title: CA1122 - DNA; A1552 vs. VCO139-Kan

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66046.gif
Strain Name: VCO139-Kan (donor DNA strain) - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 27400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 39.75; Parameter Scan Time = 14:46:06; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 59321; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 39.75; Parameter Scan Time = 14:46:06; Parameter PMT Volts = 720; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 205246; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.34; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM18504_technical_rep_1

status: Public on Mar 14 2007

type: RNA

city: Seattle

first: Joshua

middle: M

last: Akey

state: WA

address: 1705 NE Pacific St

department: Genome Sciences

country: USA

institute: University of Washington

description: Gene expression data from B lymphoblastoid cell lines grown according to Coriell instructions.

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the UW Center for Expression Arrays.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: B lymphoblastoid cell line

label_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Human Focus Array.

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

tag: YORUBA


title: GM18522_technical_rep_2


title: GM18504_technical_rep_2


title: CA1060 - DNA; A1552 vs. AIIISGC#3

status: Public on Apr 25 2007

type: genomic

city: Stanford

first: Melanie

last: Blokesch

state: CA

address: 279 Campus Drive

department: Medical School

institute: Stanford University

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66065.gif
Strain Name: AIIISGC#3 - replicate

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 27880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.59; Parameter Scan Time = 12:24:02; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59522; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.59; Parameter Scan Time = 12:24:02; Parameter PMT Volts = 730; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 205447; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch

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

molecule: genomic DNA

organism: Vibrio cholerae

label_protocol: not provided

extract_protocol: not provided


title: CA1136 - DNA; A1552 vs. AIIISGC#1

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66060.gif
Strain Name: AIIISGC#1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 430, 27860; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.26; Parameter Scan Time = 11:45:10; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.26; Parameter Scan Time = 11:45:10; Parameter PMT Volts = 730; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 205408; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM18522_technical_rep_1


title: GM19138_technical_rep_2


title: CB452- DNA; A1552 vs. ApO139#2

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68804.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1170, 27440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 42.82; Parameter Scan Time = 11:44:06; Parameter PMT Volts = 470; Parameter Scan Date = 2006-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 61990; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 42.82; Parameter Scan Time = 11:44:06; Parameter PMT Volts = 690; Parameter Scan Date = 2006-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 207917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM19138_technical_rep_1


title: CA1123 - DNA; A1552 vs. VCO139-Kan

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66047.gif
Strain Name: VCO139-Kan (donor DNA strain) - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 27400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 39.90; Parameter Scan Time = 14:52:38; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 59328; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 39.90; Parameter Scan Time = 14:52:38; Parameter PMT Volts = 730; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 205253; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.34; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: CA1137 - DNA; A1552 vs. AIIISGC#1

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66061.gif
Strain Name: AIIISGC#1 - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 430, 27860; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.30; Parameter Scan Time = 11:50:11; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59489; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.30; Parameter Scan Time = 11:50:11; Parameter PMT Volts = 720; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 205414; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: CA1125 - DNA; A1552 vs. AIISGC#1

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66049.gif
Strain Name: AIISGC#1  - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 370, 27450; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.12; Parameter Scan Time = 15:07:16; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 59343; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.12; Parameter Scan Time = 15:07:16; Parameter PMT Volts = 720; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 205267; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.35; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: CA1057- DNA; A1552 vs. AIIISGC#2

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66062.gif
Strain Name: AIIISGC#2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1150, 27970; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.31; Parameter Scan Time = 11:57:51; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59497; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.31; Parameter Scan Time = 11:57:51; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59497; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: CA1058 - DNA; A1552 vs. AIIISGC#2

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66063.gif
Strain Name: AIIISGC#2  - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 990, 27950; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.42; Parameter Scan Time = 12:07:35; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59507; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.42; Parameter Scan Time = 12:07:35; Parameter PMT Volts = 720; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 205432; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: CA1108 - DNA; A1552 vs. VCO139-Kan

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66074.gif
Strain Name: VCO139-Kan (donor DNA strain) - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 27330; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.15; Parameter Scan Time = 11:09:16; Parameter PMT Volts = 550; Parameter Scan Date = 2005-12-07; Parameter Pixel Size = 10; Parameter Laser on time = 59192; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.15; Parameter Scan Time = 11:09:16; Parameter PMT Volts = 690; Parameter Scan Date = 2005-12-07; Parameter Pixel Size = 10; Parameter Laser on time = 205117; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.35; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM18507_technical_rep_1


title: GM18507_technical_rep_2


title: CA1059 - DNA; A1552 vs. AIIISGC#3

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66064.gif
Strain Name: AIIISGC#3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 27880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.44; Parameter Scan Time = 12:14:32; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 59513; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.44; Parameter Scan Time = 12:14:32; Parameter PMT Volts = 730; Parameter Scan Date = 2005-12-10; Parameter Pixel Size = 10; Parameter Laser on time = 205438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM18501_technical_rep_2


title: GM10851_technical_rep_1

tag: CEPH


title: GM06995_technical_rep_2


title: GM10851_technical_rep_2


title: GM10845_technical_rep_2


title: GM07349_technical_rep_1


title: GM18871_technical_rep_1


title: GM07349_technical_rep_2


title: GM07029_technical_rep_1


title: GM18871_technical_rep_2


title: GM06995_technical_rep_1


title: GM10845_technical_rep_1


title: GM10856_technical_rep_2


title: GM18501_technical_rep_1


title: GM07029_technical_rep_2


title: P3_AS_HeLaS3_RNuP+_C89_B1

status: Public on May 25 2007

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

address: 3380 Central Expressway

institute: Affymetrix, Inc.

