title: day 0 ductus arteriosus replicate 2

status: Public on Sep 30 2007

type: RNA

city: Setagaya

first: Yoji

last: Sato

state: Tokyo

address: 1-18-1 Kami-yoga

department: Cell. Gene Thpy. Prod.

country: Japan

institute: NIHS

description: Wister, day 0, ductus arteriosus, without maternal vitamin A administration

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0 (MAS5), normalization value: 1, target intensity for scaling: 2500

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: ductus arteriosus

label_protocol: standard Affymetrix procedures (One-Cycle cDNA synthesis)

extract_protocol: Pooled tissues were obtained from Wister rats on the day of birth (n>=120).  After excision, the tissues were immediately frozen in liquid nitrogen and stored at -80oC.  Total RNA was isolated from the pooled tissues using TRIzol (Invitrogen).  After treatment with DNaseI (Promega), a second clean-up was performed on the isolated RNA, using RNeasy Mini (QIAGEN).


title: embryonic day 21 ductus arteriosus with maternal vitamin A replicate 1

description: Wister, embryonic day 21, ductus arteriosus, with maternal vitamin A administration

extract_protocol: Pooled tissues were obtained from Wister rat embryos on embryonic day 21 (n>=120).  After excision, the tissues were immediately frozen in liquid nitrogen and stored at -80oC.  Total RNA was isolated from the pooled tissues using TRIzol (Invitrogen).  After treatment with DNaseI (Promega), a second clean-up was performed on the isolated RNA, using RNeasy Mini (QIAGEN).


title: embryonic day 19 ductus arteriosus with maternal vitamin A replicate 1

description: Wister, embryonic day 19, ductus arteriosus, with maternal vitamin A administration

extract_protocol: Pooled tissues were obtained from Wister rat embryos on embryonic day 19 (n>=120).  After excision, the tissues were immediately frozen in liquid nitrogen and stored at -80oC.  Total RNA was isolated from the pooled tissues using TRIzol (Invitrogen).  After treatment with DNaseI (Promega), a second clean-up was performed on the isolated RNA, using RNeasy Mini (QIAGEN).


title: day 0 ductus arteriosus with maternal vitamin A replicate 2

description: Wister, day 0, ductus arteriosus, with maternal vitamin A administration


title: embryonic day 19 ductus arteriosus with maternal vitamin A replicate 2

tag: Wister, embryonic day 19, ductus arteriosus, with maternal vitamin A administration


title: embryonic day 19 ductus arteriosus replicate 2

description: Wister, embryonic day 19, ductus arteriosus, without maternal vitamin A administration


title: day 0 ductus arteriosus with maternal vitamin A replicate 1

tag: Wister, day 0, ductus arteriosus, with maternal vitamin A administration


title: embryonic day 21 ductus arteriosus replicate 2

description: Wister, embryonic day 21, ductus arteriosus, without maternal vitamin A administration


title: embryonic day 21 ductus arteriosus replicate 1

tag: Wister, embryonic day 21, ductus arteriosus, without maternal vitamin A administration


title: day 0 aorta replicate 2

description: Wister, day 0, aorta, without maternal vitamin A administration

source_name: aorta


title: embryonic day 21 aorta replicate 1

description: Wister, embryonic day 21, aorta, without maternal vitamin A administration


title: embryonic day 21 ductus arteriosus with maternal vitamin A replicate 2

tag: Wister, embryonic day 21, ductus arteriosus, with maternal vitamin A administration


title: embryonic day 19 aorta replicate 2

description: Wister, embryonic day 19, aorta, without maternal vitamin A administration


title: embryonic day 19 aorta replicate 1

tag: Wister, embryonic day 19, aorta, without maternal vitamin A administration


title: embryonic day 21 aorta replicate 2

tag: Wister, embryonic day 21, aorta, without maternal vitamin A administration


title: day 0 aorta replicate 1

tag: Wister, day 0, aorta, without maternal vitamin A administration


title: embryonic day 19 ductus arteriosus replicate 1

tag: Wister, embryonic day 19, ductus arteriosus, without maternal vitamin A administration


title: round 3, 20 g/L EtOH, replicate 2

status: Public on Sep 23 2007

city: Cambridge

first: Joel

last: Moxley

state: MA

address: 77 Massachusettes Ave

country: USA

institute: MIT

description: round 3, 20 g/L EtOH

data_processing: Bioconductor with RMA background correction, qspline normalization, and Li-Wong expression value summaries

organism: Escherichia coli

source_name: DH5-alpha (Invitrogen)

label_protocol: The extracted RNA was processed by Ambion Services using the Affymetrix protocols with the exception of Ambion ArrayScript substituted for SuperScript and Vivaspin Concentrators substituted for Qiagen cleanup columns.

extract_protocol: Strains were cultured at 37C with 225 rpm orbital shaking in 30 mL LB medium supplemented with 34 ug/mL of chloramphenicol with the indicated ethanol concentration in 50 mL closed conical tubes.  The cultures harvested at approximately OD 0.5.  Protocols from RNAprotect Bacteria Reagent and RNeasy mini spin kit were followed.

tag: genetic and environmental variation indicated in Sample_title


title: round 3, 40 g/L EtOH, replicate 1

description: round 3, 40 g/L EtOH


title: wild type, 20 g/L EtOH, replicate 2

description: wild type, 20 g/L EtOH


title: wild type, 20 g/L EtOH, replicate 1

description: wild type, 20 g/L EtOH


title: wild type, 20 g/L EtOH, replicate 3

description: wild type, 20 g/L EtOH


title: round 3, 0 g/L EtOH, replicate 2

description: round 3, 0 g/L EtOH


title: round 3, 20 g/L EtOH, replicate 3

description: round 3, 20 g/L EtOH


title: round 1, 0 g/L EtOH, replicate 1

description: round 1, 0 g/L EtOH


title: round 2, 0 g/L EtOH, replicate 2

description: round 2, 0 g/L EtOH


title: round 1, 0 g/L EtOH, replicate 2

description: round 1, 0 g/L EtOH


title: round 1, 0 g/L EtOH, replicate 3

description: round 1, 0 g/L EtOH


title: round 3, 20 g/L EtOH, replicate 1

description: round 3, 20 g/L EtOH


title: round 3, 40 g/L EtOH, replicate 2

description: round 3, 40 g/L EtOH


title: round 3, 40 g/L EtOH, replicate 3

description: round 3, 40 g/L EtOH


title: round 2, 0 g/L EtOH, replicate 1

description: round 2, 0 g/L EtOH


title: round 3, 0 g/L EtOH, replicate 1

description: round 3, 0 g/L EtOH


title: round 2, 0 g/L EtOH, replicate 3

description: round 2, 0 g/L EtOH


title: day 0 ductus arteriosus replicate 1

tag: Wister, day 0, ductus arteriosus, without maternal vitamin A administration


title: mod090_100nM-1

status: Public on Sep 27 2007

city: Stanford

first: Ling-Chun

last: Chen

state: CA

address: 318 Campus Drive

department: Molecular Pharmacology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68036.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1140, 5840; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 16:21:40; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73128; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 16:21:40; Parameter PMT Volts = 640; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243031; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen

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

organism: Mus musculus

source_name: Stratagene Mouse Reference total RNA

label_protocol:
4.1.1 Scan arrays in Axon Scanner with settings at 550 for 635nm wavelength and 800 for 532nm wavelength.  Store image in array QC file folder labeled with array number.
4.1.2 Etch opposite corners of printed area with a diamond scriber by placing array face down between two tip boxes and holding it firmly.  Be sure not to touch printed area with tip box.
4.1.3 UV-cross-link the oligos to the arrays at 600mJ (=6000 x 100 uJoules).

4.2 Primer Annealing

4.2.1 Check the quality of the RNA by using the Agilent Bioanalyzer or running an RNA gel.  For total RNA, ribosomal RNA should be visible on a gel at approximately 1.9 and 5kb.  The bands should be sharp and clear.  If the gel bands are smeared or there are multiple peaks on the 2100 Bioanalyzer electropherogram, then the RNA has been degraded.  For mRNA, a faint smear in the range of 0.5 to 2kb should be detectable.
4.2.2 Determine the RNA concentration, by measuring the UV absorbance at 260nm using a spectrophotometer.  An A260 of 1 equals an RNA concentration of approximately 40ug/mL
4.2.3 Use 30ug for each labeling reaction.
Note:  Two separate reaction tubes are needed, one for Cy3 and one for Cy5.

