atypia and congenital features.

value: Deltoid


title: PM8

description:
TB08-243A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Highly atypical spitzoid neoplasm

value: Mel 30

value: Mel

value: Arm


title: AN1

description:
TB09-003A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound, predominantly intradermal melanocytic nevus with architectural features of congenital onset

value: Nevus 60

value: Nevus


title: AM9

description:
TB08-219 1G
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Malignant melanoma, invasive & insitu, arising in a background of dysplastic nevus

value: M


title: PM10

description:
TB08-477/478C
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading melanoma, insitu and invasive


title: PM1,PM11,PM12

description:
TB08-199 D calib
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B
These are 3 run of the same sample that were averaged

source_name: Superficial spreading (Spitzoid) melanoma, insitu & invasive

value: Thigh


title: PM2

description:
TB08-192 1H
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading melanoma, invasive and insitu


title: PM9

description:
TB08-245D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Invasive and in situ melanoma, nodular.  Note: Description of superficial spreading also in synopsis but registry only codes final diagnoses.

value: Buttock


title: AM7

description:
TB08-237 1G
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Desmoplastic melanoma with associated lentiginous component

value: Mel 60


title: PM7

description:
TB08-190A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, invasive and insitu, arising in association with a nevus

value: Trunk

value: Unknown


title: LCO-0h-rep1

description: Gene expression profile from soybean trifoliates at 15 °C

value: OAC Bayfield

value: Transferrd to low temperature at V2 stage; foliar spray performed at V3 stage


title: PN1

description:
TB08-242 A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound, predominantly intradermal melanocytic nevus

value: Nevus 30

value: F

value: Forehead


title: Control-48h-rep2

source_name: Soybean trifoliates harvested 48 h after foliar spray with distilled water

value: distilled water

value: Soybean first trifoliolate leaves


title: Control-0h-rep3

source_name: Soybean trifoliates harvested immediately after foliar spray with distilled water

value: 0 h


title: Control-48h-rep3


title: LCO-0h-rep2

value: Lipo-chitooligosaccharides (LCO)


title: LCO-48h-rep1

source_name: Soybean trifoliates harvested 48 h after foliar spray with LCO


title: Control-48h-rep1


title: AM10

description:
TB08-223 C
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Malignant melanoma in situ arising in a compound dysplastic nevus

value: Mel

value: Back

value: pTis


title: PN3

description:
TB08-188A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound melanocytic nevus with features of a congenital nevus, architectural disorder and mild cytologic atypia (aka Clark's nevus with features of congenital onset).

value: Nevus


title: PM5B

description:
TB08-195 2A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma in situ (arising in compound melanocytic nevus)

value: Mel 30

value: M

value: Abdomen


title: AM3B

description:
TB08-217 1D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Desmoplastic melanoma, invasive

value: Mel 60


title: AM8B

description:
TB09-043B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Nodular melanoma (3% in situ)

value: Flank


title: AM2B

description:
TB08-180(P) 1H
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading (outside path) and Nevoid Melanoma, invasive at WLE

value: Ear


title: AN2B

description:
TB08-233D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound predominantly intradermal melanocytic nevus with architectural features of congenital onset

value: Nevus 60


title: AM4B

description:
TB08-181 B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Nodular melanoma, invasive and insitu

value: Calf


title: AM5B

description:
TB08-211 1J
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, insitu and invasive

value: F

value: Foot


title: Control-0h-rep2

value: distilled water

value: Soybean first trifoliolate leaves

value: OAC Bayfield

value: Transferrd to low temperature at V2 stage; foliar spray performed at V3 stage


title: PM3B

description:
TB08-239 B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, superficial spreading in radial growth phase & in vertical, epithelioid, nevoid and balloon cell

value: Mel

value: Scapula


title: Control-0h-rep1

value: 0 h


title: beta-cells_diabetic condition_donor10

city: Boston

first: Lorella

last: Marselli

state: MA

address: One Joslin Place

department: Joslin Diabetes Center and the Department of Medicine

institute: Harvard Medical School

description: Gene expression data from type 2 diabetic subjects

hyb_protocol: 15ug of biotinylated cRNA was hybridized for 16hr at 45C to the Affymetrix Human X3P array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

