title: ko_0hra

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77045.gif
Compound Based Treatment: 0 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 5080; Software: type: feature extraction; Performer: Tiara,,Kawahara

source_name: universal mouse reference

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = Universal Reference; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Tiara,,Kawahara

tag: universal mouse reference

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 0h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: S6-ko 29d Skin -1

status: Public on Jan 09 2009

type: RNA

city: South San Francisco

first: Adam

middle: S

last: Adler

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77699.gif
Tissue type: 29 day skin

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 4680; Software: type: feature extraction; Performer: Adam,,Adler

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

molecule: total RNA

organism: Mus musculus

source_name: WT 29d Skin

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Skin; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

extract_protocol: not provided

tag: WT 29d Skin

source_name: S6-ko 29d Skin -1

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Skin; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen)

tag: S6-ko 29d Skin -1


title: ko_24hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77049.gif
Compound Based Treatment: 24 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5200; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 24h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: wt_1.5hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77042.gif
Compound Based Treatment: 1.5 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 5040; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = WT 1.5h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: S6-ko 29d Spleen -1

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77697.gif
Tissue type: 29 day spleen

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 4710; Software: type: feature extraction; Performer: Adam,,Adler

source_name: WT 29d Spleen

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

tag: WT 29d Spleen

source_name: S6-ko 29d Spleen -1

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: S6-ko 29d Spleen -1


title: S6-ko 29d Liver -2

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77696.gif
Tissue type: 29 day liver

source_name: WT 29d Liver

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Liver; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

tag: WT 29d Liver

source_name: S6-ko 29d Liver -2

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Liver; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: S6-ko 29d Liver -2


title: S6-ko 29d Liver -1

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77695.gif
Tissue type: 29 day liver

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 4370; Software: type: feature extraction; Performer: Adam,,Adler

source_name: S6-ko 29d Liver -1

tag: S6-ko 29d Liver -1


title: S6-ko 29d Thymus -2

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77702.gif
Tissue type: 29 day thymus

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 780, 4540; Software: type: feature extraction; Performer: Adam,,Adler

source_name: WT 29d Thymus

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Thymus; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

tag: WT 29d Thymus

source_name: S6-ko 29d Thymus -2

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Thymus; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: S6-ko 29d Thymus -2


title: wt_0hra

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77040.gif
Compound Based Treatment: 0 hours

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = WT 0h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: ko_1.5hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77047.gif
Compound Based Treatment: 1.5 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1360, 4960; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 1.5h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: ko_6hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77048.gif
Compound Based Treatment: 6 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 5160; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 6h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: shSIRT6 1.5h (S2)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68772.gif
Compound Based Treatment: 1.5 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 4720; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78240; Parameter Laser Power = 3.56; Parameter Scan Time = 11:06:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 248248; Parameter Laser Power = 3.43; Parameter Scan Time = 11:06:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.03; Performer: Adam,,Adler

organism: Homo sapiens

source_name: Stratagene Universal Reference

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = Universal Reference; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

extract_protocol: not applicable

tag: Stratagene Universal Reference

source_name: shSIRT6 1.5h (S2)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = shS6 1.5h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: shSIRT6 1.5h (S2)


title: pSR 0h (P1)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68767.gif
Compound Based Treatment: 0 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 4160; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78161; Parameter Laser Power = 3.56; Parameter Scan Time = 09:47:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.78; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 248169; Parameter Laser Power = 3.38; Parameter Scan Time = 09:47:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.78; Performer: Adam,,Adler

source_name: pSR 0h (P1)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = pSR 0h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: pSR 0h (P1)


title: SIRT6null_3weekpups_spleen6

description:
Simple annotation: Transcription, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76633.gif
Tissue type: 21 day spleen

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 5200; Software: type: feature extraction; Performer: Tiara,,Kawahara

source_name: wildtype tissue (pool of 3 wt littermates)

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 21d Spleen; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Tiara,,Kawahara

source_name: SIRT6 null tissue

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 21d Spleen; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara

tag: SIRT6 null tissue


title: Populus balsamifera_20071015_Seedling_continuous_light_6d_1

status: Public on Jan 15 2009

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

country: Canada

institute: University of Toronto

description: Affymetrix protocol: Fluidics script: EukGE-WS2v5

hyb_protocol: Affymetrix protocol: Eukaryotic sample and array processing: Eukaryotic target hybridization

scan_protocol: Affymetrix protocol: GeneChip® Scanner 3000 7G Affymetrix 00-0073

data_processing: MAS5.0, scaled to 500

label: biotin

organism: Populus balsamifera

source_name: Populus balsamifera seedlings, 6 days old, contiuous light

label_protocol: Affymetrix protocol: Eukaryotic sample and array processing: One-cycle target labeling assay

growth_protocol: Seedlings were germinated in a continuous light growth chamber on wetted filter paper in petri plates with a constant temperature of 21°C. They were grown in this way for five days. On the 6th day, whole seedlings were collected and were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted. Each sample comprises pooled material from 20 individuals.

extract_protocol: Trizol method (Invitrogen, Burlington, ON, Canada)

tag: Whole seedling - 20 individuals

tag: Seedlot number 20071015

tag: 6 days post germination

tag: Continuous light


title: shSIRT6 6h (S3)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68773.gif
Compound Based Treatment: 6 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 4720; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78256; Parameter Laser Power = 3.56; Parameter Scan Time = 11:22:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 248264; Parameter Laser Power = 3.43; Parameter Scan Time = 11:22:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: Adam,,Adler

source_name: shSIRT6 6h (S3)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = shS6 6h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: shSIRT6 6h (S3)


title: wt_0hrb

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77041.gif
Compound Based Treatment: 0 hours

source_name: universal mouse reference

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = Universal Reference; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Tiara,,Kawahara

tag: universal mouse reference


title: ko_0hrb

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77046.gif
Compound Based Treatment: 0 hours

