title: female patient 079 - Cy3

description: Analysis genomic DNA female patient 079

source_name: Genomic DNA isolated from blood female patient 079

source_name: A reference pool of genomic DNA isolated from 10 male blood donors


title: male patient 089 - Cy3

status: Public on Sep 16 2005

type: genomic

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Analysis genomic DNA male patient 089

hyb_protocol: Test and reference samples were mixed with 120 µg human Cot-1 DNA, co-precipitated and resuspended in 120 µl of a hybridization solution containing 50% formamide, 10% dextran sulfate, 2X SCC, 4% SDS and 10 µg/µl yeast tRNA. Overnight hybridization and post-hybridization washing procedures were performed using a GeneTac Hybridization Station

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4200AL fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: The log2 transformed test over reference ratio for each clone was normalized by subtracting its local mean log2 test over reference ratio obtained by a weighted median filter (Yin and Yang 1996). This filter averages the log ratios of autosomal clones weighted by a Gaussian with its mean at the spot to be normalized and a standard deviation of one physical millimetre on the array.

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA isolated from blood male patient 089

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy3-dUTP

tag: Genomic DNA isolated from blood

source_name: A reference pool of genomic DNA isolated from 10 female blood donors

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy5-dUTP


title: male patient 081 - Cy3

description: Analysis genomic DNA male patient 081

source_name: Genomic DNA isolated from blood male patient 081


title: male patient 030 - Cy5

description: Analysis genomic DNA male patient 030

source_name: Genomic DNA isolated from blood male patient 030


title: male patient 017 - Cy5

description: Analysis genomic DNA male patient 017

source_name: Genomic DNA isolated from blood male patient 017


title: male patient 122 - Cy5

description: Analysis genomic DNA male patient 122

source_name: Genomic DNA isolated from blood male patient 122


title: male patient 250 - Cy5

description: Analysis genomic DNA male patient 250

source_name: Genomic DNA isolated from blood male patient 250


title: male patient 027 - Cy5

description: Analysis genomic DNA male patient 027

source_name: Genomic DNA isolated from blood male patient 027


title: female patient 111 - Cy3

description: Analysis genomic DNA female patient 111

source_name: Genomic DNA isolated from blood female patient 111


title: male patient 030 - Cy3

description: Analysis genomic DNA male patient 030


title: female patient 093 - Cy3

description: Analysis genomic DNA female patient 093

source_name: Genomic DNA isolated from blood female patient 093


title: male patient 062 - Cy3

description: Analysis genomic DNA male patient 062

source_name: Genomic DNA isolated from blood male patient 062


title: female patient 075 - Cy3

description: Analysis genomic DNA female patient 075

source_name: Genomic DNA isolated from blood female patient 075


title: male patient 113 - Cy3

description: Analysis genomic DNA male patient 113

source_name: Genomic DNA isolated from blood male patient 113


title: father patient 023 - Cy3

description: Analysis genomic DNA father patient 023

source_name: Genomic DNA isolated from blood father patient 023


title: mother patient 166 - Cy3

description: Analysis genomic DNA mother patient 166

source_name: Genomic DNA isolated from blood mother patient 166


title: mother patient 023 - Cy3

description: Analysis genomic DNA mother patient 023

source_name: Genomic DNA isolated from blood mother patient 023


title: female patient 055 - Cy5

description: Analysis genomic DNA female patient 055

source_name: A reference pool of genomic DNA isolated from 10 male blood donors

source_name: Genomic DNA isolated from blood female patient 055


title: male patient 194 - Cy3

description: Analysis genomic DNA male patient 194

source_name: Genomic DNA isolated from blood male patient 194

source_name: A reference pool of genomic DNA isolated from 10 female blood donors


title: father patient 080 - Cy3

description: Analysis genomic DNA father patient 080

source_name: Genomic DNA isolated from blood father patient 080


title: father patient 123 - Cy3

description: Analysis genomic DNA father patient 123

source_name: Genomic DNA isolated from blood father patient 123


title: mother patient 080 - Cy3

description: Analysis genomic DNA mother patient 080

source_name: Genomic DNA isolated from blood mother patient 080


title: female patient 005 - Cy3

description: Analysis genomic DNA female patient 005

source_name: Genomic DNA isolated from blood female patient 005


title: mother patient 198 - Cy3

description: Analysis genomic DNA mother patient 198

source_name: Genomic DNA isolated from blood mother patient 198


title: female patient 166 - Cy5

description: Analysis genomic DNA female patient 166

source_name: Genomic DNA isolated from blood female patient 166


title: mother patient 313 - Cy3

description: Analysis genomic DNA mother patient 313

source_name: Genomic DNA isolated from blood mother patient 313


title: male patient 319 - Cy3

description: Analysis genomic DNA male patient 319

source_name: Genomic DNA isolated from blood male patient 319


title: male patient 094 - Cy5

description: Analysis genomic DNA male patient 094

source_name: Genomic DNA isolated from blood male patient 094


title: male patient 319 - Cy5

description: Analysis genomic DNA male patient 319


title: mother patient 055 - Cy3

description: Analysis genomic DNA mother patient 055

source_name: Genomic DNA isolated from blood mother patient 055


title: mother patient 058 - Cy3

description: Analysis genomic DNA mother patient 058

source_name: Genomic DNA isolated from blood mother patient 058


title: father patient 058 - Cy3

description: Analysis genomic DNA father patient 058

source_name: Genomic DNA isolated from blood father patient 058


title: father patient 198 - Cy3

description: Analysis genomic DNA father patient 198

source_name: Genomic DNA isolated from blood father patient 198


title: female patient 024 - Cy3

description: Analysis genomic DNA female patient 024

source_name: Genomic DNA isolated from blood female patient 024

source_name: A reference pool of genomic DNA isolated from 10 male blood donors


title: female patient 079 - Cy5

description: Analysis genomic DNA female patient 079

source_name: Genomic DNA isolated from blood female patient 079


title: father patient 055 - Cy3

description: Analysis genomic DNA father patient 055

source_name: Genomic DNA isolated from blood father patient 055


title: father patient 313 - Cy3

description: Analysis genomic DNA father patient 313

source_name: Genomic DNA isolated from blood father patient 313


title: male patient 070 - Cy3

description: Analysis genomic DNA male patient 070

source_name: Genomic DNA isolated from blood male patient 070

source_name: A reference pool of genomic DNA isolated from 10 female blood donors


