title: IMP2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing IMP2

tag: Mutant strain carrying IMP2 under an inducible GAL1 promoter


title: 0_GCN4 overexpression mutant vs. Empty vector, replicate 1

status: Public on Sep 14 2006

type: RNA

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

country: USA

institute: Celgene Corporation

data_processing: The microarray data was spatially-detrended and Lowess-smoothed, giving the normalized log ratio of intensity for each spot in the mutant strain versus the WT strain and the average log intensity for each spot in the two strains.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Control strain with empty vector

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter

source_name: Mutant strain overexpressing 0_GCN4

tag: Mutant strain carrying 0_GCN4 under an inducible GAL1 promoter


title: HAA1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing HAA1

tag: Mutant strain carrying HAA1 under an inducible GAL1 promoter


title: 0_GCN4 overexpression mutant vs. Empty vector, replicate 2


title: IMP2 overexpression mutant vs. Empty vector, replicate 1


title: ASK10 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ASK10

tag: Mutant strain carrying ASK10 under an inducible GAL1 promoter


title: SWI5 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing SWI5

tag: Mutant strain carrying SWI5 under an inducible GAL1 promoter


title: ASK10 overexpression mutant vs. Empty vector, replicate 1


title: GTS1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing GTS1

tag: Mutant strain carrying GTS1 under an inducible GAL1 promoter


title: HAA1 overexpression mutant vs. Empty vector, replicate 1


title: 12.5_GCN4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing 12.5_GCN4

tag: Mutant strain carrying 12.5_GCN4 under an inducible GAL1 promoter


title: GTS1 overexpression mutant vs. Empty vector, replicate 2


title: PDR1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing PDR1

tag: Mutant strain carrying PDR1 under an inducible GAL1 promoter


title: HAP3 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing HAP3

tag: Mutant strain carrying HAP3 under an inducible GAL1 promoter


title: FKH1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing FKH1

tag: Mutant strain carrying FKH1 under an inducible GAL1 promoter


title: TEC1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing TEC1

tag: Mutant strain carrying TEC1 under an inducible GAL1 promoter


title: PDR1 overexpression mutant vs. Empty vector, replicate 1


title: TEC1 overexpression mutant vs. Empty vector, replicate 1


title: SWI5 overexpression mutant vs. Empty vector, replicate 2


title: MAC1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MAC1

tag: Mutant strain carrying MAC1 under an inducible GAL1 promoter


title: NDT80 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing NDT80

tag: Mutant strain carrying NDT80 under an inducible GAL1 promoter


title: IME1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing IME1

tag: Mutant strain carrying IME1 under an inducible GAL1 promoter


title: NDT80 overexpression mutant vs. Empty vector, replicate 1


title: GAL4 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing GAL4

tag: Mutant strain carrying GAL4 under an inducible GAL1 promoter


title: IME1 overexpression mutant vs. Empty vector, replicate 1


title: MAC1 overexpression mutant vs. Empty vector, replicate 1


title: HAP3 overexpression mutant vs. Empty vector, replicate 2


title: FKH1 overexpression mutant vs. Empty vector, replicate 1


title: PPR1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing PPR1

tag: Mutant strain carrying PPR1 under an inducible GAL1 promoter


title: PIP2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing PIP2

tag: Mutant strain carrying PIP2 under an inducible GAL1 promoter


title: RIM101 overexpression mutant vs. Empty vector, replicate 1

source_name: Control strain with empty vector

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter

source_name: Mutant strain overexpressing RIM101

tag: Mutant strain carrying RIM101 under an inducible GAL1 promoter


title: PIP2 overexpression mutant vs. Empty vector, replicate 1


title: LYS14 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing LYS14

tag: Mutant strain carrying LYS14 under an inducible GAL1 promoter


title: GLN3 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GLN3

tag: Mutant strain carrying GLN3 under an inducible GAL1 promoter


title: LYS14 overexpression mutant vs. Empty vector, replicate 2


title: OAF1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing OAF1

tag: Mutant strain carrying OAF1 under an inducible GAL1 promoter


title: CAD1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing CAD1

tag: Mutant strain carrying CAD1 under an inducible GAL1 promoter


title: GLN3 overexpression mutant vs. Empty vector, replicate 1


title: OAF1 overexpression mutant vs. Empty vector, replicate 1


title: PPR1 overexpression mutant vs. Empty vector, replicate 2


title: ZAP1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ZAP1

tag: Mutant strain carrying ZAP1 under an inducible GAL1 promoter


title: CAD1 overexpression mutant vs. Empty vector, replicate 2


title: ARG80 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing ARG80

tag: Mutant strain carrying ARG80 under an inducible GAL1 promoter


title: ARG80 overexpression mutant vs. Empty vector, replicate 2


title: ZAP1 overexpression mutant vs. Empty vector, replicate 1


title: YPR015C overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing YPR015C

tag: Mutant strain carrying YPR015C under an inducible GAL1 promoter


title: RIM101 overexpression mutant vs. Empty vector, replicate 2


title: YHP1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing YHP1

tag: Mutant strain carrying YHP1 under an inducible GAL1 promoter


title: YHP1 overexpression mutant vs. Empty vector, replicate 1


title: UPC2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing UPC2

tag: Mutant strain carrying UPC2 under an inducible GAL1 promoter


title: YOX1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing YOX1

tag: Mutant strain carrying YOX1 under an inducible GAL1 promoter


title: YOX1 overexpression mutant vs. Empty vector, replicate 2


title: XBP1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing XBP1

tag: Mutant strain carrying XBP1 under an inducible GAL1 promoter


title: YRR1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing YRR1

tag: Mutant strain carrying YRR1 under an inducible GAL1 promoter


title: YPR015C overexpression mutant vs. Empty vector, replicate 2


title: YRR1 overexpression mutant vs. Empty vector, replicate 2


title: YAP1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing YAP1

tag: Mutant strain carrying YAP1 under an inducible GAL1 promoter


title: XBP1 overexpression mutant vs. Empty vector, replicate 1


title: YAP1 overexpression mutant vs. Empty vector, replicate 2


title: 12.5_GCN4 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing 12.5_GCN4

tag: Mutant strain carrying 12.5_GCN4 under an inducible GAL1 promoter


title: STP3 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing STP3

tag: Mutant strain carrying STP3 under an inducible GAL1 promoter


title: TOS8 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing TOS8

tag: Mutant strain carrying TOS8 under an inducible GAL1 promoter

source_name: Control strain with empty vector

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter


title: STP3 overexpression mutant vs. Empty vector, replicate 2


title: STE12 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing STE12

tag: Mutant strain carrying STE12 under an inducible GAL1 promoter


title: STP2 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing STP2

tag: Mutant strain carrying STP2 under an inducible GAL1 promoter


title: STP2 overexpression mutant vs. Empty vector, replicate 2


title: UPC2 overexpression mutant vs. Empty vector, replicate 1


title: SUT1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing SUT1

tag: Mutant strain carrying SUT1 under an inducible GAL1 promoter


title: SPT2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing SPT2

tag: Mutant strain carrying SPT2 under an inducible GAL1 promoter


title: SWI4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing SWI4

tag: Mutant strain carrying SWI4 under an inducible GAL1 promoter


title: SWI4 overexpression mutant vs. Empty vector, replicate 1


title: SUT1 overexpression mutant vs. Empty vector, replicate 2


title: STE12 overexpression mutant vs. Empty vector, replicate 2


title: TOS8 overexpression mutant vs. Empty vector, replicate 1


title: SPT2 overexpression mutant vs. Empty vector, replicate 1


title: SKN7 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing SKN7

tag: Mutant strain carrying SKN7 under an inducible GAL1 promoter


title: GAL4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GAL4

tag: Mutant strain carrying GAL4 under an inducible GAL1 promoter


title: SPS18 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing SPS18

tag: Mutant strain carrying SPS18 under an inducible GAL1 promoter


title: SOK2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing SOK2

tag: Mutant strain carrying SOK2 under an inducible GAL1 promoter


title: SOK2 overexpression mutant vs. Empty vector, replicate 1


title: SIP4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing SIP4

tag: Mutant strain carrying SIP4 under an inducible GAL1 promoter


title: SKN7 overexpression mutant vs. Empty vector, replicate 2


title: SIP4 overexpression mutant vs. Empty vector, replicate 1


title: RSC30 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing RSC30

tag: Mutant strain carrying RSC30 under an inducible GAL1 promoter


title: SFP1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing SFP1

tag: Mutant strain carrying SFP1 under an inducible GAL1 promoter


title: SFP1 overexpression mutant vs. Empty vector, replicate 2


title: RSC30 overexpression mutant vs. Empty vector, replicate 1


title: SPS18 overexpression mutant vs. Empty vector, replicate 2


title: ROX1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ROX1

tag: Mutant strain carrying ROX1 under an inducible GAL1 promoter


title: ROX1 overexpression mutant vs. Empty vector, replicate 1


title: RFX1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing RFX1

tag: Mutant strain carrying RFX1 under an inducible GAL1 promoter


title: RME1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing RME1

tag: Mutant strain carrying RME1 under an inducible GAL1 promoter


title: RFX1 overexpression mutant vs. Empty vector, replicate 1


title: RGM1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing RGM1

tag: Mutant strain carrying RGM1 under an inducible GAL1 promoter


title: RAP1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing RAP1

tag: Mutant strain carrying RAP1 under an inducible GAL1 promoter

source_name: Control strain with empty vector

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter


title: RME1 overexpression mutant vs. Empty vector, replicate 1


title: PUT3 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing PUT3

tag: Mutant strain carrying PUT3 under an inducible GAL1 promoter


title: PUT3 overexpression mutant vs. Empty vector, replicate 1


title: MSN4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MSN4

tag: Mutant strain carrying MSN4 under an inducible GAL1 promoter


title: MSN2 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MSN2

tag: Mutant strain carrying MSN2 under an inducible GAL1 promoter


title: PHO4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing PHO4

tag: Mutant strain carrying PHO4 under an inducible GAL1 promoter


title: PHO4 overexpression mutant vs. Empty vector, replicate 1


title: MOT3 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing MOT3

tag: Mutant strain carrying MOT3 under an inducible GAL1 promoter


title: MSN4 overexpression mutant vs. Empty vector, replicate 1


title: MSN2 overexpression mutant vs. Empty vector, replicate 1


title: MOT3 overexpression mutant vs. Empty vector, replicate 2


title: MGA1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MGA1

tag: Mutant strain carrying MGA1 under an inducible GAL1 promoter


title: MET4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MET4

tag: Mutant strain carrying MET4 under an inducible GAL1 promoter


title: MIG1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MIG1

tag: Mutant strain carrying MIG1 under an inducible GAL1 promoter


title: MET4 overexpression mutant vs. Empty vector, replicate 1


title: MGA1 overexpression mutant vs. Empty vector, replicate 1


title: RAP1 overexpression mutant vs. Empty vector, replicate 1


title: RGM1 overexpression mutant vs. Empty vector, replicate 2


title: rapamycin treated_3 3h

city: Boston

first: Scott

middle: A.