4.2.4 Adjust 30ug of RNA to 12uL for each reaction with RNase-free water.
4.2.5 Add 2uL of oligo-dT-(V) (2ug/ul).
4.2.6 Add 10ng Doping Controls for each channel.
4.2.7 Mix well by pipetting and spin briefly.
4.2.8 Denature the primer and template by incubating the reaction in a 70C heat block for 10 minutes.
4.2.9 Place the reactions on ice for 5 minutes.

4.3 Reverse Transcription and Labeling

4.3.1 Working at room temperature, add the following components:

5X Superscript Buffer:		6.0uL
0.1M DTT:			3.0uL
50X dNTPs:			0.6uL
Superscript RT (200U/uL)	2.4uL
Cy3 or Cy5:			3.0uL
Final Volume of Reaction:	29uL

4.3.2 Mix well by pipetting and briefly centrifuge .
4.3.3 Place in a heat block at 42C and incubate for 2 hours.
4.3.4 Add 1.0uL of Superscript II RT (200U/ul) and incubate another 30 minutes.
4.3.5 Add 1.5uL of 500mM EDTA to stop the reaction.
4.3.6 Add 1.5uL of 500mM NaOH, mix well and incubate at 70C for 10 minutes to degrade RNA.
4.3.7 Add 1.5uL of 500mM HCl to neutralize the reaction.

Purification of probe using Qiagen Qiaquick PCR purification kit

4.3.8 Preheat 55uL of RNase free water per Cy3/Cy5 reaction in a microfuge tube by incubating at 40C.
4.3.9 In a separate tube, combine the Cy3 and Cy5 and add 70uL of DNase-free water.
4.3.10 Add 500uL of Buffer PB.
4.3.11 Mix thoroughly by pipetting and transfer to Qiaquick column.
4.3.12 Centrifuge at ~13,000 rpm for 1 minute, discard flowthrough.
4.3.13 To wash, add 750uL of Buffer PE and centrifuge at ~13,000 rpm for 1 minute.
4.3.14 Discard the flow-through and repeat the wash and centrifugation step (5.3.7).
4.3.15 Discard the flow-through and centrifuge for 2.5 min at ~13,000 rpm to elute any remaining buffer.
4.3.16 Transfer column to a new 1.5mL microfuge tube and carefully apply 50uL of preheated DNase-free water to the center of the column membrane.
4.3.17 Incubate for 1 minute at room temperature.
4.3.18 Elute cleaned labeled probe by centrifugation at ~13,000 rpm for 4 minutes.
4.3.19 Using the Nanodrop under nucleic acids, microarrays, take 1ul of each sample check the dye incorporation.  For a 40K array, an acceptable dye incorporation is 30pmol per channel.
Dry the samples in a speedvac (~1 hour).  Cover speedvac with foil to avoid photobleaching of the probes.

tag: Stratagene Mouse Reference total RNA


title: mod088_Con1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68034.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5920; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.28; Parameter Scan Time = 16:10:13; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73115; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.28; Parameter Scan Time = 16:10:13; Parameter PMT Volts = 620; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243019; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: mod092_Con2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68038.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 16:33:03; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73138; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 16:33:03; Parameter PMT Volts = 640; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243041; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: mod091_1uM-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68037.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1250, 5680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 16:27:16; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73132; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.49; Parameter Scan Time = 16:27:16; Parameter PMT Volts = 630; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243035; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: ICI-resistant_MCF7_DMSO_rep03

status: Public on Sep 14 2007

city: Bloomington

first: Henry

last: Paik

state: IN

department: Medical Sciences

institute: Indiana University

description:
Annotations
		[Cell Culture]
	Chip Type	[HG-U133_Plus_2]
	Chip Type Company	[Affymetrix]
	Organism Cell Line	[MCF7]
	Organism Scientific Name	[Homo Sapiens]
	Sample Preparation Amount	[value undefined]
	Sample Preparation Amount Unit	[value undefined]
	Sample Preparation Hour	[value undefined]
	Sample Preparation Minute	[value undefined]
	Sample Preparation Protocol Description	[Qiagen RNeasy]
	Sample Preparation Protocol Name	[Qiagen RNeasy]
	Sample Preparation Purity	[value undefined]
	Sample Preparation Staging	[value undefined]

data_processing: Raw Scaled Signal Count

label: Biotin

organism: Homo sapiens

source_name: ICI resistant MCF7, DMSO treated (control), 4hr

tag: Annotations

tag: [Cell Culture]

tag: Chip Type	[HG-U133_Plus_2]

tag: Chip Type Company	[Affymetrix]

tag: Organism Cell Line	[MCF7]

tag: Organism Scientific Name	[Homo Sapiens]


title: wild type, 0 g/L EtOH, replicate 2

description: wild type, 0 g/L EtOH


title: ICI-resistant_MCF7_DMSO_rep02

tag: Sample Preparation Amount	[value undefined]

tag: Sample Preparation Amount Unit	[value undefined]

tag: Sample Preparation Hour	[value undefined]

tag: Sample Preparation Minute	[value undefined]

tag: Sample Preparation Protocol Description	[Qiagen RNeasy]

tag: Sample Preparation Protocol Name	[Qiagen RNeasy]

tag: Sample Preparation Purity	[value undefined]

tag: Sample Preparation Staging	[value undefined]


title: ICI-resistant_MCF7_DMSO_rep01


title: OHT-resistant-MCF7_17b-estradiol_rep03

description:
Annotations
		[Cell Culture]
	Cell Culture Temperature Temperature Measurement	[37]
	Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]
	Chip Type	[HG-U133_Plus_2]
	Compound Treatment Amount	[10.0]
	Compound Treatment Amount Unit	[nm]
	Compound Treatment Compound Name*	[17b-estradiol]
	Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]
	Genetic Characteristic Characteristic Type	[OHT resistant]
	Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]
	Organism Scientific Name	[Homo Sapiens]

source_name: OHT resistant MCF7, 17b-estradiol treated, 4hrs

tag: Compound Treatment Amount	[10.0]

tag: Compound Treatment Amount Unit	[nm]


title: ICI-resistant_MCF7_DMSO_rep04


title: ICI-resistant_MCF7_17b-estradiol_rep02

description:
Annotations
		[Cell Culture]
	Chip Type	[HG-U133_Plus_2]
	Chip Type Company	[Affymetrix]
	Compound Treatment Amount	[1]
	Compound Treatment Amount Unit	[unit]
	Compound Treatment Application	[4 hours]
	Compound Treatment Compound Name*	[17b-estradiol]
	Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]
	Organism Cell Line	[MCF7]
	Organism Scientific Name	[Homo Sapiens]
	Sample Preparation Amount	[value undefined]
	Sample Preparation Amount Unit	[value undefined]
	Sample Preparation Hour	[value undefined]
	Sample Preparation Minute	[value undefined]
	Sample Preparation Protocol Description	[Qiagen RNeasy]
	Sample Preparation Protocol Name	[Qiagen RNeasy]
	Sample Preparation Purity	[value undefined]
	Sample Preparation Staging	[value undefined]

source_name: ICI resistant MCF7, 17b estradiol, 4hr

tag: Compound Treatment Amount	[1]

tag: Compound Treatment Amount Unit	[unit]


title: ICI-resistant_MCF7_17b-estradiol_rep04

tag: Annotations

tag: [Cell Culture]

tag: Compound Treatment Application	[4 hours]

tag: Compound Treatment Compound Name*	[17b-estradiol]

tag: Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]


title: OHT-resistant-MCF7_DMSO_rep04

description:
Annotations
		[Cell Culture]
	Cell Culture Temperature Temperature Measurement	[37]
	Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]
	Chip Type	[HG-U133_Plus_2]
	Compound Treatment Amount	[1.0]
	Compound Treatment Amount Unit	[unit]
	Compound Treatment Compound Name*	[DMSO (control)]
	Compound Treatment Compound Name* (DMSO (control))	[DMSO (control)]
	Genetic Characteristic Characteristic Type	[OHT resistant]
	Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]
	Organism Scientific Name	[Homo Sapiens]

source_name: OHT resistant MCF7, DMSO treated, 4hrs

tag: Chip Type	[HG-U133_Plus_2]

tag: Compound Treatment Amount	[1.0]

