title: PZQ 240 min B

city: Albuquerque

first: Anthony

last: Aragon

address: Castetter Hall Room 214

institute: University of New Mexico

description: PZQ 240 min B

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes.  Labeled cDNA was hybridized overnight at 42°C, to 7,066 S. japonicum and 12,166 S. mansoni element oligonucleotide arrays purchased from Agilent Technologies and described by Gobert and colleagues. Only the S. mansoni elements were considered in the analyses.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues.

data_processing: A preloaded S. mansoni grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians.

organism: Schistosoma mansoni

source_name: Adult Schistosoma mansoni

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Schistosome infected mice were supplied by NIAID Schistosomiasis Resource Center at the Biomedical Research Institute (Rockville, MD), through NIAID contract NO1-A1-30026. The abdomens of female SW mice were exposed to 125 S. mansoni PR-1 cercaria. Six weeks post-exposure, mice were anesthetized and worms harvested by cardiac perfusion with enriched, RPMI media (RPMI 1640 containing 20% fetal calf serum, 100 IU penicillin, 10µg/mL streptomycin). Mice were subsequently euthanized by cervical dislocation. All animal experimentation complied with the policies, regulations and guidelines mandated by the Institutional Animal Care and Use Committee, University of New Mexico. Prior to all experiments, adult worms were allowed to recover overnight in enriched RPMI media at 37 ºC in a water jacketed incubator with 5% CO2.

extract_protocol: RNA was isolated from thawed worms using an RNeasy® Mini kit (Qiagen) according to the manufacturer’s instructions, eluted with 30 µL of RNase free distilled water (dH2O) and quantified using a NanoDrop® ND-1000 spectrophotometer using ND-1000 3.3 soft-ware (NanoDrop Technologies). RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip® Kit (Agilent Technologies).

treatment_protocol: To determine the transcriptomic response of schistosomes to a sub-lethal dose of PZQ, duplicate groups (n=30, 15 male and 15 female) were exposed to a sub-lethal dose (50 µg/mL) of PZQ for 0 (prior to the addition of PZQ), 30, 60, and 240 min

tag: Adult Schistosoma mansoni PR1 strain

source_name: Reference

tag: Reference sample RNA consisted of a mixture of RNA from worms, following recovery, that were exposed to 37°C for 3.5 hours, 42°C for 3.5 hours, PAMPs (50µg/ml peptidoglycan

value: LPS:laminarin) for 6.0 hours, and PZQ (40µg/ml) for 0.5 hours at 37°C.


title: Untreated for 6h, biological rep3 (S3)

status: Public on Nov 10 2008

type: RNA

city: Bethesda

first: Xingmin

last: Feng

state: MD

address: 9000 Rockville Pike

country: USA

institute: National Institutes of Health

description: Gene expression data from untreated PBMC.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was extracted with the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: untreated for 6h


title: PZQ 0 min B

state: NM

description: PZQ 0 min B


title: PZQ 60 min B

description: PZQ 60 min B


title: PZQ 30 min B

description: PZQ 30 min B


title: PZQ 240 min A

description: PZQ 240 min A


title: LNCaP - GFP, Day2, U133B

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: no additional information

hyb_protocol: as described by Affymetrix

scan_protocol: as described by Affymetrix

data_processing: GCRMA normalization

source_name: LNCaP - GFP cDNA D2

label_protocol: as described by Affymetrix

growth_protocol: LNCaP cells were grown in the presence of T-medium (invitrogen)

extract_protocol: total RNA was extracted using the Qiagen RNeasy Mini Kit

treatment_protocol: LNCaP cells were transfected with either a SOX4 cDNA, a pool of siRNAs against SOX4 or a GFP control cDNA using DMRIE-C (Invitrogen).  24 hours post-transfection total RNA was harvested and Affymetrix expression profiling performed

tag: LNCaP prostate cancer cells


title: PZQ 30 min A

description: PZQ 30 min A


title: PZQ 60 min A

description: PZQ 60 min A


title: Untreated for 6h, biological rep1 (S1)


title: LNCaP - GFP, Day1, U133B

description: no additional information

source_name: LNCaP - GFP cDNA D1


title: PZQ 0 min A

description: PZQ 0 min A


title: Mature worm harfasted 6 weeks post infection D

data_processing: A preloaded S. mansoni grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians. Differentially expressed genes were evaluated using Significance Analysis of Microarrays (SAM), with a significance cutoff of a 2-fold increase or decrease in the 4 week p.i. sample relative to the 6 week p.i. sample.

growth_protocol: Schistosome infected mice were supplied by NIAID Schistosomiasis Resource Center at the Biomedical Research Institute (Rockville, MD), through NIAID contract NO1-A1-30026. The abdomens of female SW mice were exposed to 125 S. mansoni PR-1 cercaria. Four and six weeks post-exposure, mice were anesthetized and worms harvested by cardiac perfusion with enriched, RPMI media (RPMI 1640 containing 20% fetal calf serum, 100 IU penicillin, 10µg/mL streptomycin). Mice were subsequently euthanized by cervical dislocation. All animal experimentation complied with the policies, regulations and guidelines mandated by the Institutional Animal Care and Use Committee, University of New Mexico. Prior to all experiments, adult worms were allowed to recover overnight in enriched RPMI media at 37 ºC in a water jacketed incubator with 5% CO2.

treatment_protocol: To determine the transcriptomic differences between juvenile and mature schistosomes were harvasted 4 and 6 weeks p.i., allowed to recover over night prior to RNA isolation

tag: Reference sample RNA consisted consisted of 99% total RNA from 6 week p.i. worms with the remaining 1% coming from 4 week p.i. worms


title: Mature worm harfasted 6 weeks post infection A


title: Immature worm harvasted 4 weeks post infection D

source_name: Immature Schistosoma mansoni

tag: Immature Schistosoma mansoni PR1 strain


title: 10 ug/mL rATG treated for 24h, biological rep1 (S1)

description: Gene expression data from rATG-treated PBMC.

tag: rATG-treated for 24h


title: 10 ug/mL rATG treated for 24h, biological rep3 (S3)


title: 10 ug/mL rATG treated for 24h, biological rep2 (S2)


title: 10 ug/mL hATG treated for 24h, biological rep3 (S3)

description: Gene expression data from hATG-treated PBMC.

tag: hATG-treated for 24h


title: Mature worm harfasted 6 weeks post infection B


title: Mature worm harfasted 6 weeks post infection C


title: Immature worm harvasted 4 weeks post infection A


title: Immature worm harvasted 4 weeks post infection C


title: 10 ug/mL hATG treated for 24h, biological rep2 (S2)


title: LNCaP GFP hybridization 2 Replicate 2

description: Biological Replicate 2 of 3, Hybridization 2 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection

hyb_protocol: standard Illumina hybridization protocol

scan_protocol: standard Illumina scanning protocol

data_processing: Data processing performed with BeadStudio v3.1.3

source_name: LNCaP prostate cancer cells transfected with GFP, 24 hrs

label_protocol: standard Illumina labeling protocol

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: LNCaP cells were transfected with 500 ng of either a SOX4 or GFP expression vector using Lipofectamine2000 (Invitrogen) and total RNA harvested 24 hours post-transfection


title: Immature worm harvasted 4 weeks post infection B


title: Adult_vs_Neonatal (Slides 7 & 8)

type: other

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Foal 2 Articular Cartilage 635
Source_name_ch2 = Adult D052 Articular Cartilage 532
Source_name_ch1 = Adult D052 Articular Cartilage 635
Source_name_ch2 = Foal 2 Articular Cartilage 532

hyb_protocol: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized 48 hours at 42C

scan_protocol: DyeSaver2 was applied to each slide with one dip.  Slides were scanned with a Molecular Devices GenePix Personal 4100A Scanner using GenePix Pro 5.0

data_processing: Data analyzed by bottom-row lowess normalization, followed by SAS-based one sample t-test.

label: AlexaFluor647, AlexaFluor555

molecule: other

organism: Equus caballus

source_name: Adult Articular Cartilage

label_protocol: Invitrogen Indirect PLUS Labeling

extract_protocol: Amplified RNA from total RNA

tag: Tissue

value: Articular cartilage from a 4 year old Thoroughbred stallion ("D052" U-K stallion)

label: AlexaFluor555, AlexaFluor647

source_name: Foal Articular Cartilage

value: Articular cartilage from a 1 day old Thoroughbred filly


title: 2.5 ug/mL hATG treated for 6h, biological rep3 (S6)

tag: hATG-treated for 6h


title: LNCaP - SOX4 siRNA, Day1, U133A

description: no additional information

source_name: LNCaP - SOX4 siRNA D1


title: Adult_vs_Neonatal (Slides 9 & 10)

