title: YBL054W_2048.2_ArrayA

description: Yeast YBL054W_2048.2_ArrayA

source_name: Baker's yeast YBL054W

tag: Yeast YBL054W


title: YBR239C_2158.2_ArrayA

status: Public on Dec 26 2008

type: protein

city: Toronto

first: Lourdes

last: Pena-Castillo

state: Ontario

address: 160 College St. Room 1350

department: Banting and Best Department of Medical Research

country: Canada

institute: University of Toronto

description: Yeast YBR239C_2158.2_ArrayA

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 100 nM (unless otherwise specified) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. Slides were spun dry by centrifugation at 40 g for 5 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa488-conjugated antibody (488 nm ex, 522 nm em). Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices)

data_processing: Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score). E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots.

molecule: protein

organism: Saccharomyces cerevisiae

source_name: Baker's yeast YBR239C

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: Protein open reading frames, consisting of the pfam-defined DNA-binding domain and 15 amino acids of flanking sequence (or to the end of the full open reading frame) were cloned into pMAGIC1  by either RT-PCR from pooled yeast mRNA or by gene synthesis (DNA 2.0).  We transferred the inserts into a T7-GST-tagged variant of pML280 following.  We expressed proteins by either (i) purification from E. coli C41 DE3 cells (Lucigen), or (ii) in vitro translation reactions (Ambion ActivePro Kit) without purification.