title: female patient 313 - Cy3

description: Analysis genomic DNA female patient 313

source_name: Genomic DNA isolated from blood female patient 313


title: mother patient 113 - Cy3

description: Analysis genomic DNA mother patient 113

source_name: Genomic DNA isolated from blood mother patient 113


title: father patient 117 - Cy3

description: Analysis genomic DNA father patient 117

source_name: Genomic DNA isolated from blood father patient 117


title: mother patient 088 - Cy3

description: Analysis genomic DNA mother patient 088

source_name: Genomic DNA isolated from blood mother patient 088


title: mother patient 027 - Cy3

description: Analysis genomic DNA mother patient 027

source_name: Genomic DNA isolated from blood mother patient 027


title: female patient 024 - Cy5

description: Analysis genomic DNA female patient 024


title: male patient 013 - Cy3

description: Analysis genomic DNA male patient 013

source_name: Genomic DNA isolated from blood male patient 013


title: mother patient 017 - Cy3

description: Analysis genomic DNA mother patient 017

source_name: Genomic DNA isolated from blood mother patient 017


title: mother patient 013 - Cy3

description: Analysis genomic DNA mother patient 013

source_name: Genomic DNA isolated from blood mother patient 013


title: male patient 023 - Cy5

description: Analysis genomic DNA male patient 023

source_name: Genomic DNA isolated from blood male patient 023


title: male patient 008 - Cy5

description: Analysis genomic DNA male patient 008

source_name: Genomic DNA isolated from blood male patient 008


title: male patient 039 - Cy5

description: Analysis genomic DNA male patient 039

source_name: Genomic DNA isolated from blood male patient 039


title: father patient 166 - Cy3

description: Analysis genomic DNA father patient 166

source_name: Genomic DNA isolated from blood father patient 166

source_name: A reference pool of genomic DNA isolated from 10 male blood donors


title: father patient 113 - Cy3

description: Analysis genomic DNA father patient 113

source_name: Genomic DNA isolated from blood father patient 113


title: mother patient 076 - Cy3

description: Analysis genomic DNA mother patient 076

source_name: Genomic DNA isolated from blood mother patient 076


title: mother patient 063 - Cy3

description: Analysis genomic DNA mother patient 063

source_name: Genomic DNA isolated from blood mother patient 063


title: father patient 017 - Cy3

description: Analysis genomic DNA father patient 017

source_name: Genomic DNA isolated from blood father patient 017

source_name: A reference pool of genomic DNA isolated from 10 female blood donors


title: female patient 073 - Cy5

description: Analysis genomic DNA female patient 073

source_name: Genomic DNA isolated from blood female patient 073


title: female patient 300 - Cy5

description: Analysis genomic DNA female patient 300

source_name: Genomic DNA isolated from blood female patient 300


title: mother patient 123 - Cy3

description: Analysis genomic DNA mother patient 123

source_name: Genomic DNA isolated from blood mother patient 123


title: female patient 063 - Cy3

description: Analysis genomic DNA female patient 063

source_name: Genomic DNA isolated from blood female patient 063


title: male patient 051 - Cy5

description: Analysis genomic DNA male patient 051

source_name: Genomic DNA isolated from blood male patient 051


title: male patient 034 - Cy5

description: Analysis genomic DNA male patient 034

source_name: Genomic DNA isolated from blood male patient 034


title: father patient 063 - Cy3

description: Analysis genomic DNA father patient 063

source_name: Genomic DNA isolated from blood father patient 063


title: father patient 076 - Cy3

description: Analysis genomic DNA father patient 076

source_name: Genomic DNA isolated from blood father patient 076


title: father patient 051 - Cy3

description: Analysis genomic DNA father patient 051

source_name: Genomic DNA isolated from blood father patient 051


title: mother patient 051 - Cy3

description: Analysis genomic DNA mother patient 051

source_name: Genomic DNA isolated from blood mother patient 051


title: female patient 002 - Cy5

description: Analysis genomic DNA female patient 002

source_name: Genomic DNA isolated from blood female patient 002


title: male patient 046 - Cy5

description: Analysis genomic DNA male patient 046

source_name: Genomic DNA isolated from blood male patient 046


title: female patient 076 - Cy5

description: Analysis genomic DNA female patient 076

source_name: A reference pool of genomic DNA isolated from 10 male blood donors

source_name: Genomic DNA isolated from blood female patient 076


title: male patient 096 - Cy5

description: Analysis genomic DNA male patient 096

source_name: Genomic DNA isolated from blood male patient 096


title: male patient 031 - Cy5

description: Analysis genomic DNA male patient 031

source_name: Genomic DNA isolated from blood male patient 031


title: female patient 093 - Cy5

description: Analysis genomic DNA female patient 093

source_name: Genomic DNA isolated from blood female patient 093


title: Figure_5C_7

status: Public on Sep 13 2005

type: RNA

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

country: USA

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: primary rat microvascular endothelial cell RNA

data_processing: LogRatio of channels

molecule: total RNA

organism: Rattus norvegicus

source_name: Mat B III_100h Vehicle Pool

tag: Mat B III_100h Vehicle Pool

source_name: Mat B III_100h Compound A_7

tag: Mat B III_100h Compound A_7


title: Figure_5C_8

source_name: Mat B III_100h Compound A_8

tag: Mat B III_100h Compound A_8


title: male patient 013 - Cy5

description: Analysis genomic DNA male patient 013

source_name: A reference pool of genomic DNA isolated from 10 female blood donors