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 0h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: pSR 24h (P4)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68770.gif
Compound Based Treatment: 24 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 4520; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78196; Parameter Laser Power = 3.56; Parameter Scan Time = 10:23:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.36; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 248204; Parameter Laser Power = 3.43; Parameter Scan Time = 10:23:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.36; Performer: Adam,,Adler

source_name: pSR 24h (P4)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = pSR 24h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: pSR 24h (P4)


title: AJC A11

status: Public on Jan 08 2009

city: toronto

first: brian

last: knight

address: 25 orde st

institute: samuel lunenfeld research institute

description: no additional information

scan_protocol: standard protocols for Affymetrix GeneChip™3000 7G laser confocal slide scanner

data_processing: standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array using Affymetrix Expression Console software

label: Biotin

source_name: hepatic tissue, A/J, prenatal control

extract_protocol: Total Hepatic RNA was extracted from the frozen tissue using RNeasy Mini Kits with on-column RNase-free DNase Kit digestion (Quigen)

treatment_protocol: pregnant mice were either treated as controls (C) and fed ad libitum for the duration of pregnancy or were treated as restricted (R) and subjected to undernutrition restriction diet. Whole mouse livers were extracted from 27 week old offspring from C or R treated mothers and flash frozen in liquid nitrogen.

tag: male 7month old offspring


title: wt_24hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77044.gif
Compound Based Treatment: 24 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1600, 5400; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = WT 24h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: AJC A36

description: no additional information

hyb_protocol: standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array


title: B6C A26

description: no additional information

source_name: hepatic tissue, C57BL/6J, prenatal undernutrition

label_protocol: standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array


title: AJC 35

description: no additional information


title: shSIRT6 24h (S4)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68774.gif
Compound Based Treatment: 24 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 5000; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 78180; Parameter Laser Power = 3.56; Parameter Scan Time = 10:06:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.03; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 248188; Parameter Laser Power = 3.40; Parameter Scan Time = 10:06:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.03; Performer: Adam,,Adler

source_name: shSIRT6 24h (S4)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = shS6 24h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: shSIRT6 24h (S4)


title: AJC A33

description: no additional information


title: AJR A13

description: no additional information

source_name: hepatic tissue, A/J, prenatal undernutrition


title: B6R A8

description: no additional information


title: B6C A3

description: no additional information

source_name: hepatic tissue, C57BL/6J, prenatal control


title: shSIRT6 0h (S1)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68771.gif
Compound Based Treatment: 0 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 4720; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78226; Parameter Laser Power = 3.56; Parameter Scan Time = 10:52:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.85; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 248235; Parameter Laser Power = 3.43; Parameter Scan Time = 10:52:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.85; Performer: Adam,,Adler

source_name: shSIRT6 0h (S1)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = shS6 0h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: shSIRT6 0h (S1)


title: AJC 42

description: no additional information


title: S6-ko 29d Skin -2

description:
Simple annotation: aging, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77700.gif
Tissue type: 29 day skin

source_name: WT 29d Skin

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 29d Skin; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

tag: WT 29d Skin

source_name: S6-ko 29d Skin -2

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 29d Skin; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: S6-ko 29d Skin -2


title: AJR 31

description: no additional information


title: wt_6hr

description:
Simple annotation: Drug_treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77043.gif
Compound Based Treatment: 6 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1440, 5400; Software: type: feature extraction; Performer: Tiara,,Kawahara

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = WT 6h; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara


title: pSR 6h (P3)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68769.gif
Compound Based Treatment: 6 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 4360; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 78211; Parameter Laser Power = 3.56; Parameter Scan Time = 10:37:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 248219; Parameter Laser Power = 3.42; Parameter Scan Time = 10:37:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.64; Performer: Adam,,Adler

source_name: Stratagene Universal Reference

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = Universal Reference; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

source_name: pSR 6h (P3)

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = pSR 6h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: pSR 6h (P3)


title: pSR 1.5h (P2)

description:
Simple annotation: Cell-line, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68768.gif
Compound Based Treatment: 1.5 hours

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 4240; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 78269; Parameter Laser Power = 3.56; Parameter Scan Time = 11:35:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-06-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.2.4; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 248277; Parameter Laser Power = 3.43; Parameter Scan Time = 11:35:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Adam,,Adler

tag: Stratagene Universal Reference

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = pSR 1.5h; Parameter Species = Homo sapiens; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 2ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler


title: B6C 28

description: no additional information


title: Spleen S6-/- 1

description:
Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80890.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 400, 5040; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 65178; Parameter Laser Power = 3.63; Parameter Scan Time = 10:45:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.23; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 314334; Parameter Laser Power = 3.37; Parameter Scan Time = 10:45:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.23; Performer: Adam,,Adler

source_name: Spleen WT pool

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Adam,,Adler

tag: Spleen WT pool

source_name: Spleen S6-/- 1

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: Spleen S6-/- 1


title: AJR 40

description: no additional information


title: AJC A35

description: no additional information


title: B6C 24

description: no additional information


title: Spleen S6-/- RA+/- 2

description:
Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80893.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 4440; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 65204; Parameter Laser Power = 3.63; Parameter Scan Time = 11:11:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.69; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 490; Parameter Scan Power = 100; Parameter Laser on time = 314360; Parameter Laser Power = 3.38; Parameter Scan Time = 11:11:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.69; Performer: Adam,,Adler