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

data_processing: Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.

source_name: human beta-cells_diabetic

label_protocol: Amplified RNA (1 μg) was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).

extract_protocol: Total RNA was extracted from each population of laser captured β–cells using phenol-chloroform-isoamyl alcohol and precipitated with sodium acetate and glycogen carrier in isopropanol. After initial recovery and resuspension of the RNA pellet, genomic DNA contamination was removed by incubation with 10 units of DNase I for 2 hours at 37°C, in presence of 10 units of RNase inhibitor. The treatment with DNase I was followed by RNA re-extraction and precipitation. The pellet was resuspended and total RNA was amplified by T7-based linear amplification using T7-oligo-dT-primers.  Two rounds of amplification were performed using RiboAmp HS RNA Amplification Kits (Arcturus).

treatment_protocol: Pancreas specimens were obtained, placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed by 5 dips in diethylpyrocarbonate (DEPC)-treated water and dehydrated in 100% ethanol twice for 1 min, and xylene for 4 minutes, the sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer (Buffer RLT, Qiagen), for 30 minutes at 42°C, and the samples stored at -80°C.

tag: sample id

tag: disease

value: type 2 diabetes

value: beta-cells

value: pancreas

tag: gender

value: female

tag: age (years)

tag: bmi (body mass index, kg/m2)


title: PM6B

description:
TB09-044B
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading melanoma, invasive

tag: tissue

value: Mel 30

tag: age

value: Thigh


title: PM2B

description:
TB08-192 1H
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading melanoma, invasive and insitu

tag: histology

tag: percentage tumor or nevus

value: M

value: Back


title: AM6B

description:
TB08-216 F
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Lentingo malignant melanoma in situ with focus invasive melanoma

value: Mel 60

tag: sex

tag: site


title: PN2B

description:
TB08-232 2A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

value: Nevus 30

value: Nevus

value: Scalp

tag: tstage

tag: nstage


title: beta-cells_diabetic condition_donor9

tag: cell type

value: male


title: PM10B

description:
TB08-477/478C
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Superficial spreading melanoma, insitu and invasive

tag: mstage


title: PN1B

description:
TB08-242 A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound, predominantly intradermal melanocytic nevus

value: F

value: Forehead


title: PM4B

description:
TB08-231 A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

value: Mel

value: Shin


title: PM1,PM11,PM12B

description:
TB08-199 D calib
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B
These are 3 run of the same sample that were averaged

source_name: Superficial spreading (Spitzoid) melanoma, insitu & invasive


title: beta-cells_diabetic condition_donor6

value: type 2 diabetes


title: AN1B

description:
TB09-003A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound, predominantly intradermal melanocytic nevus with architectural features of congenital onset

value: Nevus 60


title: PM9B

description:
TB08-245D
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Invasive and in situ melanoma, nodular.  Note: Description of superficial spreading also in synopsis but registry only codes final diagnoses.

value: Buttock


title: beta-cells_diabetic condition_donor7

value: beta-cells

value: pancreas


title: AN3B

description:
TB08-234A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound melanocytic nevus with moderate cytological atypia and congenital features.

value: Deltoid


title: beta-cells_diabetic condition_donor5

value: female


title: beta-cells_diabetic condition_donor4


title: beta-cells_diabetic condition_donor8


title: PM8B

description:
TB08-243A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Highly atypical spitzoid neoplasm

value: Mel 30

value: M

value: Arm


title: beta-cells_diabetic condition_donor1


title: beta-cells_diabetic condition_donor3


title: AM9B

description:
TB08-219 1G
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Malignant melanoma, invasive & insitu, arising in a background of dysplastic nevus

value: Mel 60

value: Back


title: AM7B

description:
TB08-237 1G
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Desmoplastic melanoma with associated lentiginous component


title: AM1B

description:
TB08-236 1L
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, invasive, nevoid type.

