title: kernel_development_1DAP_to_35DAP_rep1_B

description: Gene expression data from maize kernel


title: Double knockout, biol rep 2 (430A)

status: Public on Apr 09 2008

type: RNA

city: San Francisco

first: Holger

last: Willenbring

state: CA

address: 35 Medical Center Way

country: USA

institute: UCSF

description: Global gene expression in adult mouse liver sample.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hours at 45 degree Celsius on MG 430A 2.0 or MG 430 2.0 GeneChip arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed in the Affymetrix GCOS version 1.4.0.036 software using the Microarray Suite version 5.0 (MAS 5.0) algorithm, and global scaling was used as the normalization method. The mean target intensity of each array was set to 350 and alpha1 and alpha2 were set to 0.05 and 0.065, respectively.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver, Fah, p21 knockout mouse off NTBC

label_protocol: Standard one cycle cDNA synthesis followed by in vitro transcription (Affymetrix) to produce biotinylated cRNA.

growth_protocol: Adult mice 10 weeks of age were used for this study.

extract_protocol: RNA isolation with RNeasy (Qiagen) from 10 mg of liver tissue stabilized with RNAlater.

treatment_protocol: Mice were either kept on NTBC or treated with water 14 days before liver analysis.

tag: Fah, p21 knockout, male, 10 weeks old, 129 strain


title: kernel_development_25DAP_to_15DAP_rep1_B

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from maize kernel

hyb_protocol: Hybridization and post hybridization wash were performed according to the protocal of the Maize Oligo Array Project (http://www.maizearray.org/).

scan_protocol: Hybridized slides were scanned by a Genepix 4000B (Axon, USA).

data_processing: Raw data from microarray hybridization, exported from GenePix suites 6.0 (Axon, USA), was imported into LIMMA with annotation and spot types. Spots with a negative flag value were assigned a weight of 0.1 in the subsequent analysis. Background-subtracted signal intensities were normalized using a two-step normalization: print-tip group loss (within-array normalization) and then between-array scale normalization.

organism: Zea mays

label_protocol: Cy5-cDNA were prepared according to the recommendations of the Maize Oligo Array Project (http://www.maizearray.org/).

growth_protocol: Natural conditions, growing season begins from May to September, on the China Agricultural University research farm in Beijing, China.

extract_protocol: Total RNA was extracted using a modified hot phenol method.

tag: Zea mays, Kernel, Development

label_protocol: Cy3-cDNA were prepared according to the recommendations of the Maize Oligo Array Project (http://www.maizearray.org/).


title: Normal, biol rep 3 (430A)

source_name: liver, Fah knockout mouse on NTBC

tag: Fah knockout, male, 10 weeks old, 129 strain


title: kernel_development_25DAP_to_15DAP_rep2_B

description: Gene expression data from maize kernel


title: kernel_development_5DAP_to_1DAP_rep2_A

description: Gene expression data from maize kernel


title: Danio_Brain_Starved_2 (X2BS2)

city: Moscow

first: Robert

middle: Edward

last: Drew

state: ID

address: Life Sciences South Rm 252

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.  This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: All analyses of microarray data were conducted using Bioconductor for R (www.R-project.org).  Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues.  The microarray data were filtered as described by Robison et al. (2008).  Filtered probesets were then normalized using Robust Multiarray Average (RMA).

label: Biotin

organism: Danio rerio

source_name: Brain

label_protocol: For each array, up to 10 ug of total RNA were converted to cDNA.  Biotinylated cRNA was then produced in vitro using the GeneChip Expression 3' amplification one-cycle target labeling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA) following the manufacturer's protocol.  After extraction, RNA from three fish was pooled for each tank for analysis.

