title: AML 47

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=740640LaserPower=4.034.17
Lot batch = shcz094

source_name: AML 47


title: AML 81

status: Public on Apr 15 2004

type: RNA

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

country: USA

institute: Stanford University

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710630LaserPower=3.44.54
Lot batch = shco045

molecule: total RNA

organism: Homo sapiens

source_name: CRH

source_name: AML 81


title: AML 20

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=3.914.46
Lot batch = shdj084

source_name: AML 20


title: AML 105

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710640LaserPower=4.014.07
Lot batch = shcz089

source_name: AML 105


title: AML 110

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710650LaserPower=4.023.13
Lot batch = shcz092

source_name: AML 110


title: AML 119

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.914.52
Lot batch = shdj083

source_name: AML 119


title: AML 38

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670600LaserPower=3.324.45
Lot batch = shco039

source_name: AML 38


title: AML 60

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=3.965.37
Lot batch = shcz112

source_name: AML 60


title: AML 48

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690620LaserPower=3.324.48
Lot batch = shco038

source_name: AML 48


title: AML 57

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=630670LaserPower=3.994.47
Lot batch = shcz227

source_name: AML 57


title: AML 102

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=3.934.73
Lot batch = shdj080

source_name: AML 102


title: AML 34

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=3.993.83
Lot batch = shcz085

source_name: AML 34


title: AML 26

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660620LaserPower=3.324.45
Lot batch = shco040

source_name: AML 26


title: AML 93

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=3.924.73
Lot batch = shdj082

source_name: AML 93


title: AML 95

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.994.58
Lot batch = shcz088

source_name: AML 95


title: AML 112

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=730640LaserPower=3.984.48
Lot batch = shcz228

source_name: AML 112


title: AML 21

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=4.214.3
Lot batch = shcz225

source_name: AML 21


title: AML 100

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680640LaserPower=3.413.81
Lot batch = shco044

source_name: CRH

source_name: AML 100


title: AML 68

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=760650LaserPower=3.873.83
Lot batch = shdj079

source_name: AML 68


title: AML 107

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710640LaserPower=3.974.2
Lot batch = shcz111

source_name: AML 107


title: AML 4

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=770630LaserPower=3.964.61
Lot batch = shcz087

source_name: AML 4


title: AML 82

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670640LaserPower=44.48
Lot batch = shco033

source_name: AML 82


title: AML 40

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680640LaserPower=3.994.48
Lot batch = shco032

source_name: AML 40


title: AML 83

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=740620LaserPower=4.255.01
Lot batch = shcz222

source_name: AML 83


title: AML 12

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=710640LaserPower=4.214.43
Lot batch = shcz224

source_name: AML 12


title: AML 88

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=4.014.45
Lot batch = shcz226

source_name: AML 88


title: AML 64

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.873.71
Lot batch = shdj077

source_name: AML 64


title: AML 103

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690630LaserPower=3.974.46
Lot batch = shco030

source_name: AML 103


title: AML 32

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=3.863.16
Lot batch = shdj076

source_name: AML 32


title: AML 99

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=4.254.82
Lot batch = shcz223

source_name: AML 99


title: AML 10

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690640LaserPower=3.994.63
Lot batch = shcz084

source_name: AML 10


title: AML 29

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650640LaserPower=4.265.31
Lot batch = shcz221

source_name: AML 29


title: AML 91

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=720650LaserPower=3.874.2
Lot batch = shdj074

source_name: AML 91


title: AML 24

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=750640LaserPower=3.873.57
Lot batch = shdj078

source_name: CRH

source_name: AML 24


title: AML 61

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=3.894.1
Lot batch = shdj073

source_name: AML 61


title: AML 77

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=700640LaserPower=3.974.42
Lot batch = shco029

source_name: AML 77


title: AML 25

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.975.01
Lot batch = shcz110

source_name: AML 25


title: AML 65

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670640LaserPower=3.994.46
Lot batch = shco031

source_name: AML 65


title: AML 15

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=3.94.02
Lot batch = shdj072

source_name: AML 15


title: AML 113

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=640650LaserPower=4.094.63
Lot batch = shcz078

source_name: AML 113


title: AML 69

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680630LaserPower=4.014.72
Lot batch = shcz219

source_name: AML 69


title: AML 1

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=44.7
Lot batch = shcz083

source_name: AML 1


title: AML 56

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660630LaserPower=3.954.69
Lot batch = shcz213

source_name: AML 56


title: AML 19

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.144.43
Lot batch = shco024

source_name: AML 19


title: AML 74

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=3.994.64
Lot batch = shcz080

source_name: AML 74


title: AML 78

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=3.774.62
Lot batch = shcz066

source_name: AML 78


title: AML 109

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=700650LaserPower=4.144.42
Lot batch = shco026

source_name: AML 109


title: AML 101

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.94.28
Lot batch = shdj071

source_name: AML 101


title: AML 2

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=3.984.69
Lot batch = shcz081

source_name: AML 2


title: AML 76

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=640650LaserPower=4.024.64
Lot batch = shcz079

source_name: CRH

source_name: AML 76


title: AML 35

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=4.144.44
Lot batch = shco028

source_name: AML 35


title: AML 46

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=700650LaserPower=4.164.44
Lot batch = shco023

source_name: AML 46


title: AML 28

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=3.574.63
Lot batch = shcz075

source_name: AML 28


title: AML 67

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.94.1
Lot batch = shdj070

source_name: AML 67


title: AML 17

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=4.144.45
Lot batch = shco027

source_name: AML 17


title: AML 30

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.873.98
Lot batch = shdj075

source_name: AML 30


title: AML 108

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=650650LaserPower=3.534.52
Lot batch = shcz077

source_name: AML 108


title: AML 58

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.564.56
Lot batch = shcz065

source_name: AML 58


title: AML 85

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=750630LaserPower=3.534.65
Lot batch = shcz063

source_name: AML 85


title: AML 43

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=700650LaserPower=3.64.71
Lot batch = shcz074

source_name: AML 43


title: AML 13

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=720640LaserPower=3.514.67
Lot batch = shcz062

source_name: AML 13


title: AML 62

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.544.6
Lot batch = shcz064

source_name: AML 62


title: AML 96

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.584.19
Lot batch = shcz211

source_name: AML 96


title: AML 53

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=690650LaserPower=3.664.75
Lot batch = shcz067