tag: Yeast YBR239C


title: YAP3_4535.1_ArrayB.2

description: Yeast YAP3_4535.1_ArrayB.2

source_name: Baker's yeast YAP3

tag: Yeast YAP3


title: XBP1_4495.1_ArrayB

description: Yeast XBP1_4495.1_ArrayB

source_name: Baker's yeast XBP1

tag: Yeast XBP1


title: TYE7_2097.2_ArrayA

description: Yeast TYE7_2097.2_ArrayA

source_name: Baker's yeast TYE7

tag: Yeast TYE7


title: UME6_2040.2_ArrayA

description: Yeast UME6_2040.2_ArrayA

source_name: Baker's yeast UME6

tag: Yeast UME6


title: YPL230W_2051.3_ArrayA

description: Yeast YPL230W_2051.3_ArrayA

source_name: Baker's yeast YPL230W

tag: Yeast YPL230W


title: SWI5_2037.2_ArrayA

description: Yeast SWI5_2037.2_ArrayA

source_name: Baker's yeast SWI5

tag: Yeast SWI5


title: TBF1_2078.2_ArrayA

description: Yeast TBF1_2078.2_ArrayA

source_name: Baker's yeast TBF1

tag: Yeast TBF1


title: XBP1_4495.2_ArrayA

description: Yeast XBP1_4495.2_ArrayA


title: TEA1_2096.3_ArrayA.2

description: Yeast TEA1_2096.3_ArrayA.2

source_name: Baker's yeast TEA1

tag: Yeast TEA1


title: UGA3_4522.2_ArrayA

description: Yeast UGA3_4522.2_ArrayA

source_name: Baker's yeast UGA3

tag: Yeast UGA3


title: STB5_4529.1_ArrayA

description: Yeast STB5_4529.1_ArrayA

source_name: Baker's yeast STB5

tag: Yeast STB5


title: TBF1_2078.1_ArrayB

description: Yeast TBF1_2078.1_ArrayB


title: TEC1_2092.2_ArrayA

description: Yeast TEC1_2092.2_ArrayA

source_name: Baker's yeast TEC1

tag: Yeast TEC1


title: STP4_2135.1_ArrayB

description: Yeast STP4_2135.1_ArrayB

source_name: Baker's yeast STP4

tag: Yeast STP4


title: TBS1_2130.2_ArrayA

description: Yeast TBS1_2130.2_ArrayA

source_name: Baker's yeast TBS1

tag: Yeast TBS1


title: SUM1_2124.3_ArrayA.1

description: Yeast SUM1_2124.3_ArrayA.1

source_name: Baker's yeast SUM1

tag: Yeast SUM1


title: STB4_2129.2_ArrayA

description: Yeast STB4_2129.2_ArrayA

source_name: Baker's yeast STB4

tag: Yeast STB4


title: SWI4_4482.2_ArrayA

description: Yeast SWI4_4482.2_ArrayA

source_name: Baker's yeast SWI4

tag: Yeast SWI4


title: SRD1_2031.3_ArrayA

description: Yeast SRD1_2031.3_ArrayA

source_name: Baker's yeast SRD1

tag: Yeast SRD1


title: SWI4_4482.1_ArrayB

description: Yeast SWI4_4482.1_ArrayB


title: STE12_4502.2_ArrayA

description: Yeast STE12_4502.2_ArrayA

source_name: Baker's yeast STE12

tag: Yeast STE12


title: TOS8_2100.1_ArrayB

description: Yeast TOS8_2100.1_ArrayB

source_name: Baker's yeast TOS8

tag: Yeast TOS8


title: UPC2_2128.2_ArrayA

description: Yeast UPC2_2128.2_ArrayA

source_name: Baker's yeast UPC2

tag: Yeast UPC2


title: SOK2_4560.1_ArrayA

description: Yeast SOK2_4560.1_ArrayA

source_name: Baker's yeast SOK2

tag: Yeast SOK2


title: SUM1_2124.4_ArrayA.2

description: Yeast SUM1_2124.4_ArrayA.2


title: SKN7_2117.2_ArrayB.2

description: Yeast SKN7_2117.2_ArrayB.2

source_name: Baker's yeast SKN7

tag: Yeast SKN7


title: SIP4_2067.2_ArrayA

description: Yeast SIP4_2067.2_ArrayA

source_name: Baker's yeast SIP4

tag: Yeast SIP4


title: SIG1_4499.2_ArrayA

description: Yeast SIG1_4499.2_ArrayA

source_name: Baker's yeast SIG1

tag: Yeast SIG1


title: SAS3_2050.2_ArrayA

description: Yeast SAS3_2050.2_ArrayA

source_name: Baker's yeast SAS3

tag: Yeast SAS3


title: SKN7_2117.2_ArrayA

description: Yeast SKN7_2117.2_ArrayA


title: STP3_4483.2_ArrayA

description: Yeast STP3_4483.2_ArrayA

source_name: Baker's yeast STP3

tag: Yeast STP3


title: RSC3_pTH2035.5_ArrayB

description: Yeast RSC3_pTH2035.5_ArrayB

source_name: Baker's yeast RSC3

tag: Yeast RSC3


title: RPN4_2137.1_ArrayB.1

description: Yeast RPN4_2137.1_ArrayB.1

source_name: Baker's yeast RPN4

tag: Yeast RPN4


title: RSC3_2035.2_ArrayA

description: Yeast RSC3_2035.2_ArrayA


title: ROX1_2099.1_ArrayA

description: Yeast ROX1_2099.1_ArrayA

source_name: Baker's yeast ROX1

tag: Yeast ROX1


title: YML081W_2152.2_ArrayA.1

description: Yeast YML081W_2152.2_ArrayA.1

source_name: Baker's yeast YML081W

tag: Yeast YML081W


title: RSC30_2087.3_ArrayA

description: Yeast RSC30_2087.3_ArrayA

source_name: Baker's yeast RSC30

tag: Yeast RSC30


title: RSC30_pTH2087.2_ArrayB

description: Yeast RSC30_pTH2087.2_ArrayB


title: SKN7_2117.1_ArrayB.1

description: Yeast SKN7_2117.1_ArrayB.1


title: ROX1_2099.1_ArrayB

description: Yeast ROX1_2099.1_ArrayB


title: RPN4_2137.2_ArrayA

description: Yeast RPN4_2137.2_ArrayA


title: RPH1_4571.1_ArrayB

description: Yeast RPH1_4571.1_ArrayB

source_name: Baker's yeast RPH1

tag: Yeast RPH1


title: RPH1_4571.2_ArrayA

description: Yeast RPH1_4571.2_ArrayA


title: RGT1_2131.2_ArrayA

description: Yeast RGT1_2131.2_ArrayA

source_name: Baker's yeast RGT1

tag: Yeast RGT1


title: RFX1_4537.2_ArrayA.1

description: Yeast RFX1_4537.2_ArrayA.1

source_name: Baker's yeast RFX1

tag: Yeast RFX1


title: RGM1_2105.1_ArrayA.1

description: Yeast RGM1_2105.1_ArrayA.1

source_name: Baker's yeast RGM1

tag: Yeast RGM1


title: RGM1_2105.1_ArrayB

description: Yeast RGM1_2105.1_ArrayB


title: REI1_2049.2_ArrayA

description: Yeast REI1_2049.2_ArrayA

source_name: Baker's yeast REI1

tag: Yeast REI1


title: REB1_4402.1_ArrayA

description: Yeast REB1_4402.1_ArrayA

source_name: Baker's yeast REB1

tag: Yeast REB1


title: RFX1_4537.3_ArrayA.2

description: Yeast RFX1_4537.3_ArrayA.2


title: REB1_4402.1_ArrayB

description: Yeast REB1_4402.1_ArrayB


title: RDS2_2062.1_ArrayA

description: Yeast RDS2_2062.1_ArrayA

source_name: Baker's yeast RDS2

tag: Yeast RDS2


title: RDR1_2112.2_ArrayA

description: Yeast RDR1_2112.2_ArrayA

source_name: Baker's yeast RDR1

tag: Yeast RDR1


title: YJL103C_4534.1_ArrayA

description: Yeast YJL103C_4534.1_ArrayA

source_name: Baker's yeast YJL103C

tag: Yeast YJL103C


title: PHO4_4536.2_ArrayA

description: Yeast PHO4_4536.2_ArrayA

source_name: Baker's yeast PHO4

tag: Yeast PHO4


title: RDS1_pTH2068.5_ArrayB

description: Yeast RDS1_pTH2068.5_ArrayB

source_name: Baker's yeast RDS1

tag: Yeast RDS1


title: PUT3_4533.2_ArrayA

description: Yeast PUT3_4533.2_ArrayA

source_name: Baker's yeast PUT3

tag: Yeast PUT3


title: PHO2_2074.2_ArrayA.1

description: Yeast PHO2_2074.2_ArrayA.1

source_name: Baker's yeast PHO2

tag: Yeast PHO2


title: PHD1_4559.2_ArrayA

description: Yeast PHD1_4559.2_ArrayA

source_name: Baker's yeast PHD1

tag: Yeast PHD1


title: PHO4_4536.1_ArrayB.1

description: Yeast PHO4_4536.1_ArrayB.1


title: PDR1_4520.1_ArrayA

description: Yeast PDR1_4520.1_ArrayA

source_name: Baker's yeast PDR1

tag: Yeast PDR1


title: MSN4_2121.2_ArrayA

description: Yeast MSN4_2121.2_ArrayA

source_name: Baker's yeast MSN4

tag: Yeast MSN4


title: MSN2_2101.1_ArrayB

description: Yeast MSN2_2101.1_ArrayB

source_name: Baker's yeast MSN2

tag: Yeast MSN2


title: OAF1_4564.1_ArrayA

description: Yeast OAF1_4564.1_ArrayA

source_name: Baker's yeast OAF1

tag: Yeast OAF1


title: NHP10_2069.3_ArrayA.3

description: Yeast NHP10_2069.3_ArrayA.3

source_name: Baker's yeast NHP10

tag: Yeast NHP10


title: NHP10_2069.1_ArrayA.1

description: Yeast NHP10_2069.1_ArrayA.1


title: PHO2_2074.1_ArrayB.2

description: Yeast PHO2_2074.1_ArrayB.2


title: MIG2_2053.1_ArrayB

description: Yeast MIG2_2053.1_ArrayB

source_name: Baker's yeast MIG2

tag: Yeast MIG2


title: MIG1_2106.1_ArrayB

description: Yeast MIG1_2106.1_ArrayB

source_name: Baker's yeast MIG1

tag: Yeast MIG1


title: PHO4_4536.1_ArrayB.2

description: Yeast PHO4_4536.1_ArrayB.2


title: MSN2_2101.2_ArrayA

description: Yeast MSN2_2101.2_ArrayA


title: MIG3_2054.2_ArrayA

description: Yeast MIG3_2054.2_ArrayA

source_name: Baker's yeast MIG3

tag: Yeast MIG3


title: MIG3_2054.1_ArrayB

description: Yeast MIG3_2054.1_ArrayB


title: PDR8_4525.1_ArrayA

description: Yeast PDR8_4525.1_ArrayA

source_name: Baker's yeast PDR8