last: Armstrong

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Children's Hospital

description: Rapamycin treated cells

data_processing: d chip normailzed (PM/MM) Method

label: Biotin

organism: Homo sapiens

source_name: T-ALL

tag: CEM-C1 cells treated with rapamycin for 3 hours


title: MET31 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing MET31

tag: Mutant strain carrying MET31 under an inducible GAL1 promoter


title: Rapamycin treated_2 3h

description: Rapamycin treated cells

tag: CEM-C1 cells treated with 10 nM rapmycin for 3 hours


title: Rapamycin treated_1 3h

description: Rapamycin treated cells

tag: CEMC1 cells treated with 10 nm rapamycin for 3 hours


title: MBP1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing MBP1

tag: Mutant strain carrying MBP1 under an inducible GAL1 promoter


title: MBP1 overexpression mutant vs. Empty vector, replicate 1


title: MET31 overexpression mutant vs. Empty vector, replicate 2


title: INO2 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing INO2

tag: Mutant strain carrying INO2 under an inducible GAL1 promoter


title: INO2 overexpression mutant vs. Empty vector, replicate 2


title: HSF1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing HSF1

tag: Mutant strain carrying HSF1 under an inducible GAL1 promoter


title: HSF1 overexpression mutant vs. Empty vector, replicate 1


title: MIG1 overexpression mutant vs. Empty vector, replicate 1


title: HMS1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing HMS1

tag: Mutant strain carrying HMS1 under an inducible GAL1 promoter


title: CEM-C1 cells treated with rapamycin_3 24h

description: rapamycin treated sample

data_processing: d chip normalized (PM/MM) method

source_name: T-ALL cells

tag: CEM-C1 cells treated with 10 nM rapamycin for 24 hours


title: HAC1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing HAC1

tag: Mutant strain carrying HAC1 under an inducible GAL1 promoter

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter


title: CEM-C1 cells treated with rapamycin_2 24h

description: rapamycin treated sample


title: CEM-C1 cells treated with rapamycin 24h

description: rapamycin treated sample

tag: CEM-C1 cells treated with 10 nm rapamycin for 24 hours


title: resistant 15

description: glucocorticoid resistant sample

data_processing: dchip normalized data (PM/MM method)

source_name: primary acute lymphoblastic leukemia

tag: pretreatment primary acute lymphoblastic leukemia


title: HAP4 overexpression mutant vs. Empty vector, replicate 1

source_name: Control strain with empty vector

source_name: Mutant strain overexpressing HAP4

tag: Mutant strain carrying HAP4 under an inducible GAL1 promoter


title: HMS1 overexpression mutant vs. Empty vector, replicate 2


title: resistant 16

description: glucocorticoid resistant sample


title: resistant 14

description: glucocorticoid resistant sample


title: DMSO treated CEM-C1 cells_3

description: DMSO treated control sample

source_name: T-ALL Cell line

tag: CEM-C1 cells treated with DMSO


title: DMSO treated CEM-C1 cells_1

description: DMSO treated control sample

tag: T-ALL cell line treated with DMSO


title: HAP4 overexpression mutant vs. Empty vector, replicate 2


title: resistant 12

description: glucocorticoid resistant sample


title: DMSO treated CEM-C1 cells_2

description: DMSO treated control sample

source_name: T-ALL cell line

tag: CEM-C1 T-ALL cell line treated with DMSO


title: HAC1 overexpression mutant vs. Empty vector, replicate 1


title: resistant 10

description: glucocorticoid resistant sample


title: GIS2 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing GIS2

tag: Mutant strain carrying GIS2 under an inducible GAL1 promoter


title: GZF3 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing GZF3

tag: Mutant strain carrying GZF3 under an inducible GAL1 promoter


title: GIS2 overexpression mutant vs. Empty vector, replicate 2


title: resitant 13

description: glucocorticoid resistant sample

source_name: pretreatment primary acute lymphoblastic leukemia

tag: primary acute lymphoblastic leukemia


title: GIS1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GIS1

tag: Mutant strain carrying GIS1 under an inducible GAL1 promoter


title: resistant 8

description: glucocorticoid resistant sample


title: resistant 6

description: glucocorticoid resistant sample


title: GIS1 overexpression mutant vs. Empty vector, replicate 1


title: resistant 5

description: glucocorticoid resistant sample


title: resistant 7

description: glucocorticoid resistant sample


title: resistant 4

description: glucocorticoid resistant sample


title: resistant 11

description: glucocorticoid resistant sample


title: GZF3 overexpression mutant vs. Empty vector, replicate 2


title: resistant 3

description: glucocorticoid resistant sample


title: GCN4-A overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GCN4-A

tag: Mutant strain carrying GCN4-A under an inducible GAL1 promoter


title: GCN4-A overexpression mutant vs. Empty vector, replicate 1


title: GAT4 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GAT4

tag: Mutant strain carrying GAT4 under an inducible GAL1 promoter


title: GAT3 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing GAT3

tag: Mutant strain carrying GAT3 under an inducible GAL1 promoter


title: Resistant 9

description: glucocorticoid resistant sample


title: sensitive 12

description: glucocorticoid sensitive

data_processing: d chip normalized (PM/MM method)


title: resistant 2

description: glucocorticoid resistant sample


title: GAT4 overexpression mutant vs. Empty vector, replicate 1


title: Resistant 1

description: glucocorticoid resistant sample


title: sensitive 10

description: glucocorticoid sensitive


title: sensitive 11

description: glucocorticoid sensitive


title: ECM22 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ECM22

tag: Mutant strain carrying ECM22 under an inducible GAL1 promoter


title: ECM22 overexpression mutant vs. Empty vector, replicate 1


title: CUP2 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing CUP2

tag: Mutant strain carrying CUP2 under an inducible GAL1 promoter


title: CST6 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing CST6

tag: Mutant strain carrying CST6 under an inducible GAL1 promoter


title: CST6 overexpression mutant vs. Empty vector, replicate 1

tag: Control strain carrying an empty 2-micron plasmid with an inducible GAL1 promoter


title: CUP2 overexpression mutant vs. Empty vector, replicate 2


title: CRZ1 overexpression mutant vs. Empty vector, replicate 1

source_name: Mutant strain overexpressing CRZ1

tag: Mutant strain carrying CRZ1 under an inducible GAL1 promoter


title: CRZ1 overexpression mutant vs. Empty vector, replicate 2


title: sensitive 8

description: glucocorticoid sensitive

tag: pretreatment primary acute lymphoblastic leukemia


title: GAT3 overexpression mutant vs. Empty vector, replicate 1


title: sensitive 7

description: glucocorticoid sensitive


title: sensitive 13

description: glucocorticoid sensitive


title: Sensitive sample 5

description: glucocorticoid sensitive


title: BYE1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing BYE1

tag: Mutant strain carrying BYE1 under an inducible GAL1 promoter


title: CAT8 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing CAT8

tag: Mutant strain carrying CAT8 under an inducible GAL1 promoter


title: BYE1 overexpression mutant vs. Empty vector, replicate 1

source_name: Control strain with empty vector


title: sensitive 9

description: glucocorticoid sensitive

source_name: primary acute lymphoblastic leukemia


title: CAT8 overexpression mutant vs. Empty vector, replicate 1


title: Sensitive sample 4

description: glucocorticoid sensitive

source_name: Primary Leukemia


title: ADR1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ADR1

tag: Mutant strain carrying ADR1 under an inducible GAL1 promoter


title: Sensitive 6

description: glucocorticoid sensitive


title: ADR1 overexpression mutant vs. Empty vector, replicate 1


title: ABF1 overexpression mutant vs. Empty vector, replicate 2

source_name: Mutant strain overexpressing ABF1

tag: Mutant strain carrying ABF1 under an inducible GAL1 promoter


title: Sensitive sample 2

description: glucocortiocid sensitive sample

source_name: primary leukemia


title: ABF1 overexpression mutant vs. Empty vector, replicate 1


title: sensitive sample 3

description: glucocortiocid sensitive sample


title: cir1 mutant vs wild type in low iron medium

city: Vancouver

first: Won Hee

last: Jung

state: British Columbia

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: Data for differentially expressed genes in the cir1 mutant compared to the wild type in low iron medium.

hyb_protocol: Hyb were performed at 55C on 70mer oligo Cryprococcus array according to the manufacturer's instructions (3DNA Array 350 kit, Genisphere).

scan_protocol: After hybridization, arrays were scanned immediumtely using the Perkin Elmer Scan Array Express

data_processing: Each channel was background corrected by subtracting the lowest 10 % of foreground signal intensity.  The two channels of each array were normalized to each other by Huber's variance stabilization algorithm, vsn.  A linear mixed effects model was applied to the normalized data in each channel.  A fixed effect was included for each array, for the dye by gene interaction, and for each combination of iron availability and/or deletion of CIR1.  Random effects were included for within-array variability (each gene appeared twice on each array), technical variability (each replicate culture was hybridized four times), and biological variability (12 replicate cultures were employed).  The changes in wild-type (low iron) vs. wild-type (high iron), wild-type (low iron) vs. cir1delta (low iron), wild-type (high iron) vs. cir1delta (high iron), and cir1delta (low iron) vs. cir1delta (high iron) were estimated with standard errors and P values based on student t statistics.  Q values were computed to adjust for the false discovery rate.

label: Cy3 or Cy5 and dye swap experiments were performed

organism: Cryptococcus deneoformans B-3501A

source_name: Cryptococcus Iron regulator (cir1) mutant in low iron medium

label_protocol: The 3DNA Array 350 kit (Genisphere) was used to label cDNA with Cy3 or Cy5

growth_protocol: Three biological replicates were grown at 30°C for 12 h in low iron medium

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

treatment_protocol: Three biological replicates for each strain were grown in 50 ml of YNB overnight at 30°C followed by growth in low iron medium at the same temperature for an additional 12 h. The latter step was added in order to eliminate any iron carryover from the rich medium.  Cultures were then harvested and washed twice with low iron medium. Cell numbers were determined and cells were transferred to 50 ml low iron medium (final density of 1.0 ´ 107 cells/ml).  Cells were grown at 30°C for another 12 h, harvested, and lyophilized for RNA extractions.

tag: serotype D cir1 mutant in low iron medium

tag: total RNA were extracted from three biological replicates after growing in low iron medium at 30 degreeC for 12 h

source_name: wild type in low iron medium

tag: wild type in low iron medium


title: cir1 mutant vs wild type in high iron medium

description: Data for differentially expressed genes in the cir1 mutant compared to the wild type in high iron medium.