source_name: AML 53


title: AML 6

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=770650LaserPower=3.544.23
Lot batch = shcz076

source_name: AML 6


title: AML 3

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=640650LaserPower=4.384.27
Lot batch = shco021

source_name: CRH

source_name: AML 3


title: HPP4_t=19

status: Public on Feb 12 2004

city: Leiden

first: Ellen

last: Sterrenburg

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Healthy primairy skeletal muscle cells (HPP4) nineteen days after initiation of fusion (t=19)

source_name: cDNA reference


title: HPP4_t=6

description: Healthy primairy skeletal muscle cells (HPP4) six days after initiation of fusion (t=6)


title: HPP4_t=10

description: Healthy primairy skeletal muscle cells (HPP4) ten days after initiation of fusion (t=10)


title: HPP4_t=22

description: Healthy primairy skeletal muscle cells (HPP4) tenty two days after initiation of fusion (t=22)


title: HPP4_t=14

description: Healthy primairy skeletal muscle cells (HPP4) fourteen days after initiation of fusion (t=14)


title: HPP4_t=1

description: Healthy primairy skeletal muscle cells (HPP4) one day after initiation of fusion (t=1)


title: AML 86

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=3.894.66
Lot batch = shdj068

source_name: AML 86


title: HPP4_t=4

description: Healthy primairy skeletal muscle cells (HPP4) four days after initiation of fusion (t=4)


title: AML 97

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=3.874.1
Lot batch = shdj067

source_name: AML 97


title: AML 9

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=3.984.7
Lot batch = shdj066

source_name: AML 9


title: AML 92

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.544.63
Lot batch = shcz209

source_name: AML 92


title: KM108_t=21

description: Healthy primairy skeletal muscle cells (KM108) twenty one days after initiation of fusion (t=21)


title: KM109 t=6(1) t=0(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and six days after fusion induction (channel 1, t=6).


title: HPP4_t=2

description: Healthy primairy skeletal muscle cells (HPP4) two days after initiation of fusion (t=2)


title: KM109 t=0(1) t=14(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and fourteen days after fusion induction (channel 2, t=14)


title: AML 50

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=720650LaserPower=3.94.53
Lot batch = shdj069

source_name: AML 50


title: KM109 t=4(1) t=0(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and four days after fusion induction (channel 1, t=4).


title: AML 14

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=640650LaserPower=4.414.08
Lot batch = shco022

source_name: AML 14


title: AML 79

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=4.564.66
Lot batch = shcz061

source_name: AML 79


title: HPP4_t=0

description: Healthy primairy skeletal muscle cells (HPP4) just before initiation of fusion (t=0)


title: AML 5

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.44.28
Lot batch = shco020

source_name: AML 5


title: AML 39

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=640650LaserPower=3.984.48
Lot batch = shdj065

source_name: AML 39


title: AML 45

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=680650LaserPower=4.564.49
Lot batch = shcz210

source_name: AML 45


title: KM109 t=14(1) t=0(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and fourteen days after fusion induction (channel 1, t=14).


title: KM109 t=0(1) t=4(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and four days after fusion induction (channel 2, t=4).


title: AML 104

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=660650LaserPower=4.394.29
Lot batch = shco019

source_name: AML 104


title: KM109 t=1(1) t=0(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and one day after fusion induction (channel 1, t=1).


title: KM109 t=0(1) t=14(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and fourteen days after fusion initiation (channel 2, t=14)


title: KM108_t=10

description: Healthy primairy skeletal muscle cells (KM108) ten days after serum initiation (t=10)


title: KM108_t=4

description: Healthy primairy skeletal muscle cells (KM108) four days after serum initiation (t=4)


title: AML 36

description:
Category: Myeloid Leukemias
Subcategory: Acute Myeloid Leukemia
Experimenter: Lars Bullinger
Scanning Software: GenePix
Software version: Pro
Scanning parameters: PMTVolts=670650LaserPower=4.524.72
Lot batch = shcz208

source_name: AML 36


title: KM108_t=1

description: Healthy primairy skeletal muscle cells (KM108) one day after serum initiation (t=1)


title: KM109 t=0(1) t=0(2) dyeswap batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1 and 2).


title: KM109_t=22

description: Healthy primary skeletal muscle cells twenty two days after initiation of fusion (t=22)


title: KM109 t=0(1) t=4(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and four days after fusion initiation (channel 2, t=4)


title: KM109 t=0(1) t=1(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and one day after fusion induction (channel 2, t=1).


title: KM109 t=0(1) t=6(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and six days after fusion initiation (channel 2, t=6)


title: KM109 t=0(1) t=1(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and one day after fusion initiation (channel 2, t=1)


title: KM109 t=14(1) t=0(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and fourteen days after fusion initiation (channel 1, t=14)


title: KM109 t=4(1) t=0(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and four days after fusion initiation (channel 1, t=4)


title: KM108_t=0

description: Healthy primairy skeletal muscle cells (KM108) just before serum initiation (t=0)


title: KM108_t=2

description: Healthy primairy skeletal muscle cells (KM108) two days after serum initiation (t=2)


title: KM109_t=14

description: Healthy primary skeletal muscle cells fourteen days after initiation of fusion (t=14)


title: KM109 t=0(1) t=0(2) dyeswap batch I

description:
Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1 and 2).
Dyeswap


title: KM109 t=0(1) t=6(2) batch II

description: Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and six days after fusion induction (channel 2, t=6).


title: KM109_t=19

description: Healthy primary skeletal muscle cells nineteen days after initiation of fusion (t=19)


title: KM109 t=1(1) t=0(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and one day after fusion initiation (channel 1, t=1)


title: KM108_t=6

description: Healthy primairy skeletal muscle cells (KM108) six days after serum initiation (t=6)


title: KM108_t=14

description: Healthy primairy skeletal muscle cells (KM108) fourteen days after initiation of fusion (t=14)


title: mtestis D6pp #2B

status: Public on Feb 01 2004

city: Pullman

first: James

last: Shima

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: Total testis RNA from BL/6-129 mice isolated using TRIzol reagent according to manufacturer's instructions. Signal intensities were scaled to a mean signal of 125.