tag: Organism Scientific Name	[Homo Sapiens]


title: mod093_10nM-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68039.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5460; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 16:04:21; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 16:04:21; Parameter PMT Volts = 620; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen

tag: Stratagene Mouse Reference total RNA

source_name: 10nM shld1-2

tag: 10nM shld1-2


title: OHT-resistant-MCF7_17b-estradiol_rep01

tag: Cell Culture Temperature Temperature Measurement	[37]

tag: Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]

tag: Genetic Characteristic Characteristic Type	[OHT resistant]

tag: Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]


title: ICI-resistant_MCF7_17b-estradiol_rep01

tag: Chip Type Company	[Affymetrix]

tag: Organism Cell Line	[MCF7]

tag: Sample Preparation Amount	[value undefined]

tag: Sample Preparation Amount Unit	[value undefined]

tag: Sample Preparation Hour	[value undefined]

tag: Sample Preparation Minute	[value undefined]

tag: Sample Preparation Protocol Description	[Qiagen RNeasy]

tag: Sample Preparation Protocol Name	[Qiagen RNeasy]

tag: Sample Preparation Purity	[value undefined]

tag: Sample Preparation Staging	[value undefined]


title: OHT-resistant-MCF7_17b-estradiol_rep02

tag: Annotations

tag: [Cell Culture]

tag: Chip Type	[HG-U133_Plus_2]

tag: Compound Treatment Amount	[10.0]

tag: Compound Treatment Amount Unit	[nm]

tag: Compound Treatment Compound Name*	[17b-estradiol]

tag: Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]

tag: Organism Scientific Name	[Homo Sapiens]


title: wild type, 0 g/L EtOH, replicate 3

description: wild type, 0 g/L EtOH

tag: genetic and environmental variation indicated in Sample_title


title: wild type, 0 g/L EtOH, replicate 1

description: wild type, 0 g/L EtOH


title: mod097_10nM-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68043.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1350, 5280; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 15:38:52; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73084; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 15:38:52; Parameter PMT Volts = 660; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 242987; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen

tag: Stratagene Mouse Reference total RNA

source_name: 10nM shld1-3

tag: 10nM shld1-3


title: mod089_10nM-1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68035.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1500, 5840; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 16:15:56; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73121; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 16:15:56; Parameter PMT Volts = 630; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: mod099_1uM-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68044.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5300; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 15:52:33; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73099; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 15:52:33; Parameter PMT Volts = 620; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243002; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: mod095_1uM-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68041.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5360; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 15:09:07; Parameter PMT Volts = 560; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73054; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 15:09:07; Parameter PMT Volts = 630; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 242957; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: mod098_100nM-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68045.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5100; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 15:45:52; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73092; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 15:45:52; Parameter PMT Volts = 620; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 242995; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen

source_name: 100nM shld1-3

tag: 100nM shld1-3


title: mod096_Con-3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68042.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1270, 5440; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 15:18:08; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73064; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 15:18:08; Parameter PMT Volts = 610; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 242967; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen


title: OHT-resistant-MCF7_DMSO_rep02

tag: Cell Culture Temperature Temperature Measurement	[37]

tag: Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]

tag: Compound Treatment Amount	[1.0]

tag: Compound Treatment Amount Unit	[unit]

tag: Compound Treatment Compound Name*	[DMSO (control)]

tag: Compound Treatment Compound Name* (DMSO (control))	[DMSO (control)]

tag: Genetic Characteristic Characteristic Type	[OHT resistant]

tag: Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]


title: OHT-resistant-MCF7_DMSO_rep01

tag: Annotations

tag: [Cell Culture]

tag: Chip Type	[HG-U133_Plus_2]


title: OHT-resistant-MCF7_DMSO_rep03


title: wt_MCF7_DMSO_rep01

description:
Annotations
		[Cell Culture]
	Cell Culture Temperature Temperature Measurement	[37]
	Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]
	Chip Type	[HG-U133_Plus_2]
	Compound Treatment Amount	[1.0]
	Compound Treatment Amount Unit	[unit]
	Compound Treatment Compound Name*	[DMSO (control)]
	Compound Treatment Compound Name* (DMSO (control))	[DMSO (control)]
	Genetic Characteristic Characteristic Type	[wt]
	Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]
	Organism Scientific Name	[Homo Sapiens]

source_name: MCF7, DMSO treated, 4hrs


title: wt_MCF7_17b-estradiol_rep03

description:
Annotations
		[Cell Culture]
	Cell Culture Temperature Temperature Measurement	[37]
	Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]
	Chip Type	[HG-U133_Plus_2]
	Compound Treatment Amount	[10.0]
	Compound Treatment Amount Unit	[nm]
	Compound Treatment Compound Name*	[17b-estradiol]
	Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]
	Genetic Characteristic Characteristic Type	[wt]
	Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]
	Organism Scientific Name	[Homo Sapiens]

source_name: MCF7, 17b-estradiol treated, 4hrs

tag: Compound Treatment Amount	[10.0]

tag: Compound Treatment Amount Unit	[nm]


title: OHT-resistant-MCF7_17b-estradiol_rep04

tag: Compound Treatment Compound Name*	[17b-estradiol]

tag: Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]

tag: Organism Scientific Name	[Homo Sapiens]


title: wt_MCF7_17b-estradiol_rep02

tag: Genetic Characteristic Characteristic Type	[wt]


title: wt_MCF7_DMSO_rep02

data_processing: Scaled Signal Count

tag: Cell Culture Temperature Temperature Measurement	[37]


title: Multiple Sclerosis Sample 3 Data

city: Dublin

first: Maureen

last: padden

address: Belfield

department: Biochemistry

country: Ireland

institute: University College Dublin

description: Human Multiple Sclerosis brain tissue

data_processing: MAS 5

source_name: Human Brain tissue

extract_protocol: Trizol RNA isolation

tag: Human Multiple Sclerosis Brain tissue


title: Multiple Sclerosis Sample 2 Data

description: Human Multiple Sclerosis brain tissue

source_name: Human Brain

tag: Multiple Sclerosis Brain tissue


title: wt_MCF7_DMSO_rep03

tag: Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]

tag: Compound Treatment Amount	[1.0]

tag: Compound Treatment Amount Unit	[unit]


title: Multiple Sclerosis Sample 1 Data

description: Multiple Sclerosis Sample 1 Brain total RNA sample.

label: Biotin-labelled cRNA targets.

source_name: Human Brain Neurological

extract_protocol: Trizol,total RNA isolation procedure

treatment_protocol: None.


title: wt_MCF7_DMSO_rep04

tag: Compound Treatment Compound Name*	[DMSO (control)]

tag: Compound Treatment Compound Name* (DMSO (control))	[DMSO (control)]


title: Female Control Data

description: Human control brain tissue

source_name: Human control brain tissue

tag: Human control brain tissue


title: Human colonocytes, Caco2 cells treated with E. coli for 2h, replicate 4

status: Public on Sep 13 2007

city: Baltimore

first: Pinaki

last: Panigrahi

state: MD

address: 22 South Greene Street, Room N5W68

department: Pediatrics

institute: University of Maryland

description: colonocytes cells, Caco2 cells

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Scan Array 5000 fluorescent scanner and image intensity data were extracted and analyzed with Imagene 4.2. analysis software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.

label_protocol: The cDNA from Caco2 RNA and Caco2 L.plantarum treated RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ?l of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.

growth_protocol: Caco2 cells cultured in DMEM containing 10% fetal calf serum. Cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 8 days and harvested by trypsinization followed by pelleting of the cells.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 ?g) was annealed with 5 ?g oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42?C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.

source_name: Caco2 cells

tag: Human colonocytes, Caco2


title: Human colonocytes, Caco2 cells treated with mix L.p. and E. coli for 2h, replicate 5

description: colonocytes cells, Caco2 cells

tag: Human colonocytes, Caco2 cells treated with mix L.p. and E.coli for 2h

extract_protocol: The RNA (30 ?g) was annealed with 5 ?g oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42?C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.