description: See publication for details

hyb_protocol: See publication for details

scan_protocol: See publication for details

data_processing: See publication for details

molecule: polyA RNA

source_name: Total Nuclear RNA from HeLa cell line

label_protocol: See publication for details

extract_protocol: Long RNA protocol - see publication for details

tag: See publication for details


title: GM18859_technical_rep_2


title: GM10860_technical_rep_1


title: GM18516_technical_rep_2


title: GM10857_technical_rep_1


title: GM18516_technical_rep_1


title: GM10856_technical_rep_1


title: GM10857_technical_rep_2


title: GM10860_technical_rep_2


title: CA1129 - DNA; A1552 vs. AIISGC#3

description:
Simple annotation: Genome comparison, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66053.gif
Strain Name: AIISGC#3  - replicate

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 380, 27120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Melanie,,Blokesch 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 = 40.62; Parameter Scan Time = 16:03:56; Parameter PMT Volts = 530; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 59398; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch 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 = 40.62; Parameter Scan Time = 16:03:56; Parameter PMT Volts = 730; Parameter Scan Date = 2005-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 205323; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Melanie,,Blokesch


title: GM18859_technical_rep_1


title: H3K18Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 3

status: Public on Mar 01 2007

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against H3K18Ac and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using H3K18Ac antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: GM06990 immunoprecipitated chromatin

source_name: Input Chromatin GM06990 cells.

extract_protocol: input chromatin

value: GM06990 input chromatin


title: H3K18Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 2 ENC1876

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me2 antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: NimbleGen

source_name: Input DNA from GM06990 cells

tag: Input DNA from GM06990 cells


title: H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 1 ENC1874

tag: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me2 antibody


title: H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 4 ENC1812


title: H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 3 ENC1811


title: p300(C-20) GM06990 RenLab ENCODE PCR tiling array replicate 3 ENC1604

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using p300(C-20) antibody


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 7 ENC1586

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody


title: H3K18Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 2


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 6 ENC1556

tag: Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 5 ENC1550


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 4 ENC1530


title: H3K27Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against H3K27Ac and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using H3K27Ac antibody


title: RNAPII(8WG16) GM06990 ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against RNAPII(8WG16) and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using RNAPII(8WG16) antibody


title: H3K4me2 GM06990 RenLab ENCODE PCR tiling array replicate 5 ENC1813


title: RNAPII(8WG16) GM06990 ENCODE NimbleGen hg17 tiling array replicate 2


title: p300(C-20) GM06990 RenLab ENCODE PCR tiling array replicate 2 ENC1603

tag: Chromatin immunoprecipitated DNA from GM06990 cells using p300(C-20) antibody


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 1 ENC1526


title: CTCF GM06990 ENCODE NimbleGen hg17 tiling array replicate 3

description: Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using CTCF antibody


title: p300(C-20) GM06990 RenLab ENCODE PCR tiling array replicate 1 ENC1423


title: H3K4me3 GM06990 ENCODE NimbleGen hg17 tiling array replicate 2

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3 and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me3 antibody


title: TAFII p250 (6B3) GM06990 ENCODE NimbleGen hg17 tiling array replicate 1

description: Chromatin immunoprecipitation was performed using antibodies against TAFII p250 (6B3) and formaldehyde crosslinked chromatin from GM06990 cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.


title: Stretch sample 121

status: Public on Jan 26 2007

city: Leicester

first: Jerry

middle: A

last: Styles

state: Leicestershire

address: Robert Kilpatrick Building, Univ. Leicester

department: Cancer Studies and Molecular Medicine

country: United Kingdom

institute: University of Leicester

description:
Changes in gene expression were analyzed using three cDNA arrays, consisting of pairs of arrays forward labeled with Cy5
and Cy3 dyes, hybridizing RNA from stretched fibroblasts against controls. All controls were pooled.

scan_protocol: Array slides were scanned using an Axon A300 scanner at the MRC Toxicology Unit, Leicester, at excitation wavelengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes respectively

data_processing:
Pixel intensity for hybridisation was determined using GenePix Pro 3.0.6 software [Axon Instruments,
Union City, CA, USA]. For dual label hybridizations there is imbalance in the measured intensity between the fluorescent channels, due to different intensities of fluorescence between equal quantities of bound dyes and also non-specific binding of the probes leading to background fluorescence. To correct for imbalance in the measured fluorescent intensities between the two fluorescent channels the data were normalized. Global normalization in which the fluorescence levels of all features are uniformly adjusted (Gant et al., 2005). The data from forward and reverse labelled arrays were normalized, condensed and t tested to determine differential gene expression (Zhang & Gant, 2004) using statistical software (NorTT) hosted by the MRC Toxicology
Unit, Leicester. The normalization procedure eliminates features that are morphologically abnormal, where there is failure of hybridization or where there is only fluorescence in one channel. Genes having a p < 0.05 in a two-tailed t test were regarded as being significantly changed in expression