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Foal 8 Articular Cartilage 635
Source_name_ch2 = Horse C064 Articular Cartilage 532
Source_name_ch1 = Horse C064 Articular Cartilage 635
Source_name_ch2 = Foal 8 Articular Cartilage 532

value: Articular cartilage from a 4 year old Thoroughbred gelding ("C064" U-K gelding)

value: Articular cartilage from a 0 day old Thoroughbred filly


title: LNCaP - SOX4 cDNA, Day1, U133A

description: no additional information

source_name: LNCaP - SOX4 cDNA D1


title: LNCaP GFP hybridization 1 Replicate 3

description: Biological Replicate 3 of 3, Hybridization 1 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection


title: 10 ug/mL hATG treated for 24h, biological rep1 (S1)


title: LNCaP GFP hybridization 2 Replicate 1

description: Biological Replicate 1 of 3, Hybridization 2 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection


title: LNCaP - SOX4 siRNA, Day2, U133A

description: no additional information

source_name: LNCaP - SOX4 siRNA D2


title: LNCaP GFP hybridization 2 Replicate 3

description: Biological Replicate 3 of 3, Hybridization 2 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection


title: LNCaP - SOX4 cDNA, Day2, U133A

description: no additional information

source_name: LNCaP - SOX4 cDNA D2


title: LNCaP - SOX4 cDNA, Day2, U133B

description: no additional information


title: 10 ug/mL rATG treated for 6h, biological rep2 (S2)

tag: rATG-treated for 6h


title: LNCaP SOX4 hybridization 2 Replicate 2

description: Biological Replicate 2 of 3, Hybridization 2 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection

source_name: LNCaP prostate cancer cells transfected with SOX4, 24 hrs


title: Untreated for 24h, biological rep2 (S2)

tag: untreated for 24h


title: LNCaP SOX4 hybridization 1 Replicate 3

description: Biological Replicate 3 of 3, Hybridization 1 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection


title: LNCaP GFP hybridization 1 Replicate 2

description: Biological Replicate 2 of 3, Hybridization 1 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection


title: Adult_vs_Neonatal (Slides 3 & 4)

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Foal 1 Articular Cartilage 635
Source_name_ch2 = Horse Cornell "1/2" Articular Cartilage 532
Source_name_ch1 = Horse Cornell "1/2" Articular Cartilage 635
Source_name_ch2 = Foal 1 Articular Cartilage 532

value: Articular cartilage from a 4 year old Thoroughbred mare

value: Articular cartilage from a 9 day old Thoroughbred colt


title: Untreated for 24h, biological rep3 (S3)


title: Adult_vs_Neonatal (Slides 1 & 2)

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Foal #4 Articular Cartilage 635
Source_name_ch2 = Horse #4 Articular Cartilage 532
Source_name_ch1 = Horse #4 Articular Cartilage 635
Source_name_ch2 = Foal #4 Articular Cartilage 532

value: Articular cartilage from a 3 day old Thoroughbred colt


title: Untreated for 6h, biological rep2 (S2)


title: LNCaP SOX4 hybridization 2 Replicate 3

description: Biological Replicate 3 of 3, Hybridization 2 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection


title: LNCaP SOX4 hybridization 1 Replicate 2

description: Biological Replicate 2 of 3, Hybridization 1 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection


title: LNCaP GFP hybridization 1 Replicate 1

description: Biological Replicate 1 of 3, Hybridization 1 of 2, LNCaP cells transfected with GFP, RNA harvested 24 hrs post-transfection


title: YFP Control IP Replicate 2 hybridized to array 1 of 2

type: genomic

description: Biological replicate 2 of 2, hybridization 1 of 2

hyb_protocol: performed by Nimblegen Systems, Inc

scan_protocol: performed by Nimblegen Systems, Inc

data_processing: Z-score normalization

molecule: genomic DNA

source_name: YFP LNCaP cells

label_protocol: performed by Nimblegen Systems, Inc

growth_protocol: LNCaP cells were grown to 95% confluency in the presence of T-medium (invitrogen)

extract_protocol: Chromatin IP performed as described in Odom et al., Science 303, 1378 (Feb 27, 2004)

tag: LNCaP cells stably infected with IRES-YFP

source_name: IP: YFP LNCaP cells


title: YFP Control IP Replicate 1 hybridized to array 1 of 2

description: Biological replicate 1 of 2, hybridization 1 of 2


title: LNCaP - GFP, Day2, U133A

description: no additional information


title: LNCaP - GFP, Day1, U133A

description: no additional information


title: Untreated for 24h, biological rep1 (S1)

description: Gene expression data from untreated PBMC.


title: LNCaP SOX4 hybridization 2 Replicate 1

description: Biological Replicate 1 of 3, Hybridization 2 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection


title: Ag-S-FY-2N-A-g306-c2-PFGband1

status: Public on Nov 08 2008

city: Seattle

first: Maitreya

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description:
Experiment design: Chromosomes from evolved strains were run on a gel and excised.  DNA from the bands is hybridized vs matched ancestor genomic DNA
Complete protocols also available as supplementary files on the Series record

hyb_protocol: reference URL : http://genomics.princeton.edu/dunham/MDPFGEarrays.pdf

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-07 Scan Time : 09:39:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

source_name: 10144 Qiagen DNA 4/6/06 (Strain Name : FY diploid)

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : reference genomic DNA http://genomics.princeton.edu/dunham/MDPFGEarrays.pdf

tag: Strain Name

value: FY diploid

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : PFGE band http://genomics.princeton.edu/dunham/MDPFGEarrays.pdf

value: S3 c2


title: Ag-S-FY-2N-A-g306-c1-DNA

description:
Experiment design: DNA from each evolved clone or population is hybridized vs DNA from the matched ancestor strain
Complete protocols also available as supplementary files on the Series record

hyb_protocol: reference URL : http://genomics.princeton.edu/dunham/MDAgilentDNA.pdf

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 11:47:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FYX genomic DNA (Strain Name : FY diploid)

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://genomics.princeton.edu/dunham/MDyeastDNAprep.pdf

source_name: 10252 genomic DNA (Strain Name : S3 c1)

value: S3 c1


title: HA-SOX4 IP Replicate 3 hybridized to array 1 of 2

description: Biological replicate 3 of 3, hybridization 1 of 2

source_name: HA-SOX4/YFP LNCaP cells

tag: LNCaP cells stably infected with HA-SOX4-IRES-YFP

source_name: IP: HA-SOX4/YFP LNCaP cells


title: Ag-S-FY-1N-B-g188-c1-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-24 Scan Time : 11:06:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 8/17/06 L5 PFG band Enzo-labeled DNA (Strain Name : S2 c1)

label_protocol: reference URL : http://genomics.princeton.edu/dunham/MDPFGEarrays.pdf

value: S2 c1

source_name: 10146 (FY4H) Qiagen Enzo-labeled DNA (Strain Name : FY haploid)

value: FY haploid


title: HA-SOX4 IP Replicate 2 hybridized to array 1 of 2

description: Biological replicate 2 of 3, hybridization 1 of 2


title: Ag-S-CEN.PK-2N-A-g303-c2-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 10:38:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 Qiagen 4/6/06 DNA (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: 6/2/05 L4 DNA (Strain Name : S7 c2)

value: S7 c2


title: Ag-S-CEN.PK-2N-A-g303-c1-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 10:54:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 6/2/05 L3 DNA (Strain Name : S7 c1)

value: S7 c1


title: Ag-S-FY-2N-B-g256-c2-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 10:22:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10144 Qiagen 4/6/06 DNA (Strain Name : FY diploid)

source_name: 5/3/05 L8 DNA (Strain Name : S4 c2)

value: S4 c2


title: Ag-S-CEN.PK-2N-B-g250-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:40:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: CEN.PK genomic DNA (Strain Name : CEN.PK diploid)

label_protocol: reference URL : http://genomics.princeton.edu/dunham/MDAgilentDNA.pdf

source_name: 10264 genomic DNA (Strain Name : S8 c1)

value: S8 c1


title: Ag-S-CEN.PK-1N-A-g297-c2-PFGband

source_name: 10148 Qiagen 4/6/06 DNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: 6/2/05 L2 DNA (Strain Name : S5 c2)

value: S5 c2


title: Ag-S-FY-1N-A-g297-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:24:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY4H genomic DNA (Strain Name : FY haploid)

source_name: 10249 genomic DNA (Strain Name : S1 c2)

value: S1 c2


title: LNCaP SOX4 hybridization 1 Replicate 1

description: Biological Replicate 1 of 3, Hybridization 1 of 2, LNCaP cells transfected with SOX4, RNA harvested 24 hrs post-transfection

source_name: LNCaP prostate cancer cells transfected with SOX4, 24 hrs


title: Ag-S-FY-2N-A-g306-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:53:14 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FYX genomic DNA (Strain Name : FY diploid)

source_name: 10253 genomic DNA (Strain Name : S3 c2)


title: Ag-S-CEN.PK-2N-B-g250-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:10:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10265 genomic DNA (Strain Name : S8 c2)

value: S8 c2


title: Ag-P-FY-2N-B-g205-c1-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-21 Scan Time : 11:21:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY4xFY5 Qiagen 7/20/06 DNA (Strain Name : FY diploid)

source_name: 4/12/06 L7 DNA (Strain Name : P4 c1)

value: P4 c1


title: Ag-S-FY-1N-A-g297-c2-PFGband

source_name: 10146 Qiagen DNA 4/6/06 (Strain Name : FY haploid)


title: Ag-S-FY-2N-B-g256-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:42:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10263 genomic DNA (Strain Name : S4 c2)


title: Ag-P-FY-2N-A-g222-c2-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-21 Scan Time : 11:45:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 4/12/06 L6 DNA (Strain Name : P3 c2)