title: mod094_100nM-2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68040.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5460; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Ling-Chun,,Chen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 15:58:29; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 73104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 15:58:29; Parameter PMT Volts = 630; Parameter Scan Date = 2006-04-07; Parameter Pixel Size = 10; Parameter Laser on time = 243007; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.47; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ling-Chun,,Chen

tag: Stratagene Mouse Reference total RNA

source_name: 100nM shld1-2

tag: 100nM shld1-2


title: Human colonocytes, Caco2 cells treated with mix L.p. and E. coli for 2h, , replicate 6

description: colonocytes cells, Caco2 cells


title: wt_MCF7_17b-estradiol_rep04

tag: Annotations

tag: [Cell Culture]

tag: Chip Type	[HG-U133_Plus_2]

tag: Compound Treatment Amount	[10.0]

tag: Compound Treatment Amount Unit	[nm]

tag: Compound Treatment Compound Name*	[17b-estradiol]

tag: Organism Cell Line	[MCF7 hormone dependent breast cancer cell line]


title: androgen-dependent prostate cancer/common reference-18

status: Public on Sep 06 2007

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

description: androgen-dependent prostate cancer versus common reference

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

source_name: androgen-dependent prostate cancer

tag: androgen-dependent prostate cancer

source_name: common reference

tag: a pool of RNA from mixed human embryo tissues


title: androgen-independent prostate cancer/common reference-4

description: androgen-independent prostate cancer versus common reference

source_name: androgen-independent prostate cancer

tag: androgen-independent prostate cancer


title: androgen-independent prostate cancer/common reference-7


title: androgen-independent prostate cancer/common reference-3


title: Human colonocytes, Caco2 cells treated with E. coli for 2h, replicate 3

description: colonocytes cells, Caco2 cells


title: androgen-independent prostate cancer/common reference-1


title: wt_MCF7_17b-estradiol_rep01

tag: Cell Culture Temperature Temperature Measurement	[37]

tag: Cell Culture Temperature Temperature Measurement Unit	[degrees celsius]

tag: Compound Treatment Compound Name* (17b-estradiol)	[17b-estradiol]

tag: Genetic Characteristic Characteristic Type	[wt]

tag: Organism Scientific Name	[Homo Sapiens]


title: ICI-resistant_MCF7_17b-estradiol_rep03

tag: Chip Type Company	[Affymetrix]

tag: Compound Treatment Amount	[1]

tag: Compound Treatment Amount Unit	[unit]

tag: Compound Treatment Application	[4 hours]

tag: Organism Cell Line	[MCF7]

tag: Sample Preparation Amount	[value undefined]

tag: Sample Preparation Amount Unit	[value undefined]

tag: Sample Preparation Hour	[value undefined]

tag: Sample Preparation Minute	[value undefined]

tag: Sample Preparation Protocol Description	[Qiagen RNeasy]

tag: Sample Preparation Protocol Name	[Qiagen RNeasy]

tag: Sample Preparation Purity	[value undefined]

tag: Sample Preparation Staging	[value undefined]


title: androgen-independent prostate cancer/common reference-8

tag: androgen-independent prostate cancer

tag: a pool of RNA from mixed human embryo tissues


title: androgen-dependent prostate cancer/common reference-17

tag: androgen-dependent prostate cancer


title: androgen-independent prostate cancer/common reference-5


title: androgen-independent prostate cancer/common reference-2


title: androgen-dependent prostate cancer/common reference-16


title: androgen-dependent prostate cancer/common reference-14


title: androgen-dependent prostate cancer/common reference-15


title: Human colonocytes, Caco2 cells treated with L. plantarum for 2h, replicate 1

status: Public on Sep 12 2007

description: colonocytes cells, Caco2 cells

label_protocol: The cDNA from Caco2 RNA and Caco2 L.plantarum treated RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.

tag: Human colonocytes, Caco2


title: androgen-dependent prostate cancer/common reference-12


title: androgen-dependent prostate cancer/common reference-11


title: androgen-dependent prostate cancer/common reference-13


title: androgen-dependent prostate cancer/common reference-10


title: androgen-dependent prostate cancer/common reference-5


title: androgen-dependent prostate cancer/common reference-7


title: androgen-dependent prostate cancer/common reference-8


title: Nomal prostate/common reference-1

status: Public on Sep 05 2007

description: normal prostate tissue versus common reference

source_name: normal prostate tissue

tag: normal prostate tissue from 20 voluntary donors with no history of prostate cancer

source_name: Common reference


title: androgen-dependent prostate cancer/common reference-3


title: Low Iron 960vs0_R

status: Public on Sep 01 2007

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in AF555 and AF647 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the iron stress time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].

hyb_protocol: AF555 and AF647 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were soaked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization

label: Alexa Fluor 555

organism: Xylella fastidiosa

source_name: low iron concentrarion, 960'

label_protocol: 20ug of total RNA was reverse transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain 9a5c isolated form CVC symptomatic Citrus (L.) Osbeck trees were grown in Periwinkle wilt (PW) broth media at 28oC with 80 rpm rotatory agitation. A culture started from a single colony was weekly passaged through serial transfers at a 1/10 dilution in PW medium.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) and residual DNA was removed by treatment with of RQ1 RNAse-free DNAse I (Promega) and RNAse inhibitor RNAseOUT (Invitrogen). The integrity of the RNA was checked by agarose gel electrophoresis, quantization performed with a NanoDrop spectrophotometer and the lack of residual DNA was checked by PCR.

treatment_protocol: Treated with 200 uM of 2,2-dipyridyl for 960 minutes.

tag: low iron concentrarion, 960'

label: Alexa Fluor 647

treatment_protocol: No treatment. Same as "Growth Protocol".


title: Low Iron 240vs0_R

source_name: low iron concentrarion, 240'

treatment_protocol: Treated with 200 uM of 2,2-dipyridyl for 240 minutes.

tag: low iron concentrarion, 240'


title: Low Iron 960vs0_L


title: Low Iron 240vs0_L


title: androgen-dependent prostate cancer/common reference-6


title: androgen-dependent prostate cancer/common reference-2


title: 49M - IRF2KO vs. Control - 6 hr LPS - repeat 2 - mAdbID:52350

city: Gaithersburg

first: Enrique

last: Zudaire

address: 8717 Grovemont Circle

department: CCR

institute: NIH

description: mAdb experiment ID: 52350

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: KO - LPS - 6 hr - repeat 2

label_protocol: Cy3 Sample Labeling Protocol - generic

extract_protocol:
Sample Extraction Protocol
Other: Extracted and purified using the RNeasy Mini Kit (Qiagen, Valencia,CA).

treatment_protocol:
Treatment type: compound
Agent: Lipopolysacharide (LPS)
Treatment dose: 35 mg/kg
Treatment time: 6 hours

tag: Strain

tag: Tissue

value: liver

tag: Developmental stage

value: adult

tag: Genotype/Genetic variation gene knock out

source_name: WT (Control) - LPS - 6 hr - repeat 2

label_protocol: Cy5 Sample Labeling Protocol - generic


title: Nomal prostate/common reference-3


title: Low Iron 0vs240_R


title: androgen-dependent prostate cancer/common reference-9


title: androgen-dependent prostate cancer/common reference-1


title: Nomal prostate/common reference-2


title: Low Iron 0vs960_L


title: Low Iron 0vs240_L


title: Low Iron 0vs015_R

source_name: low iron concentrarion, 15'

treatment_protocol: Treated with 200 uM of 2,2-dipyridyl for 15 minutes.

tag: low iron concentrarion, 15'


title: Low Iron 0vs960_R


title: Human colonocytes, Caco2 cells treated with L. plantarum for 2h, replicate 2

description: colonocytes cells, Caco2 cells

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Scan Array 5000 fluorescent scanner and image intensity data were extracted and analyzed with Imagene 4.2. analy

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the

label_protocol: The cDNA from Caco2 RNA and Caco2 L.plantarum treated RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH

growth_protocol: Caco2 cells cultured in DMEM containing 10% fetal calf serum. Cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 8 days and harvested by trypsin

extract_protocol: RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (30 ?g) was annealed with 5 ?g oligo dT12-18, and reverse-transcribed into cDNA with Superscript

extract_protocol: The RNA (30 ?g) was annealed with 5 ?g oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42?C in the presence of 0.5 mM dG


title: Low Iron 0vs060_L

source_name: low iron concentrarion, 60'

treatment_protocol: Treated with 200 uM of 2,2-dipyridyl for 60 minutes.