source_name: Genomic DNA isolated from blood male patient 013


title: female patient 088 - Cy5

description: Analysis genomic DNA female patient 088

source_name: Genomic DNA isolated from blood female patient 088


title: female patient 075 - Cy5

description: Analysis genomic DNA female patient 075

source_name: Genomic DNA isolated from blood female patient 075


title: female patient 166 - Cy3

description: Analysis genomic DNA female patient 166

source_name: Genomic DNA isolated from blood female patient 166


title: female patient 054 - Cy5

description: Analysis genomic DNA female patient 054

source_name: Genomic DNA isolated from blood female patient 054


title: female patient 038 - Cy5

description: Analysis genomic DNA female patient 038

source_name: Genomic DNA isolated from blood female patient 038


title: male patient 089 - Cy5

description: Analysis genomic DNA male patient 089

source_name: Genomic DNA isolated from blood male patient 089


title: male patient 032 - Cy5

description: Analysis genomic DNA male patient 032

source_name: Genomic DNA isolated from blood male patient 032


title: mother patient 117 - Cy3

description: Analysis genomic DNA mother patient 117

source_name: Genomic DNA isolated from blood mother patient 117

source_name: A reference pool of genomic DNA isolated from 10 male blood donors


title: Figure_5C_5

source_name: Mat B III_100h Compound A_5

tag: Mat B III_100h Compound A_5


title: male patient 058 - Cy5

description: Analysis genomic DNA male patient 058

source_name: Genomic DNA isolated from blood male patient 058


title: male patient 039 - Cy3

description: Analysis genomic DNA male patient 039

source_name: Genomic DNA isolated from blood male patient 039


title: female patient 313 - Cy5

description: Analysis genomic DNA female patient 313

source_name: Genomic DNA isolated from blood female patient 313


title: male patient 032 - Cy3

description: Analysis genomic DNA male patient 032


title: father patient 088 - Cy3

description: Analysis genomic DNA father patient 088

source_name: Genomic DNA isolated from blood father patient 088


title: Figure_5B_24

source_name: C6_24h B Vehicle Pool

tag: C6_24h B Vehicle Pool

source_name: C6_24h B Vehicle_24

tag: C6_24h B Vehicle_24


title: Figure_5B_28

source_name: C6_24h Compound B_28

tag: C6_24h Compound B_28


title: Figure_5B_29

source_name: C6_24h Compound B_29

tag: C6_24h Compound B_29


title: Figure_5B_23

source_name: C6_24h B Vehicle_23

tag: C6_24h B Vehicle_23


title: Figure_5C_3

source_name: Mat B III_100h Vehicle Pool

source_name: Mat B III_100h Vehicle_3

tag: Mat B III_100h Vehicle_3


title: Figure_5B_27

source_name: C6_24h Compound B_27

tag: C6_24h Compound B_27


title: Figure_5B_26

source_name: C6_24h Compound B_26

tag: C6_24h Compound B_26


title: Figure_5B_22

source_name: C6_24h B Vehicle_22

tag: C6_24h B Vehicle_22


title: Figure_5B_30

source_name: C6_24h Compound B_30

tag: C6_24h Compound B_30


title: Figure_5B_21

source_name: C6_24h B Vehicle_21

tag: C6_24h B Vehicle_21


title: Figure_5C_4

source_name: Mat B III_100h Vehicle_4

tag: Mat B III_100h Vehicle_4


title: Figure_5C_1

source_name: Mat B III_100h Vehicle_1

tag: Mat B III_100h Vehicle_1


title: Figure_5C_2

tag: Mat B III_100h Vehicle Pool

source_name: Mat B III_100h Vehicle_2

tag: Mat B III_100h Vehicle_2


title: Figure_5B_25

source_name: C6_24h B Vehicle_25

tag: C6_24h B Vehicle_25


title: Figure_5B_18

source_name: C6_48h B Vehicle Pool

tag: C6_48h B Vehicle Pool

source_name: C6_48h Compound B_18

tag: C6_48h Compound B_18


title: Figure_5B_20

source_name: C6_48h Compound B_20

tag: C6_48h Compound B_20


title: Figure_5B_15

source_name: C6_48h B Vehicle_15

tag: C6_48h B Vehicle_15


title: Figure_5B_19

source_name: C6_48h Compound B_19

tag: C6_48h Compound B_19


title: Figure_5B_17

source_name: C6_48h Compound B_17

tag: C6_48h Compound B_17


title: Figure_5B_12

source_name: C6_48h B Vehicle_12

tag: C6_48h B Vehicle_12


title: Figure_5B_13

source_name: C6_48h B Vehicle_13

tag: C6_48h B Vehicle_13


title: Figure_5B_16

source_name: C6_48h Compound B_16

tag: C6_48h Compound B_16


title: Figure_5B_14

source_name: C6_48h B Vehicle_14

tag: C6_48h B Vehicle_14


title: male patient 062 - Cy5

description: Analysis genomic DNA male patient 062

source_name: A reference pool of genomic DNA isolated from 10 female blood donors