value: P3 c2


title: Ag-S-FY-2N-B-g256-c1-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-07 Scan Time : 09:47:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10144 Qiagen DNA 4/6/06 (Strain Name : FY diploid)

value: S4 c1


title: Ag-S-FY-2N-B-g256-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:42:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: FY diploid

source_name: 10262 genomic DNA (Strain Name : S4 c1)


title: Ag-S-FY-1N-A-g297-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 11:55:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10248 genomic DNA (Strain Name : S1 c1)

value: S1 c1


title: Ag-P-FY-2N-A-g222-c1-PFGband

source_name: 4/12/06 L5 DNA (Strain Name : P3 c1)

value: P3 c1


title: Ag-D-CEN.PK-2N-A-g237-c2-PFGband1

source_name: 9500 Qiagen 4/6/06 DNA (Strain Name : CEN.PK diploid)

source_name: 5/4/05 L4 DNA (Strain Name : G7 c2)

value: G7 c2


title: Ag-S-FY-1N-B-g188-c2-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-24 Scan Time : 11:14:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 8/17/06 L6 PFG band Enzo-labeled DNA (Strain Name : S2 c2)

value: S2 c2

source_name: 10146 (FY4H) Qiagen Enzo-labeled DNA (Strain Name : FY haploid)

value: FY haploid


title: Ag-S-CEN.PK-2N-A-g303-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:34:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: CEN.PK genomic DNA (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: 10255 genomic DNA (Strain Name : S7 c2)

value: S7 c2


title: Ag-S-CEN.PK-2N-A-g303-c1-DNA

source_name: 10254 genomic DNA (Strain Name : S7 c1)

value: S7 c1


title: HA-SOX4 IP Replicate 1 hybridized to array 1 of 2

description: Biological replicate 1 of 3, hybridization 1 of 2

scan_protocol: performed by Nimblegen Systems, Inc

source_name: HA-SOX4/YFP LNCaP cells

source_name: IP: HA-SOX4/YFP LNCaP cells


title: Ag-S-FY-1N-B-g188-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:55:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY4H (10146) (Strain Name : FY haploid)

source_name: 10951 c1 (Strain Name : S2 c1)

value: S2 c1


title: Ag-S-CEN.PK-1N-B-g122-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-11-29 Scan Time : 11:12:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 10148 DNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: 10978c1 DNA (Strain Name : S6 c1)

value: S6 c1


title: Ag-S-FY-1N-B-g188-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:43:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10951 c2 (Strain Name : S2 c2)


title: Ag-S-CEN.PK-1N-A-g297-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:02:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 19-1-3D genomic DNA (Strain Name : CEN.PK haploid)

source_name: 10250 genomic DNA (Strain Name : S5 c1)

value: S5 c1


title: Ag-P-FY-2N-B-g205-c1-DNA-redo2

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-15 Scan Time : 12:01:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY4 x FY5 H+W DNA (Strain Name : FY diploid)

source_name: F15 11/18/05 c1 H+W DNA (Strain Name : P4 c1)


title: Ag-S-CEN.PK-1N-A-g297-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:01:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10251 genomic DNA (Strain Name : S5 c2)

value: S5 c2


title: Ag-P-FY-2N-B-g205-c2-DNA-redo2

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-15 Scan Time : 12:09:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F15 11/18/05 c2 H+W DNA (Strain Name : P4 c2)

value: P4 c2


title: pSUL1-B DNA

description:
Experiment design: DNA from 2 strains transformed with a SUL1 plasmid hybridized vs DNA from the matched ancestor strain
Complete protocols also available as supplementary files on the Series record

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-01 Scan Time : 08:55:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.1.1
Datafile type : Agilent result file

source_name: FY4 (Strain Name : FY haploid)

source_name: p-sul-1 tansforment-B (Strain Name : FY haploid pSUL1-B)

value: FY haploid pSUL1-B


title: Ag-D-CEN.PK-2N-B-g328-c3-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 11:02:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 Qiagen 4/6/06 DNA (Strain Name : CEN.PK diploid)

source_name: 5/4/05 L7 DNA (Strain Name : G8 c1)

value: G8 c1


title: Ag-P-FY-2N-B-g193-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 14:23:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file

source_name: F15 11/16/05 DNA (Strain Name : P4 population)

growth_protocol: Media : phosphate-limited chemostat media

value: P4 population

source_name: FY4 X FY5 DNA (Strain Name : FY diploid)

value: FY diploid


title: Ag-S-CEN.PK-1N-B-g122-c2-DNA

source_name: 10978c2 DNA (Strain Name : S6 c2)

value: S6 c2


title: pSUL1-A DNA

source_name: p-sul-1 tansforment-A (Strain Name : FY haploid pSUL1-A)

value: FY haploid pSUL1-A


title: Ag-P-FY-2N-A-g222-c1-DNA-redo

source_name: FY4xFY5 (Strain Name : FY diploid)

value: P3 c1


title: FY 2N extracted ty DNA vs. genomic DNA

description:
Experiment design: DNA linked to Ty1/Ty2 sequences was extracted from evolved strains and ancestor strains, and compared to ancestral extracted or genomic DNA as indicated.
Complete protocols also available as supplementary files on the Series record

hyb_protocol: reference URL : http://genomics.princeton.edu/dunham/MDTSE.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-19 Scan Time : 09:42:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4xFY5 gDNA (Strain Name : FY diploid)

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Qiagen genomic prep  http://genomics.princeton.edu/dunham/MDTSE.pdf

source_name: FY4xFY5 extracted DNA (Strain Name : FY diploid)

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Qiagen genomic prep followed by TSE http://genomics.princeton.edu/dunham/MDTSE.pdf


title: Ag-P-FY-2N-A-g222-c2-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:47:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: P3 c2


title: Ag-P-FY-2N-A-g222-pop-DNA

source_name: F16 10/6/05 DNA (Strain Name : P3 population)

value: P3 population


title: Ag-D-FY-2N-A-g238-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:59:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FYX genomic DNA (Strain Name : FY diploid)

growth_protocol: Media : glucose-limited chemostat media

source_name: F10 12/23/3 genomic DNA (Strain Name : G3 population)

value: G3 population


title: Ag-D-FY-2N-B-g237-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:51:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F11 12/23/3 c1 genomic DNA (Strain Name : G4 c1)

value: G4 c1


title: Ag-P-FY-1N-B-g316-c2-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:24:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: FY haploid

value: P2 c2


title: Ag-D-FY-2N-B-g237-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:10:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F11 12/23/3 c2 genomic DNA (Strain Name : G4 c2)

value: G4 c2


title: Ag-D-FY-2N-A-g238-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:32:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 12/23/3 c2 genomic DNA (Strain Name : G3 c2)

value: G3 c2


title: Ag-D-FY-2N-A-g238-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 13:16:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 12/23/3 c1 genomic DNA (Strain Name : G3 c1)

value: G3 c1


title: Ag-P-FY-1N-B-g316-c1-DNA-redo

source_name: FY4 (Strain Name : FY haploid)

value: P2 c1


title: Ag-D-FY-1N-B-g311-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:26:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY4H genomic DNA (Strain Name : FY haploid)

source_name: 10341c2 genomic DNA (Strain Name : G2 c2)

value: G2 c2


title: Ag-P-FY-1N-A-g186-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 14:15:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F16 11/16/05 DNA (Strain Name : P1 population)

value: P1 population

source_name: FY5 DNA (Strain Name : FY haploid)


title: Ag-P-FY-1N-A-g180-c2-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:43:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY5 (Strain Name : FY haploid)

value: P1 c1


title: Ag-D-FY-1N-B-g311-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:26:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10341c1 genomic DNA (Strain Name : G2 c1)

value: G2 c1


title: Ag-P-CEN.PK-2N-B-g201-c2-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:11:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

value: P8 c2


title: Ag-P-FY-1N-A-g180-c1-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:32:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Ag-P-FY-1N-B-g300-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 13:51:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F19 2/8/06 DNA (Strain Name : P2 population)

value: P2 population

source_name: FY4 DNA (Strain Name : FY haploid)


title: Ag-P-CEN.PK-2N-B-g201-c1-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:35:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: P8 c1


title: CEN.PK diploid Ty reference

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:21:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 genomic (Strain Name : CEN.PK diploid)

label_protocol: reference URL : http://genomics.princeton.edu/dunham/MDTSE.pdf

source_name: 9500 extraction (Strain Name : CEN.PK diploid)


title: FY 1N extracted ty DNA vs. genomic DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-13 Scan Time : 10:41:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 genomic DNA (Strain Name : FY haploid)

source_name: FY4 extracted ty DNA (Strain Name : FY haploid)


title: CEN.PK 1N extracted ty DNA vs. genomic DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-19 Scan Time : 09:42:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 alpha gDNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: 9500 alpha extracted DNA (Strain Name : CEN.PK haploid)


title: Ag-S-FY-2N-B-g256-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:36:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 x FY5 gDNA (Strain Name : FY diploid)

value: FY diploid

source_name: 10262 gDNA (Strain Name : S4 c1)

value: S4 c1


title: Ag-D-FY-1N-A-g182-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 13:38:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: FY3G genomic DNA (Strain Name : FY haploid)

value: FY haploid

source_name: 10294c1 genomic DNA (Strain Name : G1 c1)