tag: low iron concentrarion, 60'


title: Low Iron 0vs015_L


title: Low Iron 0vs060_R


title: Low Iron 060vs0_L


title: Low Iron 015vs0_R


title: Low Iron 015vs0_L


title: High Iron 960vs0_R

source_name: high iron concentrarion, 960'

treatment_protocol: Treated with 100 uM of ferric pyrophosphate for 960 minutes.

tag: high iron concentrarion, 960'


title: Low Iron 060vs0_R


title: High Iron 0vs060_L

source_name: high iron concentrarion, 60'

treatment_protocol: Treated with 100 uM of ferric pyrophosphate for 60 minutes.

tag: high iron concentrarion, 60'


title: High Iron 0vs960_R


title: High Iron 240vs0_L

source_name: high iron concentrarion, 240'

treatment_protocol: Treated with 100 uM of ferric pyrophosphate for 240 minutes.

tag: high iron concentrarion, 240'


title: High Iron 0vs240_L


title: High Iron 240vs0_R


title: High Iron 960vs0_L


title: High Iron 0vs960_L


title: High Iron 0vs240_R


title: High Iron 0vs015_R

source_name: high iron concentrarion, 15'

treatment_protocol: Treated with 100 uM of ferric pyrophosphate for 15 minutes.

tag: high iron concentrarion, 15'


title: High Iron 0vs015_L


title: androgen-dependent prostate cancer/common reference-4


title: High Iron 060vs0_R

source_name: high iron concentrarion, 60' (Alexa Fluor 647)

source_name: 28oC (Alexa Fluor 555)

tag: 28oC (Alexa Fluor 555)


title: High Iron 0vs060_R


title: High Iron 060vs0_L

tag: high iron concentrarion, 60' (Alexa Fluor 647)


title: Self-self 0vs-0_R

source_name: 28oC (Alexa Fluor 647)

tag: 28oC (Alexa Fluor 647)


title: High Iron 015vs0_R

source_name: high iron concentrarion, 15' (Alexa Fluor 647)


title: Self-self 0vs-0_L


title: Self-self 0-vs0_R


title: Self-self 0-vs0_L


title: High Iron 015vs0_L

tag: high iron concentrarion, 15' (Alexa Fluor 647)


title: Self-self 0vs0_R


title: 45M - IRF2KO vs. Control - 3 hr LPS - repeat 2 - mAdbID:48594

description: mAdb experiment ID: 48594

source_name: WT (Control) - LPS - 3 hr - repeat 2

treatment_protocol:
Treatment type: compound
Agent: Lipopolysacharide (LPS)
Treatment dose: 35 mg/kg
Treatment time: 3 hours

source_name: KO - LPS - 3 hr - repeat 2


title: 47M - IRF2KO vs. Control - Saline - 6 hr - mAdbID:48115

description: mAdb experiment ID: 48115

source_name: WT (Control) - Saline - 6 hr

treatment_protocol:
Treatment type: compound
Agent: Saline
Treatment time: 6 hours

source_name: KO - Saline - 6 hr


title: 43M - IRF2KO vs. Control - 3 hr LPS - repeat 1 - mAdbID:48593

description: mAdb experiment ID: 48593

source_name: WT (Control) - LPS - 3 hr - repeat 1

source_name: KO - LPS - 3 hr - repeat 1


title: 44M - IRF2KO vs. Control - Saline - 3 hr - mAdbID:48595

description: mAdb experiment ID: 48595

source_name: WT (Control) - Saline - 3 hr

treatment_protocol:
Treatment type: compound
Agent: Saline
Treatment time: 3 hours

source_name: KO - Saline - 3 hr


title: Self-self 0vs0_L


title: mom1-1_noHPT_leaf

status: Public on Aug 29 2007

city: Tsukuba

first: Yoshiki

last: Habu

state: Ibaraki

address: Kannondai 2-1-2

department: Institute of Agrobiological Sciences

institute: National Agriculture and Food Research Organization

description: Gene expression data from mom1-1 mutant of Arabidopsis line carrying a 1'-bar transgene at MOM1 locus

hyb_protocol: The labeled samples were mixed with 0.1 mg/mLsonicated herring sperm DNA in a hybridization buffer containing 100 mM 2-N-morpholino-ethane-sulfonic acid (MES), 1 M NaCl, 20 mM EDTA, 0.01 % Tween 20, denatured at 99 °C for 5 min, and equilibrated at 45 °C for 5 min before hybridization. The hybridization mix was then transferred to the Arabidopsis GeneChip genome array (Affymetrix) cartridge and hybridized at 45 °C for 16 h on a rotisserie at 60 rpm. The hybridized arrays were then rinsed and stained in a fluidics station (Affymetrix). They were first rinsed with wash buffer A (6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA), 0.01 % Tween 20, 0.005 % Antifoam) at 25 °C for 10 min and incubated with wash buffer B (100 mM MES, 0.1 M NaCl, 0.01 % Tween 20) at 50 °C for 20 min, then stained with Streptavidin Phycoerythrin (SAPE) (100 mM MES, 1 M NaCl, 0.05 % Tween 20, 0.005 % Antifoam, 10 mg/mL SAPE, 2 mg/mL BSA) at 25 °C for 10 min, washed with wash buffer A at 25 °C for 20 min and stained with biotinylated anti-streptavidin antibody at 25 °C for 10 min. After staining, arrays were stained with SAPE at 25 °C for 10 min and washed with wash buffer A at 30 °C for 30 min. The probe arrays were scanned twice and the intensities were averaged with a Hewlett-Packard GeneArray Scanner. (Zhu et al. (2001) Plant Physiol Biochem 39:222-242)

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

data_processing: The data were analyzed with Microarray Suite version 4.0 (MAS 4.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: seedlings, accession : Zurich, line: mom1-1 without HPT(Amedeo et al. (2000) Nature 405:203-206)

label_protocol: Biotinylated complementary RNAs (cRNAs) were in vitro transcribed from synthesized cDNA by T7 RNA polymerase (ENZO BioArray High Yield RNA Transcript Labeling Kit, Enzo). cRNAs were purified using affinity resin (Qiagen RNeasy Spin Columns) and randomly fragmented by incubating at 94 °C for 35 min in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to produce molecules of approximately 35 to 200 bases long. (Zhu et al. (2001) Plant Physiol Biochem 39:222-242)

growth_protocol: Plants were grown on soil at 22°C under a 12-hr light/dark cycle and 70 % humidity

extract_protocol: RNeasy (Qiagen) according to the manufacturer protocol

tag: Seeds were sown on soil and leaves of 3-week-old seedlings were used for total RNA extraction


title: mom1-1_leaf

description: Gene expression data from mom1-1 mutant of Arabidopsis line carrying silent HPT transgenes at A locus and a 1'-bar transgene at MOM1 locus

source_name: seedlings, accession : Zurich, line: mom1-1 (Amedeo et al. (2000) Nature 405:203-206)


title: ddm1-5_leaf

description: Gene expression data from ddm1-5 (som8) mutant of Arabidopsis line carrying silent HPT transgenes at A locus

source_name: seedlings, accession : Zurich, line: ddm1-5 (som8) (Mittelsten Scheid et al. (1998) Proc Natl Acad Sci USA 95:632-637)


title: androgen-independent prostate cancer/common reference-6

source_name: androgen-independent prostate cancer

tag: androgen-independent prostate cancer

source_name: common reference

tag: a pool of RNA from mixed human embryo tissues


title: WT7.2

status: Public on Aug 22 2007

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

country: Germany

institute: Institute for Medical Microbiology

description: blood samples were collected on admission to the ICU (that is 12 hours after trauma) in PAXgene Blood RNA System tubes (PreAnalytiX, Heidelberg, Germany) and stored at -80?C according to the   manufacturer?s recommendations (PreAnalytiX)