tag: Genomic DNA isolated from blood

source_name: Genomic DNA isolated from blood male patient 062


title: Figure_5B_10

source_name: C6_72h B Vehicle Pool

tag: C6_72h B Vehicle Pool

source_name: C6_72h Compound B_10

tag: C6_72h Compound B_10


title: Figure_5B_1

source_name: C6_72h B Vehicle_1

tag: C6_72h B Vehicle_1


title: Figure_5B_9

source_name: C6_72h Compound B_9

tag: C6_72h Compound B_9


title: Figure_5B_11

source_name: C6_48h B Vehicle_11

tag: C6_48h B Vehicle_11


title: Figure_5B_3

source_name: C6_72h B Vehicle_3

tag: C6_72h B Vehicle_3


title: female patient 240 - Cy5

description: Analysis genomic DNA female patient 240

source_name: A reference pool of genomic DNA isolated from 10 male blood donors

source_name: Genomic DNA isolated from blood female patient 240


title: Figure_5B_7

source_name: C6_72h Compound B_7

tag: C6_72h Compound B_7


title: Figure_5B_6

source_name: C6_72h Compound B_6

tag: C6_72h Compound B_6


title: Figure_5B_8

source_name: C6_72h Compound B_8

tag: C6_72h Compound B_8


title: Figure_5A_27

source_name: C6_24h A Vehicle Pool

tag: C6_24h A Vehicle Pool

source_name: C6_24h Compound A_27

tag: C6_24h Compound A_27


title: Figure_5B_2

source_name: C6_72h B Vehicle_2

tag: C6_72h B Vehicle_2


title: Figure_5B_5

source_name: C6_72h B Vehicle_5

tag: C6_72h B Vehicle_5


title: Figure_5A_30

source_name: C6_24h Compound A_30

tag: C6_24h Compound A_30


title: Figure_5A_28

source_name: C6_24h Compound A_28

tag: C6_24h Compound A_28


title: Figure_5C_6

source_name: Mat B III_100h Vehicle Pool

tag: Mat B III_100h Vehicle Pool

source_name: Mat B III_100h Compound A_6

tag: Mat B III_100h Compound A_6


title: Figure_5A_29

source_name: C6_24h Compound A_29

tag: C6_24h Compound A_29


title: Figure_5A_25

source_name: C6_24h A Vehicle_25

tag: C6_24h A Vehicle_25


title: Figure_5A_21

source_name: C6_24h A Vehicle_21

tag: C6_24h A Vehicle_21


title: Figure_5A_19

source_name: C6_48h A Vehicle Pool

tag: C6_48h A Vehicle Pool

source_name: C6_48h Compound A_19

tag: C6_48h Compound A_19


title: Figure_5A_22

source_name: C6_24h A Vehicle_22

tag: C6_24h A Vehicle_22


title: Figure_5A_26

source_name: C6_24h Compound A_26

tag: C6_24h Compound A_26


title: Figure_5A_20

source_name: C6_48h Compound A_20

tag: C6_48h Compound A_20


title: Figure_5A_18

source_name: C6_48h Compound A_18

tag: C6_48h Compound A_18


title: Figure_5A_24

source_name: C6_24h A Vehicle Pool

tag: C6_24h A Vehicle Pool

source_name: C6_24h A Vehicle_24

tag: C6_24h A Vehicle_24


title: Figure_5A_16

source_name: C6_48h Compound A_16

tag: C6_48h Compound A_16


title: Figure_5A_13

source_name: C6_48h Vehicle_13

tag: C6_48h Vehicle_13


title: Figure_5B_4

source_name: C6_72h B Vehicle Pool

tag: C6_72h B Vehicle Pool

source_name: C6_72h B Vehicle_4

tag: C6_72h B Vehicle_4


title: Figure_5A_8

source_name: C6_72h A Vehicle Pool

tag: C6_72h A Vehicle Pool

source_name: C6_72h Compound A_8

tag: C6_72h Compound A_8


title: Figure_5A_14

source_name: C6_48h Vehicle_14

tag: C6_48h Vehicle_14


title: Figure_5A_6

source_name: C6_72h Compound A_6

tag: C6_72h Compound A_6


title: Figure_5A_3

source_name: C6_72h A Vehicle_3

tag: C6_72h A Vehicle_3


title: Figure_5A_2

source_name: C6_72h A Vehicle_2

tag: C6_72h A Vehicle_2


title: Figure_5A_15

source_name: C6_48h A Vehicle Pool

tag: C6_48h A Vehicle Pool

source_name: C6_48h Vehicle_15

tag: C6_48h Vehicle_15


title: Figure_2B_bFGF_4

source_name: RHMVEC_24h bFGF_4

tag: RHMVEC_24h bFGF_4


title: Figure_5A_9

source_name: C6_72h Compound A_9

tag: C6_72h Compound A_9


title: Figure_5A_10

source_name: C6_72h Compound A_10

tag: C6_72h Compound A_10


title: Figure_5A_5

source_name: C6_72h A Vehicle_5

tag: C6_72h A Vehicle_5


title: Figure_5A_4

source_name: C6_72h A Vehicle_4

tag: C6_72h A Vehicle_4


title: Figure_2B_bFGF_3

source_name: RHMVEC_24h bFGF_3

tag: RHMVEC_24h bFGF_3


title: Figure_2B_bFGF_2

source_name: RHMVEC_24h bFGF_2

tag: RHMVEC_24h bFGF_2


title: Figure_5A_23

source_name: C6_24h A Vehicle Pool

tag: C6_24h A Vehicle Pool

source_name: C6_24h A Vehicle_23

tag: C6_24h A Vehicle_23


title: Figure_2B_ENDOGRO_1

source_name: RHMVEC_24h ENDOGRO_1

tag: RHMVEC_24h ENDOGRO_1


title: Figure_5A_12

source_name: C6_48h Vehicle_12

tag: C6_48h Vehicle_12


title: Figure_2B_ENDOGRO_3

source_name: RHMVEC_24h ENDOGRO_3

tag: RHMVEC_24h ENDOGRO_3


title: Figure_5A_17

source_name: C6_48h Compound A_17

tag: C6_48h Compound A_17


title: Figure_3D_1

description: human dermal microvascular endothelial cell RNA

source_name: HDMVEC_bFGF+Compound B_Vehicle Control

tag: HDMVEC_bFGF+Compound B_Vehicle Control

source_name: HDMVEC_24h bFGF+Compound B

tag: HDMVEC_24h bFGF+Compound B


title: Figure_2B_bFGF_1

source_name: RHMVEC_24h bFGF_1

tag: RHMVEC_24h bFGF_1


title: Figure_2B_ENDOGRO_4

source_name: RHMVEC_24h ENDOGRO_4

tag: RHMVEC_24h ENDOGRO_4


title: Figure_2B_VEGF_4

source_name: RHMVEC_24h VEGF_4

tag: RHMVEC_24h VEGF_4


title: Figure_5A_11

source_name: C6_48h A Vehicle Pool

tag: C6_48h A Vehicle Pool

source_name: C6_48h A Vehicle_11

tag: C6_48h A Vehicle_11


title: Figure_2B_ENDOGRO_2

source_name: RHMVEC_24h ENDOGRO_2

tag: RHMVEC_24h ENDOGRO_2


title: Figure_5A_7

source_name: C6_72h A Vehicle Pool

tag: C6_72h A Vehicle Pool

source_name: C6_72h Compound A_7

tag: C6_72h Compound A_7


title: Figure_2B_VEGF_3

source_name: RHMVEC_24h VEGF_3

tag: RHMVEC_24h VEGF_3


title: Figure_2B_VEGF_1

source_name: RHMVEC_24h VEGF_1

tag: RHMVEC_24h VEGF_1


title: Figure_2B_VEGF_2

source_name: RHMVEC_24h VEGF_2

tag: RHMVEC_24h VEGF_2


title: Figure_2A_bFGF_4

source_name: HDMVEC_24h bFGF_4

tag: HDMVEC_24h bFGF_4


title: Figure_5A_1

source_name: C6_72h A Vehicle_1

tag: C6_72h A Vehicle_1


title: Figure_3B_1

source_name: HDMVEC_VEGF_Vehicle Control

tag: HDMVEC_VEGF_Vehicle Control

source_name: HDMVEC_24h VEGF+Compound B

tag: HDMVEC_24h VEGF+Compound B


title: Figure_2A_bFGF_3

source_name: HDMVEC_24h bFGF_3

tag: HDMVEC_24h bFGF_3


title: Figure_2A_bFGF_1

source_name: HDMVEC_24h bFGF_1

tag: HDMVEC_24h bFGF_1


title: Figure_2A_ENDOGRO_7

source_name: HDMVEC_24h ENDOGRO_7

tag: HDMVEC_24h ENDOGRO_7


title: Figure_2A_bFGF_2

source_name: HDMVEC_24h bFGF_2

tag: HDMVEC_24h bFGF_2


title: Figure_2A_ENDOGRO_2

source_name: HDMVEC_24h ENDOGRO_2

tag: HDMVEC_24h ENDOGRO_2


title: Figure_2A_ENDOGRO_5

source_name: HDMVEC_24h ENDOGRO_5

tag: HDMVEC_24h ENDOGRO_5


title: Figure_2A_VEGF_6

source_name: HDMVEC_24h VEGF_6

tag: HDMVEC_24h VEGF_6


title: Figure_2A_ENDOGRO_6

source_name: HDMVEC_24h ENDOGRO_6

tag: HDMVEC_24h ENDOGRO_6


title: Figure_2A_VEGF_4

source_name: HDMVEC_24h VEGF_4

tag: HDMVEC_24h VEGF_4


title: Figure_2A_ENDOGRO_3

source_name: HDMVEC_24h ENDOGRO_3

tag: HDMVEC_24h ENDOGRO_3


title: Figure_2A_ENDOGRO_4

source_name: HDMVEC_24h ENDOGRO_4

tag: HDMVEC_24h ENDOGRO_4


title: Figure_2A_VEGF_5

source_name: HDMVEC_24h VEGF_5

tag: HDMVEC_24h VEGF_5


title: Figure_2A_VEGF_7

source_name: HDMVEC_24h VEGF_7

tag: HDMVEC_24h VEGF_7


title: Figure_2A_ENDOGRO_1

source_name: HDMVEC_24h ENDOGRO_1

tag: HDMVEC_24h ENDOGRO_1


title: Figure_2A_VEGF_1

source_name: HDMVEC_24h VEGF_1

tag: HDMVEC_24h VEGF_1


title: HCC_rep3_Cy5

status: Public on Sep 06 2005