value: G1 c1


title: Ag-P-CEN.PK-2N-A-g225-pop-DNA-really

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 13:43:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F18 10/6/05 DNA (Strain Name : P7 population)

value: P7 population

source_name: 9500 DNA (Strain Name : CEN.PK diploid)


title: Ag-S-FY-2N-A-g306-c1-ty

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-04 Scan Time : 11:01:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 x FY5 2/14/06 gDNA (Strain Name : FY diploid)

source_name: 10252 gDNA (Strain Name : S3 c1)

value: S3 c1


title: Ag-P-CEN.PK-2N-A-g225-c1-DNA-redo-really

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:27:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 MATa (Strain Name : CEN.PK diploid)

value: P7 c1


title: Ag-P-CEN.PK-2N-A-g225-c2-DNA-redo-really

value: P7 c2


title: Ag-D-FY-1N-A-g182-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 13:23:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10294c2 genomic DNA (Strain Name : G1 c2)

value: G1 c2


title: Ag-D-CEN.PK-2N-B-g328-c4-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 13:07:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: CEN.PK genomic DNA (Strain Name : CEN.PK diploid)

source_name: F11 3/12/4 c4 genomic DNA (Strain Name : G8 c2)

value: G8 c2


title: Ag-P-CEN.PK-1N-B-g217-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-23 Scan Time : 10:38:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500alpha H+W DNA (Strain Name : CEN.PK haploid)

source_name: F18 11/18/05 c1 DNA (Strain Name : P6 c1)

value: P6 c1


title: Ag-P-CEN.PK-1N-B-g204-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 14:07:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F18 11/16/05 DNA (Strain Name : P6 population)

value: P6 population

source_name: 9500 alpha DNA (Strain Name : CEN.PK haploid)


title: Ag-S-FY-1N-B-g188-c1-ty-redo

scan_protocol: Pixel Size : 10 Scan Date : 2007-03-27 Scan Time : 11:49:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 11069 2/14/06 gDNA (Strain Name : FY haploid)

source_name: 10951 c1 gDNA (Strain Name : S2 c1)

value: S2 c1


title: Ag-S-CEN.PK-2N-B-g250-c1-ty-redo2

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:30:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 genomic (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: 10264 extracted DNA (Strain Name : S8 c1)

value: S8 c1


title: Ag-P-CEN.PK-1N-B-g217-c2-DNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:11:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 MATalpha (Strain Name : CEN.PK haploid)

value: P6 c2


title: Ag-D-CEN.PK-2N-B-g328-c3-DNA

source_name: F11 3/12/4 c3 genomic DNA (Strain Name : G8 c1)

value: G8 c1


title: Ag-S-FY-1N-A-g297-c1-ty-redo

source_name: 10248 gDNA (Strain Name : S1 c1)

value: S1 c1


title: Ag-P-CEN.PK-1N-A-g161-c1-DNA-redo-really

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:24:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

value: P5 c1


title: Ag-D-CEN.PK-1N-D-g162-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:19:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: G6 c2


title: Ag-D-CEN.PK-1N-D-g162-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 10:40:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: G6 c1


title: Ag-S-FY-2N-B-g256-c1-RNA

description:
Experiment design: RNA from each evolved clone or population grown in chemostat culture is compared to RNA from matching ancestor strains grown in the same conditions
Complete protocols also available as supplementary files on the Series record

hyb_protocol: reference URL : http://genomics.princeton.edu/dunham/MDAgilentRNA.pdf

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 13:49:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F4 03/02/04 RNA (Strain Name : FY diploid)

growth_protocol: Media : sulfur-limited chemostat media

extract_protocol:
Extracted molecule : Total RNA
Extraction method : acid phenol prep http://genomics.princeton.edu/dunham/MDyeastRNA.pdf

value: FY diploid

source_name: F3 03/22/03 RNA (Strain Name : S4 c1)

value: S4 c1


title: Ag-D-CEN.PK-2N-A-g237-c1-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-08 Scan Time : 12:42:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F12 12/23/3 c1 genomic DNA (Strain Name : G7 c1)

value: G7 c1


title: Ag-S-FY-2N-A-g306-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 12:14:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

label_protocol: reference URL : http://genomics.princeton.edu/dunham/MDAgilentRNA.pdf

source_name: F11 01/21/03 RNA (Strain Name : S3 c2)

value: S3 c2


title: Ag-D-CEN.PK-1N-C-g164-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-04 Scan Time : 11:03:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 MATa (Strain Name : CEN.PK haploid)

value: G5 c2


title: Ag-D-CEN.PK-1N-D-g155-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 13:59:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F14 5/19/06 DNA (Strain Name : G6 population)

value: G6 population


title: Ag-P-FY-2N-B-g205-c1-ty

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-04 Scan Time : 11:01:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 x FY5 2/14/06 gDNA (Strain Name : FY diploid)

source_name: F15 11/18/05 c1 gDNA (Strain Name : P4 c1)

value: P4 c1


title: Ag-S-CEN.PK-2N-A-g303-c1-ty-redo2

source_name: 10254 extracted DNA (Strain Name : S7 c1)

value: S7 c1


title: Ag-S-CEN.PK-1N-B-g122-c1-ty-redo3

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:38:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500a genomic (Strain Name : CEN.PK haploid)

source_name: 10978c1 extracted DNA (Strain Name : S6 c1)

value: S6 c1


title: Ag-P-CEN.PK-1N-A-g161-c2-DNA-redo-really

value: P5 c2


title: Ag-S-FY-1N-B-g188-c1-RNA-replicate

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-09 Scan Time : 10:16:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F7 3/2/04 RNA (Strain Name : FY haploid)

value: FY haploid

source_name: F22 4/5/07 RNA (Strain Name : S2 c1)

value: S2 c1


title: Ag-P-FY-2N-A-g222-c2-ty

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-04 Scan Time : 10:53:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F16 10/6/05 c2 gDNA (Strain Name : P3 c2)

value: P3 c2


title: Ag-S-FY-2N-B-g256-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 12:22:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 04/11/03 RNA (Strain Name : S4 c2)

value: S4 c2


title: Ag-D-CEN.PK-2N-B-g328-c4-PFGband

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-18 Scan Time : 11:02:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9500 Qiagen 4/6/06 DNA (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: 5/4/05 L8 DNA (Strain Name : G8 c2)

value: G8 c2


title: Ag-D-CEN.PK-1N-C-g164-c1-DNA

value: CEN.PK haploid

value: G5 c1


title: Ag-S-FY-1N-A-g297-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 11:13:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F7 03/02/04 RNA (Strain Name : FY haploid)

source_name: F9 01/21/03 RNA (Strain Name : S1 c2)

value: S1 c2


title: Ag-S-CEN.PK-1N-B-g122-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-11-22 Scan Time : 13:16:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F3 11/21/3 RNA (Strain Name : CEN.PK haploid)

source_name: F19 8/21/6 RNA (Strain Name : S6 c2)

value: S6 c2


title: Ag-P-FY-1N-B-g316-c2-ty-redo4

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:21:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 (Strain Name : FY haploid)

source_name: F19 2/11/06 C2 extracted (Strain Name : P2 c2)

value: P2 c2


title: Ag-S-FY-1N-B-g188-c2-RNA-replicate

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-11 Scan Time : 10:37:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F23 8/5/06 RNA (Strain Name : S2 c2)

value: S2 c2


title: Ag-S-FY-2N-A-g306-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 14:07:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F4 03/02/04 RNA (Strain Name : FY diploid)

value: FY diploid

source_name: F11 01/13/03 RNA (Strain Name : S3 c1)

value: S3 c1


title: Ag-D-CEN.PK-1N-C-g158-pop-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 14:07:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F13 5/19/06 DNA (Strain Name : G5 population)

value: G5 population

source_name: 9500 a DNA (Strain Name : CEN.PK haploid)


title: Ag-P-FY-1N-A-g180-c2-ty

source_name: 11069 2/14/06 gDNA (Strain Name : FY haploid)

source_name: F16 11/15/5 gDNA (Strain Name : P1 c2)

value: P1 c2


title: Ag-P-FY-2N-B-g193-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:27:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F13 3/24/6 RNA (Strain Name : FY diploid)

source_name: F15 11/16/5 RNA (Strain Name : P4 population)

value: P4 population


title: Ag-P-CEN.PK-1N-A-g141-pop-DNA-really

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-26 Scan Time : 13:51:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F17 9/20/05 DNA (Strain Name : P5 population)

value: P5 population


title: Ag-P-FY-2N-B-g205-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 11:43:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F14 3/3/6 RNA (Strain Name : P4 c2)

value: P4 c2


title: Ag-P-FY-2N-B-g205-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 11:35:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 3/3/6 RNA (Strain Name : P4 c1)

value: P4 c1


title: Ag-S-CEN.PK-1N-A-g297-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:53:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500a gDNA (Strain Name : CEN.PK haploid)

source_name: 10250 gDNA (Strain Name : S5 c1)

value: S5 c1


title: Ag-P-FY-2N-A-g222-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:43:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F16 10/6/5 RNA (Strain Name : P3 population)

value: P3 population


title: Ag-P-FY-2N-A-g222-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 10:32:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 3/10/6 RNA (Strain Name : P3 c1)

value: P3 c1


title: Ag-S-FY-1N-A-g297-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:07:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F7 03/02/04 RNA (Strain Name : FY haploid)