value: Leg


title: PN3B

description:
TB08-188A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Compound melanocytic nevus with features of a congenital nevus, architectural disorder and mild cytologic atypia (aka Clark's nevus with features of congenital onset).

value: Nevus 30

value: Nevus

value: F

value: Unknown


title: PM7B

description:
TB08-190A
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Melanoma, invasive and insitu, arising in association with a nevus

value: Mel

value: Trunk


title: beta-cells_non-diabetic condition_donor9

description: Gene expression data from control subjects

source_name: human beta-cells_non-diabetic

value: non-diabetic control

value: male


title: AM10B

description:
TB08-223 C
Total RNA was reverse transcribed, preamplified  and loaded on TLDA Taqman real time assay card A and B

source_name: Malignant melanoma in situ arising in a compound dysplastic nevus

value: pTis


title: beta-cells_non-diabetic condition_donor8

value: beta-cells

value: pancreas


title: Chr16p13.11deletion patient 6

city: New York

first: Erin

middle: L.

last: Heinzen

state: NY

department: Institute for Genomic Medicine

institute: Columbia University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using robust spline normalization in R (v2.8.0).

label: biotin, cy3

source_name: blood (leukocytes)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: ABI tempus tube extraction kit, including a Dnase treatment

tag: chip processing day

tag: disease state

value: epilepsy


title: Chr16p13.11deletion patient 7


title: beta-cells_non-diabetic condition_donor10

tag: sample id


title: beta-cells_diabetic condition_donor2

description: Gene expression data from type 2 diabetic subjects

source_name: human beta-cells_diabetic

tag: disease

value: type 2 diabetes

value: female


title: beta-cells_non-diabetic condition_donor7

tag: gender


title: beta-cells_non-diabetic condition_donor4

tag: age (years)


title: beta-cells_non-diabetic condition_donor6

tag: bmi (body mass index, kg/m2)


title: Chr16p13.11deletion patient 3


title: beta-cells_non-diabetic condition_donor5

tag: tissue


title: Control (no 16p13.11 deletion) 8

value: no seizure disorder


title: beta-cells_non-diabetic condition_donor3


title: Control (no 16p13.11 deletion) 7


title: Chr16p13.11deletion patient 2


title: Control (no 16p13.11 deletion) 4


title: Control (no 16p13.11 deletion) 1


title: beta-cells_non-diabetic condition_donor1


title: Control (no 16p13.11 deletion) 3


title: Chr16p13.11deletion patient 5


title: Chicken 9A vs 3B Cy53

status: Public on Mar 19 2010

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

description: Ross 308 broiler chickens were housed in eight rooms each containing 266 birds and were raised to slaughter weight, reaching a density of 34kg/m2 at 49 days of age. The birds were fed in four meals per day and provided with ad libitum access to water.

hyb_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols), with full dye swap.

scan_protocol: Scanned on GenePix 4200A 01 Autoloader based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols). The array layout is built in each slide file.

data_processing: LOESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. S+ArrayAnalyzer 2.1 built in S-Plus 7.0 Enterprise Developer (Insightful Corporation, Seattle, Washington) was used.

organism: Gallus gallus

source_name: Liver from CTS bird 3B

label_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).

extract_protocol: A two step extraction method was used, using first Trizol then QIAGEN Rneasy  kit,  following the protocol at http://www.ark-genomics.org/protocols IGF100.00: Isolation of total RNA.

treatment_protocol: Twenty-four female birds were selected from one room and spilt into 2 groups, control (C) or crated, transported, slaughtered (CTS). C birds were killed outside the home pen by cervical dislocation immediately prior to feeding, while CTS birds experienced the normal transport to slaughter procedure (i.e. catching, crating, transport, lairage, shackling, slaughter; total 3.25h) with the entire flock after 8h food withdrawal. Liver samples were collected from all selected birds within an hour of death.