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description: Hepatocellular carcinoma - rep3 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029137

scan_protocol: Scanned images (5 um) were acquired with ScanArray Express (PerkinElmer, Boston, MA) at an excitation of 543 nm for Cy3 and 633 nm for Cy5 and at 90% power. The photomultiplier tube (PMT) settings for each fluor were set based on intensity of spiked internal alien controls to normalize among all slides in the experiment. Image files were quantified in QuantArray (PerkinElmer) and raw median signal and background values were exported to BioArray Software Environment (BASE; Saal et al. 2002) for analysis.

data_processing: Raw median signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 2-fold consistently in all features from biological replicates (n=3 per treatment) and had a p-value <0.05 by Welch’s t-test.

organism: Oncorhynchus mykiss

source_name: Hepatocellular carcinoma

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 13 months, trout were sampled for tumors. After marking the size and location of all surface tumors, a portion of each tumor and 100-200 mg of adjacent liver tissue were collected, placed separately in TRIzol Reagent (Invitogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis. Only HCC tumors (determined by histopathology) were used for microarray analysis.

tag: Strain

value: Mt. Shasta; Age:13 months; Tissue:tumor; Initiation:aflatoxin B1

source_name: Reference

treatment_protocol: Trout embryos were sham initiated with aqueous 0.01% ethanol for 30 min. At 13 months, trout were sampled for tumors. Sham-initiated trout had no tumors. Reference sample RNA was isolated from individual livers of ten sham-initiated trout and aliquots were pooled in equal amounts (ug).

value: Mt. Shasta; Age:13 months; Tissue:liver; Initiation:sham


title: HCC_rep2_Cy3

description: Hepatocellular carcinoma - rep2 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P63.13044748


title: HCC_rep2_Cy5

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029139

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: Figure_2A_VEGF_3

source_name: HDMVEC_24h VEGF_3

tag: HDMVEC_24h VEGF_3


title: Figure_2A_VEGF_2

source_name: HDMVEC_24h VEGF_2

tag: HDMVEC_24h VEGF_2


title: Control_Cy5

description: Control liver - Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P63.13044746

source_name: Control liver

treatment_protocol: Trout embryos were sham initiated with aqueous 0.01% ethanol for 30 min. At 13 months, trout were sampled for tumors. Sham-initiated trout had no tumors. Control sample RNA was isolated from individual livers of ten sham-initiated trout and aliquots were pooled in equal amounts (ug).


title: HCC_rep1_Cy5

description: Hepatocellular carcinoma - rep1 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029220


title: Control_Cy3

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P63.13044762


title: HCC_rep1_Cy3

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029221


title: NAL_rep2_Cy5

description: Non-cancerous adjacent liver - rep2 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029140

source_name: Non-cancerous adjacent liver

value: Mt. Shasta; Age:13 months; Tissue:liver (adjacent tumor); Initiation:aflatoxin B1


title: NAL_rep3_Cy5

description: Non-cancerous adjacent liver - rep3 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029138


title: NAL_rep1_Cy3

description: Non-cancerous adjacent liver - rep1 Hybridized with reference sample. Packard ScanArray Model 4000 QuantArray Genisphere labeling and hybridization kit. Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029223


title: PHYAPHYBDARK1 ATH1

status: Public on Sep 04 2005

city: Capital Federal

first: Maria

middle: Agustina

last: Mazzella

state: Buenos AIres

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI

description: For more information see Mazzella et al, 2005. Plant Cell Vol 17 (september)

hyb_protocol: Affymetrix instruction. Hybridization to ATH1 Affymetrix Arabidopsis Gene Chips

scan_protocol: Affymetrix instructions

data_processing: the scaling tab of the Affymetrix microarray suite in the mode “all probe sets” was used to standardize the trimmed mean signal of each array to the “target signal” according to manufacturer instructions.

label: Affymetrix instructions

organism: Arabidopsis thaliana

source_name: Dark grown seedlings, Ecotype: columbia. Alleles phyA-211 and phyB-9

label_protocol: Affymetrix instructions

growth_protocol: seeds were sown on 0.8% (w/v) agar

extract_protocol: Rneasy plant mini kit (Qiagen)

treatment_protocol: phyAphyB double mutant seeds incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: phyA phyB double mutants seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: PHYADARK2 ATH1

source_name: Dark grown seedlings, Ecotype: columbia. Allele phyA-211

treatment_protocol: phyA-211 mutant seeds incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: phyA-211 mutants seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: WTDARK2col ATH1

source_name: Dark grown seedlings, Ecotype: Columbia

treatment_protocol: WT seeds incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: WT seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: NAL_rep1_Cy5

description:
Non-cancerous adjacent liver - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping.  Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents.  Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene).  Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label.  cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates.  cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control.  Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation.  The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH).  Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation.  Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays.  Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P59.13029141

scan_protocol: Scanned images (5 um) were acquired with ScanArray Express (PerkinElmer, Boston, MA) at an excitation of 543 nm for Cy3 and 633 nm for Cy5 and at 90% power.  The photomultiplier tube (PMT) settings for each fluor were set based on intensity of spiked internal alien controls to normalize among all slides in the experiment.  Image files were quantified in QuantArray (PerkinElmer) and raw median signal and background values were exported to BioArray Software Environment (BASE; Saal et al. 2002) for analysis.

data_processing: Raw median signal and background values are included.  For experiment, data were background subtracted and normalized by LOWESS.  Stringent criteria were used to filter for genes that were regulated at least 2-fold consistently in all features from biological replicates (n=3 per treatment) and had a p-value <0.05 by Welch’s t-test.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min.  At 13 months, trout were sampled for tumors.  After marking the size and location of all surface tumors, a portion of each tumor and 100-200 mg of adjacent liver tissue were collected, placed separately in TRIzol Reagent (Invitogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis.  Only HCC tumors (determined by histopathology) were used for microarray analysis.