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94?C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37?C, 300 rpm. cRNA was hybridized onto microarrays at least in duplicate (technical replicates).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: A total of 22 patient samples were subjected to microarrays with at least two technical replicates per sample (total 58 arrays). Spot signals of CodeLink bioarrays were quantified using CodeLink System Software ? Batch Submission (V2.2.27) and ? Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as median centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Furthermore, the software flagged each gene value as GOOD, EMPTY, POOR, NEG or MSR defining quality measures. Only gene values flagged as GOOD or EMPTY were used for the analysis. Patients (arrays) were separated in two groups: A) 12 patients without the TNF rs1800629 A variant and B) 10 patients carrying the TNF rs1800629 A variant. Genes with missing values >= 50% of all arrays in a group were excluded from the analysis. Genes that were flagged as FALSE in > 50% of arrays in each group were also excluded from the analysis. These procedures revealed a filtered set of 8551 genes (Set1). Missing values in this filtered set were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). To detect outlier values for a particular gene in a group, all gene values > median + 3 standard deviations (SD) or < median -3 SD were flagged as BLANK. Exempted from this rule were those gene values being consistently > median + 3 SD or < median -3 SD in all technical replicates of a patient since the consistency of these values in all technical replicates of the same sample was considered as a biological feature rather than a technical outlier. All gene values that were flagged as BLANK were removed in Set1 which was then subjected to SKNN imputation. Finally, this set of 8551 genes was normalized using quantiles normalization in R (Bolstad et al. 2003) and logged (base 2).

source_name: peripheral blood

label_protocol: Total RNA were subjected to cDNA synthesis using a poly-A binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with the NanoDrop (NanoDrop Technologies) and quality was assesed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

extract_protocol: Total RNA was extracted from the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany) using the  manufacturer?s recommendations (PreAnalytiX). Total RNA was quantified with Nanodrop (NanoDrop Technologies, Rockland DE, USA) and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies GmbH, Boeblingen, Germany)

tag: Human peripheral blood collected in PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany)


title: LineA_leaf

description: Gene expression data from an Arabidopsis line carrying silent HPT transgenes at A locus

source_name: seedlings, accession : Zurich, line: A (Mittelsten Scheid et al. (1998) Proc Natl Acad Sci USA 95:632-637)


title: Zurich_leaf

source_name: seedlings, accession : Zurich


title: WT7.1


title: 46M - IRF2KO vs. Control - 6 hr LPS - repeat 1 - mAdbID:48114

description: mAdb experiment ID: 48114

source_name: WT (Control) - LPS - 6 hr - repeat 1

tag: Strain

tag: Tissue

source_name: KO - LPS - 6 hr - repeat 1


title: Human PBMC treated with Mycobacterium leprae, replicate 3

city: Rio de Janeiro

first: Ulisses

middle: Gazos

last: Lopes

state: Rio de Janeiro

address: Cidade Universitaria- CCS

department: Molecular and Structural Biology

institute: Federal University of Rio de Janeiro

description: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray GX confocal scanner (Packard/Perkin Elmer) and image intensity data were extracted and analysed with Quant Array software

hyb_protocol: Labeled cDNAs were mixed in hybridization buffer, Hybit 2 with formamide (ref HH52, http://arrayit.com ), 18H , 42C. Washing in SSC1X, SDS 0,05% (twice) and SSC 0,06X (once)

data_processing: After background correction, log base 2 expression ratios were taken to obtain the log values given in the data table

source_name: PBMC from Human donors

label_protocol: CyScribe First-srand cDNA labeling Kit (GE Healthcare) and labeled cDNA was purified with GFX columns (GE Healthcare)

extract_protocol: TRIZOL reagent, 1mL/10e6 cells

treatment_protocol: Human PBMC were isolated from Human donors by FICOLL /HYPAQUE gradient. 3X10e7 cells were seeded in 20 mL of RPMI medium supplemented with 10% FCS for 24 H

tag: Human PBMC isolated from healthy donors by FICOLL/HYPAQUE and seeded in RPMI supplemented with 10% of FCS and treated with Mycobacterium leprae

source_name: Human PBMC

treatment_protocol: Human PBMC were isolated by FICOLL/HYPAQUE gradient. 3X10e7 cells were seeded in RMPI medium supplemented with 10% FCS for 24 H. Cells were exposed to M. leprae (MOI 2:1) for 4 H


title: Human PBMC treated with Mycobacterium leprae, replicate 2

tag: Human PBMC isolated from healthy donors by FICOLL/HYPAQUE and seeded in RPMI supplemented with 10% of FCS

source_name: Human PBMC treated with M. leprae

tag: Human PBMC isolated from healthy donors and exposed to M. leprae (MOI 2:1) for 4 hours


title: Human PBMC treated with Mycobacterium leprae, replicate 1


title: WT8.1


title: WT9.2


title: WT9.1


title: MUT10.2


title: MUT8.3


title: MUT7.1


title: MUT8.2


title: MUT8.1


title: MUT10.1


title: MUT7.2


title: MUT5.3


title: MUT4.3


title: MUT5.1


title: MUT5.2


title: WT6.2


title: MUT6.1


title: WT6.3


title: MUT7.3


title: WT5.1


title: MUT6.2


title: WT5.2


title: MUT6.3


title: MUT4.1


title: WT5.3


title: MUT4.2


title: WT4.1


title: WT4.3


title: WT6.1


title: MUT2.3


title: MUT9.1


title: MUT9.2


title: WT3.1


title: WT3.3


title: MUT1.3


title: WT3.2


title: MUT2.2


title: MUT2.1


title: WT11.2


title: WT12.2


title: MUT1.2


title: WT1.1


title: 10min (additional)

status: Public on Aug 01 2007

city: Madison

first: Kai

last: Zhao

state: WI

address: 2100 University Avenue

department: Oncology

institute: Mcardle Laboratory for Cancer Research

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from a seperate culture subject to 10 minutes induction by anhydrotetracycline.

source_name: E. coli cell


title: 15min (additional)

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from a seperate culture subject to 15 minutes induction by anhydrotetracycline.


title: MUT3.1


title: MUT3.2


title: WT1.2

description: blood samples were collected on admission to the ICU (that is 12 hours after trauma) in PAXgene Blood RNA System tubes (PreAnalytiX, Heidelberg, Germany) and stored at -80°C according to the   manufacturer’s recommendations (PreAnalytiX)

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94°C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37°C, 300 rpm. cRNA was hybridized onto microarrays at least in duplicate (technical replicates). "

data_processing: A total of 22 patient samples were subjected to microarrays with at least two technical replicates per sample (total 58 arrays). Spot signals of CodeLink bioarrays were quantified using CodeLink System Software – Batch Submission (V2.2.27) and – Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as median centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Furthermore, the software flagged each gene value as GOOD, EMPTY, POOR, NEG or MSR defining quality measures. Only gene values flagged as GOOD or EMPTY were used for the analysis. Patients (arrays) were separated in two groups: A) 12 patients without the TNF rs1800629 A variant and B) 10 patients carrying the TNF rs1800629 A variant. Genes with missing values >= 50% of all arrays in a group were excluded from the analysis. Genes that were flagged as FALSE in > 50% of arrays in each group were also excluded from the analysis. These procedures revealed a filtered set of 8551 genes (Set1). Missing values in this filtered set were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). To detect outlier values for a particular gene in a group, all gene values > median + 3 standard deviations (SD) or < median -3 SD were flagged as BLANK. Exempted from this rule were those gene values being consistently > median + 3 SD or < median -3 SD in all technical replicates of a patient since the consistency of these values in all technical replicates of the same sample was considered as a biological feature rather than a technical outlier. All gene values that were flagged as BLANK were removed in Set1 which was then subjected to SKNN imputation. Finally, this set of 8551 genes was normalized using quantiles normalization in R (Bolstad et al. 2003) and logged (base 2).

extract_protocol: Total RNA was extracted from the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany) using the  manufacturer’s recommendations (PreAnalytiX). Total RNA was quantified with Nanodrop (NanoDrop Technologies, Rockland DE, USA) and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies GmbH, Boeblingen, Germany)


title: WT12.1


title: 10min

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from culture subject to 10 minutes induction by anhydrotetracycline.


title: WT10.1


title: WT2.3


title: control

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from pre-induction culture to serve as control (0 munites induction).


title: slide6_63dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

status: Public on Jul 27 2007

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Total RNA was isolated using TRI Reagent (Sigma Aldrich) according to the manufacturer’s protocol. After DNAse treatment RNA was quantified and integrity checked by electrophoresis of 1 µg RNA on 1% agarose gels containing formaldehyde stained with ethidium bromide. mRNA was isolated from total RNA using magnetic oligo-(dT)-bead (Dynabeads, Dynal). Pools of 1 µg of mRNA of each group of animals were labelled with Cy3 or Cy5 using the CyScribe Post-Labeling Kit (GE Healthcare), which involves the use of oligo-(dT) primers and random nanomers for synthesis of amino allyl-labelled first-strand cDNA and coupling of cDNA with CyDye NHS ester. Cy3/Cy5 labelled cDNAs were purified used CyScribe GFX purify kit (GE Healthcare). Cy3- and Cy5-labelled cDNAs were hybridised to the set of 13297 pig-specific 70-mer oligonucleotides (Qiagen-NRSP8) at 42 °C for 14–18 hours using the Pronto Universal Hybridization kit was used (Corning B.V. Life Science). Hybridized slides were washed once with 1× SSC, 0.2% (w/v) SDS for 10 minutes at 42 °C and twice with 0.1× SSC, 0.2% (w/v) SDS. Finally, slides were dipped into distilled water and air-dried.