value: FY haploid

source_name: F1 01/21/03 RNA (Strain Name : S1 c1)

value: S1 c1


title: Ag-P-CEN.PK-2N-B-g201-c1-ty-redo3

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:30:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 genomic (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: F17 11/18/05 C1 extracted (Strain Name : P8 c1)

value: P8 c1


title: Ag-P-CEN.PK-2N-A-g225-c1-ty-really

source_name: 9500a gDNA (Strain Name : CEN.PK diploid)

source_name: F18 10/6/5 c1 ty (Strain Name : P7 c1)

value: P7 c1


title: Ag-S-CEN.PK-2N-B-g250-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 11:18:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F3 03/02/04 RNA (Strain Name : CEN.PK diploid)

source_name: F6 02/16/03 RNA (Strain Name : S8 population)

value: S8 population


title: Ag-S-CEN.PK-2N-B-g250-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 13:33:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F11 04/11/03 RNA (Strain Name : S8 c2)

value: S8 c2


title: Ag-P-FY-2N-A-g222-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 11:11:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 3/24/6 RNA (Strain Name : FY diploid)

value: FY diploid

source_name: F14 3/10/6 RNA (Strain Name : P3 c2)

value: P3 c2


title: Ag-S-CEN.PK-2N-B-g250-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 10:49:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F4 03/22/03 RNA (Strain Name : S8 c1)

value: S8 c1


title: Ag-P-CEN.PK-1N-B-g217-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:36:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: CEN.PK haploid

source_name: F18 11/18/5 c1 gDNA (Strain Name : P6 c1)

value: P6 c1


title: Ag-P-FY-1N-A-g180-c1-RNA

source_name: F22 1/13/6 RNA (Strain Name : FY haploid)

source_name: F15 3/3/6 RNA (Strain Name : P1 c1)

value: P1 c1


title: Ag-P-FY-1N-B-g316-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 11:19:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F21 1/13/6 RNA (Strain Name : FY haploid)

source_name: F19 3/10/6 RNA (Strain Name : P2 c1)

value: P2 c1


title: Ag-S-CEN.PK-2N-A-g303-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:23:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F12 01/13/03 RNA (Strain Name : S7 c1)

value: S7 c1


title: Ag-P-FY-1N-A-g186-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 11:07:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F16 11/16/5 RNA (Strain Name : P1 population)

value: P1 population


title: Ag-P-FY-1N-A-g180-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 10:40:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F16 3/3/6 RNA (Strain Name : P1 c2)

value: P1 c2


title: Ag-P-CEN.PK-2N-B-g201-c1-RNA

source_name: F14 3/24/6 RNA (Strain Name : CEN.PK diploid)

source_name: F17 3/3/6 RNA (Strain Name : P8 c1)


title: Ag-P-CEN.PK-1N-A-g161-c1-ty-redo3-really

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:21:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 genomic (Strain Name : CEN.PK haploid)

source_name: F17 9/24/5 c1 ty (Strain Name : P5 c1)

value: P5 c1


title: Ag-P-FY-1N-B-g300-pop-RNA

value: FY haploid

source_name: F19 2/8/6 RNA (Strain Name : P2 population)

value: P2 population


title: Ag-S-CEN.PK-1N-B-g122-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 11:05:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F3 11/21/03 RNA (Strain Name : CEN.PK haploid)

source_name: F5 11/21/03 RNA (Strain Name : S6 c1)

value: S6 c1


title: Ag-S-CEN.PK-1N-A-g297-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:31:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 01/21/03 RNA (Strain Name : S5 c2)

value: S5 c2


title: Ag-D-FY-1N-B-g311-c2-ty

scan_protocol: Pixel Size : 10 Scan Date : 2007-05-04 Scan Time : 10:53:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 11069 2/14/06 gDNA (Strain Name : FY haploid)

source_name: 10341 c2 gDNA (Strain Name : G2 c2)

value: G2 c2


title: Ag-P-CEN.PK-2N-B-g190-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:59:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: CEN.PK diploid

source_name: F17 11/16/5 RNA (Strain Name : P8 population)

value: P8 population


title: Ag-D-CEN.PK-2N-A-g237-c2-DNA

scan_protocol: Pixel Size : 10 Scan Date : 2004-12-09 Scan Time : 12:42:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: CEN.PK genomic DNA (Strain Name : CEN.PK diploid)

source_name: F12 12/23/3 c2 genomic DNA (Strain Name : G7 c2)

value: G7 c2


title: Ag-D-FY-2N-A-g238-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:44:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 x FY5 gDNA (Strain Name : FY diploid)

value: FY diploid

source_name: F10 12/23/3 c1 gDNA (Strain Name : G3 c1)

value: G3 c1


title: Ag-S-CEN.PK-2N-A-g303-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 12:07:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F3 03/02/04 RNA (Strain Name : CEN.PK diploid)

source_name: F12 01/21/03 RNA (Strain Name : S7 c2)

value: S7 c2


title: Ag-P-CEN.PK-2N-A-g225-pop-RNA-really

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:35:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F14 3/24/6 RNA (Strain Name : CEN.PK diploid)

source_name: F18 10/6/5 RNA (Strain Name : P7 population)

value: P7 population


title: Ag-D-FY-1N-A-g182-c1-ty-redo3

source_name: FY4 (Strain Name : FY haploid)

source_name: 10294 c1 extracted DNA (Strain Name : G1 c1)

value: G1 c1


title: Ag-P-CEN.PK-1N-B-g217-c2-RNA

source_name: F24 1/13/6 RNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: F20 3/3/6 RNA (Strain Name : P6 c2)

value: P6 c2


title: Ag-P-CEN.PK-1N-B-g204-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:51:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F18 11/16/5 RNA (Strain Name : P6 population)

value: P6 population


title: Ag-P-CEN.PK-2N-B-g201-c2-RNA

source_name: F18 3/3/6 RNA (Strain Name : P8 c2)

value: P8 c2


title: Ag-D-FY-2N-B-g237-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:53:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F11 12/23/3 c1 gDNA (Strain Name : G4 c1)

value: G4 c1


title: Ag-S-CEN.PK-1N-A-g297-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 11:43:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F3 11/21/03 RNA (Strain Name : CEN.PK haploid)

source_name: F10 01/13/03 RNA (Strain Name : S5 c1)

value: S5 c1


title: Ag-P-CEN.PK-1N-A-g141-pop-RNA-really

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:43:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F23 1/13/6 RNA (Strain Name : CEN.PK haploid)

source_name: F17 9/20/5 RNA (Strain Name : P5 population)

value: P5 population


title: Ag-P-CEN.PK-1N-B-g217-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-05 Scan Time : 10:24:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F19 3/3/6 RNA (Strain Name : P6 c1)

value: P6 c1


title: Ag-D-CEN.PK-1N-D-g162-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-18 Scan Time : 10:23:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 3/2/04 RNA (Strain Name : CEN.PK haploid)

source_name: F23 7/4/06 RNA (Strain Name : G6 c1)

value: G6 c1


title: Ag-P-FY-1N-B-g316-c2-RNA

source_name: F21 1/13/6 RNA (Strain Name : FY haploid)

value: FY haploid

source_name: F20 3/10/6 RNA (Strain Name : P2 c2)

value: P2 c2


title: Ag-D-CEN.PK-2N-A-g237-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-06-08 Scan Time : 09:13:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500 gDNA (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: F12 12/23/3 c1 gDNA (Strain Name : G7 c1)

value: G7 c1


title: Ag-D-FY-2N-B-g237-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:23:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F14 01/16/04 RNA (Strain Name : FY diploid)

value: FY diploid

source_name: F10 01/23/04 RNA (Strain Name : G4 c2)

value: G4 c2


title: Ag-D-CEN.PK-1N-C-g164-c1-ty-redo3

scan_protocol: Pixel Size : 5 Scan Date : 2007-08-05 Scan Time : 13:38:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500a genomic (Strain Name : CEN.PK haploid)

source_name: F13 5/20/06 C1 extraction (Strain Name : G5 c1)

value: G5 c1


title: Ag-D-FY-2N-B-g237-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 11:21:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F9 01/23/04 RNA (Strain Name : G4 c1)


title: Ag-D-CEN.PK-2N-B-g328-c3-ty

source_name: F11 3/12/4 c3 gDNA (Strain Name : G8 c1)

value: G8 c1


title: Ag-D-CEN.PK-1N-C-g164-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-18 Scan Time : 10:14:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F17 1/16/04 RNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: F21 7/4/06 RNA (Strain Name : G5 c1)


title: Ag-D-CEN.PK-1N-C-g164-c2-RNA-redo

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-11 Scan Time : 10:14:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F22 7/4/06 RNA (Strain Name : G5 c2)

value: G5 c2


title: Ag-D-CEN.PK-1N-D-g162-c1-ty

scan_protocol: Pixel Size : 5 Scan Date : 2007-05-25 Scan Time : 11:36:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500a gDNA (Strain Name : CEN.PK haploid)

source_name: F14 5/20/6 c1 gDNA (Strain Name : G6 c1)


title: Ag-S-FY-2N-A-g306-c2-PFGband2

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-13 Scan Time : 10:33:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: FY4 X FY5 DNA (Strain Name : FY diploid)

source_name: 10253 band (Strain Name : S3 c2)

value: S3 c2


title: Ag-S-CEN.PK-2N-B-g250-c2-PFGband

source_name: 9500 (Strain Name : CEN.PK diploid)

source_name: 10265 band (Strain Name : S8 c2)

value: S8 c2


title: biological_replicate_1_dyeswap_A

city: Eugene

last: Miller

state: OR

address: 1229 University of Oregon

department: Institute of Molecular Biology

institute: University of Oregon

hyb_protocol: After denaturing, labeled cDNA was applied onto the microarray and covered with a coverslip, incubated in a hybridization chamber (Corning, Acton, MA), and hybridized in a 42oC water bath overnight. Following the hybridization, the microarray was washed with an SSC series and dried by centrifugation.