tag: Yeast PDR8


title: MIG2_2053.2_ArrayA

description: Yeast MIG2_2053.2_ArrayA


title: MIG1_2106.2_ArrayA

description: Yeast MIG1_2106.2_ArrayA


title: RDS1_2068.2_ArrayA

description: Yeast RDS1_2068.2_ArrayA


title: MET31_2146.2_ArrayA

description: Yeast MET31_2146.2_ArrayA

source_name: Baker's yeast MET31

tag: Yeast MET31


title: MET32_2153.2_ArrayA

description: Yeast MET32_2153.2_ArrayA

source_name: Baker's yeast MET32

tag: Yeast MET32


title: MBP1_4486.1_ArrayB.2

description: Yeast MBP1_4486.1_ArrayB.2

source_name: Baker's yeast MBP1

tag: Yeast MBP1


title: LYS14_2065.2_ArrayA

description: Yeast LYS14_2065.2_ArrayA

source_name: Baker's yeast LYS14

tag: Yeast LYS14


title: HSF1_4530.2_ArrayA

description: Yeast HSF1_4530.2_ArrayA

source_name: Baker's yeast HSF1

tag: Yeast HSF1


title: HMRA2_2071.1_ArrayB

description: Yeast HMRA2_2071.1_ArrayB

source_name: Baker's yeast HMRA2

tag: Yeast HMRA2


title: MBP1_4486.1_ArrayB.1

description: Yeast MBP1_4486.1_ArrayB.1


title: MET31_2146.1_ArrayB.2

description: Yeast MET31_2146.1_ArrayB.2


title: HMRA2_2071.2_ArrayA

description: Yeast HMRA2_2071.2_ArrayA


title: HAC1_2057.3_ArrayA

description: Yeast HAC1_2057.3_ArrayA

source_name: Baker's yeast HAC1

tag: Yeast HAC1


title: HAP1_2139.2_ArrayA

description: Yeast HAP1_2139.2_ArrayA

source_name: Baker's yeast HAP1

tag: Yeast HAP1


title: LEU3_2036.2_ArrayA

description: Yeast LEU3_2036.2_ArrayA

source_name: Baker's yeast LEU3

tag: Yeast LEU3


title: HAL9_2041.2_ArrayA

description: Yeast HAL9_2041.2_ArrayA

source_name: Baker's yeast HAL9

tag: Yeast HAL9


title: MBP1_4486.2_ArrayA

description: Yeast MBP1_4486.2_ArrayA


title: HCM1_2157.3_ArrayA.2

description: Yeast HCM1_2157.3_ArrayA.2

source_name: Baker's yeast HCM1

tag: Yeast HCM1


title: GLN3_2032.3_ArrayA.1

description: Yeast GLN3_2032.3_ArrayA.1

source_name: Baker's yeast GLN3

tag: Yeast GLN3


title: GZF3_2167.2_ArrayA

description: Yeast GZF3_2167.2_ArrayA

source_name: Baker's yeast GZF3

tag: Yeast GZF3


title: GZF3_2167.1_ArrayB

description: Yeast GZF3_2167.1_ArrayB


title: GAT4_4527.2_ArrayA

description: Yeast GAT4_4527.2_ArrayA

source_name: Baker's yeast GAT4

tag: Yeast GAT4


title: GLN3_2032.2_ArrayB.1

description: Yeast GLN3_2032.2_ArrayB.1


title: GIS1_4481.2_ArrayA

description: Yeast GIS1_4481.2_ArrayA

source_name: Baker's yeast GIS1

tag: Yeast GIS1


title: FZF1_4526.2_ArrayA

description: Yeast FZF1_4526.2_ArrayA

source_name: Baker's yeast FZF1

tag: Yeast FZF1


title: GLN3_2032.4_ArrayA.2

description: Yeast GLN3_2032.4_ArrayA.2


title: GAL4_2034.2_ArrayA

description: Yeast GAL4_2034.2_ArrayA

source_name: Baker's yeast GAL4

tag: Yeast GAL4


title: FHL1_2086.3_ArrayA.2

description: Yeast FHL1_2086.3_ArrayA.2

source_name: Baker's yeast FHL1

tag: Yeast FHL1


title: GAT3_2122.5_ArrayA.2

description: Yeast GAT3_2122.5_ArrayA.2

source_name: Baker's yeast GAT3

tag: Yeast GAT3


title: FKH2_4517.2_ArrayA

description: Yeast FKH2_4517.2_ArrayA

source_name: Baker's yeast FKH2

tag: Yeast FKH2


title: EDS1_2094.3_ArrayA.2

description: Yeast EDS1_2094.3_ArrayA.2

source_name: Baker's yeast EDS1

tag: Yeast EDS1


title: ECM23_2123.1_ArrayB

description: Yeast ECM23_2123.1_ArrayB

source_name: Baker's yeast ECM23

tag: Yeast ECM23


title: GAT1_2166.2_ArrayA

description: Yeast GAT1_2166.2_ArrayA

source_name: Baker's yeast GAT1

tag: Yeast GAT1


title: ECM23_2123.2_ArrayA

description: Yeast ECM23_2123.2_ArrayA


title: GLN3_2032.2_ArrayB.2

description: Yeast GLN3_2032.2_ArrayB.2


title: DOT6_2080.3_ArrayA

description: Yeast DOT6_2080.3_ArrayA

source_name: Baker's yeast DOT6

tag: Yeast DOT6


title: DOT6_2080.1_ArrayB.1

description: Yeast DOT6_2080.1_ArrayB.1


title: DOT6_2080.2_ArrayB.2

description: Yeast DOT6_2080.2_ArrayB.2


title: CRZ1_4531.2_ArrayA

description: Yeast CRZ1_4531.2_ArrayA

source_name: Baker's yeast CRZ1

tag: Yeast CRZ1


title: CST6_4521.2_ArrayA

description: Yeast CST6_4521.2_ArrayA

source_name: Baker's yeast CST6

tag: Yeast CST6


title: CUP9_4508.2_ArrayA

description: Yeast CUP9_4508.2_ArrayA

source_name: Baker's yeast CUP9

tag: Yeast CUP9


title: CHA4_2113.3_ArrayA.2

description: Yeast CHA4_2113.3_ArrayA.2

source_name: Baker's yeast CHA4

tag: Yeast CHA4


title: CEP3_2090.2_ArrayA

description: Yeast CEP3_2090.2_ArrayA

source_name: Baker's yeast CEP3

tag: Yeast CEP3


title: DAL80_2083.2_ArrayA

description: Yeast DAL80_2083.2_ArrayA

source_name: Baker's yeast DAL80

tag: Yeast DAL80


title: CRZ1_4531.1_ArrayB

description: Yeast CRZ1_4531.1_ArrayB


title: CIN5_2059.3_ArrayA.2

description: Yeast CIN5_2059.3_ArrayA.2

source_name: Baker's yeast CIN5

tag: Yeast CIN5


title: CAT8_4532.1_ArrayA

description: Yeast CAT8_4532.1_ArrayA

source_name: Baker's yeast CAT8

tag: Yeast CAT8


title: CBF1_2160.2_ArrayB.2

description: Yeast CBF1_2160.2_ArrayB.2

source_name: Baker's yeast CBF1

tag: Yeast CBF1


title: ADR1_4492.2_ArrayA

description: Yeast ADR1_4492.2_ArrayA

source_name: Baker's yeast ADR1

tag: Yeast ADR1


title: ASG1_2140.3_ArrayA.2

description: Yeast ASG1_2140.3_ArrayA.2

source_name: Baker's yeast ASG1

tag: Yeast ASG1


title: AZF1_2102.3_ArrayA.2

description: Yeast AZF1_2102.3_ArrayA.2

source_name: Baker's yeast AZF1

tag: Yeast AZF1


title: RIM101_2030.2_ArrayA

description: Yeast RIM101_2030.2_ArrayA

source_name: Baker's yeast RIM101

tag: Yeast RIM101


title: BDP1_2079.2_ArrayA

description: Yeast BDP1_2079.2_ArrayA

source_name: Baker's yeast BDP1

tag: Yeast BDP1


title: S2 Pol II IP vs S2 cells, ChIP input

status: Public on Dec 25 2008

type: genomic

city: Waltham

first: Joseph

last: Rodriguez

address: 415 South Street

department: Biology

country: USA

institute: Brandeis University

description: S2, PolII-ChIP

hyb_protocol: DNA was hybridized according to manufacturer's protocol on GeneChip Drosophila Tiling 2.0R. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Tiling arrays were scanned using the GeneChip Scanner 3000

data_processing: Data was processed using the Model-based Analysis of Tiling-array (MAT) software package (Johnson et al., 2006).  Both biological IP replicates were compared against the input replicates using the MAT paired option.  ChIP arrays were analyzed using a bandwidth size of 300, minimum probe gap of 300, probe number of 10 and a p-value threshold of 1e-05.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells, PolII-ChIP vs S2 cells, ChIP input; 2 replicates

label_protocol: genomic DNA was prepared according to the standard Affymetrix protocol

extract_protocol: ChIP protocol was adapted from (Andrulis et al., 2000).  Cells were harvested in 1X PBS and incubated in 0.5% formaldehyde for 15 minutes. Cells were incubated in 50mM Tris/Glycine pH 7.5 for 5 minutes. After washing, cells were resuspended in 1X PBS and Triton X-100 was added to final concentration of 0.5%.  Lysed cells were pelleted and nuclei were resuspended in ChIP Lysis Buffer.  Sarkosyl was added to a final concentration of 2%.  Samples were sonicated with Fisher Scientific Sonic Dismembrator 550 at setting 2 twice for 20 seconds.  Sonicated samples were centrifuged to remove insoluble debris.  The resulting chromatin was diluted 2-fold in Lysis Buffer prior to being stored at -80°C.    2μl of a Polyclonal RNA Polymerase II antibody was added to 150μl of chromatin and incubated overnight at 4°C. Protein G beads were blocked before being incubated with the chromatin-antibody mixture for 4 hours at 4°C. After washing, the beads were resuspended in 150μL of Elution buffer and incubated for 2 hours at 37°C. Supernatant was incubated at 65°C overnight to reverse crosslinks. DNA was purified using the PCR Purification Kit (Qiagen).