tag: protocol

value: CTS

value: liver

source_name: Liver from control bird 9A

value: Control


title: Control (no 16p13.11 deletion) 2


title: Control (no 16p13.11 deletion) 5


title: Control (no 16p13.11 deletion) 6


title: Chr16p13.11deletion patient 1


title: Chicken 5A vs 2B Cy53

source_name: Liver from CTS bird 2B

source_name: Liver from control bird 5A


title: Chicken 7A vs 9B Cy53

source_name: Liver from CTS bird 9B

source_name: Liver from control bird 7A


title: Chicken 3A vs 1B Cy35

source_name: Liver from control bird 3A

source_name: Liver from CTS bird 1B


title: Chicken 2A vs 6B Cy53

source_name: Liver from CTS bird 6B

source_name: Liver from control bird 2A


title: Chicken 4A vs 12B Cy53

source_name: Liver from CTS bird 12B

source_name: Liver from control bird 4A


title: Chicken 10A vs 7B Cy53

source_name: Liver from CTS bird 7B

source_name: Liver from control bird 10A


title: Chicken 3A vs 1B Cy53


title: Chicken 5A vs 2B Cy35


title: Chicken 9A vs 3B Cy35


title: Chr16p13.11deletion patient 4


title: Chicken 10A vs 7B Cy35


title: Chicken 7A vs 9B Cy35


title: Chicken 12A vs 4B Cy53

source_name: Liver from CTS bird 4B

source_name: Liver from control bird 12A


title: wibr3_20-wibr3_5

city: Cambridge

first: Albert

middle: W

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: c38 incubated in 5% and 20% oxygen

hyb_protocol: Agilent (human 4x44k) expression arrays were hybridized according to our laboratory method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail  consisted of 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% nlaurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetonitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing:
Microarray data were processed, normalized within-array by LOESS and  normalized between arrays by Aquantile using Limma package.
Dye swap was done in this experiment so the test samples are sometimes Cy5 or Cy3. 20% and 20%A are test while all 5% are reference.

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 2 ug total RNA

extract_protocol: Total RNA was isolated from undifferentiated hES colonies between passages 30-40 and isolated using Trizol reagent (Gibco, Invitrogen, Carlsbad, CA) according to the manufacturers protocol. RNA was subsequently treated with DNAse I in order to remove potential genomic DNA contamination using an RNAse free DNAse kit (Zymo Research, Orange County, CA).

tag: cell line

tag: oxygen concentration


title: Chicken 12A vs 4B Cy35


title: Chicken 2A vs 6B Cy35


title: wibr2_20-wibr2_5

description: c29 incubated in 5% or 20% oxygen


title: wibr2_20A-wibr2_5

description: c29 incubated in 5% oxygen or 20% oxygen acutely


title: wibr1_20A-wibr1_5

description: c22 incubated in 5% oxygen or 20% oxygen acutely


title: Chicken 8A vs 11B Cy53

source_name: Liver from CTS bird 11B

source_name: Liver from control bird 8A


title: Control siRNA, 2

city: Tokyo

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from HCT116 cells transfected with a control siRNA.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HCT116 cells, control siRNA

label_protocol: 25ng total RNA was amplified by MessageAmp™ II aRNA Amplification Kit#1751(Ambion), and 0.2 ug aRNA labeled Cyanine-3 (Cy3) using the One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HCT116 cells were cultured under 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium–nutrient mixture F-12 supplemented with 10% fetal bovine serum.

extract_protocol: RNA was prepared using the NucleoSpin RNA XS (MACHEREY-NAGEL GmbH & Co. KG,Düren) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were transfected with the annealed siRNAs for 72 h with the use of the Lipofectamine RNAi MAX reagent (Invitrogen) according to manufacturer's recommendations.