value: Mt. Shasta

tag: Age

value: 13 months

tag: Tissue

value: liver (adjacent tumor)

tag: Initiation

value: aflatoxin B1

treatment_protocol: Trout embryos were sham initiated with aqueous 0.01% ethanol for 30 min.  At 13 months, trout were sampled for tumors.  Sham-initiated trout had no tumors.  Reference sample RNA was isolated from individual livers of ten sham-initiated trout and aliquots were pooled in equal amounts (ug).

value: liver

value: sham


title: PHYAPHYBDARK2 ATH1


title: PHYADARK ATH1


title: PHYBDARK1 ATH1

source_name: Dark grown seedlings, Ecotype: columbia. Allele phyB-9

treatment_protocol: phyb9 mutant seeds incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: phy9 mutants seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: PHYBDARK2 ATH1

treatment_protocol: phybB9 mutant seeds incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: phyB-9 mutants seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: WTdarkcol1 ATH1


title: phyAphyBcry1cry2D 8K

hyb_protocol: Affymetrix instruction. Hybridization to 8  K Affymetrix Arabidopsis Gene Chips

source_name: phyAphyBcry1cry2 quadruple phortoreceptor mutant dark grown seedlings. Ecotype Lansberg erecta

extract_protocol: Rneasy plant mini kit (qiagen)

treatment_protocol: phyAphyBcry1cry2 seeds were incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: The alleles used for the generation of the quadruple  mutant were phyA-201 ,phyB-5, cry1 (hy4)  and cry2 (fha)from Ler background. phyAphyBcry1cry2 seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: PHYAPHYBDARK 2 ATH1

source_name: Dark grown seedlings, Ecotype: Columbia, Alleles: phyA-211, phyB-9

tag: phyAphyB double mutants seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 1 h of white light at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: WTD 8k

source_name: Dark grown seedlings, Ecotype: Landsberg erecta

treatment_protocol: WT seeds  incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: WT seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: phyAphyBD 8k

source_name: Dark grown seedlings phyAphyB double mutants, Ecotype, landsberg erecta

treatment_protocol: phyAphyB double mutants seeds  incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: The alleles used for the generation of the double mutant were  phyA-201 and  phyB-5 from Ler background.phyA phyB seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: cry1cry2D 8K

source_name: cry1 cry2 double mutants dark grown seedlings, Ecotype: Landsberg erecta

treatment_protocol: cry1cry2 seeds were incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested

tag: The alleles used for the generation of the double mutant were cry1 (hy4) and cry2 (fha) from Ler background.Cry1 cry2 double photoreceptor mutant seeds were sown on 0.8% (w/v) agar in clear plastic boxes and incubated at 6 degrees for 5 d. Chilled seeds were exposed to 8 h of R at 22 degrees to induce homogeneous seed germination. After 3 d in full D at 22 degrees seedlings were harvested in liquid nitrogen and total RNA was extracted by using the RNEASY Plant mini kit (Qiagen).


title: NAL_rep2_Cy3

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier. Slide# Omy004.P63.13044761


title: phyAphyBdark1 ATH1


title: 050204_PoolAvsB_1

status: Public on Sep 02 2005

city: Frederick

first: Brian

middle: D.

last: Peyser

state: MD

address: 1425 Porter St

department: Bacteriology

institute: USAMRIID

description: Two pools were created (“A” and “B”) such that 94 heterozygous yeast knockout strains were differentially represented between the two. The 94 differentially represented strains were diluted 1:1, 1:8, or 1:64 (High, Medium, or Low representation), then added to Pool B. Each strain was then diluted again from 1:2^0.33 to 1:2^5 and added to pool A. One set of strains from each representation group was not added to pool A (dilution 1:2^inf). All other strains are at equivalent representation between the two pools. See Peyser BD, et al. Nucleic Acids Res (2005) for details of the spike-in design.

hyb_protocol: Microarray hybridization: Hybridization buffer (Triton X-100 0.5%, NaCl 1 M, Tris Cl 100 mM, pH 7.5) (Ooi SL, Shoemaker DD, Boeke JD (2001) Science 294: 2552-6) was supplemented with 1 mM DTT just before use. Slides were incubated in 5 ml volumes of hybridization buffer in six-compartment polypropylene boxes (Alpha Rho Inc., Fitchberg MA, USA) and rocked in a 42C hybridization oven (Robbins 400, Robbins Scientific). After a 30 min incubation in buffer, with oligonucleotides U1c, U2c, D1c, and D2c added to 0.25 µM each to block spurious binding sites, the solution was replaced with buffer at 42C containing a 1:500 dilution of each TAG PCR product. Incubations were at 42C for 16 hrs in the dark. Microarray washing: Slides were removed to a Coplin staining jar that was filled with wash buffer at 23C. The buffer consisted of 6x SSPE + 0.5% Triton X-100 (Ooi SL et al. 2001) supplemented with 1 mM DTT as with the hybridization buffer. After 10 cycles of slow withdrawal and reimmersion over 10 min, slides were treated the same way in a second Coplin jar identical to the first except for the use of 1x SSPE. Slides were then ready for scanning. Also see Yuan DS, et al. Nucleic Acids Res (2005).

scan_protocol: Microarray scanning: Images were acquired at 10 µm resolution using a GenePix 4000B scanner (Axon Instruments) and analyzed using GenePix Pro 5.1 software (Axon Instruments), with laser power and photomultiplier tube voltages adjusted manually based on preliminary scans. Also see Yuan DS, et al. Nucleic Acids Res (2005).

data_processing: VALUE = RAW Ch1/Ch2. See Peyser BD, et al. Nucleic Acids Res (2005) for analysis and summarized values for each knockout strain.

organism: Saccharomyces cerevisiae

source_name: Pool A

label_protocol: TAG PCR: Primers were purified by HPLC. Reaction mixes (20 µl/tube) for UPTAG or DNTAG PCR contained 10 µl of 2x ExTaq Premix (Takara), 0.5 µM primer 1 (U1 or D1), 5.0 µM primer 2 (U2c or D2c, 5'-labeled with either Cy3 or Cy5 dye), and ~50 ng genomic DNA. PCR cycling parameters were 94C 3 min; 95C 10 sec, 50C 20 sec, 72C 20 sec for 50 cycles; 4C. After PCR, blocking oligonucleotides (U1 and U2.3, or D1 and D2.3) were added to 10 µM, without further denaturation. EDTA 10 mM was also added as a precaution against residual polymerase-associated exonuclease activity. Also see Yuan DS, et al. Nucleic Acids Res (2005).