source_name: Cryptococcus Iron regulator (cir1) mutant in high iron medium

growth_protocol: Three biological replicates were grown at 30°C for 12 h in high iron medium

treatment_protocol: Three biological replicates for each strain were grown in 50 ml of YNB overnight at 30°C followed by growth in low iron medium at the same temperature for an additional 12 h. The latter step was added in order to eliminate any iron carryover from the rich medium.  Cultures were then harvested and washed twice with high iron medium. Cell numbers were determined and cells were transferred to 50 ml high iron medium containing 100 micro M FeEDTA (final density of 1.0 ´ 107 cells/ml).  Cells were grown at 30°C for another 12 h, harvested, and lyophilized for RNA extractions.

tag: serotype D cir1 mutant in high iron medium

tag: total RNA were extracted from three biological replicates after growing in high iron medium at 30 degreeC for 12 h

source_name: wild type in high iron medium

tag: wild type in high iron medium


title: cir1 mutant high iron medium vs low iron medium

description: Data for differentially expressed genes in the cir1 mutant in high iron medium compared to low iron medium.

hyb_protocol: Hyb were performed 16 h at 55C on 70mer oligo Cryprococcus array according to the manufacturer's instructions (3DNA Array 350 kit, Genisphere).

treatment_protocol: Three biological replicates were grown in 50 ml of YNB overnight at 30°C followed by growth in low iron medium at the same temperature for an additional 12 h. The latter step was added in order to eliminate any iron carryover from the rich medium.  Cultures were then harvested and washed twice with low iron medium. Cell numbers were determined and cells were transferred to 50 ml low iron medium or high iron medium containing 100 micro M FeEDTA (final density of 1.0 ´ 107 cells/ml).  Cells were grown at 30°C for another 12 h, harvested, and lyophilized for RNA extractions.

tag: total RNA were extracted from three biological replicates after growing in high iron medium or low iron medium for 12 h at 30C


title: wild type high iron medium vs low iron medium

description: Data for differentially expressed genes in the wild type strain in high iron medium compared to low iron medium.

source_name: wild type strain in high iron medium

tag: serotype D wild type in high iron medium

source_name: wild type strain in low iron medium

tag: serotype D wild type in low iron medium


title: Sustantia Nigra MME Sample1 Codelink

status: Public on Sep 13 2006

city: Rochester

first: Howard

middle: J

last: Federoff

state: NY

address: 601 Elmwood Ave Box 645

department: Center for Aging and Developmental Biology

institute: University of Rochester

description: Need to specify

hyb_protocol: Hybridized according to the manufacturer's protocol (Amersham Biosciences)

scan_protocol: Detection using an Axon 4000B scanner (Axon Instruments, Foster City, CA) and quantitation using Codelink Scanning and Expression Analysis software (version 2.3)

data_processing: Median Normalized data acquired from Codelink platform and utilized for analysis

label: Biotinylated UTP & CTP

organism: Mus musculus

source_name: Pooled Sustantia Nigra C57BL/6 MPTP Injection

label_protocol: Enzo IVT Protocol

extract_protocol: Trizol

treatment_protocol: Mice received 2 injections

tag: Strain

value: C57BL/6  Gender:Male  Age:10 weeks  TissueL Substantia Nigra(SN) disected bilaterally from six like-treated mice.


title: op50 5/29 new N2 4hrs

city: Palo Alto

first: Michael

last: Shapira

state: CA

address: 300 Pasteur Dr. Lane Bldg. room L309

department: Genetics

institute: Stanford University

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19660.gif; format: GIF
Infection: OP50
Measurement: time(relative) 4 h

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

organism: Caenorhabditis elegans

source_name: N2 worms exposed to E. coli OP50- 4 hours

source_name: Common reference- Mixed stage N2 worm culture


title: sensitive sample 1

description: Glucocorticoid resistant in vitro

data_processing: data normalized with dchip (PM/MM)

source_name: leukemia

tag: pre treatment primary leukemia


title: Substantia Nigra MME Sample4 Codelink

description: Need to specify

scan_protocol: Detection using an Axon 4000B scanner (Axon Instruments, Foster City, CA) and quantitation using the Codelink Scanning and Expression Analysis software (version 2.3)

data_processing: Raw intensity data acquired from Codelink platfor

source_name: Pooled Sustantia Nigra C57BL/6 MPTP MME

treatment_protocol: Mice received 4 injections of MPTP-HCL (30MG/KG, IP). The first and second doses were separated by 16 hr. Mice were killed 24hr after final injection. (MML-Mouse MPTP Early)The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prpared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)

tag: Strain C57BL/6 Gender:Male Age:10 weeks Tissue

value: Substantia Nigra(SN) disected bilaterally from six like-treated mice


title: Substantia Nigra MME Sample3 Codelink

description: Need to specify

data_processing: Raw Intensity data acquired from Codelink Platform

treatment_protocol: Mice received 4 injections of MPTP-HCL (30mg/kp; IP).  The first and second doses were separated by 16hr.  Mice were killed 24hr after injection.  The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prepared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)

tag: Strain C57BL/6  Gender

value: Male  Age:10 weeks  Tissue:Substantia Nigra(SN) disected bilaterally from six like-treated mice.


title: Sustantia Nigra MML Sample2 Codelink

description: Need to specify

data_processing: Raw intensity data acquired from Codelink Platform; Used Median Normalized Value for Analysis

source_name: Pooled Substantia Nigra C57BL/6 MPTP Injection

treatment_protocol: Mice received 4 injections of MPTP-HCL (30mg/kg; IP).  The first and second doses were separated by 16 hr.  Mice wew killed 24hr after injection.  The SN was dissected bilaterally from six like-trated mice, pooled and RNA was prepared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)

tag: Age

value: 10 Weeks

tag: Tissue

value: Substantia Nigra(SN) dissected bilaterally from six like-treated mice.


title: Substantia Nigra MML Sample4 Codelink

description: Need to specify

scan_protocol: Detection using an Axon 400B scanner (Axon INstruments, Foster City, CA) and quantitation using the Codelink Scanning and Expression Analysis software (version 2.3)

data_processing: Raw intensity data acquired from Codelink; Median Normalized data used in analysis

source_name: Pooled Substantia Nigra C57/BL MPTP Injected Late

treatment_protocol: Mice received 4 injections of MPTP-HCL(30mg/kg, IP).  The first and second doses were separated by 16 hrs.  Mice were killed 7d after final injection (MML - Mouse MPTP Late).  The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prepared from Trizol homogenates per the manufacturer's protocol (Invitrogen)

value: C57/BL, Gender:Male, Age:10 weeks, Tissue:Substantia Nigra (SN) disected bilaterally from six like-treated mice.


title: Substantia Nigra Control Sample3 Codelink

description: Need to specify

source_name: Pooled Substantia Nigra C57bl/6 Saline injection

treatment_protocol: Mice received 4 injections of 0.9% sterile saline, of equal volume to treatment group. The first and second doses were separated by 16 hr. Mice were killed 24hr or 7d after injection. The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prpared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)


title: Sustantia Nigra MML Sample3 Codelink

description: Need to specify

source_name: Pooled Sustantia Nigra C57/BL MPTP Injected Late

value: C57/BL, Gender:Male, Age:10 weeks, Tissue:Substantia Nigra (SN) disected bilaterally from six like-treated mice


title: Substantia Nigra Control Sample4 Codelink

description: Need to specify

source_name: Pooled Substantia Nigra C57BL/6 Saline injection


title: pa14 4/22 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28291.gif; format: GIF
Infection: PA14
Measurement: time(relative) 24 h

source_name: N2 worms exposed to P. aeruginosa PA14- 24 hours

tag: Common reference- Mixed stage N2 worm culture


title: Substantia Nigra MME Sample2 Codelink

description: Need to specify


title: pa14 12hr 4/26 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29509.gif; format: GIF
Infection: PA14
Measurement: time(relative) 12 h

source_name: N2 worms exposed to P. aeruginosa PA14- 12 hours


title: op50 12hr 4/26 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29508.gif; format: GIF
Infection: OP50
Measurement: time(relative) 12 h

source_name: N2 worms exposed to E. coli OP50- 12 hours


title: pa14 5/29 n2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27967.gif; format: GIF
Infection: PA14
Measurement: time(relative) 4 h

source_name: N2 worms exposed to P. aeruginosa PA14- 4 hours


title: pa14 4/23 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28290.gif; format: GIF
Infection: PA14
Measurement: time(relative) 24 h

tag: N2 worms exposed to P. aeruginosa PA14- 24 hours


title: op50 n2 11/19 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/28186.gif; format: GIF
Infection: OP50
Measurement: time(relative) 24 h

source_name: N2 worms exposed to E. coli OP50- 24 hours


title: pa14 5/7 n2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27966.gif; format: GIF
Infection: PA14
Measurement: time(relative) 4 h

tag: N2 worms exposed to P. aeruginosa PA14- 4 hours


title: op50 4/22 n2 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28264.gif; format: GIF
Infection: OP50
Measurement: time(relative) 24 h

tag: N2 worms exposed to E. coli OP50- 24 hours


title: op50 4/21 n2 24hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28263.gif; format: GIF
Infection: OP50
Measurement: time(relative) 24 h


title: pa14 12hr 4/25 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29511.gif; format: GIF
Infection: PA14
Measurement: time(relative) 12 h

tag: N2 worms exposed to P. aeruginosa PA14- 12 hours


title: Substantia Nigra Control Sample2 Codelink

description: Need to specify

source_name: Pooled Sustantia Nigra C57BL/6 Saline injection


title: op50 6/29 N2 4hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19596.gif; format: GIF
Infection: OP50
Measurement: time(relative) 4 h

source_name: N2 worms exposed to E. coli OP50-4 hours


title: op50 12hrs 4/24 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29692.gif; format: GIF
Infection: OP50
Measurement: time(relative) 12 h

tag: N2 worms exposed to E. coli OP50- 12 hours


title: op50 12hr 4/25 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29510.gif; format: GIF
Infection: OP50
Measurement: time(relative) 12 h


title: pa14 12hrs 4/24 n2

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29691.gif; format: GIF
Infection: PA14
Measurement: time(relative) 12 h