scan_protocol: After washing, the microarray was immediately scanned using Genepix 4000B scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA) with several different laser intensities.

data_processing: GenePix Pro 3.0 image analysis software (Axon Instruments) was used to measure fluorescence signal intensities of the array elements. Ratios were normalized to the overall difference in signal intensities from each channel. Microarray data was transferred to Microsoft Excel, which was also used for calculations and data sorting. The median (M) of the ratio of Cy3 and Cy5 signal intensities of each array element was used for the analysis. The median of the medians (MeM) and maximum of the medians (MaM) were calculated from the medians that were obtained from a single experiment scored using several different laser intensities. Data was sorted according to the median of the MeMs and median of the MaMs (Table S1). Candidate genes were picked from the list of the aggregate result of the microarray, considering the results from each experiment (MeM and MaM) and scanned images. Genes that showed inconsistent results in the dye-swap experiment were removed from further analyses.

organism: Danio rerio

source_name: 48h sox9a, sox9b double mutants

label_protocol: For each experiment, 20 μg of total RNA from wild-type or mutant embryos was used to synthesize cDNA labeled with Cy3 or Cy5-dUTP (PerkinElmer, Boston, MA) using SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA). The Cy3 labeled cDNA was mixed with Cy5 labeled cDNA and purified with QIAquick PCR purification kit (Qiagen, Valencia, CA), dried in a speed vac (Savant, Farmingdale, NY) and resuspended in hybridization buffer (50% formamide, 5 x SSC, 1% SDS, 1 mg/ml calf thymus DNA).

extract_protocol: Total RNA was extracted from embryos using TRI reagent (Molecular Research Center, Inc. Cincinnati, OH). RNA quantity was measured using NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmingon, DE). Approximately 1 μg of total RNA was extracted from individual embryos at 2 dpf.

tag: whole 48h zebrafish sox9a, sox9b double mutant embryos

source_name: 48h wildtype

tag: whole 48h zebrafish wildtype embryos


title: Ag-D-FY-2N-B-g237-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 10:57:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F14 01/16/04 RNA (Strain Name : FY diploid)

source_name: F11  12/23/03 RNA (Strain Name : G4 population)

value: G4 population


title: Ag-D-FY-1N-B-g311-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:46:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F15 01/16/04 RNA (Strain Name : FY haploid)

source_name: F10 01/16/04 RNA (Strain Name : G2 c2)

value: G2 c2


title: biological_replicate_2_dyeswap_A


title: Ag-S-FY-2N-A-g306-c1-PFGband

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-13 Scan Time : 10:41:56 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 10252 band (Strain Name : S3 c1)

value: S3 c1


title: biological_replicate_2_dyeswap_B


title: Ag-D-FY-2N-A-g238-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 12:46:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F7 01/23/04 RNA (Strain Name : G3 c1)

value: G3 c1


title: Ag-D-CEN.PK-1N-C-g158-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:51:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F17 1/16/4 RNA (Strain Name : CEN.PK haploid)

source_name: F13 5/19/6 RNA (Strain Name : G5 population)

value: G5 population


title: Ag-D-FY-2N-A-g238-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-19 Scan Time : 12:34:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F8 01/23/04 RNA (Strain Name : G3 c2)

value: G3 c2


title: Ag-D-CEN.PK-1N-D-g162-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-18 Scan Time : 10:30:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 3/2/04 RNA (Strain Name : CEN.PK haploid)

source_name: F24 7/4/06 RNA (Strain Name : G6 c2)

value: G6 c2


title: biological_replicate_3_dyeswap_B


title: Ag-D-FY-2N-A-g238-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 14:07:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 12/23/03 RNA (Strain Name : G3 population)

value: G3 population


title: biological_replicate_3_dyeswap_A


title: Ag-S-CEN.PK-2N-B-g250-c1-PFGband

value: CEN.PK diploid

source_name: 10264 band (Strain Name : S8 c1)

value: S8 c1


title: biological_replicate_1_dyeswap_B


title: FeCit_0.5h_rep5

city: Ithaca

first: Philip

middle: Alan

last: Bronstein

state: NY

address: Cornell University Plant Science Building RM334

department: Plant Microbe Interaction Research Unit

institute: USDA-ARS

hyb_protocol: Using Flexmidi_Euk2v3 fluidics protocol from Affymetrix with a modifcation in wash temperature B on a Fluidic station FS450

scan_protocol: Scanned on a GeneChip scanner 3000-7G with 4-color upgrade and array autoloader

data_processing: microarray data was processed using gcrma v2.10 in R

label: Biotin

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 0.5h

label_protocol: Using standard Affymetrix protocols

growth_protocol: Pseudomonas syringae DC3000 was grown in iron limiting medium overnight in bioreactors at a temperature of 25C, supplements were added at OD600 ~0.3

extract_protocol: Samples pelleted and RNA was isolated using Rneasy kit (Qiagen, Carlsbad, CA) following manufacture’s instructions; with the exception that lyzozyme was used at a concentration of 5 mg/ml.  RNA was treated with DNase I (Ambion, Austin, TX) to remove residual DNA and then cleaned and concentrated using the MinElute kit (Qiagen)

treatment_protocol: Addition of iron citrate or sodium citrate to increase  final concentration by 50 uM


title: NaCit_4h_rep5

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 4h


title: NaCit_0h_rep5

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0h


title: FeCit_4h_rep5

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 4h


title: Ag-D-FY-1N-B-g311-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 11:43:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

value: FY haploid

source_name: F9 01/16/04 RNA (Strain Name : G2 c1)

value: G2 c1


title: NaCit_0.5h_rep5

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0.5h


title: Ag-D-FY-1N-A-g182-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 11:10:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F16 01/16/04 RNA (Strain Name : FY haploid)

source_name: F8 01/16/04 RNA (Strain Name : G1 c2)

value: G1 c2


title: FeCit_4h_rep4


title: Ag-S-CEN.PK-1N-A-g297-c1-PFGband

source_name: 9500a (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: 10250 gel band (Strain Name : S5 c1)

value: S5 c1


title: Ag-S-CEN.PK-1N-B-g122-c2-PFGband1

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-13 Scan Time : 10:25:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 10978 c2 bottom band (Strain Name : S6 c2)

value: S6 c2


title: Ag-S-CEN.PK-1N-B-g122-c1-PFGband2

source_name: 10978 c1 top band (Strain Name : S6 c1)

value: S6 c1


title: NaCit_4h_rep4


title: Ag-D-CEN.PK-2N-B-g328-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 13:17:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 01/16/04 RNA (Strain Name : CEN.PK diploid)

source_name: F11 03/12/04 RNA (Strain Name : G8 population)

value: G8 population


title: NaCit_0.5h_rep4


title: FeCit_0h_rep4

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 0h


title: FeCit_0.5h_rep4


title: Ag-P-CEN.PK-1N-B-g217-c2-PFGband

scan_protocol: Pixel Size : 5 Scan Date : 2007-07-19 Scan Time : 10:08:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: 9500alpha gDNA (Strain Name : CEN.PK haploid)

source_name: F18 11/18/5 c2 band (Strain Name : P6 c2)

value: P6 c2


title: FeCit_0h_rep5


title: Ag-D-CEN.PK-2N-B-g328-c3-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 11:54:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F19 01/15/05 RNA (Strain Name : G8 c1)

value: G8 c1


title: Ag-P-CEN.PK-1N-B-g217-c1-PFGband

source_name: F18 11/18/5 c1 band (Strain Name : P6 c1)

value: P6 c1


title: NaCit_0h_rep4

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0h


title: Ag-D-CEN.PK-2N-B-g328-c4-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 13:09:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F20 01/15/05 RNA (Strain Name : G8 c2)

value: G8 c2


title: NaCit_4h_rep3

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 4h


title: FeCit_4h_rep3

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 4h


title: Ag-D-CEN.PK-2N-A-g237-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 13:41:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F12 12/23/03 RNA (Strain Name : G7 population)

value: G7 population


title: Ag-D-CEN.PK-2N-A-g237-c2-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 12:54:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F14 01/23/04 RNA (Strain Name : G7 c2)

value: G7 c2


title: NaCit_0.5h_rep3

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0.5h


title: FeCit_0h_rep3


title: Ag-D-CEN.PK-2N-A-g237-c1-PFGband

source_name: 9500 (Strain Name : CEN.PK diploid)

source_name: F12 12/23/03 c1 band (Strain Name : G7 c1)

value: G7 c1


title: SUL1 amp segregation MD6-A4

description:
Experiment design: DNA from each segregant derived from an evolved strain is hybridized vs DNA from the matched ancestor strain
Complete protocols also available as supplementary files on the Series record