source_name: Spleen S6-/- RA+/- 2

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko RelAhet Spleen; Parameter Species = Mus musculus; Performer: Adam,,Adler
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Adam,,Adler

tag: Spleen S6-/- RA+/- 2


title: AJR 32

description: no additional information


title: Spleen S6-/- RA+/- 3

description:
Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80894.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 480, 4840; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 65213; Parameter Laser Power = 3.63; Parameter Scan Time = 11:20:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 490; Parameter Scan Power = 100; Parameter Laser on time = 314369; Parameter Laser Power = 3.38; Parameter Scan Time = 11:20:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.84; Performer: Adam,,Adler

source_name: Spleen S6-/- RA+/- 3

tag: Spleen S6-/- RA+/- 3


title: Spleen S6-/- 2

description:
Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80891.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 4920; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 65186; Parameter Laser Power = 3.63; Parameter Scan Time = 10:53:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 314342; Parameter Laser Power = 3.37; Parameter Scan Time = 10:53:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.36; Performer: Adam,,Adler

source_name: Spleen S6-/- 2

tag: Spleen S6-/- 2


title: B6R 22

description: no additional information


title: B6R 20

description: no additional information


title: Spleen S6-/- RA+/- 1

description:
Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/80892.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 4920; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 65195; Parameter Laser Power = 3.63; Parameter Scan Time = 11:02:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.51; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2008-08-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.2; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 314351; Parameter Laser Power = 3.38; Parameter Scan Time = 11:02:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [84947]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.51; Performer: Adam,,Adler

source_name: Spleen S6-/- RA+/- 1

tag: Spleen S6-/- RA+/- 1


title: B6R 19

description: no additional information


title: AJR 14

description: no additional information


title: AJR 15

description: no additional information


title: AJR 18

description: no additional information


title: AJC 10

description: no additional information


title: AJR 17

description: no additional information


title: B6R 6

description: no additional information


title: AJC 12

description: no additional information


title: B6C 1

description: no additional information


title: B6C 2

description: no additional information


title: B6C 4

description: no additional information


title: V-F27 Monarch Butterfly Fall Vehicle Treated Female 27

status: Public on Jan 01 2009

city: Worcester

first: Steven

last: Reppert

state: MA

address: 364 Plantation St

department: Neurobiology

institute: University of Massachusetts Medical School

description: Nimblegen commercial protocol is located at http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf

hyb_protocol: Nimblegen commercial protocol

scan_protocol: Nimblegen commercial protocol

data_processing: Nimblegen commercial protocol

organism: Danaus plexippus

source_name: Fall Vehicle Treated Female

label_protocol: Nimblegen commercial protocol

extract_protocol:
Extracted using Qiagen RNeasy Mini kit
Amplified using Nugen Ovation kit

treatment_protocol:
14 days Light/Dark cycle
Lights on: 7:00 AM
Lights off: 6:00 PM
Temperature (light): 23 oC
Temperature (dark): 12 oC
topical treatment of vehicle (acetone) on day 1 and day 3

tag: dissected brain

tag: Wild caught 10/30/07


title: V-F29 Monarch Butterfly Fall Vehicle Treated Female 29


title: V-M14 Monarch Butterfly Fall Vehicle Treated Male 14

source_name: Fall Vehicle Treated Male


title: V-M18 Monarch Butterfly Fall Vehicle Treated Male 18


title: V-F04 Monarch Butterfly Fall Vehicle Treated Female 04


title: V-M19 Monarch Butterfly Fall Vehicle Treated Male 19


title: V-F24 Monarch Butterfly Fall Vehicle Treated Female 24


title: V-M13 Monarch Butterfly Fall Vehicle Treated Male 13


title: M-F30 Monarch Butterfly Fall Methoprene Treated Female 30

source_name: Fall Methoprene Treated Female

treatment_protocol:
14 days Light/Dark cycle
Lights on: 7:00 AM
Lights off: 6:00 PM
Temperature (light): 23 oC
Temperature (dark): 12 oC
Topical treatment of 200 µg of methoprene on day 1 and day 3


title: V-F22 Monarch Butterfly Fall Vehicle Treated Female 22


title: M-F24 Monarch Butterfly Fall Methoprene Treated Female 24


title: V-M10 Monarch Butterfly Fall Vehicle Treated Male 10


title: M-F23 Monarch Butterfly Fall Methoprene Treated Female 23


title: M-F27 Monarch Butterfly Fall Methoprene Treated Female 27


title: F-F13 Monarch Butterfly Fall Female 13

source_name: Fall Female

treatment_protocol:
2 days Light/Dark cycle
Lights on: 7:09 AM
Lights off: 5:54 PM
Temperature: 20 C


title: F-F21 Monarch Butterfly Fall Female 21


title: M-M04 Monarch Butterfly Fall Methoprene Treated Male 04

source_name: Fall Methoprene Treated Male


title: M-M08 Monarch Butterfly Fall Methoprene Treated Male 08


title: F-F14 Monarch Butterfly Fall Female 14


title: F-F03 Monarch Butterfly Fall Female 03


title: F-M32 Monarch Butterfly Fall Male 32

source_name: Fall Male


title: M-F20 Monarch Butterfly Fall Methoprene Treated Female 20


title: M-M13 Monarch Butterfly Fall Methoprene Treated Male 13


title: S-F23 Monarch Butterfly Summer Female 23

source_name: Summer Female

treatment_protocol:
2 days Light/Dark cycle
Lights on: 5:38 AM
Lights off: 8:09 PM
Temperature: 20 C

tag: Wild caught 7/30/07


title: F-F18 Monarch Butterfly Fall Female 18


title: M-M15 Monarch Butterfly Fall Methoprene Treated Male 15


title: M-M03 Monarch Butterfly Fall Methoprene Treated Male 03


title: F-M29 Monarch Butterfly Fall Male 29


title: F-M23 Monarch Butterfly Fall Male 23


title: S-F21 Monarch Butterfly Summer Female 21


title: SIRT6null_3weekpups_spleen11

description:
Simple annotation: Transcription, Knock-out
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76634.gif
Tissue type: 21 day spleen