tag: S2, PolII-ChIP


title: ARO80_2088.2_ArrayA

description: Yeast ARO80_2088.2_ArrayA

source_name: Baker's yeast ARO80

tag: Yeast ARO80


title: ABF2_2116.1_ArrayB

description: Yeast ABF2_2116.1_ArrayB

source_name: Baker's yeast ABF2

tag: Yeast ABF2


title: ACE2_2082.2_ArrayA

description: Yeast ACE2_2082.2_ArrayA

source_name: Baker's yeast ACE2

tag: Yeast ACE2


title: AZF1_2102.2_ArrayA.1

description: Yeast AZF1_2102.2_ArrayA.1


title: hESC-1 Cy3

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

institute: McMaster Stem Cell and Cancer Research Institute (SCC-RI)

description: Array comparative genomic hybridization analysis of normal hESC-1 cultures.

hyb_protocol: See manufacturer's website.

scan_protocol: Arrays were then scanned on a ScanArray Gx Plus microarray scanner (PerkinElmer) or the Genepix 4000B scanner (Molecular Devices)

data_processing: Arrays were analyzed with SpectralWare 2.2.4 (PerkinElmer).

organism: Homo sapiens

source_name: Human embryonic stem cells

label_protocol: See manufacturer's website.

extract_protocol: Genomic DNA was extracted using using the AllPrep DNA/RNA Mini Kit (Qiagen).

tag: Cell line

tag: Gender

value: Female

source_name: Promega Male

extract_protocol: Performed by PerkinElmer.

tag: Promega Male Genomic DNA


title: Variant hESC-1 A2B5 Cy5

description: Array comparative genomic hybridization analysis of variant hESC-1 neural precursor cultures

source_name: Variant human embryonic stem cell neural precursor cultures


title: ADR1_4492.1_ArrayB.2

description: Yeast ADR1_4492.1_ArrayB.2


title: Variant hESC-1 A2B5 Cy3


title: hESC-1 Cy5


title: ACE2_2082.1_ArrayB

description: Yeast ACE2_2082.1_ArrayB


title: Variant hESC-1 Cy5

description: Array comparative genomic hybridization analysis of variant hESC-1 cultures.

source_name: Variant human embryonic stem cells (v-hESC-1)


title: Variant hESC-1

type: RNA

description: Gene expression array analysis using variant hESCs normalized to the median hybridization intensity.

hyb_protocol: See manufacturer's website

scan_protocol: See manufacturer's website

data_processing: Background levels of hybridization were subtracted, and gene expression was normalized to the median hybridization intensity.

molecule: total RNA

label_protocol: Amplified RNA was labeled with the TrueLabeling-AMP™ 2.0 kit.

extract_protocol: Total RNA was extracted from frozen normal hESC, vhESC, EP2102 pellets using the RNeasy kit (Qiagen).

tag: Variant human embryonic stem cell line (H9)


title: Variant hESC-2 Cy3

description: Array comparative genomic hybridization analysis of variant hESC-2 cultures.

source_name: Variant human embryonic stem cells (v-hESC-2)

tag: Promega Male genomic DNA


title: ABF1_4505.2_ArrayA

description: Yeast ABF1_4505.2_ArrayA

source_name: Baker's yeast ABF1

tag: Yeast ABF1


title: S2 drosha knockdown,biological replicate 2

description: S2 drosha RNAi

hyb_protocol: cDNA was hybridized according to manufacturer's protocol on GeneChip Drosophila Tiling 1.0R. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Data was processed using the Model-based Analysis of Tiling-array (MAT) software package (Johnson et al., 2006).  RNA arrays were analyzed using a bandwidth size of 150, minimum probe gap of 300, probe number of 5 and p-value threshold of 1e-05.

source_name: S2 cells treated with drosha dsRNA

label_protocol: cDNA was prepared according to the standard Affymetrix protocol

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

tag: S2, drosha dsRNA


title: Variant hESC-2

tag: Variant human embryonic stem cells (H9)


title: Variant hESC-2 Cy5

value: female

tag: Promega Male genomic DNA.


title: hESC-1 1

description: Gene expression array analysis using normal hESCs normalized to the median hybridization intensity.

tag: Normal human embryonic stem cell line (H9)


title: S2 drosha knockdown,biological replicate 1

description: S2 drosha RNAi


title: S2 dicer knockdown,biological replicate 2

description: S2 dicer RNAi

source_name: S2 cells treated with dicer dsRNA

tag: S2, dicer dsRNA


title: ABF2_2116.1_ArrayA.1

description: Yeast ABF2_2116.1_ArrayA.1


title: Ep2102 1-1

description: Gene expression array analysis using EP2102 normalized to the median hybridization intensity.

source_name: EP2102 cells

extract_protocol:
Total RNA was extracted from frozen normal hESC, vhESC,
EP2102 pellets using the RNeasy kit (Qiagen).

tag: Human embryonal carcinoma cell line


title: hESC-1 2


title: S2 dicer knockdown,biological replicate 1

description: S2 dicer RNAi


title: Variant hESC-1 Cy3


title: S2 control,biological replicate 2

description: S2, control

source_name: S2 cells, control

tag: S2, control


title: Ep2102 1-2


title: S2 control,biological replicate 1

description: S2, control


title: V1799_Patient with Amyotrophic Lateral Sclerosis

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a patient with ALS

hyb_protocol: Hybridisation was done overnight at 42C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

scan_protocol: Slides were scanned using an Agilent scanner.  PMT settings: 100/100%

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalised by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Mar. 2007)

source_name: DNA isolated from EBV-transformed lymphoblastoid cell line

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

extract_protocol: DNA was extracted from patient cell line using the QIAamp Blood DNA Midi Kit

tag: female ALS patient

source_name: DNA isolated from EBV-transformed cell line (reference)

extract_protocol: DNA was extracted from EBV-transformed lymphoblastoid cell line using standard phenol-chloroform extraction procedures

tag: healthy female donor


title: V926_Patient with Amyotrophic Lateral Sclerosis

scan_protocol: Slides were scanned using an Agilent scanner. PMT settings: 100/100%

tag: male ALS patient

tag: healthy male donor


title: V918_Patient with Amyotrophic Lateral Sclerosis


title: ratbladder_SCI_7days

city: Pittsburgh

first: Silvia

last: Wognum

state: PA

address: 100 Technology Drive

department: Bioengineering

institute: University of Pittsburgh

hyb_protocol: Fifteen to twenty micrograms of cRNA were fragmented by incubating in a buffer containing 200mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc at 958C for 35 min. The fragmented cRNAs were then hybridized with a pre-equilibrated Affymetrix chip at 458C for 14–16 h. After the hybridization cocktails were removed, the chips were then washed in a fluidic station with low-stringency buffer (6x SSPE, 0.01% Tween-20, 0.005% antifoam) for 10 cycles (2 mixes/cycle) and stringent buffer (100 mM MES, 0.1 M NaCl, and 0.01% Tween-20) for 4 cycles (15 mixes/cycle), and stained with SAPE (Strepto-avidin Phycoerythrin). This was followed by incubation with biotinylated mouse anti-avidin antibody, and restained with SAPE.