treatment_protocol: Groups of eight females of the same age were randomly assigned to each of twelve 3-L tanks (10 cm wide x 15 cm tall x 25 cm deep) arranged on the same shelf of a flow-through rearing system.  Test tanks were assigned to starved or control treatments in an alternating manner so that treatments were uniformly distributed across fish ages and tank location.  Fish in the starved treatment received no food for 21 days, while fish in the control treatment continued to be fed to apparent satiety three times daily.

tag: Strain

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:8172005, Start date:432006, Mean Mass:266.2, Mean Length:24.2, Mean SGR:-0.586, Mean GSI:0.046


title: kernel_development_15DAP_to_10DAP_rep2_B

description: Gene expression data from maize kernel


title: kernel_development_15DAP_to_10DAP_rep1_B

description: Gene expression data from maize kernel


title: Danio_Brain_Starved_1 (X2BS1)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10252005, Start date:432006, Mean Mass:265.3, Mean Length:25.7, Mean SGR:-0.907, Mean GSI:0.055


title: Danio_Brain_Control_2 (X2BC2)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10182005, Start date:432006, Mean Mass:422.0, Mean Length:26.5, Mean SGR:0.207, Mean GSI:0.105


title: kernel_development_10DAP_to_5DAP_rep2_B

description: Gene expression data from maize kernel


title: Danio_Brain_Control_4 (X2BC4)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9232005, Start date:432006, Mean Mass:631.5, Mean Length:28.8, Mean SGR:0.232, Mean GSI:0.152


title: kernel_development_5DAP_to_1DAP_rep1_B

description: Gene expression data from maize kernel


title: Normal, biol rep 2 (430A)

source_name: liver, wildtype mouse on NTBC

tag: wildtype, male, 10 weeks old, 129 strain


title: kernel_development_5DAP_to_1DAP_rep2_B

description: Gene expression data from maize kernel


title: SCG from P0 NGF/Bax double null mouse sample 2 moe430A

city: Baltimore

first: David

middle: D

last: Ginty

state: MD

address: 725 N. Wolfe St.

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description: standard protocol was applied by JHMI microarray core facility

hyb_protocol: 16 hour at 45C with rotation(60RPM) as described by affymetrix in their  gene chip expression analysis technical manual, 2004.

scan_protocol: Using affymetrix gene chip scanner 3000 7G and default parameters described by the manufacturer in their gene chip expression analysis technical manual 2004

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer's specifications. Global scaling of images to target intensity of 150.

label_protocol: One round amplification protocol for total RNA following Affymetrix specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT Kit. (www.affymetrix.com, genchip expression analysis, technical manual, 2003)

extract_protocol: RNA was isolated using the RNeasy kit (Qiagen)

tag: age

tag: superior cervical ganglia


title: SCG from P0 bax/ngf double null mouse sample 1 moe430A

source_name: superior cervical ganglia from bax/ngf double null mouse


title: Danio_Brain_Control_3 (X2BC3)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:8172005, Start date:432006, Mean Mass:452.8, Mean Length:26.4, Mean SGR:0.148, Mean GSI:0.123


title: Danio_Brain_Control_1 (X2BC1)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10182005, Start date:432006, Mean Mass:410.3, Mean Length:25.7, Mean SGR:0.214, Mean GSI:0.119


title: SCG from P0 bax null mouse sample 2 moe430A

source_name: Dissected superior cervical ganglia from P0 bax null mice


title: kernel_development_10DAP_to_5DAP_rep1_B

description: Gene expression data from maize kernel


title: Normal, biol rep 1 (430A)

source_name: liver, wildtype mouse on water


title: SCG from P0 bax null mouse sample 1 moe430A


title: SCG from P0 Bax null mouse sample 2 moe430B


title: mock Hek293 FLAG-Ago2 IP (4)

status: Public on Apr 08 2008

city: Stanford

first: Daniel

last: Hogan

address: 279 Campus Dr B439

institute: Stanford University

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67131.gif
Measurement: mass(absolute) 0 ug