organism: Mus musculus

source_name: total RNA from D6 postpartum mouse testis


title: mtestis D35pp #2B

source_name: total RNA from D35 postpartum mouse testis


title: mtestis D56pp #2B

source_name: total RNA from D56 postpartum mouse testis


title: mtestis D3pp #2B

source_name: total RNA from D3 postpartum mouse testis


title: mtestis D30pp #2B

source_name: total RNA from D30 postpartum mouse testis


title: mtestis D8pp #2B

source_name: total RNA from D8 postpartum mouse testis


title: mtestis D18pp #2B

source_name: total RNA from D18 postpartum mouse testis


title: mtestis D20pp #2B

source_name: total RNA from D20 postpartum mouse testis


title: mtestis D10pp #2B

source_name: total RNA from D10 postpartum mouse testis


title: KM109_t=2

description: Healthy primary skeletal muscle cells two days after initiation of fusion (t=2)

source_name: cDNA reference


title: mtestis D0pp #2B

source_name: total RNA from D0 postpartum mouse testis


title: mtestis D14pp #2B

source_name: total RNA from D14 postpartum mouse testis


title: KM109 t=0(1) t=0(2) batch I

description:
Timecourse experiment hybridized to human oligo array part I.
Healthy human primary myoblasts (KM109) just before fusion (channel 1 and 2).


title: KM109_t=4

description: Healthy primary skeletal muscle cells four days after initiation of fusion (t=4)


title: KM109_t=1

description: Healthy primary skeletal muscle cells one day after initiation of fusion (t=1)


title: KM109_t=0

description: Healthy primary skeletal muscle cells just before initiation of fusion (t=0)


title: KM109_t=10

description: Healthy primary skeletal muscle cells ten days after initiation of fusion (t=10)


title: mtestis D6pp #1B


title: mtestis D56pp #1B


title: mtestis D35pp #1B


title: mtestis D8pp #1B


title: mtestis D30pp #1B


title: mtestis D3pp #1B


title: mtestis D20pp #1B


title: KM109 t=6(1) t=0(2) batch I

description: Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 2, t=0) and six days after fusion initiation (channel 1, t=6)


title: mtestis D56pp #2C


title: mtestis D30pp #2C


title: KM109 t=0(1) t=0(2) batch II

description:
Timecourse experiment hybridized to human oligo array part II.
Healthy human primary myoblasts (KM109) just before fusion (channel 1 and 2).


title: mtestis D3pp #2C


title: mtestis D14pp #1B


title: mtestis D20pp #2C


title: mtestis D0pp #1B


title: mtestis D6pp #2C


title: mtestis D35pp #2C


title: mtestis D18pp #2C


title: mtestis D18pp #1B


title: mtestis D8pp #2C


title: mtestis D6pp #1C


title: mtestis D8pp #1C


title: mtestis D14pp #2C


title: mtestis D20pp #2A


title: mtestis D10pp #1C


title: mtestis D18pp #2A


title: mtestis D10pp #1B


title: mtestis D6pp #2A


title: mtestis D10pp #2C


title: mtestis D3pp #1C


title: mtestis D35pp #1C


title: mtestis D3pp #2A


title: mtestis D56pp #2A


title: mtestis D10pp #2A


title: mtestis D30pp #1C


title: mtestis D56pp #1C


title: mtestis D0pp #2A


title: mtestis D14pp #1C


title: mtestis D8pp #2A


title: mtestis D18pp #1C


title: mtestis D35pp #2A


title: mtestis D14pp #2A


title: mtestis D30pp #2A


title: mtestis D0pp #2C


title: mtestis D20pp #1C


title: mtestis D0pp #1C


title: KM109_t=6

description: Healthy primary skeletal muscle cells six days after initiation of fusion (t=6)


title: mtestis D8pp #1A


title: mtestis D30pp #1A


title: mtestis D0pp #1A

description: Total testis RNA from BL/6-129 mice isolated using TRIzol reagent according to manufacturer's instructions.  Signal intensities were scaled to a mean signal of 125.


title: mtestis D6pp #1A


title: mtestis D56pp #1A


title: mtestis D35pp #1A


title: mtestis D20pp #1A


title: mtestis D10pp #1A


title: mtestis D3pp #1A


title: mtestis D14pp #1A


title: mtestis D18pp #1A


title: HCT116-CloneK 4Gy 24hr PartA R1

status: Public on Dec 07 2003

city: Ottawa

first: Felix

middle: M.

last: Mesak

state: ON

address: 503 Smyth Rd. 3rd Floor

department: Centre for Cancer Therapeutics

country: Canada

institute: Ottawa Regional Cancer Centre

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).

Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12256971_19k3A

source_name: Control HCT116-Clone10 cells (Cy3)

source_name: XR sensitive HCT116-CloneK cells (Cy5)


title: HCT116-CloneK 4Gy 6hr PartA R1

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12263219_19k3A


title: HCT116-CloneK 4Gy 24hr PartA R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12263227_19k3A


title: HCT116-CloneK 4Gy 10min PartB R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257504_19k3B


title: HCT116-CloneK 4Gy 6hr PartB R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12262658_19k3B

source_name: Control HCT116-Clone10 cells (Cy5)

source_name: XR sensitive HCT116-CloneK cells (Cy3)


title: HeLa cell control

status: Public on Oct 19 2003

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description:
HeLa cell RNA control
Keywords = SARS
Keywords = coronavirus
Keywords = viral discovery
Keywords = viruses
Keywords = respiratory infection

source_name: HeLa cell total RNA


title: HCT116-CloneK 4Gy 6hr PartB R1

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12262656_19k3B


title: HCT116-CloneK 4Gy 10min PartA R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12263220_19k3A


title: HCT116-CloneK 4Gy 10min PartB R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257502_19k3B


title: HCT116-CloneK 4Gy 24hr PartB R1

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257501_19k3B


title: HCT116-CloneK 4Gy 10min PartB R1

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257500_19k3B


title: HCT116-CloneK 4Gy 6hr PartA R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12263224_19k3A


title: HCT116-CloneK 4Gy 10min PartA R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12256972_19k3A


title: Infected culture

description:
Infected Vero cell culture supernatant
Keywords = SARS
Keywords = coronavirus
Keywords = viral discovery
Keywords = viruses
Keywords = respiratory infection

organism: Viruses

source_name: viral culture supernatant total nucleic acid


title: HCT116-CloneK 4Gy 24hr PartB R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257503_19k3B