value: colon cancer

tag: sirna

value: control


title: CD44 siRNA, 1

description: Gene expression data from HCT116 cells transfected with CD44 siRNA.

source_name: HCT116 cells, CD44 siRNA


title: Chicken 8A vs 11B Cy35


title: CD44 siRNA, 2


title: Chicken 1A vs 10B Cy53

source_name: Liver from CTS bird 10B

source_name: Liver from control bird 1A


title: beta-cells_non-diabetic condition_donor2

source_name: human beta-cells_non-diabetic


title: Splenic rat Ly49s3+ NK cells

status: Public on Mar 18 2010

city: Oslo

first: Marit

last: Inngjerdingen

address: Sognsvannsveien 20

department: Institute of Immunology

country: Norway

institute: Oslo University Hospital, Rikshospitalet and University of Oslo

description: Gene expression in Ly49s3+ NK cells.

hyb_protocol: Three µg of total RNA were used to generate cRNA, subsequently hybridized to the Affymetrix GeneChip® Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The array was scanned using GeneArray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: Splenic Ly49s3+ NK cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Tri Reagent extraction of total RNA was performed according to the manufacturer's instructions (Sigma-Aldrich).

treatment_protocol: Mononuclear spleen cells prepared by Lymphoprep separation, and enriched for NK cells by precoating cells with anti-TCRαβ, anti-CD68, anti-CD5, anti-Igκ-chain, and anti-CD45RA supernatants followed by depletions with anti-mouse IgG-coated Dynabeads (Invitrogen Dynal). The enriched population was stained with antibodies towards rat CD3, NKR-P1A, Ly49s3, and NKR-P1B. Single-positive NKR-P1B+ or Ly49s3+ NK cells (CD3-NKR-P1A+) were sorted in a FACS-Diva (BD Biosciences), and the purity of sorted cells was above 90%. Cells were lysed in Tri Reagent (Sigma-Aldrich) for total RNA harvest.

tag: strain

tag: age

value: 8-12 weeks

value: spleen

value: Ly49s3+ NK cells


title: Chicken 1A vs 10B Cy35


title: wibr3_20A-wibr3_5

description: c38 incubated in 5% oxygen or 20% oxygen acutely


title: Chicken 4A vs 12B Cy35


title: Splenic rat NKR-P1B+ NK cells

description: Gene expression in NKR-P1B+ NK cells.

source_name: Splenic NKR-P1B+ NK cells

value: NKR-P1B+ NK cells


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_sample from sample from subject 9F10, sex= Male, infection= Mock, day= 0

hyb_protocol: hybridized at a constant temperature of 45◦C for approximately 16 hours

scan_protocol: GeneChips were scanned using the standard Affymetrix GeneChip Scanner

data_processing: The data were analyzed with EC using MAS5

organism: Macaca fascicularis

label_protocol: All tonsil swab RNA (average 4.2 μg per swab) was used for cDNA synthesis as described (2). In vitro transcription labeling with biotinylated UTP and CTP was performed according to the manufacturer’s recommendations (Enzo Diagnostics) for 10 h at 37 °C. Amplified cRNA was purified as described above. The quality and size of cRNA was verified with an Agilent 2100 Bioanalyzer System (Agilent Technologies)

growth_protocol: GAS strain MGAS5005 (GenBank CP000017), genetically representative of contemporary serotype M1 strains, was grown as previously described (11, 12)

extract_protocol: Tonsil swabs were immediately frozen on dry ice.The swabs contained a mixture of epithelial and inflammatory cells, but microscopic examination indicated that the majority of cells were epithelial cells. Host cells were lysed using the FastPrep FP 120 system and Lysing Matrix D Tube (MP Biomedicals) with 500 μL phenol:chloroform (5:1) at pH 4.5 (Applied Biosystems), 500 μL CRSR-”GREEN” (MP Biomedicals), and 300 μL of 5 mM arunocarboxylic acid. RNA was purified in 96-well format as described (1). RNA quantity was determined with an Agilent 2100 Bioanalyzer System (Agilent Technologies)