scan_protocol: Pixel Size : 10 Scan Date : 2007-03-27 Scan Time : 11:57:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DBY10148 (Strain Name : CEN.PK haploid)

source_name: MD6-A4 (Strain Name : S5 c1 x ancestor-C)

value: S5 c1 x ancestor-C


title: SUL1 amp segregation MD6-A5

source_name: MD6-A5 (Strain Name : S5 c1 x ancestor-D)

value: S5 c1 x ancestor-D


title: FeCit_0.5h_rep3

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 0.5h


title: FeCit_4h_rep2


title: Ag-D-FY-1N-A-g182-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-18 Scan Time : 10:15:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F16 01/16/04 RNA (Strain Name : FY haploid)

value: FY haploid

source_name: F7 01/16/04 RNA (Strain Name : G1 c1)

value: G1 c1


title: FeCit_0.5h_rep2


title: NaCit_4h_rep2


title: NaCit_0h_rep3


title: Ag-D-CEN.PK-2N-A-g237-c1-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2005-02-17 Scan Time : 10:57:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F13 01/16/04 RNA (Strain Name : CEN.PK diploid)

value: CEN.PK diploid

source_name: F13 01/23/04 RNA (Strain Name : G7 c1)


title: NaCit_0.5h_rep2


title: self/self CEN.PK PK-lim redo

scan_protocol: Pixel Size : 10 Scan Date : 2004-11-12 Scan Time : 11:05:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: F10 4/2/4 total RNA (Strain Name : CEN.PK diploid)

growth_protocol: Media : phosphate/potassium-limited chemostat media

source_name: F1 10/17/3 total RNA (Strain Name : CEN.PK diploid)


title: FeCit_0h_rep2

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 0h


title: FeCit_4h_rep1

source_name: Pseudomonas syringae DC3000 subjected to FeCit for 4h


title: SUL1 amp segregation MD6-A3

value: CEN.PK haploid

source_name: MD6-A3 (Strain Name : S5 c1 x ancestor-B)

value: S5 c1 x ancestor-B


title: Ag-D-CEN.PK-2N-A-g237-c2-PFGband2

source_name: 9500 gDNA (Strain Name : CEN.PK diploid)

source_name: F12 12/23/3 c2 band (Strain Name : G7 c2)


title: FeCit_0.5h_rep1


title: SUL1 amp segregation MD6-A2

source_name: MD6-A2 (Strain Name : S5 c1 x ancestor-A)

value: S5 c1 x ancestor-A


title: SUL1 amp segregation MD55-A5

scan_protocol: Pixel Size : 10 Scan Date : 2007-03-27 Scan Time : 11:33:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: DBY10144 (Strain Name : FY haploid)

source_name: MD55-A5 (Strain Name : S4 c2-D)

value: S4 c2-D


title: NaCit_4h_rep1

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 4h


title: SUL1 amp segregation MD55-A2

source_name: MD55-A2 (Strain Name : S4 c2-A)

value: S4 c2-A


title: SUL1 amp segregation MD55-A4

source_name: MD55-A4 (Strain Name : S4 c2-C)

value: S4 c2-C


title: NaCit_0h_rep2

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0h


title: Ag-P-CEN.PK-2N-A-g225-c2-RNA-diploidref

scan_protocol: Pixel Size : 5 Scan Date : 2007-09-14 Scan Time : 08:54:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.3.1
Datafile type : Agilent result file

source_name: F14 3/24/06 (Strain Name : CEN.PK diploid)

value: P7 c2


title: Ag-P-CEN.PK-1N-A-g161-c2-RNA-haploidref

source_name: F23 1/13/06 (Strain Name : CEN.PK haploid)

value: P5 c2


title: Ag-P-CEN.PK-1N-A-g161-c1-RNA-haploidref

value: P5 c1


title: SUL1 amp segregation MD55-A3

source_name: MD55-A3 (Strain Name : S4 c2-B)

value: S4 c2-B


title: NaCit_0.5h_rep1

source_name: Pseudomonas syringae DC3000 subjected to NaCit for 0.5h


title: FeCit_0h_rep1


title: NaCit_0h_rep1


title: Ag-P-CEN.PK-2N-A-g225-c1-RNA-diploidref

value: P7 c1


title: SUL1 amp segregation MD54-A4

scan_protocol: Pixel Size : 10 Scan Date : 2007-03-27 Scan Time : 11:41:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: MD54-A4 (Strain Name : S4 c1-C)

value: S4 c1-C


title: AOS_R10

status: Public on Nov 07 2008

city: Maastricht

first: Arie

last: van Erk

address: UNS 40

country: Netherlands

institute: BiGCaT Bioinformatics

description: cardiac biopsy

hyb_protocol: Use of Affymetrix GeneChip HT Hybridization, Wash, and Stain kit on the GeneChip Array Station. Hybridization @ 45 degrees Celsius using Affymetrix eukariotic target hybridization protocol; washing using GeneChip Operating Software and protocol FS450_0001

scan_protocol: Scanning using GeneChip Scanner 3000

data_processing: MAS-5 algorithm for the affymetrix files

source_name: AOS

label_protocol: Affymetrix 2-cycle cDNA synthesis protocol

growth_protocol: Samples were snap frozen in liquid nitrogen, stored at -80 degrees Celsius

extract_protocol: RNeasy mini protocol (Qiagen)

tag: tissue

value: cardiac left ventricle

tag: Amp nr

tag: Arie nr

tag: age

tag: sex

value: f

tag: bsa

tag: valve

value: ND

tag: ef

tag: lvedd

tag: ava

tag: lvmi


title: SUL1 amp segregation MD54-A3

value: FY haploid

source_name: MD54-A3 (Strain Name : S4 c1-B)

value: S4 c1-B


title: AOS_R09

description: cardiac biopsy

value: m


title: SUL1 amp segregation MD54-A2

source_name: MD54-A2 (Strain Name : S4 c1-A)

value: S4 c1-A


title: AOS_R06

description: cardiac biopsy


title: hFSF_rep3

city: Beijing

first: hongkui

last: deng

address: Yiheyuan Road 5#, Haidian District

department: College of Life Sciences

country: China

institute: Peking University

description: gene expression comparation of iPS production

hyb_protocol: The Human OneArray was hybridized using 1.5× OneArrayTM Hybridization Buffer for 16 h at 60℃; then washed in Wash Buffer 1, 2 and 3 accroding to the manufacturer's instruction.

scan_protocol: Arrays were scanned using GenePix 4000B scanner (Molecular Devices)  according to the manufacturer’s protocol

data_processing: After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12311 probes for further quantile normalization. The median of each sample was used for hierarchical clustering. Complete-linkage hierarchical clustering was performed using cluster 3.0 with Spearman rank correlation coefficient as gene distances measurement, and Pearson correlation coefficient as sample distances measurement (Attached in supplementary data).

source_name: human fetal skin fibroblast, hFSF (rep 3)

label_protocol: cDNA were synthesized by reverse transcription using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) with oligo(dT) primer that contain a T7 RNA polymerase promoter sequence, according to the manufacturer’s instruction. In vitro transcription was then performed with the purified cDNA and amino allyl UTP was incorporated during transcription to produce amino allyl modified aRNA that was subsequently coupled to cy5 dye label by reacting at 25℃ for 2h.

growth_protocol: Human fibroblasts were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone) containing 10% fetal bovine serum (FBS, Gibco). hES cells, iPS cells and Pre-iPS cells were maintained on Mitomycin C-treated MEFs in hES Cell culture medium consisting of 80% DMEM/F12 (Invitrogen), 20% Knockout serum replacement (KSR) (Invitrogen), 1 mM L-glutamine, 1% non-essential amino acids, 0.1 mM beta-mercaptoethanol (all from Invitrogen) and 4 ng/ml basic fibroblast growth factor bFGF (P&A Biotech).

extract_protocol: Total RNA was isolated from cells using TRIzol (Invitrogen) according to the manufacturer’s protocol.

tag: fibroblast


title: AOS_R07

description: cardiac biopsy


title: SUL1 amp segregation MD54-A5

source_name: MD54-A5 (Strain Name : S4 c1-D)

value: S4 c1-D


title: hFSF_rep1

source_name: human fetal skin fibroblast, hFSF (rep 1)


title: Ag-D-CEN.PK-1N-D-g155-pop-RNA

scan_protocol: Pixel Size : 10 Scan Date : 2007-01-30 Scan Time : 10:59:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: F13 3/2/4 RNA (Strain Name : CEN.PK haploid)

value: CEN.PK haploid

source_name: F14 5/19/6 RNA (Strain Name : G6 population)

value: G6 population


title: AOS_R08

description: cardiac biopsy


title: AOS_R05

description: cardiac biopsy


title: AOS_R03

description: cardiac biopsy


title: hAFF_rep2

source_name: human adult foreskin fibroblast, hAFF (rep 2)

tag: Age


title: hAFF_rep1

source_name: human adult foreskin fibroblast, hAFF (rep 1)


title: hFSF_rep2

source_name: human fetal skin fibroblast, hFSF (rep 2)


title: AOS_R04

description: cardiac biopsy


title: hAFF_rep3

source_name: human adult foreskin fibroblast, hAFF (rep 3)


title: AOS_R02

description: cardiac biopsy


title: AOS_N09

description: cardiac biopsy


title: AOS_R01

description: cardiac biopsy


title: AOS_N10

description: cardiac biopsy


title: hFSF-4PU-Pre-iPS-2_rep3

description: gene expression comparation of iPS production, 4F represents OCT4/SOX2/c-Myc/KLF4