source_name: Human pelvic fibroblasts

growth_protocol:
Cell culture:
The specimens were placed immediately in a cold Hanks’ Balanced Salt Solution, HBSS, (Gibco, Paisley, Scotland, UK) and transferred to the tissue culture laboratory for immediate processing. They were minced into 1 mm3 pieces, the tissue fragments were treated with Collagenase type I (Gibco, Paisley, Scotland, UK) 1% in HBSS and incubated at 370C for 2 hours with gentle rotation. The supernatant (containing the fibroblasts) was washed with HBSS and Medium 199 Earle’s MOD Salts (Gibco, Paisley, Scotland, UK) supplemented with 15% fetal bovine serum heat inactivated (Gibco, Paisley, Scotland, UK) and 1% antibiotic/antimycotic solution (10 000 U penicillin, 10 mg streptomycin, 25 μg amphotericin B per ml, Sigma-Aldrich, Dorset, UK), and then spun down twice to remove collagenase. The same stock of growth medium was used in the whole experiment. The pellets were resuspended in growth medium, plated in 25-cm2 tissue culture flasks with Nunclon surface (Nalge Nunc International Corporation, Hereford, UK) and incubated at 370C in humidified air with 5% carbon dioxide (CO2). The medium was changed on alternate days and confluent fibroblasts cells were passaged into a 75-cm2 flask (Nalge Nunc International Corporation, Hereford, UK) using 0.1% trypsin-EDTA (Gibco, Paisley, Scotland, UK) for 10 minutes at 370C. The fibroblasts were then frozen in liquid nitrogen for long term storage.
Preparation of cells for treatment:
The fibroblasts were raised up from freezing and re-cultured in the same conditions described before. Fibroblasts from the 4th to 6th passages were used for experimentation.
They were seeded (5x104 cells/well) onto two BioFlex® plates; 6-well, flexible, with Collagen-I coated elastomer membrane bottoms (FlexCell International Corporation, Pennsylvania, USA), and allowed to grow. The fibroblasts were serum-starved for 48 hours, by using 1% charcoal/dextran treated fetal bovine serum (HyClone, Logan, Utah, USA) added to Medium 199 Earle’s MOD Salts supplemented medium, to achieve quiescence, and then they were cultured with 20% charcoal/dextran treated fetal bovine serum the same growth medium. For the following 4 days, individual wells were subjected to different treatment regimens.
Chronic cyclical mechanical strain:
The Flexercell Stress Unit (FlexCell International Corporation, McKeesport, Pennsylvania, USA) provides the equipment for the application of mechanical strain to cultured cells in vitro. The plates are housed within a manifold and subjected to a pre-calibrated computer-controlled vacuum. This apparatus allows strains to be equibiaxial over the majority of the elastomer membrane areas. Release of the vacuum relaxes the membranes to their resting conditions. Software driven controls of the solenoid valves that regulate the vacuum make it possible to generate various strain amplitudes, durations, frequencies and overall profiles of mechanical strains on cell monolayers {Hsieh, 2000 #278;Stanley, 2000 #277}. The cells were exposed to stretch (21%)-relaxation (0%) cycles of 12 hours each at a frequency of 1 Hz for four days. The manifold of The Flexercell Stress Unit and the corresponding BioFlex static plate was kept in the same incubator at 370C in humidified air with 5% CO2.

extract_protocol:
Preparation of RNA: Fibroblasts derived from three different subjects were used. Eight BioFlex plates of subconfluent fibroblasts were obtained from each cell source. Four plates were exposed to stretch for 96h and the other four were used for the static wells as the comparator described earlier. Total RNA was extracted from fibroblasts as previously described by Green et al (Green et al., 2001). Its quantity and purity were assessed by using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and Agilent RNA 6000 Nano Assay (RNA Nano reagent kit guide, part number: G2941-90126) according to the manufacturer’s instructions. The ratio of 18s and 28s peaks was used to assess RNA quality. Only RNA of A260 / A280 > 1.9
was used giving an Agilent trace with no evidence of RNA degradation.

treatment_protocol:
Stretch experiments:
Preparation of cells for treatment: Fibroblasts from the 4th to 6th passages were seeded (5x104 cells/well) into 6-well BioFlex® flexible plates with Collagen-I coated elastomer membrane bottoms (FlexCell International Corporation, McKeesport, Pennsylvania, USA), and allowed to grow. They were serum-starved for 48h, by using 1% charcoal/dextran treated heat-inactivated fetal bovine serum (HyClone, Logan, Utah, USA
added to the tissue culture medium to achieve quiescence, and then they were cultured with 15% of the same serum added to the tissue culture medium.
Chronic cyclical mechanical stretch: The Flexercell Stress Unit (FlexCell International Corporation, McKeesport, Pennsylvania, USA) provides the equipment for the application of stretch to cultured cells in vitro. The plates are housed within a manifold and subjected to a pre-calibrated computer-controlled vacuum stretch (Hsieh et al., 2000, Stanley et al., 2000). The cells were exposed to stretch amplitude of (21%)-relaxation (0%) cycles of 12h each, at a frequency of 1 Hz, for 96h, at 37oC in humidified air with 5% CO2. The corresponding BioFlex® static plate was kept in the same incubator