title: Acetaminophen 4 hr 3 vs PBS 4hr

status: Public on Oct 03 2003

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
One replicate of "Acet" group
Keywords = spinal cord

organism: Rattus norvegicus

source_name: Acetaminophen-treated 4 hr spinal cord cultures

source_name: Pooled PBS-treated 4 hr spinal cord cultures


title: HCT116-CloneK 4Gy 24hr PartB R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12257363_19k3B


title: Water negative control

description:
No template, water only, control
Keywords = SARS
Keywords = coronavirus
Keywords = viral discovery
Keywords = viruses
Keywords = respiratory infection

source_name: water negative control


title: Control culture

description:
Uninfected Vero cell culture control
Keywords = SARS
Keywords = coronavirus
Keywords = viral discovery
Keywords = viruses
Keywords = respiratory infection


title: Acetaminophen 4 hr 2 vs PBS 4hr


title: HCT116-CloneK 4Gy 6hr PartB R3

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12262657_19k3B


title: HCT116-CloneK 4Gy 6hr PartA R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 6 hours after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12263223_19k3A


title: HCT116-CloneK 4Gy 10min R1

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 10 minutes after XR from different batches and pooled together. RNA extraction was done using Rneasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12256957_19k3A


title: NS398 4 hr 1 vs DMSO 4hr

description:
One replicate of "NS398" group
Keywords = spinal cord

source_name: NS398-treated 4 hr spinal cord cultures

source_name: Pooled DMSO-treated 4 hr spinal cord cultures


title: NS398 4 hr 3 vs DMSO 4hr


title: NS398 4 hr 2 vs DMSO 4hr


title: HCT116-CloneK 4Gy 24hr PartA R2

description:
A cDNA microarray between X-radiation (XR) sensitive cell clone HCT116-Clone K and unirradiated control HCT116-Clone10 cells, a cell clone which has similar XR response with parental HCT116 cells. HCT116-CloneK cells were treated with XR at dose 4 Gy. Their total mRNA was collected 24 hours after XR from different batches and pooled together. RNA extraction was done using RNeasy Mini kit (Qiagen Inc.). Total mRNA from HCT116-CloneK or HCT116-Clone10 was labeled either with Cy5 or Cy3. This experiment was repeated three times with one of them was a reciprocal labeling. The arrays were scanned with ScanArray Express (Packard Bioscience). Acquired images were analyzed using QuantArray software version 3.0 (Packard Bioscience). The data was transformed with an Excel VBA macro Normaliser2 software (Institute for Biological Sciences, NRC, Ottawa, ON, Canada). Normaliser2 filtered the data by identifying problems with a spot on the array (flagging), which was then removed from the data set according to the set threshold i.e. spot intensity signal/sub array background less than 2.5, less than 5% spot intensity, and ignore spots with streak or damage.
Note: FLAGS: IF, Ignore Filter; SB1 or 2, Substract Background CH1 or CH2; LI1 or 2, Low Intensity CH1 or CH2; HI1 or 2, High Intensity CH1 or CH2. VALUE: Ratio (Log2)(Regression SubArray Normalised)(LogIntensity)(SubArray Bkgd Subtracted).
Keywords = X-radiation (XR), XR sensitive, colorectal cancer cells, HCT1116
Lot batch = ChipNo12256990_19k3A


title: MP 4 hr 3 vs PBS 4hr

description:
One replicate of "MP" group
Keywords = spinal cord

source_name: MP-treated 4 hr spinal cord cultures


title: Acetaminophen 4 hr 1 vs PBS 4hr


title: Indomethacin 4 hr 3 vs ETOH 4hr

description:
One replicate of "Indo" group
Keywords = spinal cord

source_name: Indomethacin-treated 4 hr spinal cord cultures

source_name: Pooled ETOH-treated 4 hr spinal cord cultures


title: Indomethacin 4 hr 2 vs ETOH 4hr


title: CKINs 4 hr 1 vs PBS 4hr

description:
One replicate of "CKIN" group
Keywords = spinal cord

source_name: CKIN-treated 4 hr spinal cord cultures


title: Indomethacin 4 hr 1 vs ETOH 4hr


title: 4 hr unpooled 2 vs PBS 4hrpooled

description:
One replicate of "Injured 4 hr" group
Keywords = spinal cord

source_name: Unpooled PBS-treated 4 hr spinal cord cultures


title: MP 4 hr 1 vs PBS 4hr


title: MP 4 hr 2 vs PBS 4hr


title: CKINs 4 hr 3 vs PBS 4hr


title: 4 hr unpooled 1 vs PBS 4hrpooled


title: DLJ 6

status: Public on Aug 19 2003

city: Manchester

first: Dawn

last: Jones

country: United Kingdom

institute: UMIST

description:
FY23 labelled with Cy3
DJ28 labelled with Cy5
Keywords = PDE2, Ras/cAMP pathway

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae DJ28

source_name: Saccharomyces cerevisiae FY23


title: CT2 vs PBS 4 hr pooled

description:
One replicate of "Uninjured" group
Keywords = spinal cord

source_name: Freshly dissected rat spinal cord


title: CT3 vs PBS 4 hr pooled


title: 4 hr unpooled 3 vs PBS 4hrpooled


title: UV_fhCMV-H-1

status: Public on Sep 08 2003

city: Seattle

first: Lynn

last: Graf

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
Target Source: human foreskin fibroblasts exposed to UV-inactivated cytomegalovirus.
Clinical  isolate fhCMV-H of CMV, genotype gB3.