data_processing: Microarrays were scanned using the 428 Array Scanner (Affymetrix). Spots were quantified and quality filtering was applied using ImaGene5 software version 5.6 (BioDiscovery). Each spot had to pass a number of quality criteria including spot consistency, minimum intensity levels, and minimum signal-to-background ratio. The subtracted signal median of genes that passed filtering was analysed further with TIGR Microarray Data Analysis System (MIDAS) that allows performing normalisation steps: per spot, intensity dependent (lowess fit). Filtered and normalized expression data were analyzed using TIGR Multiexperiment Viewer (MEV). The t-test was conducted of each stage and the set of p-values for each stage was converted to a set of q values using the software program QVALUE. To compare all stages between DL and Pi, variance analysis (ANOVA, p < 0.05) was used and these subsequent analyses were compared using hierarchical clustering.

molecule: polyA RNA

organism: Sus scrofa

tag: 3rd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 63 dpc

tag: 3rd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 63 dpc


title: WT11.1


title: 5min

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from culture subject to 5 minutes induction by anhydrotetracycline.


title: MUT3.3


title: WT10.2


title: slide4_63dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 1st pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 63 dpc

tag: 1st pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 63 dpc


title: WT2.2


title: WT2.1


title: Bovine_H893_cy5_861_cy3

status: Public on Jun 30 2007

city: Columbia

first: Zhilin

last: Liu

state: MO

address: 920 East Campus Dr., ASRC S140

institute: University of Missouri-Columbia

description: The hybridization was carried out using the 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA) according to the manufacture?s instructions. For each hybridization, 5?g of total RNA of each follicle sample were used. After hybridization, the slides were scanned using an Axon GenePix 4000B scanner (Axon Instruments Inc., Union City, CA) at 5?m resolution, and the image was analyzed using GenePix Pro 4.0.1.12 software (Axon Instruments Inc., Union City, CA). The result files and the image were linked together and stored in the local BioArray Software Environment (BASE) database (Saal et al., 2002).

data_processing: The result data were first filtered to remove all control spots, 3נSSC, and blank spots. Then the background-corrected-median-intensities were normalized using a pin-based-lowess-normalization within BASE. The log ratio of chanel 1 VS. chanel 2 were then outputed together with the raw data for each spot of all the arrays.

organism: Bos taurus

source_name: Bovine ovarian follicle H893

extract_protocol: RNAqueous-Midi kit, (Ambion Inc., Austin, Texas)

tag: ovarian follicle,  9mm, tube A, weight 0.0469g

source_name: Bovine ovarian follicle 861

tag: ovarian follicle,  8.5mm, tube A, weight 0.0604g


title: TSA 0 Control 2

status: Public on Aug 02 2007

address: Gaffky Str. 20

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94gr.C for 20 minutes. For hybridization on CodeLink bioarrays, 10 μg of fragmented cRNA in 260 μl of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37gr.C / 300 rpm. cRNA of each group was hybridized in duplicate (technical replicates). In total, 10 bioarrays (2 arrays per group) were processed in parallel using the CodeLink Shaker Kit and CodeLink Parallel Processing Kit (Amersham Biosciences).

data_processing: Spot signals of the CodeLink bioarrays were quantified using CodeLink Expression Software 1.21 based on ImaGene 5.5 (BioDiscovery, Marina Del Ray, CA). The image segmentation and quantification process is outlined in the ImaGene 5.5 user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds (0.062 to 0.211) for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Data of 10 arrays (two replicates per group) were subjected to data analysis. Genes with missing values >= 50% in all arrays were excluded from the analysis. The remaining missing values were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). Microarray data containing 9897 genes were normalized using quantiles normalization in R (Bolstad et al. 2003).

source_name: testis

growth_protocol: Animals were kept under controlled conditions of light, temperature and humidity receiving water and standard food ad libitum.

extract_protocol: Total RNA was extracted from frozen tissue of 3 animals per group using the RNeasy Mini Kit (Qiagen, Germany). The material from each group was pooled. Both quality and quantity of RNA was checked by Agilent 2100 Bioanalyzer and UV spectrophotometer.

treatment_protocol: TSA was resolved in dimethylsulfoxide and PBS. 15 animals were divided into 5 groups each containing 3 mice. Group 1 received only the carrier and were sacrificed after 10h (control). Groups 2 - 5 received 60ug/day/mouse TSA applied by one subcutaneous injection and were sacrificed after 2.5h (group 2), 5h (group 3), 7.5h (group 4) and 10h (group 5).

tag: Balb-c mice, age

value: 9 week, gender:male, tissue:testis


title: WT1.3


title: 5min (additional)

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from a seperate culture subject to 5 minutes induction by anhydrotetracycline.


title: 15min

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from culture subject to 15 minutes induction by anhydrotetracycline.


title: control (additional)

description:
This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). Purified RNA was reverse-transcribed to cDNA, labeled and hybridized to Affymetrix GeneChip E. coli Antisense Genome Arrays as recommended in the technical manual (www.affymetrix.com). Meanwhile, we measured the protein level of sigma32 during the time course. The changes of some sigma32?dependent genes were also determined in a DnaK null mutant to examine the anti-sigma function of the gene.
This sample is taken from pre-induction culture to serve as control.


title: WT4.2


title: slide5_63dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 2nd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 63 dpc

tag: 2nd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 63 dpc


title: WT8.2


title: NFIA P16WT3

status: Public on Mar 30 2007

city: Hamburg

first: Yong Wee

last: Wong

address: 94 Falkenried Str

institute: Center for Molecular Neurobiology

description: Total RNA extracted from mouse brain

hyb_protocol: Procedures for cDNA synthesis, labeling and hybridization were carried out according to the manufacturer's protocol (Affymetrix). All experiments were performed using Affymetrix mouse genome Genechip U74A version 2. Briefly, 15mg of total RNA were used for first strand cDNA synthesis with an HPLC-purified T7-(dT)24 primer. Synthesis of biotin-labeled cRNA was carried out using the ENZO RNA transcript labeling kit (Affymetrix). For hybridization, 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45oC for 16 hours. Genechips were washed and stained with streptavidin-phycoerythrin using the microfluidic workstation™ (Affymetrix) and scanned with a laser scanner (Agilent Technologies).

data_processing: RMA, normalised to 50th percentile

source_name: NFIA P16WT3

extract_protocol: Total RNA was extracted from the entire brain of NF-I-A-deficient and wild-type control mice (n=3 each) using TRIzol (Invitrogen) according to the manufacturer’s instructions. Further purification of RNA was performed with the RNeasy Mini Kit (Qiagen). Total RNA concentration was determined using a spectrophotometer at 260 nm and 280 nm wavelength. To check RNA integrity, total RNA was separated in a 1% agarose gel containing formaldehyde, and the intensity ratio of 28S and 18S ribosomal RNA bands was assessed after ethidium bromide staining.

tag: cRNA

tag: postnatal day 16

tag: WT


title: NMC_3

status: Public on Apr 01 2007

city: Chiyoda-ku

first: Naoki

last: Tanimura

address: 2-3 Kanda-Nishikicho

department: Science Solutions Division

institute: Mizuho Information & Research Institute, Inc.

description: SM/C-2.6 is described in Exp. Cell Res. 2004 296(2); 245-255. Mouse 430A array was used.

hyb_protocol: 45･C x 16hr (Hybridization oven 640)

data_processing: Affymetrix MAS 5.0 with p-value cuttoffs of 0.04 and 0.06 for present, marginal, and absent.

source_name: Non myogenic cells

label_protocol: Used Affymetrix two-cycle biotin aRNA synthesis kit.

extract_protocol: Used Qiagen Rneasy Mini Kit according to instructions therein.