tag: Source of fibroblasts:

label_protocol: cDNA arrays, consisting of pairs of arrays labeled with Cy5 and Cy3 dyes, hybridizing RNA from stretched fibroblasts against controls. All controls were pooled. Microarray hybridization and analysis were performed as previously described (Turton et al., 2001). Changes in gene expression were analysed hybridizing RNA from treated cells against pooled controls. In this study Cy3 was added to control samples and Cy5 to treated samples.

tag: Three tissue samples were collected from uterine specimens of abdominal hysterectomy performed on premenopausal Caucasian women with no history of uterine prolapse. The supra-cervical area was cut (5 mm thick slices) with a scalpel to obtain the medial ends of the cardinal ligament. Every patient had to sign a consent form preoperatively, allowing the use of tissues removed at surgery for research purposes. The local ethics committee has approved this research program.


title: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of 10 tiss, bio rep 3 WRR_52hpf_rep3 (WRR52_4)

status: Public on Jan 25 2007

city: West Lafayette

first: Yuk Fai

last: Leung

state: IN

address: 915 W. State Street

department: Biological Sciences

institute: Purdue University

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 3

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.

label: Biotin

organism: Danio rerio

label_protocol: Thirty-three nanograms of total RNA were labeled by Affymetrix GeneChip Two-Cycle Target Labeling protocol.

growth_protocol: Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.

extract_protocol: Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.

treatment_protocol: Ten tissues were dissected from developing embryos according to: Leung YF, Ma P, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retinal Pigment Epithelium in vivo. 2007;48:881-890., and pooled as one biological replicate.

tag: Strain

value: AB

tag: Genotype

value: Wild-type

tag: Age

tag: Tissue

value: Retina with Retinal pigment epithelium attached


title: Stretch sample 118

description:
Changes in gene expression were analyzed using three cDNA arrays, consisting of pairs of arrays forward labeled with Cy5
and Cy3 dyes, hybridizing RNA from stretched fibroblasts against controls.  All controls were pooled.

scan_protocol: Array slides were scanned using an Axon A300 scanner at the MRC Toxicology Unit, Leicester, at excitation wavelengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes respectively.

data_processing:
Pixel intensity for hybridisation was determined using GenePix Pro 3.0.6 software [Axon Instruments,
Union City, CA, USA]. For dual label hybridizations there is imbalance in the measured intensity between the fluorescent channels, due to different intensities of fluorescence between equal quantities of bound dyes and also non-specific binding of the probes leading to background fluorescence. To correct for imbalance in the measured fluorescent intensities between the two fluorescent channels the data were normalized. Global normalization in which the fluorescence levels of all features are uniformly adjusted (Gant et al., 2005). The data from forward and reverse labelled arrays were normalized, condensed and t tested to determine differential gene expression (Zhang & Gant, 2004)  using statistical software (NorTT) hosted by the MRC Toxicology
Unit, Leicester. The normalization procedure eliminates features that are morphologically abnormal, where there is failure of hybridization or where there is only fluorescence in one channel. Genes having a p < 0.05 in a two-tailed t test were regarded as being significantly changed in expression

label_protocol: cDNA arrays, consisting of pairs of arrays labeled with Cy5 and Cy3 dyes, hybridizing RNA from stretched fibroblasts against controls.  All controls were pooled.  Microarray hybridization and analysis were performed as previously described (Turton et al., 2001). Changes in gene expression were analysed hybridizing RNA from treated cells against pooled controls. In this study Cy3 was added to control samples and Cy5 to treated samples.

treatment_protocol:
Stretch experiments:
Preparation of cells for treatment: Fibroblasts from the 4th to 6th passages were seeded (5x104 cells/well) into 6-well BioFlex® flexible plates with Collagen-I coated elastomer membrane bottoms (FlexCell International Corporation, McKeesport, Pennsylvania, USA), and allowed to grow. They were serum-starved for 48h, by using 1% charcoal/dextran treated heat-inactivated fetal bovine serum (HyClone, Logan, Utah, USA
added to the tissue culture medium to achieve quiescence, and then they were cultured with 15% of the same serum added to the tissue culture medium.
Chronic cyclical mechanical stretch: The Flexercell Stress Unit (FlexCell International Corporation, McKeesport, Pennsylvania, USA) provides the equipment for the application of stretch to cultured cells in vitro. The plates are housed within a manifold and subjected to a pre-calibrated computer-controlled vacuum stretch (Hsieh et al., 2000, Stanley et al., 2000). The cells were exposed to stretch amplitude of (21%)-relaxation (0%) cycles of 12h each, at a frequency of 1 Hz, for 96h, at 37oC in humidified air with 5% CO2. The corresponding BioFlex® static plate was kept in the same incubator.