scan_protocol: Affymetrix  HP ChipScanner (G-7 scanner). Software: GCOS1.4

data_processing: GCOS1.4, normalized through scaled target intensity.

organism: Rattus norvegicus

source_name: urinary bladder muscle post-spinal cord injury (7 days)

label_protocol: The purified cDNA were incubated at 37 degC for 4 h in an in vitro transcription reaction to produce cRNA labeled with biotin using MEGAscriptTM system (Ambion, Inc., Austin, TX).

growth_protocol: No specific protocol. Normal animal keeping, specific for spinalized animals, under DLAR protocol.

extract_protocol: Total RNA was isolated using Trizol reagent, and purified with Qiagen RNeasy kit

treatment_protocol:
bladder harvested under halothane anesthesia 7 days post-spinalization;
muscle layer dissected and snap-frozen in liquid nitrogen.

tag: strain

value: Sprague Dawley

tag: gender

value: female ,

tag: age/weight

tag: animal protocol:

tag: An PE-10 intrathecal catheter (Clay-Adams, Parsippany, New Jersey) was implanted at the level of the L6 to S1 spinal cord after laminectomy at the Th11 vertebra with the rat under halothane anesthesia. The end of the catheter was heat sealed and placed subcutaneously. At 3 to 4 days after intrathecal catheter implantation spinal cord transection was performed between Th9 to Th10 with the rat under halothane anesthesia. After T9 laminectomy the dura and spinal cord were cut with scissors and a sterile Gelform sponge (The Upjohn Co., Kalamazoo, Michigan) was placed between the cut ends of the spinal cord. The overlying muscle and skin were sutured. Postoperatively the animals were treated with antibiotics (ampicillin, 150 mg./kg. intramuscularly) for 7 days. The bladder of spinalized rats was manually emptied twice daily.

tag: tissues

value: urinary bladder muscle


title: ratbladder_SCI_25d

source_name: urinary bladder muscle post-spinal cord injury (25 days)

treatment_protocol:
bladder harvested under halothane anesthesia 25 days post-spinalization;
muscle layer dissected and snap-frozen in liquid nitrogen.

tag: An PE-10 intrathecal catheter (Clay-Adams, Parsippany, New Jersey) was implanted at the level of the L6 to S1 spinal cord after laminectomy at the Th11 vertebra with the rat under halothane anesthesia. The end of the catheter was heat sealed and placed subcutaneously. At 3 to 4 days after intrathecal catheter implantation spinal cord transection was performed between Th9 to Th10 with the rat under halothane anesthesia. After T9 laminectomy the dura and spinal cord were cut with scissors and a sterile Gelform sponge (The Upjohn Co., Kalamazoo, Michigan) was placed between the cut ends of the spinal cord. The overlying muscle and skin were sutured. Postoperatively the animals were treated with antibiotics (ampicillin, 150 mg./kg. intramuscularly) for 7 days. The bladder of spinalized rats was manually emptied twice daily until reflex voiding recovered, 14 days after spinalization.


title: V1285_Patient with Amyotrophic Lateral Sclerosis

scan_protocol: Slides were scanned using an Axon4000B.


title: V1771_Patient with Amyotrophic Lateral Sclerosis


title: V1109_Patient with Amyotrophic Lateral Sclerosis


title: V925_Patient with Amyotrophic Lateral Sclerosis


title: V1751_Patient with Amyotrophic Lateral Sclerosis


title: V1275aPatient with Amyotrophic Lateral Sclerosis


title: V1753_Patient with Amyotrophic Lateral Sclerosis


title: V1266_Patient with Amyotrophic Lateral Sclerosis


title: V1800_Patient with Amyotrophic Lateral Sclerosis


title: V1286_Patient with Amyotrophic Lateral Sclerosis


title: V916_Patient with Amyotrophic Lateral Sclerosis


title: V1043_Patient with Amyotrophic Lateral Sclerosis


title: CUP9_4508.1_ArrayB

description: Yeast CUP9_4508.1_ArrayB

source_name: Baker's yeast CUP9

tag: Yeast CUP9


title: V1752_Patient with Amyotrophic Lateral Sclerosis


title: V1254_Patient with Amyotrophic Lateral Sclerosis


title: ECM22_2066.2_ArrayA

description: Yeast ECM22_2066.2_ArrayA

source_name: Baker's yeast ECM22

tag: Yeast ECM22


title: V1270_Patient with Amyotrophic Lateral Sclerosis


title: Rsc8 ChIP in a wild-type background

description: Rsc8-IP vs. Input genomic DNA in a wild-type background

hyb_protocol: Competitively hybridized 1ug of DNA from channels 1 and 2 against each other on NimbleGEn 385k feature, 32bp whole genome tiling array in a Maui SL Mixer with a Maui hybrdization system overnight at 42C.

scan_protocol: Array was scanned on GenePix 4000B scanner as per NimbleGen guidelines

data_processing: The data was prepared using NimbleScan's GFF generating algorithm from the supplementary PAIR files, the VALUE reported is the normalized log2ratio from NimbleScan. The normalization is the default done by NimbleScan. Specifically, the log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: Rsc8-IP genomic DNA from wild-type Saccharomyces cerevisiae carrying Rsc8-TAP

label_protocol: Cy5 labeled primers and Klenow, as per NimbleGen labeling protocol

growth_protocol: Cells were grown at 22°C (permissive) until mid-log phase, then an equal volume of hot medium was added to equilibrate the culture to 37°C (restrictive). After 7 hours of growth at restrictive conditions, formaldehyde was added to a final concentration of 1% and cells were crosslinked for 20 mins.

extract_protocol: After formaldehyde crosslinking, cells were homogenized and extracts were sonicated on a Branson Sonifier 450 to shear the chromatin to an average size of ~500 bp. A single pulldown was performed with IgG sepharose beads and following decrosslinking and LM-PCR amplification of purified IP DNA, the sample was labeled and hybridized on a Nimblegen array.

tag: BY4741, his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rsc8-TAP::HIS3MX6

source_name: Input genomic DNA from wild-type Saccharomyces cerevisiae carrying Rsc8-TAP

label_protocol: Cy3 labeled primers and Klenow, as per NimbleGen labeling protocol

extract_protocol: After formaldehyde crosslinking, cells were homogenized and extracts were sonicated on a Branson Sonifier 450 to shear the chromatin to an average size of ~500 bp. A small fraction of the chromatin extract was decrosslinked and following LM-PCR amplification of purified input DNA, the sample was labeled and hybridized on a Nimblegen array.


title: ratbladder_SCI_3days

source_name: urinary bladder muscle post-spinal cord injury

treatment_protocol:
bladder harvested under halothane anesthesia 3 days post-spinalization;
muscle layer dissected and snap-frozen in liquid nitrogen.