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 4640; Software: type: feature extraction; Performer: Tiara,,Kawahara

source_name: wildtype tissue (pool of 3 wt littermates)

label_protocol:
not provided
Biological Sample - Channel 1; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in Channel 1 (green).; Protocol Type = Biological Sample; Parameter Tissue type = WT 21d Spleen; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy3; Performer: Tiara,,Kawahara

source_name: SIRT6 null tissue

label_protocol:
not provided
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Tissue type = S6ko 21d Spleen; Parameter Species = Mus musculus; Performer: Tiara,,Kawahara
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Amount of extract labeled = 15ug of aRNA; Parameter Type of label = Cy5; Performer: Tiara,,Kawahara

tag: SIRT6 null tissue


title: F-M10 Monarch Butterfly Fall Male 10


title: S-M07 Monarch Butterfly Summer Male 07

source_name: Summer Male


title: S-F22 Monarch Butterfly Summer Female 22


title: S-M10 Monarch Butterfly Summer Male 10


title: F-M07 Monarch Butterfly Fall Male 07


title: B6C A25

description: no additional information

source_name: hepatic tissue, C57BL/6J, prenatal control

tag: male 7month old offspring


title: S-F20 Monarch Butterfly Summer Female 20


title: S-M11 Monarch Butterfly Summer Male 11


title: S-M04 Monarch Butterfly Summer Male 04


title: S-F19 Monarch Butterfly Summer Female 19


title: S-M03 Monarch Butterfly Summer Male 03


title: GBM DNA hypermethylome: TSA vs mock in neurosphere HSR-GBM1

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: TSA vs mock in neurosphere HSR-GBM1

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

source_name: Mock treated neurosphere HSR-GBM1 cells

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 1x PBS for 96 hours

tag: Human GBM neurosphere HSR-GBM1 cells

source_name: TSA treated neurosphere HSR-GBM1 cells

treatment_protocol: 300 nanomolar TSA for 18 hour

tag: Human GBM neurosphere HSR-GBM1 cells treated with TSA


title: GBM DNA hypermethylome: TSA vs mock in D54MG

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: TSA vs mock in D54MG

source_name: Mock treated D54MG cells

tag: D54MG human GBM cell line

source_name: TSA treated D54MG cells

tag: D54MG human GBM cell line treated with TSA


title: GBM DNA hypermethylome: 5-AZA vs mock in D54MG

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: 5-AZA vs mock in D54MG

source_name: 5-AZA treated D54MG cells

treatment_protocol: 5 micromolar 5-AZA for 96 hours

tag: D54MG human GBM cell line treated with 5-AZA


title: GBM DNA hypermethylome: 5-AZA vs mock in T98G

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: 5-AZA vs mock in T98G

source_name: Mock treated T98G cells

tag: T98G human GBM cell line

source_name: 5-AZA treated T98G cells

tag: T98G human GBM cell line treated with 5-AZA


title: SHR - 6 week old - biol rep 2

city: Leiden

first: klaas

last: koop

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: SHR - 6 week old - biol rep 2

hyb_protocol: Hybridization and scanning were performed by the Leiden Genome Technology Center according to standard protocols (www.lgtc.com)

data_processing: Preprocessing of the data was performed with the GC Robust Multiarray Average (GCRMA) package in the R-environment (www.r-project.org ; www.bioconductor.org)

organism: Rattus norvegicus

source_name: isolated glomeruli

label_protocol: Biotin-labeled cRNA was produced using the Ambion MessageAmp II-Biotin Enhanced kit (Ambion, www.ambion.com), according to the manufacturer’s instructions.

growth_protocol: The animals were treated as described in Koop, K et al. Selective loss of podoplanin protein expression accompanies proteinuria and precedes alterations in podocyte morphology in a spontaneous proteinuric rat model. Am J Pathol. 2008 Aug;173(2):315-26

extract_protocol: RNA was isolated from the glomeruli using the TRIzol (Invitrogen) method, and purified with Qiagen RNeasy mini columns (Qiagen, www.qiagen.com).

tag: non-proteinuric rat strain


title: GBM DNA hypermethylome: 5-AZA vs mock in U-87 MG

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: 5-AZA vs mock in U-87 MG

source_name: Mock treated U-87 MG cells

tag: U-87 MG human GBM cell line

source_name: 5-AZA treated U-87 MG cells

tag: U-87 MG human GBM cell line treated with 5-AZA


title: GBM DNA hypermethylome: 5-AZA vs mock in neurosphere HSR-GBM1

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: 5-AZA vs mock in neurosphere HSR-GBM1

tag: Human GBM neurosphere HSR-GBM1

source_name: 5-AZA treated neurosphere HSR-GBM1 cells

tag: human GBM neurosphere HSR-GBM1 treated with 5-AZA


title: SHR - 4 week old - biol rep 1

description: SHR - 4 week old - biol rep 1

scan_protocol: Hybridization and scanning were performed by the Leiden Genome Technology Center according to standard protocols (www.lgtc.com)