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 3 ENC1529


title: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of 10 tiss, bio rep 2 WRR_52hpf_rep2 (WRR52_3)

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 2


title: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of 10 tiss, bio rep 1 1 WRR_52hpf_rep1 (WRR52_1)

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 1


title: Stretch sample 119

label_protocol: cDNA arrays, consisting of pairs of arrays labeled with Cy5 and Cy3 dyes, hybridizing RNA from stretched fibroblasts against controls. All controls were pooled. Microarray hybridization and analysis were performed as previously described (Turton et al., 2001). Changes in gene expression were analysed hybridizing RNA from treated cells against pooled controls. In this study Cy3 was added to control samples and Cy5 to treated samples

tag: Three tissue samples were collected from uterine specimens of abdominal hysterectomy performed on premenopausal Caucasian women with no history of uterine prolapse. The supra-cervical area was cut (5 mm thick slices) with a scalpel to obtain the medial ends of the cardinal ligament. Every patient had to sign a consent form preoperatively, allowing the use of tissues removed at surgery for research purposes. The local ethics committee has approved this research program


title: CTCF GM06990 ENCODE NimbleGen hg17 tiling array replicate 2


title: TAFII p250 (6B3) GM06990 ENCODE NimbleGen hg17 tiling array replicate 3


title: H3K27Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 1


title: TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 2 ENC1527


title: TAFII p250 (6B3) GM06990 replicate 3

status: Public on Jan 01 2007

label_protocol: Cy3 input Cy5 sample NimbleGen


title: H3K4me3 GM06990 replicate 3

tag: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me3 antibody


title: H3K4me3 GM06990 ENCODE NimbleGen hg17 tiling array replicate 3


title: H3K27Ac GM06990 ENCODE NimbleGen hg17 tiling array replicate 3


title: RNAPII(8WG16) GM06990 ENCODE NimbleGen hg17 tiling array replicate 1


title: TAFII p250 (6B3) GM06990 ENCODE NimbleGen hg17 tiling array replicate 2


title: CTCF GM06990 ENCODE NimbleGen hg17 tiling array replicate 1


title: H3K4me3 GM06990 ENCODE NimbleGen hg17 tiling array replicate 1


title: TAFII p250 (6B3) GM06990 replicate 2


title: TAFII p250 (6B3) GM06990 replicate 1


title: H3K4me1 GM06990 replicate 3

source_name: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me1 antibody


title: H3K4me1 GM06990 replicate 1

tag: Chromatin immunoprecipitated DNA from GM06990 cells using H3K4me1 antibody


title: CTCF GM06990 replicate 1

tag: Chromatin immunoprecipitated DNA from GM06990 cells using CTCF antibody


title: H3K4me3 GM06990 replicate 2


title: H3K4me3 GM06990 replicate 1


title: CTCF GM06990 replicate 3


title: CTCF GM06990 replicate 2


title: PriMk_Expt3_Day7_rep2

status: Public on Nov 09 2006

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description: Study of in vitro megakaryocyte differentiation

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

growth_protocol: Cultured as described (Yang et al., Stem Cells 2002;20:320-328) with TPO, IL-3, and Flt3-ligand in serum free X-VIVO media

extract_protocol: Mk cells immunomagnetically selected using anti-CD41a-PE (Coulter; Fullerton, CA) and anti-PE magnetic beads (Miltenyi; Auburn, CA), followed by Agilent RNA isolation mini-kit

treatment_protocol: Cultured for 7 days

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 20, Caucasian, nonsmoker

source_name: Universal Reference RNA

tag: Pooled RNA from 10 human cell lines


title: PriMk_Expt3_Day9_rep1

treatment_protocol: Cultured for 9 days


title: PriMk_Expt3_Day12_rep1

treatment_protocol: Cultured for 12 days


title: PriMk_Expt3_Day7_rep1


title: PriMk_Expt3_Day4_rep1

extract_protocol: Agilent RNA isolation mini-kit

treatment_protocol: Cultured for 4 days


title: PriMk_Expt3_Day0_rep2

treatment_protocol: Uncultured


title: PriMk_Expt2_Day9_rep2

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, female donor, age 21, Caucasian, nonsmoker


title: PriMk_Expt2_Day5_rep2

treatment_protocol: Cultured for 5 days


title: PriMk_Expt3_Day3_rep1

treatment_protocol: Cultured for 3 days


title: PriMk_Expt3_Day0_rep1


title: PriMk_Expt2_Day12_rep1


title: H3K4me1 GM06990 replicate 2

tag: Input DNA from GM06990 cells


title: PriMk_Expt2_Day0_rep1


title: PriMk_Expt2_Day9_rep1


title: PriMk_Expt2_Day3_rep1


title: PriMk_Expt2_Day5_rep1


title: PriMk_Expt2_Day0_rep2


title: PriMk_Expt1_Day9_rep1

tag: Culture initiated from G-CSF mobilized peripheral blood CD34-positive hematopoietic stem and progenitor cell donation, male donor, age 24, Caucasian


title: PriMk_Expt2_Day4_rep1


title: PriMk_Expt1_Day12_rep1


title: PriMk_Expt2_Day1_rep1

treatment_protocol: Cultured for 1 days


title: PriMk_Expt2_Day4_rep2


title: PriMk_Expt1_Day7_rep1


title: RNA Polymerase II ChIP-chip on GM06990 cells using monoclonal antibody (8WG16) Sample 3

status: Public on Nov 30 2006

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description: RNA polymerase II ChIP-chip in ENCODE region in GM06990 cells using monoclonal anti-Pol II (8WG16) antibody