value: 170g at start

tag: animal protocol

value: under halothane anesthesia, a complete laminectomy at the T9–T10 spinal level was performed:

tag: An PE-10 intrathecal catheter (Clay-Adams, Parsippany, New Jersey) was implanted at the level of the L6 to S1 spinal cord after laminectomy at the Th11 vertebra with the rat under halothane anesthesia. The end of the catheter was heat sealed and placed subcutaneously. At 3 to 4 days after

tag: intrathecal catheter implantation spinal cord transection was performed between Th9 to Th10 with the rat under halothane anesthesia. After T9 laminectomy the dura and spinal cord were cut with scissors and a sterile Gelform sponge (The Upjohn Co., Kalamazoo, Michigan) was placed between the cut ends of the spinal cord. The overlying muscle and skin were sutured. Postoperatively the animals were treated with antibiotics (ampicillin, 150 mg./kg. intramuscularly) for 7 days. The bladder of spinalized rats was manually emptied twice daily.


title: V1251_Patient with Amyotrophic Lateral Sclerosis


title: V1020_Patient with Amyotrophic Lateral Sclerosis


title: V1019_Patient with Amyotrophic Lateral Sclerosis


title: V125_Patient with Amyotrophic Lateral Sclerosis


title: Rsc8 ChIP in a rsc3-1 background

description: Rsc8-IP vs. Input genomic DNA in a rsc3-1 background

source_name: Rsc8-IP genomic DNA from rsc3-1 Saccharomyces cerevisiae carrying Rsc8-TAP

tag: BY4741, his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rsc3-1::kanR rsc8-TAP::HIS3MX6

source_name: Input genomic DNA from rsc3-1 Saccharomyces cerevisiae carrying Rsc8-TAP


title: ratbladder_normalcontrol

source_name: urinary bladder muscle healthy (normal control)

growth_protocol: No specific protocol. Normal animal keeping under DLAR protocol.

treatment_protocol:
bladder harvested under halothane anesthesia;
muscle layer dissected and snap-frozen in liquid nitrogen.


title: V1092_Patient with Amyotrophic Lateral Sclerosis

tag: female ALS patient

tag: healthy female donor


title: V1275_Patient with Amyotrophic Lateral Sclerosis

tag: male ALS patient

tag: healthy male donor


title: V1282_Patient with Amyotrophic Lateral Sclerosis


title: V74_Patient with Amyotrophic Lateral Sclerosis


title: V146_Patient with Amyotrophic Lateral Sclerosis


title: AFT2_4507.2_ArrayA

description: Yeast AFT2_4507.2_ArrayA

source_name: Baker's yeast AFT2

tag: Yeast AFT2


title: V1013_Patient with Amyotrophic Lateral Sclerosis


title: V1880aPatient with Amyotrophic Lateral Sclerosis


title: V1178_Patient with Amyotrophic Lateral Sclerosis


title: V1168_Patient with Amyotrophic Lateral Sclerosis


title: V1182_Patient with Amyotrophic Lateral Sclerosis


title: V1165_Patient with Amyotrophic Lateral Sclerosis


title: V1088_Patient with Amyotrophic Lateral Sclerosis


title: V1186_Patient with Amyotrophic Lateral Sclerosis


title: V1106_Patient with Amyotrophic Lateral Sclerosis


title: V1284_Patient with Amyotrophic Lateral Sclerosis


title: V1280_Patient with Amyotrophic Lateral Sclerosis


title: V50_Patient with Amyotrophic Lateral Sclerosis


title: V962_Patient with Amyotrophic Lateral Sclerosis


title: V1045_Patient with Amyotrophic Lateral Sclerosis


title: V10_Patient with Amyotrophic Lateral Sclerosis


title: V1082_Patient with Amyotrophic Lateral Sclerosis


title: V1081_Patient with Amyotrophic Lateral Sclerosis


title: V1180_Patient with Amyotrophic Lateral Sclerosis


title: V971_Patient with Amyotrophic Lateral Sclerosis


title: V1087_Patient with Amyotrophic Lateral Sclerosis


title: ASG1_2140.2_ArrayA.1

description: Yeast ASG1_2140.2_ArrayA.1

source_name: Baker's yeast ASG1

tag: Yeast ASG1


title: V1179_Patient with Amyotrophic Lateral Sclerosis


title: V1060_Patient with Amyotrophic Lateral Sclerosis


title: V1044_Patient with Amyotrophic Lateral Sclerosis


title: V991_Patient with Amyotrophic Lateral Sclerosis


title: V968_Patient with Amyotrophic Lateral Sclerosis


title: V1287_Patient with Amyotrophic Lateral Sclerosis


title: V1072_Patient with Amyotrophic Lateral Sclerosis


title: V1058_Patient with Amyotrophic Lateral Sclerosis


title: V1046_Patient with Amyotrophic Lateral Sclerosis


title: V1066_Patient with Amyotrophic Lateral Sclerosis


title: V1021_Patient with Amyotrophic Lateral Sclerosis


title: V1057_Patient with Amyotrophic Lateral Sclerosis


title: V1055_Patient with Amyotrophic Lateral Sclerosis


title: V1274_Patient with Amyotrophic Lateral Sclerosis


title: V1059_Patient with Amyotrophic Lateral Sclerosis


title: V967_Patient with Amyotrophic Lateral Sclerosis


title: P7-1

status: Public on Dec 24 2008

city: Innsbruck

first: Michael

last: Rudnicki

state: Tirol

address: Anichstrasse 35

department: Dept of Nephrology

country: Austria

institute: University of Innsbruck

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69904.gif
Disease State: progressive
Individual: 21

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 4480; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.81; Parameter Scan Time = 08:37:17; Parameter PMT Volts = 540; Parameter Scan Date = 2006-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 12540; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.81; Parameter Scan Time = 08:37:17; Parameter PMT Volts = 740; Parameter Scan Date = 2006-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 12554; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.90; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

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

source_name: Stratagene Universal Human Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: 1 ug STR  aRNA 2rounds vom 27.04.04

source_name: 1 ug PD 28-T aRNA 2rounds

extract_protocol: RNA was isolated using Pico Pure; RNA Isolation Kit (all Arcturus, Mountain View, CA). We performed two rounds of linear RNA amplification using RiboAmp; RNA Amplification Kit (Arcturus, Mountain View, CA). Reference RNA was as well amplified twice.

tag: 1 ug PD 28-T aRNA 2rounds


title: P6-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69903.gif
Disease State: progressive
Individual: 20

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1780, 4690; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 11:14:51; Parameter PMT Volts = 520; Parameter Scan Date = 2006-08-02; Parameter Pixel Size = 10; Parameter Laser on time = 12455; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 11:14:51; Parameter PMT Volts = 690; Parameter Scan Date = 2006-08-02; Parameter Pixel Size = 10; Parameter Laser on time = 12469; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.09; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 24-T aRNA 2rounds

tag: 1 ug PD 24-T aRNA 2rounds


title: P4-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65942.gif
Disease State: progressive
Individual: 18

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4120; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.49; Parameter Scan Time = 10:38:07; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11844; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 23.49; Parameter Scan Time = 10:38:07; Parameter PMT Volts = 650; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11859; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.93; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 14 no DNase aRNA 2rounds

tag: 1 ug PD 14 no DNase aRNA 2rounds


title: P4-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65944.gif
Disease State: progressive
Individual: 18

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5120; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.62; Parameter Scan Time = 07:57:39; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-22; Parameter Pixel Size = 10; Parameter Laser on time = 11880; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.62; Parameter Scan Time = 07:57:39; Parameter PMT Volts = 630; Parameter Scan Date = 2005-11-22; Parameter Pixel Size = 10; Parameter Laser on time = 11894; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.11; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: P3-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65945.gif
Disease State: progressive
Individual: 17