treatment_protocol: Infection of cynomolgus macaques and sample preparation has been described extensively (11, 12). Briefly, animals were GAS-culture negative and had negligible antistreptolysin O titers, indicating no recent history of GAS exposure. Twenty animals were subjected to a mock-inoculation protocol (PBS only) for 5 weeks, rested for 4weeks, and inoculated in the upper respiratory tractwith 107 CFUsMGAS5005. Blood, saliva, and throat swabs were collected on days 0, 1, 2, 4, 7, 9, 16, 23, 32, 45, 58, 72, and 86.Only the first nine time-points were studied because specimens collected during days 0 to 32 had matching comparator specimens from the mock-infection protocol. Thirty-two clinical and laboratory parameters were measured by the same veterinarian during mock and infection periods

tag: monkey

value: cynomolgus

tag: subject id

value: Male

tag: infection type

value: Mock

tag: time point (day)


description: Gene expression data from_sample from sample from subject 9F08, sex= Male, infection= Mock, day= 2


title: Control siRNA, 1

tag: cell type


description: Gene expression data from_sample from sample from subject 9F06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 9F05, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 9F03, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 9F02, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 9E10, sex= Male, infection= GAS, day= 0

value: GAS


description: Gene expression data from_sample from sample from subject 9E08, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 9F09, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 9F07, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 9E06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 9C06, sex= Female, infection= Mock, day= 7

value: Female


description: Gene expression data from_sample from sample from subject 9C09, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 9C10, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 9C07, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 9C05, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 9E07, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 9E05, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 9E09, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 9C08, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 9E04, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 9F04, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 9C04, sex= Female, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 9E02, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 9E03, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 9C03, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 9C02, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 9B09, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 9B10, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 9B07, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 9B08, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 9B04, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 9B06, sex= Female, infection= GAS, day= 7


title: wibr1_20-wibr1_5

description: c22 incubated in 5% or 20% oxygen


description: Gene expression data from_sample from sample from subject 8F10, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 9B02, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 9B03, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 9B05, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 8F08, sex= Female, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 8F05, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 8F07, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 8F09, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 8F04, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 8F06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 8E06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 8F03, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 8E08, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 8F02, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 8E10, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 8E04, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 8E07, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 8E05, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 8C10, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 8E09, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 8E03, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 8C09, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 8E02, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 8C08, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 8C07, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 8C03, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 8C05, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 8B07, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 8C04, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 8C06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 8B06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 8C02, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 8B04, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 8B10, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 8B05, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 8B09, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 8B08, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 8B03, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 8B02, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 7F10, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 7F07, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 7E10, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 7F02, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 7F06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 7F09, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 7F05, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 7E09, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 7F04, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 7F03, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 7F08, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 7E08, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 7E07, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 7E04, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 7E06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 7E02, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 7C10, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 7E05, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 7C07, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 7B08, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 7E03, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 7C09, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 7C05, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 7B10, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 7C03, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 7C06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 7C04, sex= Female, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 7C02, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 7C08, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 7B06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 7B07, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 7B05, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 7B09, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 6F09, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 7B04, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 6F08, sex= Female, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 6F06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 7B02, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 6F05, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 6F04, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 7B03, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 6F02, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 6F07, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 6F03, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 6E10, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 6E08, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 6E07, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 6E03, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 6B10, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 6C10, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 6E05, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 6C06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 6E02, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 6E04, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 6B09, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 6C03, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 6C07, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 6C08, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 6C09, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 6E09, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 6B08, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 6C02, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 6C05, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 6C04, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 6F10, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 6B03, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 6B04, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 6B07, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 6B06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 6B05, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 6B02, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 5F09, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 6E06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 5F10, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 5F06, sex= Female, infection= Mock, day= 7