HFF were plated in T75 flasks at approximately 80% confluence. The next day
the supernatant was removed and replaced with the CMV viral inoculum (MOI of
3) in a total volume of 7 mls of RPMI supplemented with 5% FBS. Virus was UV-inactivated on ice in a UV Stratalinker 2400. To ensure that the virus was UV-inactivated, yet not heat inactivated, pilot studies were conducted in which samples of each virus strain were subjected to increasing amount of UV light. These test samples were incubated with HFF for 2 hours at 37ºC and either fixed with 50% acetone/50% methanol at 8 hours post-infection (hpi) and stained using antibodies to CMV IE1 and pp65 or allowed to replicate for 24 hr. If the inoculum failed to produce CPE, was not positive for IE1 staining, but was positive for pp65 staining, it was considered UV-inactivated.The virus was permitted to absorb for 2 hours at 37 C and 5% CO2. The supernatants were incubated at the same time as the infected cultures. The inoculum was removed, the cells were washed 2 times with Hank's buffer, and media was replaced.
Uninfected and infected fibroblasts were harvested at 24 hpi by brief trypsinization followed by pelleting of the cells.
All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with
Superscript II reverse transcriptase for 2h at 42 C in the presence of 0.5mM
dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP.
After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with
a Microcon-30 concentrator. The cDNA from uninfected and infected fibroblasts
was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix
4000A fluorescent scanner and image intensity data were extracted and
analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression values were mean centered and linear transformed to obtain the log and linear values given in the data table.
Keywords = cytomegalovirus,  glycoprotein B

source_name: CMV-exposed  foreskin fibroblasts (HFF)

source_name: uninfected HFF


title: UV_fhCMV-T-2

description:
Target Source: human foreskin fibroblasts exposed to UV-inactivated cytomegalovirus.
Clinical  isolate fhCMV-T of CMV, genotype gB1.

HFF were plated in T75 flasks at approximately 80% confluence. The next day
the supernatant was removed and replaced with the CMV viral inoculum (MOI of
3) in a total volume of 7 mls of RPMI supplemented with 5% FBS. Virus was UV-inactivated on ice in a UV Stratalinker 2400. To ensure that the virus was UV-inactivated, yet not heat inactivated, pilot studies were conducted in which samples of each virus strain were subjected to increasing amount of UV light. These test samples were incubated with HFF for 2 hours at 37ºC and either fixed with 50% acetone/50% methanol at 8 hours post-infection (hpi) and stained using antibodies to CMV IE1 and pp65 or allowed to replicate for 24 hr. If the inoculum failed to produce CPE, was not positive for IE1 staining, but was positive for pp65 staining, it was considered UV-inactivated.The virus was permitted to absorb for 2 hours at 37 C and 5% CO2. The supernatants were incubated at the same time as the infected cultures. The inoculum was removed, the cells were washed 2 times with Hank's buffer, and media was replaced.
Uninfected and infected fibroblasts were harvested at 24 hpi by brief trypsinization followed by pelleting of the cells.
All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with
Superscript II reverse transcriptase for 2h at 42 C in the presence of 0.5mM
dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP.
After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with
a Microcon-30 concentrator. The cDNA from uninfected and infected fibroblasts
was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix
4000A fluorescent scanner and image intensity data were extracted and
analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression values were mean centered and linear transformed to obtain the log and linear values given in the data table.
Keywords = cytomegalovirus
Keywords = glycoprotein B

source_name: UV-CMV exposed human foreskin fibroblasts (HFF)

source_name: uninfected fibroblasts


title: CKINs 4 hr 2 vs PBS 4hr


title: DLJ 2

description:
DJ28 labelled with Cy3
FY23 labelled with Cy5
Keywords = PDE2, Ras/cAMP pathway


title: DLJ 5


title: DLJ 10


title: CT1 vs PBS 4 hr pooled

description: One replicate of "Uninjured" group.


title: DLJ 9


title: DLJ 7


title: DLJ 4


title: DLJ 1

status: Public on Aug 15 2003


title: UV_fhCMV-T-1

description:
Target Source: human foreskin fibroblasts exposed to UV-inactivated cytomegalovirus.
Clinical  isolate fhCMV-T of CMV, genotype gB1.

HFF were plated in T75 flasks at approximately 80% confluence. The next day
the supernatant was removed and replaced with the CMV viral inoculum (MOI of
3) in a total volume of 7 mls of RPMI supplemented with 5% FBS. Virus was UV-inactivated on ice in a UV Stratalinker 2400. To ensure that the virus was UV-inactivated, yet not heat inactivated, pilot studies were conducted in which samples of each virus strain were subjected to increasing amount of UV light. These test samples were incubated with HFF for 2 hours at 37ºC and either fixed with 50% acetone/50% methanol at 8 hours post-infection (hpi) and stained using antibodies to CMV IE1 and pp65 or allowed to replicate for 24 hr. If the inoculum failed to produce CPE, was not positive for IE1 staining, but was positive for pp65 staining, it was considered UV-inactivated.The virus was permitted to absorb for 2 hours at 37 C and 5% CO2. The supernatants were incubated at the same time as the infected cultures. The inoculum was removed, the cells were washed 2 times with Hank's buffer, and media was replaced.
Uninfected and infected fibroblasts were harvested at 24 hpi by brief trypsinization followed by pelleting of the cells.
All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. The RNA (25 ug) was annealed with 5 ug oligo dT12-18, and reverse-transcribed into cDNA with
Superscript II reverse transcriptase for 2h at 42 C in the presence of 0.5mM
dGTP, 0.5mM dCTP, 0.5mM dATP, 0.3mM dTTP, 0.2mM amino-allyl dUTP.
After hydrolysis of RNA in 0.2M NaOH, Tris was removed from the reaction with
a Microcon-30 concentrator. The cDNA from uninfected and infected fibroblasts
was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 ul of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix
4000A fluorescent scanner and image intensity data were extracted and
analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression values were mean centered and linear transformed to obtain the log and linear values given in the data table.
Keywords = cytomegolvirus
Keywords = glycoprotein B

source_name: UV-CMV-exposed human foreskin fibroblasts (HFF)