treatment_protocol: The animals were treated as described in Koop, K et al. Selective loss of podoplanin protein expression accompanies proteinuria and precedes alterations in podocyte morphology in a spontaneous proteinuric rat model. Am J Pathol. 2008 Aug;173(2):315-26


title: SHR - 4 week old - biol rep 2

description: SHR - 4 week old - biol rep 2


title: SHR - 6 week old - biol rep 1

description: SHR - 6 week old - biol rep 1


title: Dahl SS - 4 week old - biol rep 1

description: Dahl SS - 4 week old - biol rep 1

tag: proteinuric rat strain


title: Dahl SS - 6 week old - biol rep 1

description: Dahl SS - 6 week old - biol rep 1


title: GBM DNA hypermethylome: TSA vs mock in T98G

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: TSA vs mock in T98G

source_name: TSA treated T98G cells

tag: T98G human GBM cell line treated with TSA


title: Dahl SS - 6 week old - biol rep 2

description: Dahl SS - 6 week old - biol rep 2


title: Dahl SS - 4 week old - biol rep 2

description: Dahl SS - 4 week old - biol rep 2


title: GBM DNA hypermethylome: TSA vs mock in U-87 MG

description: Identification of the GBM DNA hypermethylome revealed by gene expression profiling: TSA vs mock in U-87 MG

source_name: TSA treated U-87 MG cells

tag: U-87 MG human GBM cell line treated with TSA


title: CDC53 down-regulated vs. control C. albicans cells Replicate 4

city: Montreal

first: Katharina

last: Trunk

state: Quebec

address: 2950 chemin Polytechnique

institute: IRIC-Université de Montréal

description: replicate 4 of 4, for normalization test/reference Cy3/Cy5

hyb_protocol: The microarray slides were dipped sequentially in 0.2% SDS and water and immediately pre-hybridized for 1 hour at 42°C with 5X SSC, 0.1% SDS and 0.1 mg/ml BSA and subsequently washed twice for 5 min with 0.1X SSC and once for 30 sec with water and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer (Roche) with yeast tRNA (Invitrogen) and salmon sperm DNA (Sigma) in a SlideBooster hybridization chamber (Advalytix). The slides were washed twice with SSC-0.1% SDS, once with 1X SSC and once with 0.1X SSC. Slides were dried by centrifugation.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: control strain KTY3

label_protocol: 25 to 30 µg of total RNA was reverse transcribed using oligo(dT)23VN (V=A,C,G) in the presence of Cy5-dCTP or Cy3-dCTP (Amersham) and Superscript III reverse transcriptase (Invitrogen) . Thereafter, template RNA was degraded by adding 0.05 units of RNase H (USB) and 0.05 ug of RNase A (Pharmacia) followed by incubation for 30 min at 37°C. The labeled cDNAs were purified with Illustra Cyscribe GFX purification kit (Amersham).

growth_protocol: o/n cultures grown in YPD were diluted to OD 0.005 in fresh YPD with 20 µg/ml Doxycycline and grown for 12 h at 30°C

extract_protocol: 10 ml of C. albicans cultures were centrifuged, washed once in ice-cold water, centrifuged and the pellets were quickly frozen at –80°C. Total RNA was isolated using a hot phenol extraction protocol. Pellets were resuspended in 250 µl of TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5 % SDS). 250 µl of Phenol (acid-equilibrated pH 4.7) were added to each sample, the suspensions were vortexed and incubated at 65°C for 1 h. After centrifugation the upper phase was transferred to a new tube. Two more extractions (1x phenol, 1x chloroform/isoamylacolohl 24:1) were carried out. Total RNA was precipitated using sodium acetate/ethanol, washed once with 80% ethanol and dissolved in water. RNA quantification was assessed by absorbance reading at 260 nm (Nanodrop) and its quality was assessed using an Agilent 2100 Bioanalyzer (Santa Clara, CA).

tag: 12 h growth in the presence of 20 µg/ml Doxycycline

source_name: CDC53 conditional strain KTY31


title: CDC53 down-regulated vs. control C. albicans cells Replicate 3

description: replicate 3 of 4, for normalization test/reference Cy5/Cy3


title: CDC53 down-regulated vs. control C. albicans cells Replicate 2

description: replicate 2 of 4, for normalization test/reference Cy3/Cy5

source_name: control strain KTY3 replicate


title: CDC53 down-regulated vs. control C. albicans cells Replicate 1

description: replicate 1 of 4, for normalization test/reference Cy5/Cy3


title: 9h post DNA Damage P53 WT MEFs

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

description: Total RNA poly-A labeled RNA were hybridized to custom arrays

hyb_protocol: Nimblegen Hybridization protocol (http://www.nimblegen.com)

scan_protocol: Arrays were scanned using AXON 5uM scanner

data_processing: Probe signal intensity (ie, Sample VALUEs) obtained using the NimbleScan software provided by Nimblegen.  The .gff files (linked below as supplementary files) were also generated with NimbleScan.

source_name: P53 Inducible MEFs

label_protocol: Nimblegen ChIP labeling protocol (http://www.nimblegen.com)

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). The RNA was treated with DNaseI (Roche) before 2ug of each was used to generate cDNA with the Superscript III kit (Invitrogen). Poly-T was used to prime the cDNA synthesis. The cDNA was purified with phenol chloroform isoamyl alcohol and precipitated before being sent to Nimblegen to be analyzed for gene expression.

tag: CRE-LOX inducible P53 WT cells were exposed to a DNA damaging agent (Doxyrubicin) and profiled across time.