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

source_name: RNA Polymerase II ChIP in GM06990 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from Pol II-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: GM06990 cells were grown in RPMI medium supplemented with 15% FBS and antibiotics (kanamycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-Pol II monoclonal antibody (Covance MMS-126R). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Monoclonal antibody for Pol II (8WG16)

source_name: IgG control ChIP in GM06990 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: GM06990 cells were grown in RPMI medium supplemented with 15% FBS and antibiotics (kanamycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with normal rabbit IgG (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: IgG reference


title: Tetra-acetylated Histone H4 ChIP-chip on GM06990 cells Sample 1

description: Tetra-acetylated Histone H4 ChIP-chip in ENCODE region in GM06990 cells

source_name: Tetra-acetylated Histone H4 ChIP in GM06990 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from acetylated Histone H4-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: GM06990 cells were grown in RPMI medium supplemented with 15% FBS and antibiotics (kanamycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-acetyl-Histone H4 rabbit polyclonal antiserum (Upstate 06-866). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Tetra-acetylated Histone H4 antibody


title: PriMk_Expt3_Day4_rep2


title: PriMk_Expt1_Day5_rep2


title: PriMk_Expt1_Day3_rep1


title: PriMk_Expt1_Day5_rep1


title: Tetra-acetylated Histone H4 ChIP-chip on GM06990 cells Sample 3


title: Tetra-acetylated Histone H4 ChIP-chip on GM06990 cells Sample 2


title: RNA Polymerase II ChIP-chip on GM06990 cells using monoclonal antibody (8WG16) Sample 2


title: PriMk_Expt1_Day4_rep2


title: PriMk_Expt1_Day2_rep1

treatment_protocol: Cultured for 2 days


title: PriMk_Expt1_Day1_rep1


title: PriMk_Expt1_Day0_rep1


title: CHRF_Expt4_PMA_7d_rep1

description: CHRF-288 model of megakaryocyte differentiation

source_name: CHRF cells, PMA 7d

growth_protocol: Grown in IMDM with 10% heat inactivated fetal bovine serum, 37degC, 5% CO2

extract_protocol: Adherent cells removed by trypsinization followed by Agilent RNA isolation mini-kit

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 7d

tag: Megakaryoblastic cell line (Witte et al., Cancer 1986; 58(2):238-44), origin male 17-month old with megakaryoblastic leukemia


title: CHRF_Expt4_PMA_9d_rep1

source_name: CHRF cells, PMA 9d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 9d


title: PriMk_Expt1_Day2_rep2


title: PriMk_Expt1_Day0_rep2


title: CHRF_Expt4_PMA_6h_rep2

source_name: CHRF cells, PMA 6h

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 6h


title: PriMk_Expt2_Day7_rep1


title: CHRF_Expt4_PMA_5d_rep2

source_name: CHRF cells, PMA 5d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 5d


title: PriMk_Expt3_Day5_rep1


title: PriMk_Expt1_Day4_rep1


title: CHRF_Expt4_PMA_5d_rep1


title: RNA Polymerase II ChIP-chip on GM06990 cells using monoclonal antibody (8WG16) Sample 1


title: PriMk_Expt2_Day2_rep1


title: CHRF_Expt4_PMA_4d_rep1

source_name: CHRF cells, PMA 4d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 4d


title: CHRF_Expt4_None_0_rep1

source_name: CHRF cells, untreated

treatment_protocol: No treatment


title: CHRF_Expt4_PMA_6h_rep1


title: CHRF_Expt4_PMA_1h_rep2

source_name: CHRF cells, PMA 1h

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 1h


title: CHRF_Expt4_PMA_3h_rep1

source_name: CHRF cells, PMA 3h

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 3h


title: CHRF_Expt4_PMA_1d_rep1

source_name: CHRF cells, PMA 1d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 1d


title: CHRF_Expt3_PMA_5d_rep2


title: CHRF_Expt3_PMA_9d_rep2


title: CHRF_Expt4_PMA_1h_rep1


title: CHRF_Expt3_PMA_9d_rep1


title: CHRF_Expt4_None_0_rep2


title: CHRF_Expt4_PMA_3d_rep1

source_name: CHRF cells, PMA 3d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 3d


title: CHRF_Expt3_PMA_3h_rep1


title: CHRF_Expt4_PMA_1d_rep2


title: CHRF_Expt3_PMA_2d_rep1

source_name: CHRF cells, PMA 2d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 2d