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 15:19:14; Parameter PMT Volts = 630; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 269419; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 15:19:14; Parameter PMT Volts = 720; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 634329; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.38; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

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)

organism: Homo sapiens

source_name: amplifed RNA from HEK293T cell lysate

label_protocol: not provided

extract_protocol: not provided

tag: amplifed RNA from HEK293T cell lysate

source_name: amplified RNA after FLAG-Ago2 affinity purification

tag: Measurement

value: mass(absolute) 0 ug


title: Ago2 Hek293 FLAG-Ago2 Expression (7)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76449.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 17:25:35; Parameter PMT Volts = 298; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43592; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 17:25:35; Parameter PMT Volts = 342; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43592; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.01; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: UNIVERSAL REFERENCE

tag: UNIVERSAL REFERENCE

source_name: amplified RNA from HEK293T cells

tag: amplified RNA from HEK293T cells


title: mock Hek293 FLAG-Ago2 IP (14)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69834.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.75; Parameter Scan Time = 14:45:32; Parameter PMT Volts = 482; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24556; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.31; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.75; Parameter Scan Time = 14:45:32; Parameter PMT Volts = 474; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24556; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: amplified RNA from HEK293T cell lysate

tag: amplified RNA from HEK293T cell lysate

tag: amplified RNA after FLAG-Ago2 affinity purification


title: mock Hek293 FLAG-Ago2 IP (6)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67133.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.11; Parameter Scan Time = 17:25:07; Parameter PMT Volts = 630; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 269469; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.11; Parameter Scan Time = 17:25:07; Parameter PMT Volts = 720; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 634379; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (10)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67816.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.44; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 451; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 5981; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.50; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.44; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 452; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 5981; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP +miR-124 (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69827.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 12:54:33; Parameter PMT Volts = 453; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24446; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 12:54:33; Parameter PMT Volts = 448; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24445; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

value: concentration(absolute) 60 nM


title: Ago2 Hek293 FLAG-Ago2 IP +miR-1 (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69744.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.75; Parameter Scan Time = 18:53:14; Parameter PMT Volts = 441; Parameter Scan Date = 2006-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 22293; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.42; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.75; Parameter Scan Time = 18:53:14; Parameter PMT Volts = 431; Parameter Scan Date = 2006-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 22292; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.38; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: amplified RNA after affinity purification


title: mock Hek293 FLAG-Ago2 IP (3)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67130.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 15:01:06; Parameter PMT Volts = 630; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 269401; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 15:01:06; Parameter PMT Volts = 720; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 634311; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.39; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 Expression (5)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76437.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 14:36:28; Parameter PMT Volts = 308; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43423; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 14:36:28; Parameter PMT Volts = 336; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43423; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.02; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (5)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67132.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 7520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 15:35:04; Parameter PMT Volts = 630; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 269434; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.67; Parameter Scan Time = 15:35:04; Parameter PMT Volts = 720; Parameter Scan Date = 2006-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 634344; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.37; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: aRNA lysate

tag: aRNA lysate

source_name: aRNA after affinity purification

tag: aRNA after affinity purification


title: mock Hek293 FLAG-Ago2 IP (11)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67824.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 18:51:45; Parameter PMT Volts = 453; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6377; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 18:51:45; Parameter PMT Volts = 488; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6377; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (7)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69750.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 19:59:39; Parameter PMT Volts = 463; Parameter Scan Date = 2006-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 22359; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 19:59:39; Parameter PMT Volts = 460; Parameter Scan Date = 2006-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 22359; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.36; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

value: mass(absolute) 10 ug


title: mirna Ago2 ip #3

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72689.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 21:08:27; Parameter PMT Volts = 451; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17842; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 21:08:27; Parameter PMT Volts = 426; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17842; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: Ago2 total RNA

tag: Ago2 total RNA

source_name: Ago2 ip RNA

tag: Ago2 ip RNA


title: mock Hek293 FLAG-Ago2 IP (13)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69823.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.38; Parameter Scan Time = 13:16:53; Parameter PMT Volts = 459; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24468; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.38; Parameter Scan Time = 13:16:53; Parameter PMT Volts = 463; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24468; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.42; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mirna Ago2 ip #1