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 7 mut

status: Public on Sep 12 2006

city: Carlsbad

first: Aimee

last: Jackson

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: For details please see: Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, and Linsley PS. RNA (2006) 12(7):1179-1187

data_processing: Local background correction

source_name: HeLa

tag: HeLa, mock,

tag: HeLa, 193-MAPK14, pos 7 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 6 mut

tag: HeLa, 193-MAPK14, pos 6 mut


title: Hela, mock vs. HeLa, Luc

tag: Hela,  mock

tag: HeLa, Luc


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 8 mut

tag: HeLa, 193-MAPK14, pos 8 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 10 mut

tag: HeLa, 193-MAPK14, pos 10 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 4 mut

tag: HeLa, 193-MAPK14, pos 4 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 12 mut

tag: HeLa, 193-MAPK14, pos 12 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 9 mut

tag: HeLa, 193-MAPK14, pos 9 mut


title: pa14 4/21 n2 24hrs

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28296.gif; format: GIF
Infection: PA14
Measurement: time(relative) 24 h


title: pa14 629new 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19659.gif; format: GIF
Infection: PA14
Measurement: time(relative) 4 h

source_name: N2 worms exposed to P. aeruginosa PA14 - 4 hours

source_name: Common reference- mixed stage N2 worms culture


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 14 mut

tag: HeLa, 193-MAPK14, pos 14 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 3 mut

tag: HeLa, 193-MAPK14, pos 3 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, normal

tag: HeLa, 193-MAPK14, normal


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 17 mut

tag: HeLa, 193-MAPK14, pos 17 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 16 mut

tag: HeLa, 193-MAPK14, pos 16 mut


title: Substantia Nigra Control Sample1 Codelink

description: Need to specify

data_processing: Raw intensity data acquired from Codelink platform

treatment_protocol: Mice received 4 injections of 0.9% sterile saline, of equal volume to treatment group.  The first and second doses were separated by 16 hr.  Mice were killed 24hr or 7d after injection.  The SN was dissected bilaterally from six like-treated mice, pooled and RNA was prpared from Trizol homogenates per the manufacturer's protocol. (Invitrogen)

tag: Strain C57BL/6 Gender:Male Age:10 weeks Tissue


title: op50 5/07 N2 4hr

description:
Simple annotation: Pathogen, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19293.gif; format: GIF
Infection: OP50
Measurement: time(relative) 4 h

source_name: N2 worms exposed to E. coli OP50- 4 hours

source_name: Common reference- Mixed stage N2 worm culture


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 1 mut

tag: HeLa, 193-MAPK14, pos 1 mut


title: HeLa, mock, 24 hr vs. HeLa, PIK3CB-6338, 24 hr

tag: HeLa, mock, 24 hr

tag: HeLa, PIK3CB-6338, 24 hr


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 15 mut

tag: HeLa, mock,

tag: HeLa, 193-MAPK14, pos 15 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 19 mut

tag: HeLa, 193-MAPK14, pos 19 mut


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 3 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 3 mut, 24 hr, b


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 18 mut

tag: HeLa, 193-MAPK14, pos 18 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 11 mut

tag: HeLa, 193-MAPK14, pos 11 mut


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 1 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 5 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 5 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 2 mut, 24 hr, b


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 2 mut

tag: HeLa, 193-MAPK14, pos 2 mut


title: HeLa, mock, vs. HeLa, 193-MAPK14, pos 13 mut

tag: HeLa, 193-MAPK14, pos 13 mut


title: HeLa, mock, 24 hr vs. HeLa, PIK3CB-6340, 24 hr

tag: HeLa, PIK3CB-6340, 24 hr


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 4 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 4 mut, 24 hr, b


title: Ped. Normal #3

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67440.gif

source_name: 4 ug of Amplified Stratagene Universal Reference

source_name: 4 ug of 1 round amplified Ped. Normal whole blood RNA (PAXgene kit)


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 8 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 8 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 6 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 6 mut, 24 hr, b


title: Ped. Normal #11

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67550.gif

tag: 4 ug of Amplified Stratagene Universal Reference

source_name: 4 ug of 1 round amplified Ped. ITP whole blood RNA (PAXgene kit)


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 7 mut, 24 hr, b

tag: HeLa, mock, 24 hr

tag: HeLa, 193-MAPK14, pos 7 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 10 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 10 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 14 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 14 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 9 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 9 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 15 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 15 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 13 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 13 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 18 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 18 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 16 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 16 mut, 24 hr, b


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 12 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 12 mut, 24 hr, b


title: Adult Refractory. ITP #7

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67546.gif

source_name: 4 ug of Amplified Stratagene Universal Reference (CTP2 Ref)

source_name: 4 ug of 1 round amplified Normal whole blood RNA (PAXgene kit)


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 17 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 17 mut, 24 hr, b


title: HeLa, mock, 24hr vs. HeLa, MAPK14, normal, 24hr

tag: HeLa, mock, 24hr

tag: HeLa, MAPK14, normal, 24hr


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, c

tag: HeLa, 193-MAPK14, pos 1 mut, 24 hr, c


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 19 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 19 mut, 24 hr, b


title: Ped. Normal #1

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67438.gif

tag: 4 ug of Amplified Stratagene Universal Reference (CTP2 Ref)

tag: 4 ug of 1 round amplified Ped. Normal whole blood RNA (PAXgene kit)


title: Ped. Normal #2

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67439.gif

tag: 4 ug of Amplified Stratagene Universal Reference


title: Ped. Acute ITP #6

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67443.gif

tag: 4 ug of 1 round amplified Ped. ITP whole blood RNA (PAXgene kit)


title: Ped. Acute ITP #9

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67548.gif


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, c

tag: HeLa, mock, 24 hr

tag: HeLa, 193-MAPK14, pos 2 mut, 24 hr, c


title: Ped. Acute ITP #4

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67441.gif


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 1 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 5 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 5 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 10 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 10 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 11 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 11 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 2 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 4 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 4 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 6 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 6 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 12 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 12 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 9 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 9 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 3 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 3 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 13 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 13 mut, 24 hr, a


title: HeLa, mock , 24 hr vs. HeLa, MAPK14-193 , 24 hr

tag: HeLa, mock , 24 hr

tag: HeLa, MAPK14-193 , 24 hr


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 7 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 7 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 14 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 14 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 15 mut, 24 hr, a

tag: HeLa, mock, 24 hr

tag: HeLa, 193-MAPK14, pos 15 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 16 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 16 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 19 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 19 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 17 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 17 mut, 24 hr, a


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 8 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 8 mut, 24 hr, a


title: Female BALB/c Lacrimal Testosterone, biological rep 3 (CodeLink)

first: Nathaniel

last: Treister

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Lacrimal gland gene expression from ovarectomized mice treated with testosterone for 14 days.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on a GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse 20K I Bioarray. Bioarrays were washed and stained with streptavidin-Alexa 647 and washed again.

scan_protocol: Bioarrays were scanned with a ScanArray Express HT scanner using ScanArray Express software.

data_processing: Data were analyzed with the CodeLink Image Analysis software using the default settings and normalized using global scaling to a median target intensity  on each array of 1.0.

label: biotin

source_name: Lacrimal glands from testosterone treated female BALB/c mice ( glands pooled from 5-6 mice).

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

extract_protocol: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 18 mut, 24 hr, a

tag: HeLa, 193-MAPK14, pos 18 mut, 24 hr, a


title: Hela mock 24hr vs. HeLa PLk1319, 24 hr

tag: Hela mock 24hr

tag: HeLa PLk1319, 24 hr


title: Female BALB/c Lacrimal Placebo, biological rep 3 (CodeLink)

description: Lacrimal gland gene expression from ovarectomized mice treated with placebo for 14 days.

source_name: Lacrimal glands from placebo treated female BALB/c mice ( glands pooled from 5-6 mice).

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.


title: Female BALB/c Lacrimal Placebo, biological rep 1 (CodeLink)


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 11 mut, 24 hr, b

tag: HeLa, 193-MAPK14, pos 11 mut, 24 hr, b


title: saline vs injection muscimol (slide 2)

status: Public on Sep 09 2006

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

description:
Auratus goldfish genome project: slide 2; AURATUS goldfish genome project: Muscimol treatment in hypothalamus
Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17- alpha EE2 (Physiological Genomics).  Further sequence information found at www.auratus.ca

data_processing: Array quality filter test used; Intensity-dependent Lowess normalization

organism: Carassius auratus

source_name: Carassius auratus; hypothalamus; i.p. saline control

tag: Female adult goldfish

tag: tissue

value: hypothalamus

tag: Control i.p. injection of 0.6% saline

tag: 6 hour treatment

tag: Sexually regressed animals (mid-August)

tag: Adults approx. 2-3 years of age

source_name: Carassius auratus; hypothalamus; i.p injection muscimol

tag: single i.p. injection muscimol 1 ug/gram body weight


title: Female BALB/c Lacrimal Testosterone, biological rep 1 (CodeLink)


title: Female BALB/c Lacrimal Testosterone, biological rep 2 (CodeLink)


title: injection muscimol vs saline (slide 31)

description:
Auratus goldfish genome project: slide 31; Muscimol treatment in hypothalamus
Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17- alpha EE2 (Physiological Genomics).  Further sequence information found at www.auratus.ca

tag: Dye swap with 2


title: HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, normal, 24 hr

tag: HeLa, mock, 24 hr

tag: HeLa, 193-MAPK14, normal, 24 hr


title: Rat liver_PCB153_13 week_rep1

status: Public on Sep 08 2006

city: Buffalo

first: Bladimir

middle: Jason

last: Ovando

address: 102 Farber Hall

department: Pharmacology & Toxicology

institute: University at Buffalo

description: Tissues were obtained from a 2-year cancer bioassay investigating the relative carcinogenic potencies of the AhR ligands 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) and 3,3´,4,4´,5-pentachlorobiphenyl (PCB126); the non-AhR ligand 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB153) and the binary mixture of PCBs 126 and 153. Female Harlan Sprague-Dawley rats were exposed for 13 weeks, 5 days a week via oral gavage to toxic equivalent doses of TCDD, PeCDF, PCB126, PCB153, the binary mixture of PCBs 126 and 153 or a vehicle control of corn oil:acetone (99:1).