title: DLJ 8


title: MGRef Cy3 vs 12APFb Cy5 700600GEO

status: Public on Jul 25 2003

city: New Haven

first: Tong-Ruei

last: Li

state: CT

address: 333 Cedar St. Rm#NSB386

department: Department of Genetics

institute: Yale University School of Medicine

description:
The MIAME Checklist
Experiment Design:
· Type of experiment: for example, is it a comparison of normal vs. diseased tissue, a time course, or is it designed to study the effects of a gene knock-out?
Comparisons between the midgut at time points 18 hr. BPF, 4 hr. BPF, PF, 2 hr. APF, 3 hr. APF, 4 hr. APF, 5 hr. APF, 6 hr. APF, 8 hr. APF, 10 hr. APF and 12 hr. APF., vs. a reference sample. Reference sample is a mixture of the midgut samples at time points 18 hr. BPF, 4 hr. BPF, PF, 2 hr. APF, 3 hr. APF, 4 hr. APF, 5 hr. APF, 6 hr. APF, 8 hr. APF, and 12 hr. APF (BPF: before puparium formation; PF: puparium formation, also known as WPP (white prepupa); APF: after puparium formation).  Animal staging is according to Andres, A.J. & Thummel, C.S. Methods for quantitative analysis of transcription in larvae and prepupae. in Methods in Cell Biology, Volume 44. Drosophila melanogaster: Practical Uses in Cell and Molecular Biology., Vol. 44 (eds. Goldstein, L.S.B. & Fyrberg, E.A.) 565-573 (Academic Press, San Diego, 1994)). The reference sample is a mixture of the above-described samples. RNA samples from Drosophila melanogaster (Canton S strain) were amplified according to Baugh, L. R., Hill, A. A., Brown, E. L., and Hunter, C. P. (2001). Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29, E29. Samples from the midgut at one stage were hybridized against the reference sample on each microarray.
· Experimental factors: the parameters or conditions tested, such as time, dose, or genetic variation.
Each array tested differences in gene expression at different times in development in the midgut.
· The number of hybridizations performed in the experiment.
Three replicate hybridizations for each tissue using independent samples.
· The type of reference used for the hybridizations, if any.
The reference sample is a mixture of the samples from different stages.
· Hybridization design: if applicable, a description of the comparisons made in each hybridization, whether to a standard reference sample, or between experimental samples. An accompanying diagram or table may be useful.
See above.
· Quality control steps taken: for example, replicates or dye swaps.
No dye swaps were used. Three replicates for each stage.
· URL of any supplemental websites or database accession numbers
Samples used, extract preparation and labeling:
· The origin of the biological sample (for instance, name of the organism, the provider of the sample) and its characteristics: for example, gender, age, developmental stage, strain, or disease state. See above. Tissues/Organs were dissected from at least 12 individuals for each sample.
· Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques. Animals were grown on standard corn meal medium with 0.05% bromophenol blue at 25 degrees Celsius.
· Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol
Total RNA was extracted using TriZOL. 2 ug of total RNA from each sample was amplified with T7 RNA polymerase using a one-round linear amplification protocol. RNA extraction and amplification were according to Baugh, L. R., Hill, A. A., Brown, E. L., and Hunter, C. P. (2001). Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29, E29.
· Labeling protocol(s).
Priming step with random hexamers. Labeling step using Superscript II, buffer, DTT, dUTP-Cy3, dUTP-Cy5 and free nucleotides. Cleanup using Qiagen PCR cleanup kit. Hybridization to slide in a TE, SSC, SDS solution with poly-A as a blocker. Hybridization chambers from DIE-TECH, incubated for 10 minutes at 42 degrees followed by approximately 15-hour incubation at 64 degrees. Three washes with successively more dilute solutions of SSC, including SDS in the first wash, then a centrifuge spin to dry. Arrays were stored in the dark until scanned. See K.P. White and K.C. Burtis "Drosophila microarrays: from arrayer construction to hybridization" in Drosophila Protocols, Cold Spring Harbor Press, 2000 for microarray protocols.
· External controls (spikes).
Hybridization procedures and parameters:
· The protocol and conditions used during hybridization, blocking and washing.
See above.
Measurement data and specifications:
· The quantitations based on the images.
Images were gridded and spots were quantified with GenePix software (Axon Instruments)
· The set of quantitations from several arrays upon which the authors base their conclusions. While access to images of raw data is not required (although its value is unquestionable), authors should make every effort to provide the following:
o Type of scanning hardware and software used: this information is appropriate for a materials and methods section.
Slides were scanned on an Axon 4000B scanner using Genepix Pro 3.0 software.
o Type of image analysis software used: specifications should be stated in the materials and methods.
The program GenePix Pro 3.0 from Axon Instruments was used to analyse the data.
o A description of the measurements produced by the image-analysis software and a description of which measurements were used in the analysis.
(F635 Median - B635), (F532 Median - B532), and (Ratio of Medians) were the raw measurements produced by the software. The detailed information for these measurements is available at http://www.axon.com/manuals/GenePix_Pro_4.0_User_Guide_Rev_E.pdf
o The complete output of the image analysis before data selection and transformation (spot quantitation matrices).
See *.xls files attached.
o Data selection and transformation procedures.
Data for all spots are filtered. For a spot to pass quality control, 3 conditions need to be met: (1). There is no automatic or manual flag during image gridding using GenePix Pro software. (2). For this spot, at least 1 channel is of at least 75% of the pixels are one SD above background. (3). The net signal noise ratio should be at least 1 for at least one channel. For the channel at 635 nm wavelength, the signal noise ratio is the ratio between (F635_median-B635_median) and the background median. The background median is the bigger of the median of B635-median of all the spots on the whole array, and B-median of this spot. For the channel at 532 nm wavelength, F532_median and B532_median are used. Ratios between net signals are log2 transformed and analyzed as detailed in the paper.
o Final gene expression data table(s) used by the authors to make their conclusions after data selection and transformation (gene expression data matrices).
See the web tables attached for the paper. Additionally, see the column for Passed and normalized ratio of median in the *.xls files attached. Data before and after data selection is in one file.
Array Design:
· General array design, including the platform type (whether the array is a spotted glass array, an in situ synthesized array, etc.); surface and coating specifications (when known - often commercial suppliers do not provide this data); and the availability of the array (the name or make of commercially available arrays).
Spotted array using PCR fragments of approximately 95% of the genes in the D. melanogaster BDGP genome. Slides were coated with polylysine, printed using a GeneMachines OmniGrid printer with DNA suspended in 3X SSC, and postprocessed using the DCE protocol of Diehl, F., Grahlmann, S., Beier, M. & Hoheisel, J.D. "Manufacturing DNA microarrays of high spot homogeneity and reduced background signal." Nucleic Acids Research 29, e38 (2001).
· For each feature (spot) on the array, its location on the array and the ID of its respective reporter (molecule present on each spot) should be given.
The KP numbers identify these and can be tied to the data files. The ID of the respective reporter is included in the Excel file Web Table PCR Primer and Amplicon Sequence.xls.
· For each reporter, its type (e.g., cDNA or oligonucleotide) should be given, along with information that characterizes the reporter molecule unambiguously, in the form of appropriate database reference(s) and sequence (if available).
The FBGN and CG numbers, primer pairs, sequences, and KP number (to tie them to the spots on the array) are all listed in the Excel file Web Table PCR Primer and Amplicon Sequence.xls.
· For commercial arrays: a reference to the manufacturer should be provided, including a catalogue number and references to the manufacturer's website if available.
· For non-commercial arrays, the following details should be provided:
o The source of the reporter molecules: for example, the cDNA or oligo collection used, with references.
o The method of reporter preparation.
o The spotting protocols used, including the array substrate, the spotting buffer, and any post-printing processing, including cross-linking.
o Any additional treatment performed prior to hybridization.
We followed a sequence of decreasingly stringent tests to pick optimal primer pairs for the PCR fragments on the arrays. For each gene, we looked for (first) a 500b to 2kb sequence at the 3' end and, failing this, (second) two 200b to 500b sequences in:(1) coding sequence, completely within an EST clot, and unduplicated (BLAST<=10^-4); (2) coding sequence, partially within an EST clot, unduplicated; (3) coding sequence, unduplicated; (4) exon, completely within an EST clot, unduplicated; (5) exon, partially within an EST clot, unduplicated; (6) exon, unduplicated; (7) sequence less than 2kb at the 3' end. See above for the other details about making these arrays.
Sample hybridized to platform version GEO_Dmel20010730arrayplatform
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development