tag: Strain

tag: Age

value: 8--12 weeks

tag: Cell

value: SM/C-2.6 (-)CD45(-) cells from hind limb muscles, immediately after sorting. <1% cells are myogenic cells.


title: NFIA P16WT2

description: Total RNA extracted from mouse brain

source_name: NFIA P16WT2


title: QSC_2

scan_protocol: GeneArray Scanner

source_name: Satellite cells in quiescent state

label_protocol: GeneChip® Eukayotic Small Sample Target Labeling Assay Version II

value: SM/C-2.6 (+) cells from hind limb muscles, immediately after sorting .  >97% cells are Pax7(+)


title: NMC_4


title: NMC_2


title: ASC_1

source_name: Satellite cells in activated state

growth_protocol: DMEM, 20% FCS, 2.5ng/ml bFGF

value: SM/C-2.6 (+)cells from hind limb muscles, cultured for 4 days.  >99% cells are MyoD(+).


title: QSC_4


title: NMC_1


title: ASC_4


title: NFIA P16KO3

description: Total RNA extracted from mouse brain

source_name: NFIA P16KO3

tag: NFIA deficient


title: ASC_2


title: NFIA P16KO1

description: Total RNA extracted from mouse brain

source_name: NFIA P16KO1


title: NFIA P16KO2

description: Total RNA extracted from mouse brain

source_name: NFIA P16KO2


title: NFIA E18WT1

description: total RNA extracted from mouse brain

data_processing: RMA, nomralised to 50th percentile

source_name: NFIA E18WT1

tag: embryonic day 18


title: QSC_3


title: NFIA P16WT1

description: Total RNA extracted from mouse brain

source_name: NFIA P16WT1


title: NFIA E18KO1

description: RNA extracted from mouse brain

data_processing: RMA, normalized by 50th percentile

source_name: NFIA E18KO1


title: NFIA E18KO3

description: total RNA extracted from mouse brain

source_name: nfia E18KO3


title: ASC_3


title: QSC_1

label_protocol: GeneChip® Eukayotic Small Sample Target Labeling Assay Version II.


title: genotype A35 developing seed at 5 days after anthesis, biological rep1

status: Public on Mar 25 2007

city: Winnipeg

first: Mark

last: Jordan

state: Manitoba

address: 195 Dafoe Rd.

department: Cereal research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description: Gene expression data from field grown developing seeds 5 days after anthesis

hyb_protocol: Following fragmentation, the labelled samples were mixed with 0.1 mg/ml sonicated herring sperm DNA in hybridization buffer (100mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCL, 20mM EDTA, 0.01% Tween 20, 0.5 mg/ml BSA, 10% DMSO), denatured at 99°C for 5 min then added to GeneChip Wheat Genome Array (Affymetrix) according to manufacturer instructions and hybridized for 16 h at 45°C in a rotisserie oven at 60 rpm. Following hybridization the arrays were washed and stained in the Affymetrix fluidics station 450 according to standard protocol (Section 2.3.3 of the Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000.

data_processing: The raw data in the Affymetrix CEL files of all 78 arrays representing two biological replicates of each of 39 genotypes were subjected to quantile normalization using Robust Multi-Array Average (RMA) (Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193) followed by normalization to the median.

organism: Triticum aestivum

source_name: developing seed collected from field grown material 5 days after anthesis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix). mRNA was used for first and second strand cDNA synthesis using the One Cycle cDNA Synthesis Kit (Affymetrix, http://www.affymetrix.com) following the manufacturers instructions. The resulting cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) according to instructions and then used to make purified biotin labelled cRNA using the GeneChip IVT labelling kit and the GeneChip Sample Cleanup Module (Affymetrix). The resulting labelled cRNA was quantified and the yield and size distribution of labelled fragments checked by electrophoresis using the Agilent Bioanalyzer. The labelled cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and stored at -20°C.

growth_protocol: The 39 lines and parental lines were grown as 1.47 m rows in three replications in a 7x7 (49 entry) lattice design at Winnipeg, Manitoba in 2004. Each replicate had a unique randomization

extract_protocol: Total RNA was extracted from frozen seed using a modification of the protocol described at http://plantsciences.montana.edu/wheat-transformation/molecular.htm. The content of a 2 mL tube full of frozen seeds was ground to a fine powder in liquid nitrogen using a mortar and pestle. Ground seed was transferred to 50 mL Oak Ridge tubes and 7.5 mL of extraction buffer was added. [50 mL Extraction Buffer contained 35 mL nuclease-free water, 2.5 mL 1M Tris, pH 9.0. 5 mL 2M NaCl, 5 mL 10% Sarcosyl, 2 mL 0.5M EDTA,  pH 8.0, 250 ?L 1M DTT]. After vortexing well, 3.75 mL phenol and 3.75 mL chloroform/isoamyl alcohol (49:2) were added and samples vortexed again. Samples were centrifuged 10 min at 13,000 rpm in a Sorvall model RC5C at 4 using an SS-34 rotor. A total of 7.5 mL of the upper aqueous phase was transferred to a clean Oak Ridge tube, 15 mL Trizol was added and the sample was vortexed. A volume of 3 mL of choloroform was added and the sample was vortexed again. Samples were centrifuged 10 min at 13,000 rpm in the Sorvall at 4. A volume of 15 mL of the upper aqueous phase was transferred to a fresh Oak Ridge tube and 10 mL of chloroform was added and the sample was vortexed. Samples were centrifuged again in the Sorvall at 13,000 rpm for 10 min at 4. A volume of 12 mL of the upper phase was transferred to a fresh Oak Ridge tube and the RNA precipitated by adding 1,200 uL of 3M sodium acetate and 24 mL of absolute ethanol. Samples were left at -80 overnight then centrifuged at 14,000 rpm at 4 in the Sorvall for 20-30 minutes to precipitate the RNA. The pellet was rinsed with 70% ethanol, lightly dried and re-suspended in 1 mL of nuclease-free water. RNA concentration was quantified using a spectrophotometer. All solutions and equipment used in this procedure were RNAse-free. Messenger RNA was enriched from total RNA using the Poly(A) Purist MAG kit  (Ambion, http://www.ambion.com) according to the protocol provided by the manufacturer. Messenger RNA was checked for quality and quantified by micro-chromatography using an Agilent 2000 Bioanalyzer and the RNA 6000 Nano Assay Kit both purchased from Agilent Technologies (http://www.agilent.com). Quantification was carried out according to the instructions provided with the kit.

treatment_protocol: spikes were tagged when anthers were visible, enough developing seeds to fill a 2mL tube were isolated from each spike 5 days after tagging and flash frozen in liquid nitrogen

tag: Genotype

value: A35 from RL4452 x AC Domain mapping population

value: developing seed 5 days after anthesis


title: genotype A35 developing seed at 5 days after anthesis, biological rep2


title: NFIA E18WT2

description: total RNA extracted from mouse brain

source_name: NFIA E18WT2


title: NFIa E18KO2

description: RNA extracted from brain

source_name: nfia E18KO2


title: genotype F87 developing seed at 5 days after anthesis, biological rep1

value: F87 from RL4452 x AC Domain mapping population


title: genotype F87 developing seed at 5 days after anthesis, biological rep2


title: genotype F82 developing seed at 5 days after anthesis, biological rep1

value: F82 from RL4452 x AC Domain mapping population


title: genotype F38b developing seed at 5 days after anthesis, biological rep1

value: F38b from RL4452 x AC Domain mapping population


title: genotype A91 developing seed at 5 days after anthesis, biological rep2

value: A91 from RL4452 x AC Domain mapping population


title: genotype A91 developing seed at 5 days after anthesis, biological rep1


title: genotype H8 developing seed at 5 days after anthesis, biological rep2

value: H8 from RL4452 x AC Domain mapping population


title: genotype G13 developing seed at 5 days after anthesis, biological rep2

value: G13 from RL4452 x AC Domain mapping population


title: genotype C10 developing seed at 5 days after anthesis, biological rep2

value: C10 from RL4452 x AC Domain mapping population


title: genotype B33 developing seed at 5 days after anthesis, biological rep2

value: B33 from RL4452 x AC Domain mapping population


title: genotype F38b developing seed at 5 days after anthesis, biological rep2


title: genotype C10 developing seed at 5 days after anthesis, biological rep1


title: genotype H8 developing seed at 5 days after anthesis, biological rep1