data_processing: Gene traffic by Iobion using GCRMA method

organism: Rattus norvegicus

source_name: Rat liver_PCB153_13 week_rep1

extract_protocol: Qiagen RNeasy Kit with Dnase treatment

treatment_protocol: Treatment regimen: 13 weeks, 5 days/week, oral gavage

tag: Organism

value: Female Sprague Dawley Rats

tag: Tissue

value: Liver

tag: Treatment

value: 1000ug/kg/day PCB153

tag: Rat IDs


title: HeLa, mock, 24 hrs vs. HeLa, 1721-PLK-772, 24 hrs

description: For details please see: Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, and Linsley PS. RNA (2006) 12(7):1179-1187

tag: HeLa, mock, 24 hrs


title: Rat liver_Binary_13 week_rep1

source_name: Rat liver_Binary_13 week_rep1

value: 1000ng/kg/day PCB126 & 1000ug/kg/day PCB153


title: Rat liver_PCB126_13 week_rep1

source_name: Rat liver_PCB126_13 week_rep1

value: 1000ng/kg/day PCB126


title: Rat liver_Binary_13 week_rep3

source_name: Rat liver_Binary_13 week_rep3


title: saline vs injection muscimol (slide 46)

description:
Auratus goldfish genome project: slide 46; Muscimol treatment in hypothalamus
Further details for techniques and protocols for our microarray hybridizations and normalizations can be found in Martyniuk et al. Gene expression profiling in the brain of male goldfish exposed to 17- alpha EE2 (Physiological Genomics).  Further sequence information found at www.auratus.ca


title: Rat liver_PCB126_13 week_rep3

source_name: Rat liver_PCB126_13 week_rep3


title: Female BALB/c Lacrimal Placebo, biological rep 2 (CodeLink)


title: Rat liver_PCB126_13 week_rep2

source_name: Rat liver_PCB126_13 week_rep2


title: HT29tTSTetOH1_PLK1_Doxycycline_0ng/ml_24h vs. HT29tTSTetOH1_PLK1_Doxycycline_50ng/ml_24h

source_name: HeLa


title: Rat liver_PCB153_13 week_rep3

source_name: Rat liver_PCB153_13 week_rep3


title: Rat liver_Binary_13 week_rep2

source_name: Rat liver_Binary_13 week_rep2


title: Rat liver_PCB153_13 week_rep2

source_name: Rat liver_PCB153_13 week_rep2


title: Ped. Acute ITP #5

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67442.gif

source_name: 4 ug of Amplified Stratagene Universal Reference

source_name: 4 ug of 1 round amplified Ped. ITP whole blood RNA (PAXgene kit)


title: Rat liver_PeCDF_13 week_rep3

source_name: Rat liver_PeCDF_13 week_rep3

value: 200ng/kg/day PeCDF


title: Rat liver_PeCDF_13 week_rep1

source_name: Rat liver_PeCDF_13 week_rep1


title: Rat liver TCDD_13 week_rep1

source_name: Rat liver_TCDD_13 week_rep1

value: 100ng/kg/day TCDD


title: Rat liver TCDD_13 week_rep2

source_name: Rat liver_TCDD_13 week_rep2


title: Rat liver control_13 week_rep6

source_name: Rat liver_vehicle control_13 week_rep6

value: corn oil:acetone (99:1; vehicle control)


title: Rat liver TCDD_13 week_rep3

source_name: Rat liver_TCDD_13 week_rep3

tag: Female Sprague Dawley Rats


title: Rat liver_PeCDF_13 week_rep2

source_name: Rat liver_PeCDF_13 week_rep2


title: Rat liver control_13 week_rep5

source_name: Rat liver_vehicle control_13 week_rep5

tag: Rat IDs:32 & 50


title: MAQC_GEX_1_D3

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

data_processing: The data values are the number of molecules normalized to 1,000,000 ACTB molecules.

label: Caliper

source_name: MAQC sample D, i.e., MAQC samples A and B mixed at 25%:75% ratio (A:B).

label_protocol: Standardized RT (StaRT)-PCR (TM) is a quantitative competitive template PCR platform that provides numerical quantification of transcript abundance values at endpoint of PCR over the full range observed in human tissues (more than six orders of magnitude).  Following reverse transcription, cDNA molecules representing each gene are measured in relation to a known number of its respective internal standard cDNA molecules.

tag: MAQC sample


title: Rat liver control_13 week_rep4

source_name: Rat liver_vehicle control_13 week_rep4


title: MAQC_GEX_1_D1


title: MAQC_GEX_1_D2


title: MAQC_GEX_1_C2

source_name: MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).


title: Rat liver control_13 week_rep1

description: Tissues were obtained from a 2-year cancer bioassay investigating the relative carcinogenic potencies of the AhR ligands 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) and 3,3´,4,4´,5-pentachlorobiphenyl (PCB126); the non-AhR ligand 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB153) and the binary mixture of PCBs 126 and 153. Female Harlan Sprague-Dawley rats were exposed for 13 weeks, 5 days a week via oral gavage to toxic equivalent doses of TCDD, PeCDF, PCB126, PCB153, the binary mixture of PCBs 126  and 153  or a vehicle control of corn oil:acetone (99:1).

source_name: Rat liver_vehicle control_13 week_rep1


title: MAQC_GEX_1_C3


title: Ped. Normal #10

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67549.gif

tag: 4 ug of Amplified Stratagene Universal Reference

tag: 4 ug of 1 round amplified Ped. ITP whole blood RNA (PAXgene kit)


title: dmso11-19b

city: Chapel Hill

first: Nancy

last: DeMore

state: NC

address: 3010 Old Clinic Rd., CB 7213

department: Surgery

institute: UNC @ Chapel Hill

data_processing: Lowess

source_name: Reference RNA

tag: Modified version of the Stratagene Human Universal

source_name: Breast tumor

tag: MDA-MB-435 cells treated with DMSO 1:1000


title: MAQC_GEX_1_C1


title: MAQC_GEX_1_A3

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)


title: MAQC_GEX_1_B3

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: MAQC_GEX_1_B2


title: MAQC_GEX_1_B1


title: 2me11-2

tag: MDA-MB-435 cells treated with 2uM 2-methoxyestradiol


title: 2me11-19b

tag: MDA-MB-435 cells treated with 2UM 2-methoxyestradiol


title: dmso11-22b


title: dmso11-2

tag: modified version of the Stratagene Human Universal


title: 2me11-22b

tag: MDA-MB-435 cells treated with 2-methoxyestradiol 2uM


title: MAQC_GEX_1_A2


title: MAQC_GEX_1_A1


title: 2me11-19a

data_processing: lowess


title: dmso11-19a


title: Rat liver control_13 week_rep3

source_name: Rat liver_vehicle control_13 week_rep3


title: Rat liver control_13 week_rep2

source_name: Rat liver_vehicle control_13 week_rep2


title: 2me11-22a


title: dmso11-22a


title: MAQC_BIO1_1_B4

scan_protocol: Slides were scanned with a confocal LuxScan scanner (CapitalBio Corp.). The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).

data_processing: The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).  Median-scaling of background-subtracted intensity was applied to each array to make median equal to 1000.

label_protocol: Fluorescent-labeled DNA (Cy3) was produced through Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described in detail (Guo, Y. et al. J. Virol. 79, 14392-14403, 2005). Briefly, double-stranded cDNA containing T7 RNA polymerase promoter sequence was synthesized with 5 ug of total RNA using Reverse Transcription System, RNase H, DNA polymerase I and T4 DNA polymerase, according to the manufacturer’s recommended protocol (Promega).


title: MAQC_BIO1_1_B3


title: MAQC_BIO1_1_A5


title: MAQC_BIO1_1_A2


title: MAQC_BIO1_1_B1


title: MAQC_BIO1_1_A3


title: MAQC_AFX_L_RDL_5

description: The samples were randomly labeled and each test site was provided an aliquot of each sample.  To avoid potential confounding factors in experimental implementation, the identity of the RNA samples was kept unknown to the test sites before data were submitted to FDA/NCTR.

hyb_protocol: Affymetrix GeneChip Operating Software (GCOS) is used to automate the control of GeneChip Fluidics Stations and Scanners.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The CEL file data were analyzed with BioConductor to generate probeset level data using the justPlier() function.  Probe-level data were quantile normalized before PLIER summarization per test site (across 36 arrays).  An offset value of 16 was then added to each probeset-level data point.

source_name: Sample type L_RDL (Liver Riddelliine)

label_protocol: The samples were processed following Affymetrix one-cycle sample preparation protocol with 5 ug of total RNA (Please refer to GeneChip Expression Analysis Technical Manual for details) and hybridized to Rat Genome 230 2.0 arrays.

treatment_protocol: Groups of six 6-week-old Big Blue rats were gavaged with riddelliine (1 mg/kg body weight) or aristolochic acid (10 mg/kg body weight) five times a week for 12 weeks or Big Blue rats were fed a diet of 8% comfrey roots for 12 weeks.  The animals were sacrificed after 12 weeks of treatment, and the tissues were isolated, frozen quickly in liquid nitrogen and stored at –80 °C.

tag: MAQC rat toxicogenomics samples used in Guo L. et al., Nature Biotechnology, 24(9), 2006.


title: MAQC_BIO1_1_B2


title: MAQC_BIO1_1_A4


title: MAQC_BIO1_1_A1


title: MAQC_AFX_L_RDL_1


title: MAQC_BIO_1_sB2

description: Sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5), sB (B/B, Cy3/Cy5).  The human genome-wide long oligonucleotide microarray was constructed inhouse at CapitalBio Corporation, Beijing, China.

scan_protocol: Slides were scanned with a confocal LuxScan scanner (CapitalBio Corp.). For two-color microarrays, the scanning setting for the Cy3 and Cy5 channels was manually balanced by visual inspection of the external control spots. The data from the obtained images were extracted with SpotData software (CapitalBio Corp.).

data_processing: The data from the obtained images were extracted with SpotData software (CapitalBio Corp.). The raw data were submitted to MAQC and further normalized by using linear-scaling and LOWESS.

label_protocol: Fluorescent-labeled DNA (Cy3 and Cy5-dCTP) was produced through Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described in detail (Guo, Y. et al. J. Virol. 79, 14392-14403, 2005). Briefly, double-stranded cDNA containing T7 RNA polymerase promoter sequence was synthesized with 5 ug of total RNA using Reverse Transcription System, RNase H, DNA polymerase I and T4 DNA polymerase, according to the manufacturer’s recommended protocol (Promega).


title: MAQC_AFX_L_CTR_5

source_name: Sample type L_CTR (Liver Control)


title: MAQC_AFX_L_RDL_2


title: MAQC_AFX_L_RDL_6


title: MAQC_AFX_L_RDL_3


title: MAQC_BIO_1_sA1


title: MAQC_BIO_1_sA2


title: MAQC_AFX_L_RDL_4


title: MAQC_BIO_1_B3


title: MAQC_BIO_1_B5


title: MAQC_BIO_1_sB5


title: MAQC_BIO_1_B4


title: MAQC_BIO_1_sB3


title: MAQC_BIO_1_sA4


title: MAQC_BIO_1_sB1


title: MAQC_BIO_1_sA5


title: MAQC_BIO_1_sA3


title: MAQC_BIO_1_sB4


title: MAQC_BIO_1_B2


title: MAQC_AFX_L_CTR_6


title: MAQC_BIO1_1_B5


title: MAQC_AFX_L_CTR_4


title: MAQC_BIO_1_A5


title: MAQC_BIO_1_B1


title: MAQC_AFX_L_CTR_1


title: MAQC_AFX_L_CFY_6

source_name: Sample type L_CFY (Liver Comfrey)


title: MAQC_AFX_L_CTR_2


title: MAQC_BIO_1_A1


title: MAQC_BIO_1_A4


title: MAQC_AFX_L_AA_4

source_name: Sample type L_AA (Liver Aristolochic Acid)


title: MAQC_AFX_K_CTR_1

source_name: Sample type K_CTR (Kidney Control)


title: MAQC_BIO_1_A3


title: MAQC_AFX_L_AA_5


title: MAQC_AFX_L_CFY_3


title: MAQC_AFX_K_CTR_4


title: MAQC_AFX_K_AA_6

source_name: Sample type K_AA (Kidney Aristolochic Acid)