title: 6h post DNA Damage P53 WT MEFs

hyb_protocol: Nimblegen Hyb protocol (http://www.nimblegen.com)


title: 3h post DNA Damage P53 KO MEFs


title: P53 WT MEFs 0h Post DNA Damage


title: Mouse ES Replicate 2 Array 4

source_name: Mouse ES v6.5

tag: Mouse Embryonic Stem Cells V6.5


title: 6h post DNA Damage P53 KO MEFs


title: 9h post DNA Damage P53 KO MEFs


title: Whole Embryo E13.5 Replicate 1

source_name: Whole Embryo

tag: Whole Embryo E13.5


title: 3h post DNA Damage P53 Wt MEFs


title: Whole Embryo E9.5 Replicate 2

tag: Whole Embryo E9.5


title: Mouse ES Replicate 2 Array 1


title: Mouse Embryonic Fibroblasts (MEF) lincRNA Expression_rep2

source_name: MEF

tag: Genotype

value: 129SvJae x C57BL/6; Timepoint:Embryonic day 13.5; Passages:4-6


title: Mouse ES Replicate 1 Array 2


title: P53 KO MEFs 0h Post DNA Damage


title: Mouse ES Replicate 2 Array 2


title: Whole Embryo E13.5 Replicate 2


title: Mouse ES Replicate 1 Array 4


title: Mouse ES Replicate 2 Array 3


title: Mouse ES Replicate 1 Array 3


title: Whole Embryo E10.5 Replicate 2

tag: Whole Embryo E10.5


title: Ambion Ovary

source_name: Ambion

tag: Ambion Ovary RNA


title: Whole Embryo E9.5 Replicate 1


title: Mouse ES Replicate 1 Array 1


title: Universal RNA

source_name: Startagene

extract_protocol: stratagene

tag: Universal RNA Pool


title: Neural Precursor Cells (NPC) lincRNA Expression_rep2

source_name: NPC

value: 129SvJae x C57BL/6


title: Dendridic Cells TLR2 Stimulated

source_name: Bone Marrow Dendridic Cells

tag: Dendridic Cells TLR2 Stimulated


title: Ambion Testes

source_name: Abion

tag: Ambion Testes RNA


title: Mouse Hindlimb E10.5

source_name: Embryonic Hindlimb

tag: Mouse Hindlimb


title: Mouse Lung Fibroblasts (MLF) lincRNA Expression_rep1

description: MLF total RNA poly-A labeled RNA were hybridized to custom arrays

source_name: Mouse lung Fibroblasts


title: Dendridic Cells TLR4 Stimulated

tag: BMDC TLR4 Stimulated


title: Mouse Forelimb E10.5

source_name: Embryonic Forelimb

tag: Mouse Forelimb E10.5


title: Mouse Lung Fibroblasts (MLF) lincRNA Expression_rep2

source_name: MLF


title: Dendridic Cells Unstimulated

tag: BMDC Unstimulated


title: Dendridic Cells TLR9 Stimulated

tag: Dendridic Cells TLR9 Stimulated


title: Mouse Hindlimb E9.5


title: NIZOB2244W

status: Public on Dec 31 2008

type: genomic

city: Nijmegen

first: Jumamurat

last: Bayjanov

address: Geert-Groteplein

institute: CMBI

description: NIZOB2244W is a L.lactis subsp. lactis strain isolated from plant.

hyb_protocol: According to standard NimbleGen protocol (http://www.nimblegen.com/products/cgh/index.html)

data_processing: R package "fields" was used to normalize hybridisation data. Initially, a smooth three dimensional surface was fitted to the data. For each individual spot the height of the surface at the position of that spot is then subtracted from its raw signal intensity value. The height of this surface at a specific position represents the local average signal. In order to avoid negative values the overall mean of the smooth fit is added to all signal intensities.

molecule: genomic DNA

organism: Lactococcus lactis subsp. lactis

extract_protocol: DNA was isolated using the QiaAmp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's protocol for the isolation of genomic DNA from Gram-positive bacteria.

tag: strain NIZOB2244W


title: N42

description: N42 is a L.lactis subsp. lactis strain isolated from plant.

scan_protocol: According to standard NimbleGen protocol (http://www.nimblegen.com/products/cgh/index.html)

tag: strain N42


title: Mouse Hindlimb E13.5


title: Mouse Forelimb E13.5

tag: Mouse Forelimb E13.5


title: NCDO895

description: NCDO895 is a L.lactis subsp. lactis strain isolated from dairy products.

label_protocol: According to standard NimbleGen protocol (http://www.nimblegen.com/products/cgh/index.html)

tag: strain NCDO895


title: NCDO763

description: NCDO763 is a L.lactis subsp. cremoris strain isolated from dairy products.

organism: Lactococcus cremoris

tag: strain NCDO763


title: Ambion Brain lincRNA Expression

tag: Ambion Brain Total RNA


title: P7266

description: P7266 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain P7266


title: UC317

description: UC317 is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain UC317


title: P7304

description: P7304 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain P7304


title: Mouse Forelimb E9.5

tag: Mouse Forelimb E9.5


title: MG1363

description: MG1363 is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain MG1363


title: ML8

description: ML8 is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain ML8


title: Mouse ES Cells

source_name: Mouse ES V6.5

tag: Mouse Embryonic Stem Cells V6.5


title: SK11

description: SK11 is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain SK11


title: Mouse Embryonic Fibroblasts (MEF) lincRNA Expression_rep1

description: MEF poly-adenylated RNA was hybridized

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). The RNA was treated with DNaseI (Roche) before 2ug of each was used to generate cDNA with the Superscript III kit (Invitrogen). Random hexamers were used to prime the cDNA synthesis. The cDNA was purified with phenol chloroform isoamyl alcohol and precipitated before being sent to Nimblegen to be analyzed for gene expression.