organism: Drosophila melanogaster

source_name: 635nm (Cy5) channel, midgut at time point 12 hr. after puparium formation

source_name: 532nm (Cy3) channel, reference sample


title: MGRef Cy3 vs 12APFa Cy5 680590GEO

description:
The MIAME Checklist
Experiment Design:
· Type of experiment: for example, is it a comparison of normal vs. diseased tissue, a time course, or is it designed to study the effects of a gene knock-out?
Comparisons between the midgut at time points 18 hr. BPF, 4 hr. BPF, PF, 2 hr. APF, 3 hr. APF, 4 hr. APF, 5 hr. APF, 6 hr. APF, 8 hr. APF, 10 hr. APF and 12 hr. APF., vs. a reference sample. Reference sample is a mixture of the midgut samples at time points 18 hr. BPF, 4 hr. BPF, PF, 2 hr. APF, 3 hr. APF, 4 hr. APF, 5 hr. APF, 6 hr. APF, 8 hr. APF, and 12 hr. APF (BPF: before puparium formation; PF: puparium formation, also known as WPP (white prepupa); APF: after puparium formation).  Animal staging is according to Andres, A.J. & Thummel, C.S. Methods for quantitative analysis of transcription in larvae and prepupae. in Methods in Cell Biology, Volume 44. Drosophila melanogaster: Practical Uses in Cell and Molecular Biology., Vol. 44 (eds. Goldstein, L.S.B. & Fyrberg, E.A.) 565-573 (Academic Press, San Diego, 1994)). The reference sample is a mixture of the above-described samples. RNA samples from Drosophila melanogaster (Canton S strain) were amplified according to Baugh, L. R., Hill, A. A., Brown, E. L., and Hunter, C. P. (2001). Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29, E29. Samples from the midgut at one stage were hybridized against the reference sample on each microarray.
· Experimental factors: the parameters or conditions tested, such as time, dose, or genetic variation.
Each array tested differences in gene expression at different times in development in the midgut.
· The number of hybridizations performed in the experiment.
Three replicate hybridizations for each tissue using independent samples.
· The type of reference used for the hybridizations, if any.
The reference sample is a mixture of the samples from different stages.
· Hybridization design: if applicable, a description of the comparisons made in each hybridization, whether to a standard reference sample, or between experimental samples. An accompanying diagram or table may be useful.
See above.
· Quality control steps taken: for example, replicates or dye swaps.
No dye swaps were used. Three replicates for each stage.
· URL of any supplemental websites or database accession numbers
Samples used, extract preparation and labeling:
· The origin of the biological sample (for instance, name of the organism, the provider of the sample) and its characteristics: for example, gender, age, developmental stage, strain, or disease state. See above. Tissues/Organs were dissected from at least 12 individuals for each sample.
· Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques. Animals were grown on standard corn meal medium with 0.05% bromophenol blue at 25 degrees Celsius.
· Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol
Total RNA was extracted using TriZOL. 2 ug of total RNA from each sample was amplified with T7 RNA polymerase using a one-round linear amplification protocol. RNA extraction and amplification were according to Baugh, L. R., Hill, A. A., Brown, E. L., and Hunter, C. P. (2001). Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29, E29.
· Labeling protocol(s).
Priming step with random hexamers. Labeling step using Superscript II, buffer, DTT, dUTP-Cy3, dUTP-Cy5 and free nucleotides. Cleanup using Qiagen PCR cleanup kit. Hybridization to slide in a TE, SSC, SDS solution with poly-A as a blocker. Hybridization chambers from DIE-TECH, incubated for 10 minutes at 42 degrees followed by approximately 15-hour incubation at 64 degrees. Three washes with successively more dilute solutions of SSC, including SDS in the first wash, then a centrifuge spin to dry. Arrays were stored in the dark until scanned. See K.P. White and K.C. Burtis "Drosophila microarrays: from arrayer construction to hybridization" in Drosophila Protocols, Cold Spring Harbor Press, 2000 for microarray protocols.
· External controls (spikes).
Hybridization procedures and parameters:
· The protocol and conditions used during hybridization, blocking and washing.
See above.
Measurement data and specifications:
· The quantitations based on the images.
Images were gridded and spots were quantified with GenePix software (Axon Instruments)
· The set of quantitations from several arrays upon which the authors base their conclusions. While access to images of raw data is not required (although its value is unquestionable), authors should make every effort to provide the following:
o Type of scanning hardware and software used: this information is appropriate for a materials and methods section.
Slides were scanned on an Axon 4000B scanner using Genepix Pro 3.0 software.
o Type of image analysis software used: specifications should be stated in the materials and methods.
The program GenePix Pro 3.0 from Axon Instruments was used to analyse the data.
o A description of the measurements produced by the image-analysis software and a description of which measurements were used in the analysis.
(F635 Median - B635), (F532 Median - B532), and (Ratio of Medians) were the raw measurements produced by the software. The detailed information for these measurements is available at http://www.axon.com/manuals/GenePix_Pro_4.0_User_Guide_Rev_E.pdf
o The complete output of the image analysis before data selection and transformation (spot quantitation matrices).
See *.xls files attached.
o Data selection and transformation procedures.
Data for all spots are filtered. For a spot to pass quality control, 3 conditions need to be met: (1). There is no automatic or manual flag during image gridding using GenePix Pro software. (2). For this spot, at least 1 channel is of at least 75% of the pixels are one SD above background. (3). The net signal noise ratio should be at least 1 for at least one channel. For the channel at 635 nm wavelength, the signal noise ratio is the ratio between (F635_median-B635_median) and the background median. The background median is the bigger of the median of B635-median of all the spots on the whole array, and B-median of this spot. For the channel at 532 nm wavelength, F532_median and B532_median are used. Ratios between net signals are log2 transformed and analyzed as detailed in the paper.
o Final gene expression data table(s) used by the authors to make their conclusions after data selection and transformation (gene expression data matrices).
See the web tables attached for the paper. Additionally, see the column for Passed and normalized ratio of median in the *.xls files attached. Data before and after data selection is in one file.
Array Design:
· General array design, including the platform type (whether the array is a spotted glass array, an in situ synthesized array, etc.); surface and coating specifications (when known - often commercial suppliers do not provide this data); and the availability of the array (the name or make of commercially available arrays).
Spotted array using PCR fragments of approximately 95% of the genes in the D. melanogaster BDGP genome. Slides were coated with polylysine, printed using a GeneMachines OmniGrid printer with DNA suspended in 3X SSC, and postprocessed using the DCE protocol of Diehl, F., Grahlmann, S., Beier, M. & Hoheisel, J.D. "Manufacturing DNA microarrays of high spot homogeneity and reduced background signal." Nucleic Acids Research 29, e38 (2001).
· For each feature (spot) on the array, its location on the array and the ID of its respective reporter (molecule present on each spot) should be given.
The KP numbers identify these and can be tied to the data files. The ID of the respective reporter is included in the Excel file Web Table PCR Primer and Amplicon Sequence.xls.
· For each reporter, its type (e.g., cDNA or oligonucleotide) should be given, along with information that characterizes the reporter molecule unambiguously, in the form of appropriate database reference(s) and sequence (if available).
The FBGN and CG numbers, primer pairs, sequences, and KP number (to tie them to the spots on the array) are all listed in the Excel file Web Table PCR Primer and Amplicon Sequence.xls.
· For commercial arrays: a reference to the manufacturer should be provided, including a catalogue number and references to the manufacturer's website if available.
· For non-commercial arrays, the following details should be provided:
o The source of the reporter molecules: for example, the cDNA or oligo collection used, with references.
o The method of reporter preparation.
o The spotting protocols used, including the array substrate, the spotting buffer, and any post-printing processing, including cross-linking.
o Any additional treatment performed prior to hybridization.
We followed a sequence of decreasingly stringent tests to pick optimal primer pairs for the PCR fragments on the arrays. For each gene, we looked for (first) a 500b to 2kb sequence at the 3' end and, failing this, (second) two 200b to 500b sequences in:(1) coding sequence, completely within an EST clot, and unduplicated (BLAST<=10^-4); (2) coding sequence, partially within an EST clot, unduplicated; (3) coding sequence, unduplicated; (4) exon, completely within an EST clot, unduplicated; (5) exon, partially within an EST clot, unduplicated; (6) exon, unduplicated; (7) sequence less than 2kb at the 3' end. See above for the other details about making these arrays.
Sample hybridized to platform version GEO_Dmel200102arrayplatform
Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development