title: MAQC_AFX_L_CTR_3


title: MAQC_AFX_L_CFY_5


title: MAQC_AFX_K_CTR_5


title: MAQC_BIO_1_A2


title: MAQC_AFX_L_CFY_4


title: MAQC_AFX_K_CTR_3


title: MAQC_AFX_L_CFY_1


title: MAQC_AFX_L_CFY_2


title: MAQC_AFX_L_AA_6


title: MAQC_AFX_K_CTR_6


title: MAQC_AFX_K_CTR_2


title: MAQC_AFX_L_AA_3


title: MAQC_AFX_L_AA_2


title: MAQC_AFX_K_AA_4


title: MAQC_AFX_L_AA_1


title: MAQC_AFX_K_AA_5


title: MAQC_AFX_K_AA_2


title: MAQC_AFX2_L_RDL_5


title: MAQC_AFX_K_AA_1


title: MAQC_AFX_K_AA_3


title: MCK-PPARa rep 2

city: St. Louis

first: Brian

last: Finck

state: MO

address: 660 S. Euclid Ave

institute: Washington University

description: Muscle RNA from muscle-specific PPARalpha overexpressing transgenic mouse

source_name: Gastrocnemius muscle PPARalpha overexpressing transgenic mouse

extract_protocol: RNAzol B -followed manufacturers protocol

tag: Gastrocnemius muscle from transgenic mouse overexpressing PPARalpha


title: MAQC_AFX2_L_RDL_1


title: MAQC_AFX2_L_RDL_3


title: MCK-PPARa rep 1

description: Muscle RNA from muscle-specific PPARalpha overexrpessing transgenic mouse

source_name: Gastrocnemius muscle from PPARalpha overexpressing mouse

tag: Gastrocnemius muscle for transgenic mouse overexpressing PPARalpha in a skeletal muscle-specific manner


title: MAQC_AFX2_L_CTR_3


title: MAQC_AFX2_L_CTR_5


title: Non-transgenic mouse rep 1

description: Muscle RNA from littermate control mice for muscle-specific PPARalpha overexrpessing transgenic mice

source_name: gastrocnemius muscle wild-type mouse

tag: Gastrocnemius muscle wild-type mouse - control mouse for PPARalpha overexpressing


title: MAQC_AFX2_L_RDL_6


title: Non-transgenic mouse rep 2

source_name: Gastrocnemius muscle wild-type mouse

tag: Gastrocnemius muscle wild-type mouse - control mouse for PPARalpha overexpressing -rep 2


title: MAQC_AFX2_L_RDL_2


title: MAQC_AFX2_L_CTR_6


title: MAQC_AFX2_L_RDL_4


title: MAQC_AFX2_L_CFY_5


title: MAQC_AFX2_L_CTR_1


title: MAQC_AFX2_L_CFY_1


title: MAQC_AFX2_L_CFY_3


title: MAQC_AFX2_L_CTR_4


title: MAQC_AFX2_L_CTR_2


title: MAQC_H25K1_3_B5

hyb_protocol: Hybridization was done manually in TeleChem Hybridization cassettes using LifterSlip(TM) (Erie Company).  cRNAs were labeled independently and not pooled prior to hybridization.  In one-color experiments, Cy3-labeled cDNA samples were denatured independently and one sample applied to each microarray.  Hybridization mixes (55 ul total volume) consisted of 38.5 ul labeled cDNA, 5.5 ul 2% SDS, 7.0 ul 20X SSC, 3.0 ul poly dA (5 ug/ul) and 1.0 ul Cotl DNA (1 ug/ul).  Hybridization cassettes and slides were pre-heated to 55°C before samples were added and 3X SSC was added into humidity grooves in the cassette. Samples were applied to the microarrays and hybridized for 16 hrs at 55°C in a water bath.  Post-hybridization, slides were washed (10 min, 2X SSC/0.1% SDS at 42°C; 10 min, 0.2X SSC/0.1% SDS at 42°C; 10 min, 0.2X SSC at 22°C twice) prior to centrifugation in 50-ml conical tubes at 201 x g for 5 minutes to dry.

scan_protocol: Scanning was performed on Axon 4200A or 4200B instruments at a PMT yielding 1% or less saturated spots.

data_processing: All one-color and two-color images were analyzed using Axon GenePix Pro 5.0 software and raw data were provided in the form of one tab-delimited text (.gpr) file per microarray.  The raw data were submitted to MAQC and further normalized by using median-scaling.

label_protocol: 2 ug of each sample was amplified using a Genisphere SenseAmp Plus Amplification kit (generating amplified poly A tailed senseRNA), according to the manufacturer’s recommended protocol.  The resulting tailed senseRNA was reverse transcribed with amino-allyl indirect labeling using a SuperScriptTM Indirect cDNA Labeling Kit (Invitrogen) with slight modifications.  Each first strand cDNA generation reaction used 5 µg of senseRNA with Superscript II and aa-dUTP at 42°C for 2 hrs.  cDNA was purified using a MinElute PCR Purification Kit and conjugated with mono-functional Cy3 or Cy5 dye aliquot (GE Healthcare) for 1 hr at 22°C in the dark.  Dye-conjugated cDNA was purified with a MinElute PCR Purification Kit.  Dye:base labeling efficiency was determined at this point for all dye-conjugated cDNA.


title: MAQC_H25K1_3_B4


title: MAQC_AFX2_L_CFY_6


title: MAQC_AFX2_L_CFY_2


title: MAQC_AFX2_L_AA_5


title: MAQC_AFX2_L_AA_3


title: MAQC_AFX2_L_CFY_4


title: MAQC_AFX2_L_AA_1


title: MAQC_AFX2_L_AA_4


title: MAQC_AFX2_K_CTR_5


title: MAQC_H25K1_3_B2


title: MAQC_AFX2_L_AA_6


title: MAQC_H25K1_3_A4


title: MAQC_AFX2_L_AA_2


title: MAQC_AFX2_K_CTR_1


title: MAQC_AFX2_K_CTR_6


title: MAQC_AFX2_K_CTR_4


title: MAQC_H25K1_3_B1


title: MAQC_H25K1_3_B3


title: MAQC_AFX2_K_CTR_3


title: MAQC_AFX2_K_AA_1


title: MAQC_AFX2_K_CTR_2


title: MAQC_AFX2_K_AA_3


title: MAQC_AFX2_K_AA_5


title: MAQC_H25K1_3_A5


title: MAQC_AFX2_K_AA_2


title: MAQC_AFX2_K_AA_6


title: MAQC_H25K1_3_A3


title: MAQC_H25K1_2_B4


title: MAQC_H25K1_2_B5


title: MAQC_AFX2_K_AA_4


title: MAQC_H25K1_2_B2


title: MAQC_H25K1_3_A2


title: MAQC_H25K1_2_B3


title: MAQC_H25K1_3_A1


title: MAQC_H25K1_2_A3


title: MAQC_H25K1_2_A4


title: MAQC_H25K1_1_B2


title: MAQC_H25K1_2_B1


title: MAQC_H25K1_1_A4


title: MAQC_H25K1_1_B3


title: MAQC_H25K1_1_A5


title: MAQC_H25K1_2_A2


title: MAQC_H25K1_1_B1


title: MAQC_H25K1_1_B4


title: MAQC_H25K1_1_B5


title: MAQC_H25K1_1_A3


title: MAQC_H25K_2_sB3

description: H25K two-color sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5), and sB (B/B, Cy3/Cy5).  Only test site 2 submitted two-color H25K data.

data_processing: All images were analyzed using Axon GenePix Pro 5.0 software and raw data were provided in the form of one tab-delimited text (.gpr) file per microarray.  The raw data were submitted to MAQC and further normalized by using median-scaling and LOWESS.


title: MAQC_H25K1_1_A1


title: MAQC_AG1_3_D2

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 8.5 (P/N G2567AA).  AG1 data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745).

data_processing: Data were transformed by setting all measurements less than 5.0 to 5.0.  Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present.  All data points were median scaled using the median signal intensity value for data points labeled as Present.

source_name: MAQC sample D, i.e., MAQC samples A and B mixed at 25%:75% ratio (A:B).

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol (AG1).  These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.  The microarrays used were Agilent’s Whole Human Genome Oligo Microarrays (P/N G4112A).  Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.  Labeled cRNAs were generated from 500 ng of total RNA for each of AG1 and AGL using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).  Agilent’s Stabilization and Drying Solution was used in processing all microarrays.


title: MAQC_H25K_2_sA5


title: MAQC_H25K1_2_A1


title: MAQC_H25K_2_sB5


title: MAQC_H25K1_1_A2


title: MAQC_H25K_2_sB1


title: MAQC_H25K1_2_A5


title: MAQC_AG1_3_C4

source_name: MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).


title: MAQC_AG1_3_D3


title: MAQC_AG1_3_C5


title: MAQC_AG1_3_D1


title: MAQC_H25K_2_sA4


title: MAQC_H25K_2_sB2


title: MAQC_AG1_3_D5


title: MAQC_H25K_2_sA3


title: MAQC_H25K_2_sB4


title: MAQC_AG1_3_D4


title: MAQC_AG1_3_C2


title: MAQC_AG1_3_C3


title: MAQC_AG1_3_B5


title: MAQC_AG1_3_B4


title: MAQC_H25K_2_sA2


title: MAQC_H25K_2_sA1


title: MAQC_H25K_2_B8


title: MAQC_H25K_2_B9


title: MAQC_AG1_3_C1


title: MAQC_H25K_2_B3


title: MAQC_H25K_2_B2


title: MAQC_AG1_3_B2


title: MAQC_H25K_2_B4


title: MAQC_AG1_3_B1


title: MAQC_AG1_3_B3


title: MAQC_AG1_3_A5


title: MAQC_AG1_3_A3


title: MAQC_H25K_2_B6


title: MAQC_H25K_2_B7


title: MAQC_AG1_3_A4


title: MAQC_H25K_2_B5


title: MAQC_AG1_L_RDL_3

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol (AG1).  These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.  The microarrays used were Agilent’s Whole Rat Genome Oligo Microarrays (P/N G4131A).  Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.  Labeled cRNAs were generated from 500 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).  Agilent’s Stabilization and Drying Solution was used in processing all microarrays.