growth_protocol: Knockout strains were grown on YPD agar, then pooled. Aliquots of pooled yeast were frozen in glycerol at -80C.

extract_protocol: Preparation of genomic DNA: Genomic DNA was prepared using the Masterpure Yeast DNA kit from Epicentre (Madison, WI) according to manufacturer’s instructions.

treatment_protocol: Spike-in dilutions.  See Peyser BD, et al. Nucleic Acids Res (2005) for details of the spike-in design.

tag: Saccharomyces cerevisiae heterozygous knockout strains

source_name: Pool B


title: 050614_SelfSelf_4


title: 050204_SelfSelf_2


title: vastus lateralis biopsy, 67 year-old healthy sedentary male (#74B)

status: Public on Sep 01 2005

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

description:
Needle biopsies were obtained from the vastus lateralis muscle of 6 healthy, sedentary, 67±2.5 year-old males before and after 3 months of training.  RNA was extracted using Trizol. Targets were produced using standard Affymetrix procedures from about 4ug of total RNA.
Keywords = microarray, exercise, fitness, elderly, training effect

source_name: vastus lateralis biopsy


title: vastus lateralis biopsy, 68 year-old healthy sedentary male (#58)


title: vastus lateralis biopsy, 76 year-old healthy sedentary male (#47)


title: 050204_SelfSelf_3

description:
Two pools were created (“A” and “B”) such that 94 heterozygous yeast knockout strains were differentially represented between the two. The 94 differentially represented strains were diluted 1:1, 1:8, or 1:64 (High, Medium, or Low representation), then added to Pool B. Each strain was then diluted again from 1:2^0.33 to 1:2^5 and added to pool A. One set of strains from each representation group was not added to pool A (dilution 1:2^inf). All other strains are at equivalent representation between the two pools.

See Peyser BD, et al. Nucleic Acids Res (2005) for details of the spike-in design.

hyb_protocol: Microarray hybridization: Hybridization buffer (Triton X-100 0.5%, NaCl 1 M, Tris Cl 100 mM, pH 7.5) (Ooi SL, Shoemaker DD, Boeke JD (2001) Science 294: 2552-6) was supplemented with 1 mM DTT just before use. Slides were incubated in 5 ml volumes of hybridization buffer in six-compartment polypropylene boxes (Alpha Rho Inc., Fitchberg MA, USA) and rocked in a 42C hybridization oven (Robbins 400, Robbins Scientific). After a 30 min incubation in buffer, with oligonucleotides U1c, U2c, D1c, and D2c added to 0.25 µM each to block spurious binding sites, the solution was replaced with buffer at 42C containing a 1:500 dilution of each TAG PCR product. Incubations were at 42C for 16 hrs in the dark.  Microarray washing: Slides were removed to a Coplin staining jar that was filled with wash buffer at 23C. The buffer consisted of 6x SSPE + 0.5% Triton X-100 (Ooi SL et al. 2001) supplemented with 1 mM DTT as with the hybridization buffer. After 10 cycles of slow withdrawal and reimmersion over 10 min, slides were treated the same way in a second Coplin jar identical to the first except for the use of 1x SSPE. Slides were then ready for scanning.  Also see Yuan DS, et al. Nucleic Acids Res (2005).

scan_protocol: Microarray scanning: Images were acquired at 10 µm resolution using a GenePix 4000B scanner (Axon Instruments) and analyzed using GenePix Pro 5.1 software (Axon Instruments), with laser power and photomultiplier tube voltages adjusted manually based on preliminary scans.  Also see Yuan DS, et al. Nucleic Acids Res (2005).

label_protocol:
TAG PCR: Primers were purified by HPLC. Reaction mixes (20 µl/tube) for UPTAG or DNTAG PCR contained 10 µl of 2x ExTaq Premix (Takara), 0.5 µM primer 1 (U1 or D1), 5.0 µM primer 2 (U2c or D2c, 5'-labeled with either Cy3 or Cy5 dye), and ~50 ng genomic DNA. PCR cycling parameters were 94C 3 min; 95C 10 sec, 50C 20 sec, 72C 20 sec for 50 cycles; 4C. After PCR, blocking oligonucleotides (U1 and U2.3, or D1 and D2.3) were added to 10 µM, without further denaturation. EDTA 10 mM was also added as a precaution against residual polymerase-associated exonuclease activity.

Also see Yuan DS, et al. Nucleic Acids Res (2005).


title: vastus lateralis biopsy, 66 year-old healthy sedentary male (#68)

description:
Needle biopsies were obtained from the vastus lateralis muscle of 6 healthy, sedentary, 67±2.5 year-old males before and after 3 months of training.  RNA was extracted using Trizol. Targets were produced using standard Affymetrix procedures from about 4ug of total RNA.
Keywords = microarray, exercise, fitness, elderly, training effect"


title: 050204_SelfSelf_1


title: vastus lateralis biopsy, 67 year-old healthy trained male (#90)


title: Figure_3C_1

source_name: HDMVEC_bFGF_Vehicle Control

tag: HDMVEC_bFGF_Vehicle Control

source_name: HDMVEC_24h bFGF

tag: HDMVEC_24h bFGF


title: stem_mutant35S32-6_rep2

city: Davis

first: Andrew

last: Groover

address: 1100 West Chiles Rd

department: Institute of Forest Genetics

institute: USDA Forest Service

description: While clones 35S-32-6 and 35S-32-3-1 carry the same T-DNA construct, they represent independent transformation events.  Each clone was assayed by two independent RNA preps from pooled plants, which are represented here as replications.

hyb_protocol: Hybridization by NimbleGen company.

scan_protocol: Scan by NimbleGen company.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA) expressed as log2.  For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

label: biotin

organism: Populus tremula x Populus alba

source_name: 35S32-6 clone, overexpressing Populus ARK1 gene

label_protocol: Labeling by NimbleGen company.

growth_protocol: Plants grown in standard tissue culture conditions for Populus alba X P. tremula clone INRA 717 described by Han et al 2000.

extract_protocol: Ground in liquid N, bead beat in Qiagen buffer RLT, then isolated by Qiagen RNAeasy.

tag: Populus alba X P. tremula clone INRA 717, tranformed with T-DNA carrying cauliflower mosaic virus promoter 35S driving expression of the Populus ARK1 KNOX class homeodomain protein, ortholog of SHOOTMERISTEMLESS from Arabidopsis. Entire, defoliated stems sampled.