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72687.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:52:50; Parameter PMT Volts = 383; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17827; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:52:50; Parameter PMT Volts = 396; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17827; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 3.04; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (4)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67826.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 18:01:25; Parameter PMT Volts = 460; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6327; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 18:01:25; Parameter PMT Volts = 489; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6327; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 Expression (6)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76439.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.94; Parameter Scan Time = 15:59:53; Parameter PMT Volts = 294; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43506; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.94; Parameter Scan Time = 15:59:53; Parameter PMT Volts = 327; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43506; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-1Expression (3)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76445.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.81; Parameter Scan Time = 16:27:30; Parameter PMT Volts = 314; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.81; Parameter Scan Time = 16:27:30; Parameter PMT Volts = 322; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.00; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (9)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67815.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.56; Parameter Scan Time = 12:39:24; Parameter PMT Volts = 456; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6005; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.49; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.56; Parameter Scan Time = 12:39:24; Parameter PMT Volts = 461; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6005; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mirna Ago2 vs C #3

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72686.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:39:05; Parameter PMT Volts = 424; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17813; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:39:05; Parameter PMT Volts = 473; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17813; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: mock total RNA

tag: mock total RNA


title: mirna Ago2 vs C #1

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72693.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 160, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 21:48:51; Parameter PMT Volts = 578; Parameter Scan Date = 2007-02-20; Parameter Pixel Size = 10; Parameter Laser on time = 58386; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 21:48:51; Parameter PMT Volts = 603; Parameter Scan Date = 2007-02-20; Parameter Pixel Size = 10; Parameter Laser on time = 58385; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mirna Ago2 vs C #2

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72685.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:25:21; Parameter PMT Volts = 427; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17799; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 20:25:21; Parameter PMT Volts = 492; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17799; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.98; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-1Expression (4)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76453.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.75; Parameter Scan Time = 17:53:08; Parameter PMT Volts = 290; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43620; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.75; Parameter Scan Time = 17:53:08; Parameter PMT Volts = 339; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.98; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (7)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67813.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 23:11:41; Parameter PMT Volts = 462; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.19; Parameter Scan Time = 23:11:41; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (12)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67829.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 11:45:20; Parameter PMT Volts = 610; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 286666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 11:45:20; Parameter PMT Volts = 650; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 651576; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (8)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67814.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.38; Parameter Scan Time = 15:29:48; Parameter PMT Volts = 437; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6175; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.38; Parameter Scan Time = 15:29:48; Parameter PMT Volts = 466; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6175; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67812.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.50; Parameter Scan Time = 16:20:22; Parameter PMT Volts = 442; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6226; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.50; Parameter Scan Time = 16:20:22; Parameter PMT Volts = 462; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6226; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (5)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69812.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.63; Parameter Scan Time = 14:01:08; Parameter PMT Volts = 480; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24512; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.63; Parameter Scan Time = 14:01:08; Parameter PMT Volts = 457; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24512; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.42; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-1Expression (2)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76443.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 15:04:13; Parameter PMT Volts = 304; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43451; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 15:04:13; Parameter PMT Volts = 325; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43450; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.01; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP +miR-124 (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72575.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.69; Parameter Scan Time = 14:23:20; Parameter PMT Volts = 491; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.69; Parameter Scan Time = 14:23:20; Parameter PMT Volts = 453; Parameter Scan Date = 2006-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 24534; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mirna Ago2 ip #4