title: MAQC_AG1_L_RDL_4


title: MAQC_H25K_2_B10


title: MAQC_AG1_L_RDL_5


title: MAQC_AG1_3_A1


title: MAQC_AG1_L_RDL_6


title: MAQC_AG1_3_A2


title: MAQC_AG1_2_D5


title: MAQC_AG1_L_RDL_2


title: MAQC_AG1_L_RDL_1


title: MAQC_H25K_2_A8


title: MAQC_AG1_2_D4


title: MAQC_AG1_L_CTR_2


title: MAQC_H25K_2_B1


title: MAQC_AG1_L_CTR_6


title: MAQC_AG1_L_CTR_3


title: MAQC_H25K_2_A9


title: MAQC_AG1_L_CTR_4


title: MAQC_H25K_2_A7


title: MAQC_AG1_2_D2


title: MAQC_AG1_L_CTR_5


title: MAQC_AG1_L_CFY_4


title: MAQC_AG1_2_D3


title: MAQC_AG1_L_CTR_1


title: MAQC_H25K_2_A6


title: MAQC_AG1_L_CFY_6


title: MAQC_H25K_2_A5


title: MAQC_AG1_L_CFY_5


title: MAQC_AG1_2_C4


title: MAQC_AG1_L_CFY_1


title: MAQC_AG1_2_C3


title: MAQC_AG1_L_CFY_2


title: MAQC_AG1_L_CFY_3


title: MAQC_H25K_2_A3


title: MAQC_AG1_L_AA_5


title: MAQC_AG1_2_D1


title: MAQC_H25K_2_A4


title: MAQC_AG1_2_C2


title: MAQC_H25K_2_A2


title: MAQC_H25K_2_A1


title: MAQC_AG1_L_AA_4


title: MAQC_AG1_L_AA_1


title: MAQC_AG1_K_CTR_6


title: MAQC_AG1_K_CTR_5


title: MAQC_AG1_L_AA_3


title: MAQC_AG1_L_AA_2


title: MAQC_AG1_2_C5


title: MAQC_AG1_K_CTR_4


title: MAQC_AG1_L_AA_6


title: MAQC_H25K_2_A10


title: MAQC_AG1_2_C1


title: MAQC_AG1_K_CTR_3


title: MAQC_AG1_K_AA_5


title: MAQC_AG1_K_CTR_1


title: MAQC_AG1_2_B5


title: MAQC_AG1_K_CTR_2


title: MAQC_AG1_2_B2


title: MAQC_NMC_1_B4

description: Sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5).  The slides were printed by the Norwegian Microarray Consortium.

scan_protocol: Slides were scanned using an Agilent G2505B scanner at 10 micron resolution.

data_processing: Images were processed and quantified using GenePix Pro 6.0.0.56. The data were filtered (or flagged) on the basis of signal levels and spot quality.  The raw data were submitted to MAQC and further normalized by using LOWESS.


title: MAQC_NMC_1_B5


title: MAQC_AG1_2_B3


title: MAQC_AG1_K_AA_4


title: MAQC_NMC_1_B3


title: MAQC_AG1_K_AA_6


title: MAQC_AG1_2_B1


title: MAQC_AG1_K_AA_3


title: MAQC_NMC_1_B2


title: MAQC_NMC_1_B1


title: MAQC_GEH_2Fail_D5

scan_protocol: All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.

data_processing: The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.  These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment.  In the MAQC study, for all microarray platforms, genes which were not detected (i.e., 'absent') were excluded from subsequent analyses.   The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background.   Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).

label_protocol: MAQC total RNA samples were processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Human Whole Genome bioarrays (catalog #300026).


title: MAQC_AG1_K_AA_2


title: MAQC_AG1_K_AA_1


title: MAQC_AG1_2_A4


title: MAQC_AG1_2_A5


title: MAQC_GEH_2Fail_D4


title: MAQC_AG1_2_A3


title: MAQC_GEH_2Fail_D3


title: MAQC_NMC_1_A4


title: MAQC_GEH_2Fail_D2


title: MAQC_GEH_2Fail_C5


title: MAQC_GEH_2Fail_D1


title: MAQC_NMC_1_A5


title: MAQC_NMC_1_A3


title: MAQC_AG1_2_A2


title: MAQC_NMC_1_A1


title: MAQC_NMC_1_A2


title: MAQC_GEH_2Fail_C2


title: MAQC_GEH_2Fail_C1


title: MAQC_GEH_2Fail_C3


title: MAQC_AG1_1_D4


title: MAQC_GEH_2Fail_C4


title: MAQC_GEH_2Fail_B5


title: MAQC_AG1_1_D5


title: MAQC_GEH_2Fail_B4


title: MAQC_AG1_1_D3


title: MAQC_AG1_2_A1


title: MAQC_AG1_1_D2


title: MAQC_GEH_2Fail_B2


title: MAQC_GEH_2Fail_B3


title: MAQC_NCI_4_B5

description: NCI sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5).  This is the second (and different) printing of the NCI.

scan_protocol: Slides were scanned using an Axon 4000B instrument at 10 micron resolution.  All scans were performed at 100% laser power, but the PMT setting varied from slide-to-slide depending on the labeling and hybridization outcomes.  Thus, the intensity of the signals among the slides will vary, but the Cy3/Cy5 ratios will be much less variable.

data_processing: Images were processed and quantified using GenePix 4.0 or higher software (Axon Instruments, Union City, CA).  The data were filtered (or flagged) on the basis of signal levels and spot quality.  The raw data were submitted to MAQC and further normalized by using median-scaling and LOWESS.

label_protocol: Labeling of probes, hybridization of slides and scanning was done essentially as described [Petersen, D. et al. BMC Bioinformatics 6, 63. 2005]


title: MAQC_GEH_2Fail_B1


title: MAQC_NCI_4_B3


title: MAQC_NCI_4_B2


title: MAQC_NCI_4_B4


title: MAQC_AG1_1_D1


title: MAQC_GEH_2Fail_A4


title: MAQC_GEH_2Fail_A3


title: MAQC_GEH_2Fail_A2


title: MAQC_GEH_2Fail_A1


title: MAQC_NCI_4_B1


title: MAQC_NCI_4_A5


title: MAQC_GEH_2Fail_A5


title: MAQC_AG1_1_C4


title: MAQC_AG1_1_C3


title: MAQC_AG1_1_C5


title: MAQC_NCI_4_A1


title: MAQC_NCI_4_A4


title: MAQC_NCI_4_A2


title: MAQC_NCI_4_A3


title: MAQC_NCI_3r_sA2


title: MAQC_NCI_3r_B4


title: MAQC_AG1_1_B4


title: MAQC_AG1_1_C2


title: MAQC_NCI_3r_sA1


title: MAQC_AG1_1_B3


title: MAQC_AG1_1_B5


title: MAQC_AG1_1_C1


title: MAQC_AG1_2_B4


title: MAQC_AG1_1_B2


title: MAQC_NCI_3Fail_D5

description: NCI sample-pair convention: A (A/A, Cy3/Cy5), B (B/A, Cy3/Cy5), C (C/A, Cy3/Cy5), and D (D/A, Cy3/Cy5).  MAQC sample A was used as the common reference sample (Cy5; channel 2) in NCI two-color experiments.  Test sites NCI_2 and NCI3 failed in the first round of experiments due to protocol issues.  The failed hybridizations are named as NCI_2Fail and NCI_3Fail.  NCI_2 repeated part of the experiment with 14 hybridizations.

data_processing: Images were processed and quantified using GenePix 4.0 software (Axon Instruments, Union City, CA).  The data were filtered (or flagged) on the basis of signal levels and spot quality.  The raw data were submitted to MAQC and further normalized by using LOWESS.


title: MAQC_NCI_3r_B3


title: MAQC_NCI_3r_B2


title: MAQC_AG1_1_A5


title: MAQC_AG1_1_B1


title: MAQC_NCI_3r_A4


title: MAQC_AG1_1_A2


title: MAQC_NCI_3Fail_D4


title: MAQC_QGN_1_D3

data_processing: Background signals were determined in the absence of RNA samples and subtracted from signals obtained in the presence of RNA samples. Because QuantiGene(R) assay measures RNA directly, no data normalization against a reference gene is required in the data analysis.

label: Luminescence

label_protocol: The QuantiGene(R) assays were performed according to the procedure of QuantiGene(R) Reagent System (Panomics).  It is a branched DNA (bDNA) technology.


title: MAQC_AG1_1_A4


title: MAQC_NCI_3Fail_D1


title: MAQC_NCI_3r_A3


title: MAQC_NCI_3Fail_C5


title: MAQC_NCI_3Fail_D2


title: MAQC_QGN_1_D2


title: MAQC_NCI_3r_A2


title: MAQC_NCI_3r_B1


title: MAQC_NCI_3r_A1


title: MAQC_QGN_1_C3


title: MAQC_ABI_L_RDL_4

hyb_protocol: Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation.  The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values.  The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values.  The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise.  In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescence - Digoxigenin

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol.  Rat Genome Survey Microarray was used.


title: MAQC_QGN_1_D1


title: MAQC_AG1_1_A1


title: MAQC_NCI_3Fail_C2


title: MAQC_AG1_1_A3


title: MAQC_NCI_3Fail_C1


title: MAQC_NCI_3Fail_C3


title: MAQC_NCI_3Fail_C4


title: MAQC_ABI_L_RDL_6


title: MAQC_NCI_3Fail_B5


title: MAQC_QGN_1_C2


title: MAQC_NCI_3Fail_D3


title: MAQC_QGN_1_B3


title: MAQC_ABI_L_RDL_5


title: MAQC_QGN_1_C1


title: MAQC_QGN_1_B1


title: MAQC_ABI_L_RDL_2


title: MAQC_QGN_1_B2


title: MAQC_ABI_L_RDL_3


title: MAQC_QGN_1_A3


title: MAQC_QGN_1_A1


title: MAQC_EPP_3_D5

description: MAQC sample

hyb_protocol: The DualChip(R) hybridization was carried out overnight (16 hours) at 60°C according to the DualChip(R) instruction manual.

scan_protocol: Eppendorf platform is an open system. Different scanner technologies and settings have been used by the different test sites.

data_processing: Each array was scanned at three different PMT gain settings. Eppendorf has developed specialized data analysis scheme treating the scanning, the background correction and normalization in a suited framework for low density arrays generating array to array gene expression ratio. The data sets submitted are divided in two groups. The first data set provides gene expression ratio comparing two samples and constitutes the standard result for the Eppendorf platform.

label_protocol: A reverse transcription with indirect labeling was performed using 10 ug of total RNA. The internal standard mixture was used for quantification/ normalization and estimation of experimental variation [de Longueville F, et al. Biochem. Pharmacol. 64, 137-49, 2002; Chen & Bittner. J. Biomedical Optics 2, 364-374, 1997].  Each DualChip(R) consists of two identical microarrays on the same slide, with two separate hybridization frames. This DualChip®-concept enables two complete gene expression experiments to be run on the same slide, using a one-color labeling technique.