tag: Genotype


title: N41

description: N41 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain N41


title: LMG8520

description: LMG8520 is a L.lactis subsp. lactis strain isolated from plant.

organism: Lactococcus lactis subsp. hordniae

tag: strain LMG8520


title: Neural Precursor Cells (NPC) lincRNA Expression_rep1

description: NPC total RNA poly-A labeled RNA were hybridized to custom arrays

source_name: Mouse NPC


title: KF201

description: KF201 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF201


title: Li-1

description: Li-1 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain Li-1


title: M20

description: M20 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain M20


title: LMG9449

description: LMG9449 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain LMG9449


title: wts03h.72slide7

city: Chicago

first: Christopher

middle: David

last: Brown

state: IL

department: Human Genetics

institute: University of Chicago

description: no additional information

hyb_protocol: Samples were hybridized to a PCR spotted whole genome Drosophila microarray as previously described (Li and White 2003, PMID: 12852852).

scan_protocol: Slides were scanned on a GenePix 4000B at 560 (red) and 530 (green) PMT.

data_processing: The developmental time course gene expression data was obtained from wild-type, as well as FTZ and EVE mutant flies.  Probes not present in all the arrays, flagged, and BLANK probes were removed from the data before the normalization.  This resulted in 13,229 probes included per array.  All data analyses were conducted in Perl and R (R Development Core Team).  Background subtraction was performed with the normexp function (offset=50) in the LIMMA package using median foreground and background intensities.  Within-array normalization was performed with print-tip loess, between array normalization was performed by quantile normalization, as implemented in the LIMMA package (6).  Differentially expressed genes were identified using an empirical Bayes methodology (Smyth 2004), with a false discovery rate of 0.001 (Benjamini and Hochberg 1995), also implemented in the LIMMA package.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryos,wild type,3hours AEL

label_protocol: RNA samples were directly compared to a Drosophila common reference sample collected throughout embryogenesis from 0-22h as previously described (Arbeitman et al., 2002).

extract_protocol: Trizol

treatment_protocol: ftz and eve mutant flies were maintained over GFP balancers.  Desired stages were collected and genotyped for microarrays as previously described (Ghanim and White 2006, PMID: 17068956).

tag: experimental genotype

source_name: Reference

tag: Common reference RNA, collected from embryos throughout embryogenesis (0-22h)


title: LMG6897T

description: LMG6897T is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain LMG6897T


title: KW10

description: KW10 is a L.lactis subsp. cremoris strain isolated from plant.

tag: strain KW10


title: wts03h.73slide6

description: no additional information


title: KF282

description: KF282 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF282


title: LMG9446

description: LMG9446 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain LMG9446


title: KF134

description: KF134 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF134


title: KF147

description: KF147 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF147


title: LMG14418

description: LMG14418 is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain LMG14418


title: KF196

description: KF196 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF196


title: DRA4

description: DRA4 is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain DRA4


title: K337

description: K337 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain K337


title: KF67

description: KF67 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF67


title: KF24

description: KF24 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF24


title: KF146

description: KF146 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF146


title: wts03h.71slide8

description: no additional information


title: E34

description: E34 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain E34


title: KF7

description: KF7 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain KF7


title: AM2

description: AM2 is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain AM2


title: LMG8526

description: LMG8526 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain LMG8526


title: IL1403

description: IL1403 is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain IL1403


title: FG2

description: FG2 is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain FG2


title: K231

description: K231 is a L.lactis subsp. lactis strain isolated from plant.

tag: strain K231


title: ATCC19435T

description: ATCC19435T is a L.lactis subsp. lactis strain isolated from dairy products.

tag: strain ATCC19435T


title: wt06h.30slide12

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,6hours AEL

tag: experimental genotype

tag: Common reference RNA, collected from embryos throughout embryogenesis (0-22h)


title: wt07h.31slide13

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,7hours AEL


title: wt09h.33slide58

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,9hours AEL


title: HP

description: HP is a L.lactis subsp. cremoris strain isolated from dairy products.

source_name: HP

tag: strain HP


title: wt08h.22slide57

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,8hours AEL


title: wt09h.23slide73

description: no additional information


title: wt08h.32slide56

description: no additional information


title: wt10h.34slide60

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,10hours AEL


title: wt10h.24slide97

description: no additional information


title: wt07h.21slide74

description: no additional information


title: V4

description: V4 is a L.lactis subsp. cremoris strain isolated from dairy products.