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72690.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 21:22:09; Parameter PMT Volts = 404; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17856; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 21:22:09; Parameter PMT Volts = 454; Parameter Scan Date = 2007-03-12; Parameter Pixel Size = 10; Parameter Laser on time = 17856; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader; Parameter Laser Power = 2.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-124 Expression (2)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76441.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 15:31:40; Parameter PMT Volts = 299; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43479; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.06; Parameter Scan Time = 15:31:40; Parameter PMT Volts = 333; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43478; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.00; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID, replicate 2

status: Public on Apr 07 2008

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Embryonic Drosophila cells, Kc167 cells

hyb_protocol: Samples were hybridized to the arrays in a volume of approximately 30 ul (5 mM TRIS, 0.5 mM EDTA, 3X SSC). The following competitors were added: 25 ug DpnI-digested Dam-fusion plasmid DNA, 100 ug yeast tRNA, 20 ug poly (dA-dT). Arrays were washed in four subsequent steps. The respective washing buffers were: 1X SSC/0.03% SDS (arrays were submerged once), 1XSSC (arrays were submerged 15 times), 0.2XSSC (20 minutes), 0.05XSSC (10 minutes).

scan_protocol: Microarrays are scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at a variable PMT (0-100%) for each channel (Red or Green), a variable resolution (5 or 10 um per pixel) and a suitable scan area.

data_processing: After removal of low quality, redundant or ambiguous proves, hybridization data of 9,993 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Su(var)3-7-Dam

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Su(var)3-7 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Su(var)3-7-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam (REFERENCE)


title: Mock Hek293 Expression (2)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72491.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 810, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.30; Parameter Scan Time = 13:52:03; Parameter PMT Volts = 500; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 337040; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.30; Parameter Scan Time = 13:52:03; Parameter PMT Volts = 520; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 701976; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67811.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.56; Parameter Scan Time = 16:45:39; Parameter PMT Volts = 462; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6251; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.56; Parameter Scan Time = 16:45:39; Parameter PMT Volts = 497; Parameter Scan Date = 2006-04-01; Parameter Pixel Size = 10; Parameter Laser on time = 6251; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-124 Expression (1)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76435.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.94; Parameter Scan Time = 14:08:58; Parameter PMT Volts = 320; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43396; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.94; Parameter Scan Time = 14:08:58; Parameter PMT Volts = 329; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43395; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.02; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 + miR-1Expression (1)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76433.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 13:41:25; Parameter PMT Volts = 307; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43368; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.88; Parameter Scan Time = 13:41:25; Parameter PMT Volts = 339; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43368; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.02; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP +miR-1 (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69785.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.38; Parameter Scan Time = 14:00:28; Parameter PMT Volts = 483; Parameter Scan Date = 2006-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 22013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.38; Parameter Scan Time = 14:00:28; Parameter PMT Volts = 429; Parameter Scan Date = 2006-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 22013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing H1-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length H1 was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: H1-Dam (EXPERIMENTAL)


title: Ago2 Hek293 FLAG-Ago2 IP +miR-124 (3)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72516.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 8560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 17:57:53; Parameter PMT Volts = 560; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 337949; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 17:57:53; Parameter PMT Volts = 480; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 702885; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.30; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Mock Hek293 Expression (1)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72490.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 810, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.08; Parameter Scan Time = 13:29:10; Parameter PMT Volts = 500; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 337017; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.08; Parameter Scan Time = 13:29:10; Parameter PMT Volts = 520; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 701954; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 IP (6)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69784.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1030, 3600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.94; Parameter Scan Time = 13:38:20; Parameter PMT Volts = 468; Parameter Scan Date = 2006-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 21991; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.32; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.94; Parameter Scan Time = 13:38:20; Parameter PMT Volts = 452; Parameter Scan Date = 2006-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 21990; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Mock Hek293 Expression (3)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72492.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 250, 1940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.44; Parameter Scan Time = 14:17:19; Parameter PMT Volts = 352; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58808; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.44; Parameter Scan Time = 14:17:19; Parameter PMT Volts = 359; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58807; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.43; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (2)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67129.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 6760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.72; Parameter Scan Time = 19:37:21; Parameter PMT Volts = 620; Parameter Scan Date = 2006-02-12; Parameter Pixel Size = 10; Parameter Laser on time = 267829; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.72; Parameter Scan Time = 19:37:21; Parameter PMT Volts = 650; Parameter Scan Date = 2006-02-12; Parameter Pixel Size = 10; Parameter Laser on time = 632739; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: amplified RNA from HEK293 cell lysate