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 3920; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.82; Parameter Scan Time = 08:14:42; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-22; Parameter Pixel Size = 10; Parameter Laser on time = 11896; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.82; Parameter Scan Time = 08:14:42; Parameter PMT Volts = 670; Parameter Scan Date = 2005-11-22; Parameter Pixel Size = 10; Parameter Laser on time = 11911; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 17 no DNase aRNA 2rounds

tag: 1 ug PD 17 no DNase aRNA 2rounds


title: P1-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58617.gif
Disease State: progressive
Individual: 15

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4560; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.07; Parameter Scan Time = 09:35:55; Parameter PMT Volts = 500; Parameter Scan Date = 2005-01-12; Parameter Pixel Size = 10; Parameter Laser on time = 10051; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.07; Parameter Scan Time = 09:35:55; Parameter PMT Volts = 670; Parameter Scan Date = 2005-01-12; Parameter Pixel Size = 10; Parameter Laser on time = 10065; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.19; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD2-T aRNA 2rounds

tag: 1 ug PD2-T aRNA 2rounds


title: S2-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54640.gif
Disease State: stable
Individual: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4280; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.83; Parameter Scan Time = 08:55:50; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-28; Parameter Pixel Size = 10; Parameter Laser on time = 8909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.83; Parameter Scan Time = 08:55:50; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-28; Parameter Pixel Size = 10; Parameter Laser on time = 8912; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.23; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug F1-T aRNA 2rounds

tag: 1 ug F1-T aRNA 2rounds


title: V1083_Patient with Amyotrophic Lateral Sclerosis

source_name: DNA isolated from EBV-transformed lymphoblastoid cell line

source_name: DNA isolated from EBV-transformed cell line (reference)


title: S4-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54469.gif
Disease State: stable
Individual: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 4680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.30; Parameter Scan Time = 09:04:12; Parameter PMT Volts = 520; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.74; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.30; Parameter Scan Time = 09:04:12; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8841; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.33; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug M8-T aRNA 2rounds

tag: 1 ug M8-T aRNA 2rounds


title: S11-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55088.gif
Disease State: stable
Individual: 11

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.72; Parameter Scan Time = 08:49:25; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9098; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.72; Parameter Scan Time = 08:49:25; Parameter PMT Volts = 690; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9100; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.26; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I14-T aRNA 2rounds

tag: 1 ug I14-T aRNA 2rounds


title: S6-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54863.gif
Disease State: stable
Individual: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4280; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.30; Parameter Scan Time = 09:14:25; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-30; Parameter Pixel Size = 10; Parameter Laser on time = 9003; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.30; Parameter Scan Time = 09:14:25; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-30; Parameter Pixel Size = 10; Parameter Laser on time = 9005; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.12; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug F2-T aRNA 2rounds

tag: 1 ug F2-T aRNA 2rounds


title: S5-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55403.gif
Disease State: stable
Individual: 5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.36; Parameter Scan Time = 08:56:23; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 9212; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.36; Parameter Scan Time = 08:56:23; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 9214; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.22; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I11-T aRNA 2rounds

tag: 1 ug I11-T aRNA 2rounds


title: S4-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53575.gif
Disease State: stable
Individual: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 4960; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.65; Parameter Scan Time = 10:22:52; Parameter PMT Volts = 520; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8632; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.65; Parameter Scan Time = 10:22:52; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8635; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.37; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: S13-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55332.gif
Disease State: stable
Individual: 13

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.73; Parameter Scan Time = 08:59:38; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-13; Parameter Pixel Size = 10; Parameter Laser on time = 9146; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.73; Parameter Scan Time = 08:59:38; Parameter PMT Volts = 690; Parameter Scan Date = 2004-08-13; Parameter Pixel Size = 10; Parameter Laser on time = 9148; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.34; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I18-T aRNA 2rounds

tag: 1 ug I18-T aRNA 2rounds


title: S1-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55406.gif
Disease State: stable
Individual: 1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.58; Parameter Scan Time = 09:36:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-25; Parameter Pixel Size = 10; Parameter Laser on time = 9241; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.58; Parameter Scan Time = 09:36:43; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-25; Parameter Pixel Size = 10; Parameter Laser on time = 9243; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.33; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I15-T aRNA 2rounds

tag: 1 ug I15-T aRNA 2rounds


title: S7-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54121.gif
Disease State: stable
Individual: 7

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 4400; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.48; Parameter Scan Time = 09:28:44; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 8759; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.48; Parameter Scan Time = 09:28:44; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-14; Parameter Pixel Size = 10; Parameter Laser on time = 8761; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.34; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug M6-T aRNA 2rounds

tag: 1 ug M6-T aRNA 2rounds


title: S8-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53848.gif
Disease State: stable
Individual: 8

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4960; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.52; Parameter Scan Time = 09:47:10; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-08; Parameter Pixel Size = 10; Parameter Laser on time = 8689; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.52; Parameter Scan Time = 09:47:10; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-08; Parameter Pixel Size = 10; Parameter Laser on time = 8692; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.34; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I1-T aRNA 2rounds

tag: 1 ug I1-T aRNA 2rounds


title: S12-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55336.gif
Disease State: stable
Individual: 12

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.43; Parameter Scan Time = 08:53:33; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-18; Parameter Pixel Size = 10; Parameter Laser on time = 9181; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.43; Parameter Scan Time = 08:53:33; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-18; Parameter Pixel Size = 10; Parameter Laser on time = 9183; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.25; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: Stratagene Universal Human Reference RNA

source_name: 1 ug F7-T aRNA 2rounds

tag: 1 ug F7-T aRNA 2rounds


title: S9-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54271.gif
Disease State: stable
Individual: 9

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 5040; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 09:07:16; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8803; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.88; Parameter Scan Time = 09:07:16; Parameter PMT Volts = 700; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8806; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.28; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I7-T aRNA 2rounds

tag: 1 ug I7-T aRNA 2rounds


title: S3-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55337.gif
Disease State: stable
Individual: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.76; Parameter Scan Time = 09:00:11; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-18; Parameter Pixel Size = 10; Parameter Laser on time = 9187; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.76; Parameter Scan Time = 09:00:11; Parameter PMT Volts = 630; Parameter Scan Date = 2004-08-18; Parameter Pixel Size = 10; Parameter Laser on time = 9190; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.35; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

tag: 1 ug STR  aRNA 2rounds vom 27.04.04

source_name: 1 ug M2-T aRNA 2rounds

tag: 1 ug M2-T aRNA 2rounds


title: S7-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55087.gif
Disease State: stable
Individual: 7

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.12; Parameter Scan Time = 08:50:46; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-13; Parameter Pixel Size = 10; Parameter Laser on time = 9137; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.12; Parameter Scan Time = 08:50:46; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-13; Parameter Pixel Size = 10; Parameter Laser on time = 9139; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.32; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: S8-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54468.gif
Disease State: stable
Individual: 8