title: DLJ 3


title: MGRef Cy3 vs 12APFc Cy5 630600GEO


title: MGRef Cy3 vs 10APFc Cy5 640600GEO

source_name: 635nm (Cy5) channel, midgut at time point 10 hr. after puparium formation


title: MGRef Cy3 vs 8APFc Cy5 600610GEO

source_name: 635nm (Cy5) channel, midgut at time point 8 hr. after puparium formation


title: MGRef Cy3 vs 8APFb Cy5 670640GEO


title: MGRef Cy3 vs 10APFa Cy5 630590GEO


title: MGRef Cy3 vs 6APFc Cy5 650620GEO

source_name: 635nm (Cy5) channel, midgut at time point 6 hr. after puparium formation


title: MGRef Cy3 vs 8APFa Cy5 660590GEO


title: MGRef Cy3 vs 5APFc Cy5 630650GEO

source_name: 635nm (Cy5) channel, midgut at time point 5 hr. after puparium formation


title: MGRef Cy3 vs 10APFb Cy5 680600GEO


title: MGRef Cy3 vs 5APFa Cy5 660580GEO


title: MGRef Cy3 vs 6APFb Cy5 680640GEO


title: MGRef Cy3 vs 6APFa Cy5 710590GEO


title: MGRef Cy3 vs 5APFb Cy5 650630GEO


title: MGRef Cy3 vs 4APFb Cy5 680620GEO

source_name: 635nm (Cy5) channel, midgut at time point 4 hr. after puparium formation


title: MGRef Cy3 vs 3APFa Cy5 670570GEO

source_name: 635nm (Cy5) channel, midgut at time point 3 hr. after puparium formation


title: MGRef Cy3 vs 4APFc Cy5 660630GEO


title: MGRef Cy3 vs 3APFc Cy5 630630GEO


title: MGRef Cy3 vs 2APFa Cy5 670580GEO

source_name: 635nm (Cy5) channel, midgut at time point 2 hr. after puparium formation


title: MGRef Cy3 vs PFc Cy5 620610GEO

source_name: 635nm (Cy5) channel, midgut at puparium formation


title: MGRef Cy3 vs 4APFa Cy5 670570GEO


title: MGRef Cy3 vs PFb Cy5 610610GEO


title: MGRef Cy3 vs 2APFb Cy5 660620GEO


title: MGRef Cy3 vs 4BPFb Cy5 610610GEO

source_name: 635nm (Cy5) channel, midgut at time point 4 hr. before puparium formation


title: MGRef Cy3 vs PFa Cy5 710580GEO


title: MGRef Cy3 vs 4BPFc Cy5 620610GEO


title: MGRef Cy3 vs 3APFb Cy5 720620GEO


title: MGRef Cy3 vs 4BPFa Cy5 710570GEO


title: MGRef Cy3 vs 2APFc Cy5 630620GEO