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 3)

tag: patial reprogrammed cells

tag: Donor

value: hFSF


title: hFSF-4PU-Pre-iPS-2_rep2

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 2)


title: hFSF-4PU-Pre-iPS-1_rep3

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 1 (rep 3)


title: hFSF-4PU-Pre-iPS-2_rep1

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 1)


title: AOS_N08

description: cardiac biopsy


title: hAFF-4U-M-iPS-3_rep3

source_name: iPS cell line derived from hAFF by 4F+UTF1-Myc, clone 3 (rep 3)

tag: Human Induced Pluripotent Stem cell

value: hAFF


title: AOS_N06

description: cardiac biopsy

source_name: AOS


title: AOS_N07

description: cardiac biopsy


title: hAFF-4U-M-iPS-3_rep2

source_name: iPS cell line derived from hAFF by 4F+UTF1-Myc, clone 3 (rep 2)


title: hFSF-4PU-Pre-iPS-1_rep1

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 1 (rep 1)


title: hAFF-4U-M-iPS-3_rep1

source_name: iPS cell line derived from hAFF by 4F+UTF1-Myc, clone 3 (rep 1)


title: AOS_N02

description: cardiac biopsy


title: AOS_N01

description: cardiac biopsy


title: control_C07

description: cardiac biopsy

source_name: control


title: hAFF-4PU-iPS-13_rep2

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 13 (rep 2)


title: AOS_N04

description: cardiac biopsy


title: hFSF-4PU-Pre-iPS-1_rep2

source_name: Pre-iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 1 (rep 2)


title: hAFF-4PU-iPS-13_rep1

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 13 (rep 1)


title: AOS_N05

description: cardiac biopsy


title: control_C05

description: cardiac biopsy


title: hAFF-4PU-iPS-13_rep3

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 13 (rep 3)


title: control_C04

description: cardiac biopsy


title: hFSF-4PU-iPS-2_rep2

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 2)


title: hFSF-4PU-iPS-2_rep3

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 3)


title: hFSF-4PU-iPS-2_rep1

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 2 (rep 1)


title: control_C06

description: cardiac biopsy


title: control_C03

description: cardiac biopsy


title: control_C01

description: cardiac biopsy


title: Duodenum_swimming_n2

city: Bangkok

first: Narattaphol

last: Charoenphandhu

address: Rama 6 Rd, Rachthevee

department: Department of Physiology

country: Thailand

institute: Faculty of Science, Mahidol University

description: Each array probes 21,910 genes and contains 22,523 oligonucleotide probes (50-bases gene-specific probe and 29-bases address sequence per probe), which were selected from the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database release 16.

hyb_protocol: Beadchips were hybridized at 58°C for 20 hours. After washing, they were blocked non-specific binding with blocking buffer at room temperature for 10 min. Hybridization was detected by incubating with 2 mL blocking buffer containing streptavidin-Cy3 for 10 min. Hybridization reagents and protocol were used according to IntelliHyb Seal's instruction (Illumina)

scan_protocol: BeadStation 500GX Genetic Analysis System is used to scan the fluorescent signals at the dual laser excitation of 532 nm and 635 nm, and emission spectrum of 550-600 nm and 650-700 nm. Image registration and data extraction are automatic.

data_processing: The Illumina’s Cubic-Spline normalization algorithm was applied to adjust sample signals to minimize the effects of variation arising from non-biological factors. Comparisons between samples from control and CMA rats were done with the t-test differential expression algorithm.

organism: Rattus norvegicus

label_protocol: Total RNA was reverse transcribed to synthesize first and second strand cDNA. After cDNA purification, it was used for in vitro transcription to synthesize biotinylated cRNA according to Illumina TotalPrep RNA Amplification Kit's instruction (Illumina)

growth_protocol: Eight-week-old female Sprague-Dawley rats were housed in the laboratory animal husbandry unit for a week prior to the experiment  under 12:12 h dark-light cycle and were fed regular pellets and distilled water ad libitum. The room had a temperature of 20-25°C and humidity of 50-60%. This study has been approved by the Institutional Animal Care and Use Committee (IACUC) of the Faculty of Science, Mahidol University, Thailand.

extract_protocol: 10-cm duodenal segments of rats were removed and cut longitudinally along the radix mesenterii to expose the mucosa. Intestinal epithelial cells were collected by scraping the mucosal surface with an ice-cold glass slide.

treatment_protocol: Rats were randomly divided into 2 groups, control and swimming groups. Swimming exercise group was assigned to perform endurance swimming for 2 weeks. Swimming rats were initially trained for a week until they could swim non stop 1 hour/day.  Swimming frequency was 5 days/week. The age-matched control  remained sedentary for 2 weeks in a swimming pool. The water temperature was maintained at 30-32°C. After exercise, rats were dried with a towel and hair dryer.

tag: SEX

value: Female

tag: STRAIN

value: Sprague Dawley

tag: AGE

value: 9 weeks


title: Duodenum_swimming_n3


title: control_C02

description: cardiac biopsy

tag: tissue

tag: Amp nr

tag: Arie nr


title: Duodenum_swimming_n6


title: AOS_N03

description: cardiac biopsy

tag: age

tag: sex

tag: bsa


title: hFSF-4PU-iPS-4_rep1

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 4 (rep 1)


title: Duodenum_control_n6

source_name: Duodenum


title: hFSF-4PU-iPS-4_rep2

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 4 (rep 2)


title: hFSF-4PU-iPS-4_rep3

source_name: iPS cell line derived from hFSF by 4F+p53si+UTF1, clone 4 (rep 3)


title: H1_rep1

source_name: H1 Human Embryonic Stem cell (rep 1)

tag: Human Embryonic Stem cell


title: Duodenum_swimming_n5


title: H1_rep3

source_name: H1 Human Embryonic Stem cell (rep 3)


title: H1_rep2

source_name: H1 Human Embryonic Stem cell (rep 2)


title: H7_rep1

source_name: H7 Human Embryonic Stem cell (rep 1)


title: Duodenum_swimming_n1


title: hAFF-4PU-iPS-9_rep1

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 9 (rep 1)


title: Duodenum_control_n1


title: H7_rep2

source_name: H7 Human Embryonic Stem cell (rep 2)


title: H7_rep3

source_name: H7 Human Embryonic Stem cell (rep 3)


title: Duodenum_control_n4


title: Duodenum_control_n5


title: hAFF-4PU-iPS-9_rep3

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 9 (rep 3)


title: Duodenum_swimming_n4


title: E9-P.gingivalis vs Pooled sample

city: Louisville

first: Amar

last: Singh

address: 501 S Preston street

department: Oral Health and Systemic Disease Research Group

institute: University of Louisville

description: E9-P. gingivalis (Cy3) / Pooled E9 sample (Cy5)

hyb_protocol: 16h, 56-59°C, PerkinElmer MPS621 cDNA arays

scan_protocol: median signal, local background correction, ScanArray 5000 XL

data_processing: Expression ratio determined from background-corrected ratios transformed to log2-space and normalized by 'loess' plots of the difference against the average; paired-slides normalization applied to the replica swaps and each array was polished to MEDIAN = 0.00 and scaled to STDEV = 0.50. Normalized data fitted to a linear model for microarray analysis using the 'limma' package (http://www.bioconductor.org).

source_name: Gingiva, E9-P.gingivalis

label_protocol: streptavidin-conjugated peroxidase and cyanine-5-tyramide, and peroxidase-conjugated anti-fluorescein and cyanine-3-tyramide

growth_protocol: 24h after challenge with 90% confluence

extract_protocol: Total cellular RNA isolated with RNeasy (Qiagen) that removes small RNAs (<200 nucleotides); RNA passing QA/QC converted to cDNA with incorporation of labeled nucleotide; each condition replicated with independent samples and the reverse-label assignments.

treatment_protocol: Stimulated with heat inactivated P. gingivalis (33277) for 24h

tag: Young and healthy subject without known systemic disease

source_name: Gingiva, Pooled E9 sample

tag: Gingiva, Pooled E9 sample


title: E28-P.gingivalis vs Pooled sample

description: E28-P. gingivalis (Cy3) / Pooled E28 sample (Cy5)

source_name: Gingiva, E28-P. gingivalis

source_name: Gingiva, Pooled E28 sample

tag: Gingiva, Pooled E28 sample


title: E9 Control vs Pooled sample

description: E9 Control (Cy3) / Pooled E9 sample (Cy5)

source_name: Gingiva, E9 Control

growth_protocol: 24h after along with challenged samples with 90% confluence

treatment_protocol: Unstimulated


title: E28 Control vs Pooled sample

description: E28 Control (Cy3) / Pooled E28 sample (Cy5)

source_name: Gingiva, E28 Control


title: Duodenum_control_n2

source_name: Duodenum


title: Duodenum_control_n3


title: hAFF-4PU-iPS-9_rep2

source_name: iPS cell line derived from hAFF by 4F+p53si+UTF1, clone 9 (rep 2)