title: MAQC_QGN_1_A2


title: MAQC_ABI_L_RDL_1


title: MAQC_EPP_3_D4

description: MAQC sample


title: MAQC_ABI_L_CTR_5


title: MAQC_NCI_3Fail_A4


title: MAQC_NCI_3Fail_B3


title: MAQC_ABI_L_CTR_6


title: MAQC_ABI_L_CTR_2


title: MAQC_NCI_3Fail_B2


title: MAQC_ABI_L_CTR_3


title: MAQC_ABI_L_CTR_4


title: MAQC_NCI_3Fail_A5


title: MAQC_EPP_3_D3

description: MAQC sample


title: MAQC_NCI_3Fail_B1


title: MAQC_ABI_L_CTR_1


title: MAQC_NCI_3Fail_B4


title: MAQC_ABI_L_CFY_5


title: MAQC_NCI_3Fail_A2


title: MAQC_EPP_3_D2

description: MAQC sample


title: MAQC_ABI_L_CFY_4


title: MAQC_ABI_L_CFY_3


title: MAQC_NCI_2Fail_D3


title: MAQC_NCI_3Fail_A1


title: MAQC_NCI_2Fail_D4


title: MAQC_ABI_L_CFY_6


title: MAQC_NCI_2Fail_D5


title: MAQC_EPP_3_D1

description: MAQC sample


title: MAQC_NCI_3Fail_A3


title: MAQC_EPP_3_C3

description: MAQC sample


title: MAQC_EPP_3_C5

description: MAQC sample


title: MAQC_ABI_L_CFY_2


title: MAQC_EPP_3_C4

description: MAQC sample


title: MAQC_NCI_2Fail_D2


title: MAQC_EPP_3_B5

description: MAQC sample


title: MAQC_EPP_3_C2

description: MAQC sample


title: MAQC_EPP_3_C1

description: MAQC sample


title: MAQC_ABI_L_CFY_1


title: MAQC_ABI_L_AA_6


title: MAQC_ABI_L_AA_3


title: MAQC_NCI_2Fail_D1


title: MAQC_ABI_L_AA_5


title: MAQC_ABI_L_AA_2


title: MAQC_EPP_3_B4

description: MAQC sample


title: MAQC_NCI_2Fail_C5


title: MAQC_NCI_2Fail_C4


title: MAQC_NCI_2Fail_C3


title: MAQC_ABI_L_AA_4


title: MAQC_NCI_2Fail_C1


title: MAQC_EPP_3_B2

description: MAQC sample


title: MAQC_ABI_K_CTR_5


title: MAQC_EPP_3_B3

description: MAQC sample


title: MAQC_ABI_L_AA_1


title: MAQC_ABI_K_CTR_6


title: MAQC_EPP_3_B1

description: MAQC sample


title: MAQC_EPP_3_A5

description: MAQC sample


title: MAQC_NCI_2Fail_B5


title: MAQC_NCI_2Fail_C2


title: MAQC_NCI_2Fail_B3


title: MAQC_ABI_K_CTR_4


title: MAQC_EPP_3_A4

description: MAQC sample


title: MAQC_ABI_K_CTR_3


title: MAQC_NCI_2Fail_B2


title: MAQC_EPP_3_A2

description: MAQC sample


title: MAQC_ABI_K_CTR_2


title: MAQC_NCI_2Fail_B1


title: MAQC_NCI_2Fail_B4


title: MAQC_EPP_3_A1

description: MAQC sample


title: MAQC_EPP_2_D5

description: MAQC sample


title: MAQC_EPP_3_A3

description: MAQC sample


title: MAQC_EPP_2_D4

description: MAQC sample


title: MAQC_ABI_K_CTR_1


title: MAQC_ABI_K_AA_6


title: MAQC_NCI_2Fail_A4


title: MAQC_NCI_2Fail_A5


title: MAQC_NCI_2Fail_A2


title: MAQC_NCI_2Fail_A3


title: MAQC_EPP_2_D2

description: MAQC sample


title: MAQC_ABI_K_AA_4


title: MAQC_ABI_K_AA_5


title: MAQC_NCI_2Fail_A1


title: MAQC_ABI_K_AA_3


title: MAQC_EPP_2_D1

description: MAQC sample


title: MAQC_GEH_L_RDL_6

data_processing: The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.  These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment.  The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background.   Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).

label_protocol: 1 ug of total RNA was processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Rat Whole Genome Bioarray (catalog #300031).


title: MAQC_ABI_K_AA_2


title: MAQC_ABI_K_AA_1


title: MAQC_NCI_2_D3


title: MAQC_EPP_2_C4

description: MAQC sample


title: MAQC_EPP_2_D3

description: MAQC sample


title: MAQC_EPP_2_C2

description: MAQC sample


title: MAQC_EPP_2_C5

description: MAQC sample


title: MAQC_EPP_2_C3

description: MAQC sample


title: MAQC_EPP_2_B5

description: MAQC sample


title: MAQC_NCI_2_D1


title: MAQC_GEH_L_RDL_2


title: MAQC_EPP_2_B4

description: MAQC sample


title: MAQC_GEH_L_RDL_4


title: MAQC_OPN_1_B4

description: Sample-pair convention: A (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5).  The data were provided by Operon.

scan_protocol: Slides were scanned using a GenePix 4000B scanner at 10 micron resolution.

data_processing: Images were processed and quantified using GenePix Pro. The data were filtered (or flagged) on the basis of signal levels and spot quality.  The raw data were submitted to MAQC and further normalized by using linear median-scaling and LOWESS.


title: rdr2, mixed stage inflorescence small RNA MPSS set

type: MPSS

city: Davis

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description:
Plants were grown in soil in growth chamber with 16
hours of light for 5 weeks. Immature inflorescence was harvested ~2 hours
after dark. Tissue included inflorescence meristem and early stage floral
buds (up to Stage 11/12). Total RNA was isolated using TRIzol reagent.

data_processing: To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The raw abundance count for each stepper was calculated as the average from all 2-step or from all 3-step runs for a given signature. The average total number of signatures sequenced in all 2-step or for all 3-step runs was also calculated within the library. The final stage to merge the data within the steppers was to calculate the normalized abundance for each stepper. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a

organism: Arabidopsis thaliana

source_name: Inflorescence tissue

tag: Ecotype


title: MAQC_GEH_L_RDL_5


title: MAQC_GEH_L_RDL_3


title: MAQC_EPP_2_B3

description: MAQC sample


title: MAQC_OPN_1_B5

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)


title: MAQC_GEH_L_RDL_1


title: MAQC_NCI_2_C2


title: MAQC_GEH_L_CTR_6


title: MAQC_NCI_2_D2


title: MAQC_GEH_L_CTR_5


title: MAQC_EPP_2_C1

description: MAQC sample


title: MAQC_NCI_2_C3


title: MAQC_GEH_L_CTR_4


title: MAQC_OPN_1_B3

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: MAQC_OPN_1_B2


title: MAQC_EPP_2_B2

description: MAQC sample


title: MAQC_NCI_2_B4


title: MAQC_NCI_2_C1


title: MAQC_NCI_2_B3


title: MAQC_GEH_L_CTR_3


title: MAQC_OPN_1_B1


title: MAQC_EPP_2_B1

description: MAQC sample


title: MAQC_NCI_2_B2


title: MAQC_EPP_2_A5

description: MAQC sample


title: MAQC_GEH_L_CTR_2


title: MAQC_EPP_2_A4

description: MAQC sample


title: MAQC_OPN_1_A5


title: MAQC_EPP_2_A2

description: MAQC sample


title: MAQC_NCI_2_B1


title: MAQC_GEH_L_CTR_1


title: MAQC_EPP_2_A3

description: MAQC sample


title: MAQC_NCI_2_A3


title: MAQC_NCI_2_A4


title: MAQC_GEH_L_CFY_5


title: MAQC_EPP_1_D5

description: MAQC sample


title: dcl234, mixed stage inflorescence small RNA 454 set

type: other

data_processing: To determine the abundance value for each signature in the library, we counded the number of occurence of each signature in the specific library to give us the Raw or the abundance value.

tag: dcl234 454 data


title: MAQC_GEH_L_CFY_2


title: MAQC_GEH_L_CFY_4


title: MAQC_OPN_1_A1


title: MAQC_OPN_1_A4


title: MAQC_NCI_2_A2


title: MAQC_GEH_L_CFY_6


title: MAQC_EPP_1_D4

description: MAQC sample


title: MAQC_EPP_1_D3

description: MAQC sample


title: MAQC_EPP_2_A1

description: MAQC sample


title: MAQC_EPP_1_D2

description: MAQC sample


title: MAQC_OPN_1_A3


title: MAQC_GEH_L_CFY_1


title: Col-0, mixed stage inflorescence small RNA 454 set

tag: Col-0 454 data


title: MAQC_NCI_1_D4

tag: MAQC sample


title: rdr2, mixed stage inflorescence small RNA 454 set

tag: rdr2 454 data


title: MAQC_NCI_2_A1


title: MAQC_OPN_1_A2


title: MAQC_NCI_1_D5


title: MAQC_GEH_L_AA_6


title: MAQC_GEH_L_AA_4


title: MAQC_NCI_1_D3


title: MAQC_EPP_1_C5

description: MAQC sample


title: MAQC_EPP_1_C4

description: MAQC sample


title: dcl1-7, mixed stage inflorescence small RNA 454 set

tag: dcl1-7 454 data


title: rdr6, mixed stage inflorescence small RNA 454 set

tag: rdr6 454 data


title: MAQC_GEH_L_AA_5


title: MAQC_NCI_1_D2


title: MAQC_NCI_1_D1


title: MAQC_EPP_1_D1

description: MAQC sample


title: MAQC_GEH_L_AA_3


title: MAQC_EPP_1_C3

description: MAQC sample


title: MAQC_GEH_L_AA_2


title: MAQC_EPP_1_C2

description: MAQC sample


title: MAQC_GEH_L_AA_1


title: MAQC_GEH_K_CTR_6


title: MAQC_NCI_1_C4


title: MAQC_GEH_K_CTR_5


title: MAQC_EPP_1_B5

description: MAQC sample


title: MAQC_EPP_1_C1

description: MAQC sample


title: MAQC_NCI_1_C3


title: MAQC_EPP_1_B3

description: MAQC sample


title: MAQC_GEH_K_CTR_4


title: MAQC_GEH_K_CTR_2


title: MAQC_NCI_1_B4


title: MAQC_NCI_1_C2


title: MAQC_EPP_1_B2

description: MAQC sample


title: MAQC_NCI_1_B2


title: MAQC_GEH_K_CTR_3


title: MAQC_NCI_1_C1


title: MAQC_NCI_1_B3


title: MAQC_GEH_K_CTR_1


title: MAQC_GEH_K_AA_5


title: MAQC_NCI_1_C5


title: MAQC_EPP_1_B1

description: MAQC sample


title: MAQC_NCI_1_B5


title: MAQC_EPP_1_A3

description: MAQC sample


title: MAQC_EPP_1_A4

description: MAQC sample


title: MAQC_EPP_1_A5

description: MAQC sample


title: MAQC_EPP_1_B4

description: MAQC sample


title: MAQC_GEH_K_AA_3


title: MAQC_EPP_1_A1

description: MAQC sample


title: MAQC_NCI_1_A3


title: MAQC_NCI_1_A4


title: MAQC_NCI_1_A2


title: MAQC_GEH_K_AA_6


title: MAQC_GEH_K_AA_4


title: MAQC_EPP_1_A2

description: MAQC sample


title: MAQC_GEH_K_AA_1


title: MAQC_NCI_1_A5