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 4680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.75; Parameter Scan Time = 08:56:40; Parameter PMT Volts = 510; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8832; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.75; Parameter Scan Time = 08:56:40; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8835; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.31; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: MG_An_144

city: Bethesda

first: Jackie

last: Lavigne

state: MD

address: 6120 Executive Blvd. Rm. 6114

department: DCEG

institute: NCI/NIH

description: Effects of calorie restriction and exercise alone or in association in mammary gland gene expression

hyb_protocol: Affymetrix recommended protocol was followed for hybridation process. Hybridation cocktail  was prepared by mixing Control oligo B2, 20X Euk. Hyb controls, Herring Sperm DNA, Acetylated BSA, 2X Hybridization Buffer  and RNase-free Water at the requested concentration. Following fragmentation, 15 ug of cRNA, were hybridized on Affymetrix GeneChip Mouse Expression Array 430A . The microarrays were than incubated for 16 hours (o/n) at 45˚C and 60rpm. (Takahashi et al Using DNA microarray analyses to elucidate the effects of genistein in androgen-responsive prostate cancer cells: identification of novel targets. Mol Carcinog 2004;41:108-19)

scan_protocol: Affymetrix equipment and recommended protocol were used for the scan process.  (Takahashi et al Using DNA microarray analyses to elucidate the effects of genistein in androgen-responsive prostate cancer cells: identification of novel targets. Mol Carcinog 2004;41:108-19)

data_processing: The signal values and detection calls of the probe sets were determined using Affymetrix GCOS (ver. 1) software.  Relative intensity variation across arrays was normalized by scaling to an average signal level of 500 counts, excluding low 2% and high 2% signals. These signal values were transformed to a logarithmic scale (base 2) for statistical calculations.

organism: Mus musculus

source_name: Bilateral thoracical C57BL/6 mouse mammary gland

label_protocol: Affymetrix recommended protocol was followed for labeling (Expression Analysis Technical Manual, 2001, Affymetrix). RNA was biotin-labeled using the Enzo Bioarray-High Yield-RNA Transcript Labeling Kit (Cat #42655-20)

extract_protocol: Total mammary gland RNA was isolated from pooled left and right thoracic mammary glands (approximately 60 mg each) prior to microarray analysis, using TRIzol extraction reagent (Invitrogen, Rockville, MD) and the RNeasy Midi Cleanup Kit (Qiagen, Valencia, CA) in accordance with the manufacturers’ protocols.  Total RNA concentration was determined by spectrophotometric evaluation of absorbance at 260 nm, and RNA integrity was confirmed by 1% agarose gel electrophoresis.  RNA quality of random samples was also tested on an Agilent 2100 bio-analyzer (Agilent Technologies, Palo Alto CA).

treatment_protocol: Female C57BL/6 mice (9 weeks old) were randomized into 4 experimental groups: 1) food consumed ad libitum (AL); 2) AL with access to running wheels (AL+EX); 3) 30% CR; and 4) 30% CR with access to running wheels (CR+EX). CR mice received 70% of calories but 100% of all other nutrients compared to AL mice.  Food consumption, weight gain, and physical activity levels were recorded for 6 weeks.  RNA samples from animal mammary glands were analysed by Affymetrix oligo-microarray platform, in particular 10 samples from AL group (control), 9 samples from AL+EX group,  9 samples from CR group and 9 samples from CR+EX group were analysed.

tag: Diet regimen

value: 30% Calorie Restriction with free access to running wheels (CR+EX)


title: S10-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55645.gif
Disease State: stable
Individual: 10

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:59:01; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-25; Parameter Pixel Size = 10; Parameter Laser on time = 9263; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:59:01; Parameter PMT Volts = 710; Parameter Scan Date = 2004-08-25; Parameter Pixel Size = 10; Parameter Laser on time = 9266; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.24; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug F8-T aRNA 2rounds

tag: 1 ug F8-T aRNA 2rounds


title: S3-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54268.gif
Disease State: stable
Individual: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 5040; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 08:44:53; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8781; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.44; Parameter Scan Time = 08:44:53; Parameter PMT Volts = 670; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8783; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.09; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: S12-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55405.gif
Disease State: stable
Individual: 12

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.31; Parameter Scan Time = 09:16:14; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 9232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.79; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.31; Parameter Scan Time = 09:16:14; Parameter PMT Volts = 670; Parameter Scan Date = 2004-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 9234; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.28; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: MG_An_140


title: P2-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65943.gif
Disease State: progressive
Individual: 16

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4120; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.31; Parameter Scan Time = 10:48:21; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11854; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.31; Parameter Scan Time = 10:48:21; Parameter PMT Volts = 660; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11869; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.07; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 19 no DNase aRNA 2rounds

tag: 1 ug PD 19 no DNase aRNA 2rounds


title: S9-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55086.gif
Disease State: stable
Individual: 9

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:20:30; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9129; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.59; Parameter Scan Time = 09:20:30; Parameter PMT Volts = 710; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9132; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.25; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: MG_An_22


title: MG_An_68


title: MG_An_70


title: MG_An_48


title: MG_An_44


title: S1-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53532.gif
Disease State: stable
Individual: 1

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 4960; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:15:30; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8626; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.13; Parameter Scan Time = 10:15:30; Parameter PMT Volts = 700; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8628; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.38; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: S11-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53838.gif
Disease State: stable
Individual: 11

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4960; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.63; Parameter Scan Time = 09:28:39; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-08; Parameter Pixel Size = 10; Parameter Laser on time = 8672; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.63; Parameter Scan Time = 09:28:39; Parameter PMT Volts = 690; Parameter Scan Date = 2004-07-08; Parameter Pixel Size = 10; Parameter Laser on time = 8674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.35; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: S5-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54639.gif
Disease State: stable
Individual: 5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 4680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 09:22:47; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 09:22:47; Parameter PMT Volts = 675; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 8860; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.16; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer


title: MG_An_42

value: 30% Calorie Restriction (CR)


title: MG_An_136


title: MG_An_20


title: MG_An_40


title: MG_An_66


title: MG_An_56

value: AL with free access to running wheel (AL+EX)


title: MG_An_14


title: MG_An_16


title: MG_An_46


title: MG_An_132


title: MG_An_62


title: MG_An_130


title: MG_An_58


title: CHC382T-dChip-U133A

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: see [Sandra Rebouissou, Mohamed Amessou, Gabrielle Couchy, Sandrine Imbeaud, Tina Izard, Charles Balabaud, Paulette Bioulac-Sage, Jessica Zucman-Rossi. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Submitted]

hyb_protocol: Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).

data_processing: Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].

label: Biotin

label_protocol: For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.

tag: Sample

tag: Gender

value: female;

tag: Age at onset

value: 45 years;

tag: Disease

value: Inflammatory hepatocellular adenomas (IHCA);

tag: Tissue

value: tumor liver.


title: MG_An_36


title: CHC471T-dChip-U133A

value: 30 years;


title: MG_An_34


title: CHC466T-dChip-U133A

value: 50 years;


title: MG_An_32


title: CHC364T-dChip-U133A

value: 44 years;


title: MG_An_10


title: CHC466T-RMA-U133A

data_processing: Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15].


title: MG_An_8


title: CHC471T-RMA-U133A


title: MG_An_124

value: food consumed ad libitum (AL)


title: MG_An_54


title: MG_An_122


title: MG_An_52


title: MG_An_50


title: CHC382T-RMA-U133A


title: CHC364T-RMA-U133A


title: MG_An_30


title: MG_An_28


title: MG_An_64


title: MG_An_26


title: MG_An_2


title: MG_An_4


title: S6-2

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55085.gif
Disease State: stable
Individual: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.85; Parameter Scan Time = 09:06:31; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9116; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.85; Parameter Scan Time = 09:06:31; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-11; Parameter Pixel Size = 10; Parameter Laser on time = 9118; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.34; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

tag: 1 ug F2-T aRNA 2rounds