tag: amplified RNA from HEK293 cell lysate


title: Ago2 Hek293 FLAG-Ago2 IP (8)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72512.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 16:58:23; Parameter PMT Volts = 580; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 337889; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 16:58:23; Parameter PMT Volts = 480; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 702826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 Expression (1)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72487.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 250, 1940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.69; Parameter Scan Time = 13:03:17; Parameter PMT Volts = 334; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.53; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.69; Parameter Scan Time = 13:03:17; Parameter PMT Volts = 333; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58733; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: mock Hek293 FLAG-Ago2 IP (1)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67128.gif
Measurement: mass(absolute) 0 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 20:16:04; Parameter PMT Volts = 630; Parameter Scan Date = 2006-02-12; Parameter Pixel Size = 10; Parameter Laser on time = 267868; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 20:16:04; Parameter PMT Volts = 670; Parameter Scan Date = 2006-02-12; Parameter Pixel Size = 10; Parameter Laser on time = 632778; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

source_name: amplified RNA from Hek293T cell lysate

tag: amplified RNA from Hek293T cell lysate


title: Ago2 Hek293 FLAG-Ago2 IP +miR-1 (3)

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72513.gif
Measurement: concentration(absolute) 60 nM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 11680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 17:15:23; Parameter PMT Volts = 580; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 337906; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 17:15:23; Parameter PMT Volts = 480; Parameter Scan Date = 2007-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 702843; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.27; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Ago2 Hek293 FLAG-Ago2 Expression (3)

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72489.gif
Measurement: mass(absolute) 10 ug

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 250, 1940; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.25; Parameter Scan Time = 13:56:17; Parameter PMT Volts = 336; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58787; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.55; Parameter Scan Power = 80; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.25; Parameter Scan Time = 13:56:17; Parameter PMT Volts = 342; Parameter Scan Date = 2007-02-25; Parameter Pixel Size = 10; Parameter Laser on time = 58786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.46; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 80; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, Su(var)3-7 DamID, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Adult lungs (Mu11KA)

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Avenue Box 850

department: Pediatrics

institute: University of Rochester Medical Center

description: Lung

hyb_protocol: Twenty-five micrograms of each biotin-labeled cRNA was hybridized to an Affymetrix Mu11K sub A and B chip according to the manufacturer's protocol. Four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) were included in each hybridization reaction to verify consistent hybridization efficiency. Hybridization is carried out according the Affymetrix GeneChip® Manual. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Standard Affymetrix protocol

data_processing: Chips were scanned and the intensity of signal was computed using GeneChip Analysis Suite version 3.3 (Affymetrix, Santa Clara, CA). All chip intensities were scaled to an average of 1,500 units for comparison (inter-experiment scaling) purposes.

source_name: normal lung

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: Ten micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of three individual lungs. This step was performed to minimize both biologic variability and the number of microarrays necessary to generate informative data. After pooling, RNA was re-purified using Qiagen purification kits (Valencia, CA). Target cRNA was synthesized according to manufacturer's protocol. Briefly, total RNA was reverse transcribed into a complete cDNA library (SuperScript Choice kit; Invitrogen) using a T7/T24 primer (Genset Corp., La Jolla, CA). This cDNA was subsequently in vitro transcribed into biotin-labeled cRNA (High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The resulting cRNA was fragmented and assessed for quality by gel electrophoresis.  Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols

tag: Strain

value: Swiss webster, Age:adult,Tissue:normal lung