title: CHRF_Expt4_PMA_2d_rep1


title: CHRF_Expt4_DMSO_4d_rep1

source_name: CHRF cells, DMSO 4d

treatment_protocol: Treated with 0.02% DMSO for 4d


title: CHRF_Expt3_PMA_4d_rep1


title: CHRF_Expt3_PMA_1h_rep2


title: CHRF_Expt4_DMSO_7d_rep1

source_name: CHRF cells, DMSO 7d

treatment_protocol: Treated with 0.02% DMSO for 7d


title: CHRF_Expt3_PMA_1d_rep1

source_name: Universal Reference RNA


title: CHRF_Expt3_PMA_7d_rep1


title: CHRF_Expt3_PMA_6h_rep1


title: CHRF_Expt4_PMA_12h_rep1

source_name: CHRF cells, PMA 12h

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 12h


title: CHRF_Expt3_PMA_12d_rep1

source_name: CHRF cells, PMA 12d

treatment_protocol: Treated with 10 ng/mL PMA in DMSO (0.02% final volume) for 12d


title: CHRF_Expt3_PMA_1h_rep1


title: CHRF_Expt3_PMA_5d_rep1


title: CHRF_Expt3_PMA_12h_rep1


title: CHRF_Expt3_PMA_6h_rep2


title: CHRF_Expt3_None_0_rep1


title: CHRF_Expt3_PMA_3d_rep1


title: CHRF_Expt3_None_0_rep3


title: CHRF_Expt3_DMSO_12d_rep1

source_name: CHRF cells, DMSO 12d

treatment_protocol: Treated with 0.02% DMSO for 12d


title: CHRF_Expt3_DMSO_4d_rep2


title: Affymetrix RGU34A 2HA

status: Public on Dec 01 2004

city: Dublin

first: Niamh

last: O'Sullivan

country: Ireland

institute: University College Dublin

description: This is replicate 1 of the 2 hour sample from passive avoidance trained rats.

organism: Rattus norvegicus

source_name: rat dentate gyrus


title: Affymetrix RGU34A 24HB

description: This is replicate 2 of the 24 hour sample from passive avoidance trained rats.


title: CHRF_Expt3_DMSO_4d_rep1


title: Affymetrix RGU34A 6HC

description: This is replicate 3 of the 6 hour sample from passive avoidance trained rats.


title: Affymetrix RGU34A 12HA

description: This is replicate 1 of the 12 hour sample from passive avoidance trained rats.


title: Affymetrix RGU34A 6HB

description: This is replicate 2 of the 6 hour sample from passive avoidance trained rats.


title: Affymetrix RGU34A 3HB

description: This is replicate 2 of the 3 hour sample from passive avoidance trained rats.


title: CHRF_Expt3_None_0_rep2


title: Affymetrix RGU34A Naive A

description: This is replicate 1 of the naive samples from passive avoidance trained rats.


title: Affymetrix RGU34A NaiveB

description: This is replicate 2 of the naive samples from passive avoidance trained rats.

source_name: Rat dentate gyrus


title: Affymetrix RGU34A 12HB

description: This is replicate 2 of the 12 hour sample from passive avoidance trained rats.


title: Affymetrix RGU34A 3HA

description: This is replicate 1 of the 3 hour sample from passive avoidance trained rats.


title: APL,case 3,3IF,FC

status: Public on Oct 06 2005

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description:
APL patients with FLT3 ITD, 57 years at diagnosis (4/3/02), male, GB=21.2,Hb(g/dl)=10.4, PLT=21, circulant blasts=84%, DIC yes, LDH (IU/L)=1516, fibrinogen(mg/dl)=120,bcr3, variant M3 morphology, ATRA syndrome yes.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729787

hyb_protocol: cRNA products were purified using RNeasy columns (Qiagen). Samples had to contain 10-20 picomoles of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization. 1 ug of Cy5-labelled cRNA was mixed with the same amount of Cy3-labelled reference cRNA and, then, mixed cRNAs were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridised on Agilent Human 1A Oligo Microarray (V2), ink-jet printed microarray, comprising 20,173 (60-mer) experimentally validated oligonucleotide probes (features). After hybridization for 17 h at 60°C, slides were washed according to Agilent SSPE protocol instructions and then scanned using a confocal laser scanner (Agilent Technologies).

scan_protocol: Fluorescence data were analysed with Feature Extraction Software v7.5 (Agilent Technologies).

source_name: FLT3, ITD, Cy5

label_protocol: fluorescently-labelled cRNA was generated by in vitro transcription using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

source_name: Universal Human reference Stratagene,Cy3

extract_protocol: Universal Human Reference RNA (Stratagene, Cedar Creek, TX), used as reference control in all microarray gene-profiling experiments, consisted of equal amount of total RNA from 10 human cancer cell lines.


title: Affymetrix RGU34A 24HA

description: This is replicate 1 of the 24 hour sample from passive avoidance trained rats.


title: Affymetrix RGU34A Naive C

description: This is replicate 3 of the naive samples from passive avoidance trained rats.