tag: strain V4


title: wt06h.20slide59

description: no additional information


title: wts02h.52slide71

description: no additional information

source_name: Drosophila melanogaster embryos,wild type,2hours AEL


title: wt06h.10Slide57

description: no additional information


title: wt07h.11Slide58

description: no additional information


title: ftzs03h.72slide64

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,3hours AEL


title: ftzs03h.73slide68

description: no additional information


title: ftzs02h.51slide69

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,2hours AEL


title: wt09h.13Slide81

description: no additional information


title: ftzs02h.52slide65

description: no additional information


title: wt08h.12Slide80

description: no additional information


title: ftzs02h.53slide67

description: no additional information


title: ftz10h.64slide15

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,10hours AEL


title: wt10h.14Slide24

description: no additional information


title: wts02h.51slide70

description: no additional information


title: ftz09h.63slide14

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,9hours AEL


title: ftz07h.61slide12

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,7hours AEL


title: ftz08h.62slide13

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,8hours AEL


title: ftz06h.60slide11

description: no additional information

source_name: Drosophila melanogaster embryos,ftz mutant,6hours AEL


title: ftz09h.53slide9

description: no additional information


title: ftz10h.54slide10

description: no additional information


title: ftz06h.50slide45

description: no additional information


title: ftz06h.40slide40

description: no additional information


title: eves03h.73slide96

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,3hours AEL


title: eves03h.72slide95

description: no additional information


title: ftz10h.44slide44

description: no additional information


title: ftz07h.41slide41

description: no additional information


title: eves03h.71slide94

description: no additional information


title: ftz08h.42slide42

description: no additional information


title: ftz07h.51slide7

description: no additional information


title: eves02h.51slide59

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,2hours AEL


title: eve09h.63slide38

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,9hours AEL

source_name: Reference


title: ftz09h.43slide43

description: no additional information


title: eves02h.52slide60

description: no additional information


title: eve10h.64slide39

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,10hours AEL


title: eve08h.62slide37

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,8hours AEL


title: eves02h.53slide61

description: no additional information


title: eve08h.52slide71

description: no additional information


title: eve09h.53slide84

description: no additional information


title: eve10h.54slide85

description: no additional information


title: eve06h.50slide69

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,6hours AEL


title: eve07h.51slide70

description: no additional information

source_name: Drosophila melanogaster embryos,eve mutant,7hours AEL


title: eve10h.44slide68

description: no additional information


title: eve06h.60slide86

description: no additional information


title: eve09h.43slide67

description: no additional information


title: eve07h.41slide65

description: no additional information


title: eve08h.42slide66

description: no additional information


title: ftzs03h.71slide63

description: no additional information


title: WT_Gal_AntimycinA_N2_Gen3_rep3

city: Urbana

first: Kurt

middle: E

last: Kwast

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

institute: University of Illinois at Urbana-Champaign

description: Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) in the presence of Antimycin A for three generations.  After three generations, the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of anaerobic growth in the presence of Antimycin A..  Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5).

data_processing: GenePix Pro software (v4.1) was used for spot identification and fluorescence intensity quantification.  After manually flagging and removing spots with aberrant measurements, background fluorescence was subtracted from the median Cy3 and median Cy5 fluorescence intensity values.  Any resulting negative intensity values were set to zero and a constant of one fluorescent unit was then added to all intensity values.  Outliers were identified and removed using SAS, and the log2Cy3 intensity (query cDNA) for all remaining observations on a slide was normalized against that of the log2Cy5 intensity (reference cDNA) using locally weighted linear regression (Loess).  The log2(Cy3/Cy5) ratio for each spot was calculated, and the mean log2(Cy3/Cy5) ratio across all observations on a slide was normalized to a value of zero.  The mean of the normalized log2(Cy3/Cy5) ratio for each gene was then calculated by averaging the duplicate observations on each slide and pooling replicate slides by sampling time.

organism: Saccharomyces cerevisiae

tag: Strain

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:3 generations, Replication:Rep3

value: JM43 (wild-type), Medium:SSG-TEA, Condition:a pool of RNA collected from both anaerobic and aerobic cultures


title: WT_Gal_AntimycinA_N2_Gen2_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:2 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen3_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:3 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen05_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.5 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen038_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.38 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen1_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:1 generation, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen05_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.5 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen038_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.38 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen05_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.5 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen038_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.38 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen1_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:1 generation, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen025_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.25 generations, Replication:Rep2


title: eve06h.40slide64

description: no additional information


title: WT_Gal_AntimycinA_N2_Gen025_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.25 generations, Replication:Rep4


title: WT_Gal_AntimycinA_N2_Gen025_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.25 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen1_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:1 generation, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen3_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:3 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen2_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:2 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen2_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:2 generations, Replication:Rep1

value: JM43 (wild-type), Medium:SSG-TEA, Condition:a pool of RNA collected from both anaerobic and aerobic cultures


title: wts02h.53slide9

description: no additional information


title: WT_Gal_AntimycinA_N2_Gen019_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.19 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen013_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.13 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen019_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.19 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen013_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.13 generations, Replication:Rep4


title: WT_Gal_AntimycinA_N2_Gen013_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.13 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen008_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.08 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen019_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.19 generations, Replication:Rep3


title: WT_Gal_AntimycinA_N2_Gen008_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.08 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen008_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.08 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen004_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.04 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen038_rep4

description: Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) for six generations of preconditioning.  When cell density was ≈1 Klett unit, Antimycin A (1 μM) was added into medium.  Samples were harvested after 0 (control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of aerobic growth in the presence of Antimycin A.  Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5).

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.38 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen3_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:3 generations, Replication:Rep1


title: WT_Gal_AntimycinA_N2_Gen004_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.04 generations, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen1_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:1 generation, Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen2_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:2 generations, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen2_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:2 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen05_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.5 generations, Replication:Rep1

value: JM43 (wild-type), Medium:SSG-TEA, Condition:a pool of RNA collected from both anaerobic and aerobic cultures


title: WT_Gal_AntimycinA_Air_Gen05_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.5 generations, Replication:Rep2


title: WT_Gal_AntimycinA_N2_Gen004_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:N2, Generation:0.04 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen1_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:1 generation, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen2_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:2 generations, Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen05_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.5 generations, Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen3_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:3 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen1_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:1 generation, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen3_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:3 generations, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen038_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.38 generations, Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen038_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.38 generations, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen025_rep5

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.25 generations, Replication:Rep5


title: WT_Gal_AntimycinA_Air_Gen025_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.25 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen025_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.25 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen019_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.19 generations, Replication:Rep3