title: vastus lateralis biopsy, 56 year-old healthy sedentary male (#3)


title: stem_mutant35S32-6_rep1

tag: Populus alba X P. tremula clone INRA 717, tranformed with T-DNA carrying cauliflower mosaic virus promoter 35S driving expression of the Populus ARK1 KNOX class homeodomain protein, ortholog of SHOOTMERISTEMLESS from Arabidopsis.  Entire, defoliated stems sampled.


title: vastus lateralis biopsy, 72 year-old healthy sedentary male (#23)


title: WTD ATH1


title: WTDARK2 ATH1


title: stem_WildType_C_rep1

description: Wild type control plants, grown in identical conditions as transformed experimental clones.  Wild type clones A and C are the same genotype, simply different cultures.  Each clone was assayed by two independent RNA preps from pooled plants.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA) expressed as log2. For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

source_name: Wild Type Clone C

tag: Populus alba X P. tremula clone INRA 717.  Wild type control, not transformed.


title: stem_WildType_A_rep2

source_name: Wild Type Clone A

tag: Populus alba X P. tremula clone INRA 717. Wild type control, not transformed.


title: stem_mutant35S32-3-1_rep2

description: While clones 35S-32-6 and 35S-32-3-1 carry the same T-DNA construct, they represent independent transformation events.

source_name: 35S32-3-1 clone, overexpressing Populus ARK1 gene


title: stem_WildType_A_rep1


title: stem_mutant35S32-3-1_rep1


title: stem_WildType_C_rep2


title: vastus lateralis biopsy, 66 year-old healthy trained male (#85)


title: vastus lateralis biopsy, 68 year-old healthy trained male (#80)


title: vastus lateralis biopsy, 76 year-old healthy trained male (#71)


title: LPS 8h 2

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via Vela 6

department: Experimental Oncology

country: Switzerland

institute: Institute of Southern Switzerland

description:
This sample is also known as IOSI05-015 and IRBD4
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 8h

source_name: Monocyte derived dendritic cells


title: vastus lateralis biopsy, 56 year-old healthy trained male (#56)


title: vastus lateralis biopsy, 72 year-old healthy trained male (#52)


title: LPS+R848 2h 3

description:
This sample is also known as IOSI05-021 and IRBLR93
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) and 2.5?g/ml R848 (GLSynthesis) for 2h


title: untreated 2

description:
This sample is also known as IOSI05-018 and IRBD7
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were harvested and RNA extracted


title: untreated 1

description:
This sample is also known as IOSI05-011and IRBG7
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were harvested and RNA extracted


title: LPS 2h 2

description:
This sample is also known as IOSI05-012 and IRBD1
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 2h


title: Donor 5 vg 4 hr

status: Public on Aug 25 2005

city: Bethesda

first: Jim

last: Boonyaratanakornkit

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

description:
Peripheral blood leukocytes of three human donors were isolated from blood bank buffy-coat preparations by Ficoll-Hypaque density gradient centrifugation, and T-cells were purified with high affinity negative selection human CD3+ T-cell enrichment columns.  The cells were resuspended in RPMI-1640 with 10% FCS with approximately 3-8 millions cells/mL at room temperature overnight.  T-cells were then either unactivated (1g 0 hr), activated (1g 4 hr) with a final concentration of 5 mg/mL Con A + 4 mg/mL anti-CD28 antibody and incubated for 4 hours at 37°C, or loaded onto a RPM rotating at 60°/s.  T-cells loaded on the RPM were cultured for 2 hours prior to collection or activation to allow equilibration of cells to the new environment.  After incubation, 1 mL of 4 M guanidinium isothiocyanate in 750 mM sodium citrate buffer, pH 7, with N-lauroylsarcosine and ß-mercaptoethanol was added to lyse cells and stabilize RNA.  Lysates were frozen at -80°C.
Lot batch = 2001996

source_name: T-cells, peripheral blood


title: R848 8h 2

description:
This sample is also known as IOSI05-016 and IRBD5
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 2.5?g/ml R848 (GLSynthesis) for 8h


title: LPS+R848 8h 2

description:
This sample is also known as IOSI05-017 and IRBD6
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) and 2.5?g/ml R848 (GLSynthesis) for 8 h


title: LPS 2h 3

description:
This sample is also known as IOSI05-019 and IRBL91
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 2h


title: R848 8h 3

description:
This sample is also known as IOSI05-023 and IRBR95
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 2.5?g/ml R848 (GLSynthesis) for 8h


title: LPS+R848 8h 3

description:
This sample is also known as IOSI05-024 and IRBLR96
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) and 2.5?g/ml R848 (GLSynthesis) for 8 h


title: R848 2h 3

description:
This sample is also known as IOSI05-020 and IRBR92
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated  with 2.5?g/ml R848 (GLSynthesis) for 2h


title: LPS+R848 2h 2

description:
This sample is also known as IOSI05-014 and IRBD3
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) and 2.5?g/ml R848 (GLSynthesis) for 2h


title: LPS 2h 1

description:
This sample is also known as IOSI05-005 and IRBG1
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 2h


title: LPS+R848 8h 1

description:
This sample is also known as IOSI05-010 and IRBG6
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) and 2.5?g/ml R848 (GLSynthesis) for 8 h


title: LPS 8h 1

description:
This sample is also known as IOSI05-008 and IRBG4
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 8h


title: R848 2h 2

description:
This sample is also known as IOSI05-013 and IRBD2
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated  with 2.5?g/ml R848 (GLSynthesis) for 2h


title: R848 8h 1

description:
This sample is also known as IOSI05-009 and IRBG5
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 2.5?g/ml R848 (GLSynthesis) for 8h


title: Donor 5 vg 0 hr


title: LPS 8h 3

description:
This sample is also known as IOSI05-022 and IRBL94
Sample_characteristics: Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)
Sample_data_processing: Affymetrix GCOS 1.2
Sample_extract_protocol: cells were harvested and lysed using Trizol (Invitrogen). An additional RNA clean-up step using the RNAeasy purification kit (Qiagen).
Sample_growth_protocol_ch: cultured for five days in 10cm tissue culture dishes in RPMI with 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 10 ng/ml. On day 5 MoDCs were harvested and aliquoted into 6 well plate at 0.5 106 cells/ml, 1.5 106 cells/well.
Sample_hyb_protocol: standard Affymetrix procedures, washes performed using Fluidics Station 400
Sample_label: biotin
Sample_label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA
Sample_molecule: total RNA
Sample_scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000
Sample_treatment_protocol_ch: after 2h of incubation at 37°C cells were stimulated with 10ng/ml E. coli  0111:B4 LPS Ultra-Pure (Invivogen) for 8h