title: 1.0uM_IAA_1h_2.2

status: Public on Mar 09 2004

city: Rockville

first: Julia

middle: C

last: Redman

state: MD

address: 9712 Medical Center Dr

department: Plant Genomics

institute: The Institute for Genomic Research

description:
Exposure to 1.0micromolar IAA for 1h prior to harvest; biological replicate 2, hybridization 2; scaling factor 2.7.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994

organism: Arabidopsis thaliana

source_name: whole plant, WT Col-0; biological replicate 2 of 2


title: 1.0uM_IAA_3h_2.1

description:
Exposure to 1.0micromolar IAA for 3h prior to harvest; biological replicate 2, hybridization 1; scaling factor 4.1.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Affymetrix RGU34A 6HA

description: This is replicate 1 of the 6 hour sample from passive avoidance trained rats.


title: 1.0uM_IAA_3h_2.2

description:
Exposure to 1.0micromolar IAA for 3h prior to harvest; biological replicate 2, hybridization 2; scaling factor 3.9.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 1.0uM_IAA_1h_1.2

description:
Exposure to 1.0micromolar IAA for 1h prior to harvest; biological replicate 1, hybridization 2; scaling factor 4.5.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994

source_name: whole plant, WT Col-0; biological replicate 1 of 2


title: 1.0uM_IAA_3h_1.1

description:
Exposure to 1.0micromolar IAA for 3h prior to harvest; biological replicate 1, hybridization 1; scaling factor 4.4.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 1.0uM_IAA_1h_1.1

description:
Exposure to 1.0micromolar IAA for 1h prior to harvest; biological replicate 1, hybridization 1; scaling factor 4.3.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 1.0uM_IAA_3h_1.2

description:
Exposure to 1.0micromolar IAA for 3h prior to harvest; biological replicate 1, hybridization 2; scaling factor 5.3.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: APL,case 22,1AF,GM

description:
APL patients with FLT3 TK mutation, 66 years at diagnosis (20/1/2000), female, GB=1.3,Hb(g/dl)=8.0, PLT=6, circulant blasts=29%, DIC yes, LDH (IU/L)=623, fibrinogen(mg/dl)=337,bcr1, variant M3 morphology, ATRA syndrome no.
Keywords = APL
Keywords = FLT3
Keywords = ITD
Keywords = mutation
Lot batch = US22502667_251209729783

source_name: FLT3, asp mutation, Cy5


title: Affymetrix RGU34A 0H B

description: This is replicate 2 of the 0 hours samples from passive avoidance trained rats.


title: Control_3.1

description:
Untreated control: biological replicate 3, hybridization 1; scaling factor 2.9.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994

source_name: whole plant, WT Col-0; biological replicate 3 of 3


title: 0.1uM_IAA_1h_2.2

description:
Exposure to 0.1micromolar IAA for 1h prior to harvest; biological replicate 2, hybridization 2; scaling factor 6.1.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 1.0uM_IAA_1h_2.1

description:
Exposure to 1.0micromolar IAA for 1h prior to harvest; biological replicate 2, hybridization 1; scaling factor 2.4.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_3h_1.1

description:
Exposure to 0.1micromolar IAA for 3h prior to harvest; biological replicate 1, hybridization 1; scaling factor 3.6.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Control_3.2

description:
Untreated control: biological replicate 3, hybridization 2; scaling factor 3.0.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_3h_2.2

description:
Exposure to 0.1micromolar IAA for 3h prior to harvest; biological replicate 2, hybridization 2; scaling factor 4.5.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_3h_1.2

description:
Exposure to 0.1micromolar IAA for 3h prior to harvest; biological replicate 1, hybridization 2; scaling factor 3.6.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_1h_1.1

description:
Exposure to 0.1micromolar IAA for 1h prior to harvest; biological replicate 1, hybridization 1; scaling factor 6.5.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Control_1.1 (a)

description:
Untreated control: biological replicate 1, hybridization 1 (first labeling); scaling factor 2.8.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994

source_name: whole plant, WT Col-0; biological replicate 1 of 3


title: Control_1.2 (a)

description:
Untreated control: biological replicate 1, hybridization 2 (first labeling); scaling factor 3.0.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Control_2.1

description:
Untreated control: biological replicate 2, hybridization 1; scaling factor 5.1.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994

source_name: whole plant, WT Col-0; biological replicate 2 of 3


title: 0.1uM_IAA_3h_2.1

description:
Exposure to 0.1micromolar IAA for 3h prior to harvest; biological replicate 2, hybridization 1; scaling factor 5.3.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_1h_1.2

description:
Exposure to 0.1micromolar IAA for 1h prior to harvest; biological replicate 1, hybridization 2; scaling factor 4.6.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Control_2.2

description:
Untreated control: biological replicate 2, hybridization 2; scaling factor 5.0.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: 0.1uM_IAA_1h_2.1

description:
Exposure to 0.1micromolar IAA for 1h prior to harvest; biological replicate 2, hybridization 1; scaling factor 5.8.  See series file for additional information.
Keywords = IAA
Keywords = whole plant
Keywords = indole-3-acetic acid
Lot batch = 2001994


title: Affymetrix RGU34A 0H A

description: This is replicate 1 of the 0 hours samples from passive avoidance trained rats.


title: Affymetrix RGU34A 2HB

description: This is replicate 2 of the 2 hour sample from passive avoidance trained rats.