title: Monocyte sample 194

description:
sample 194
9965581144_F


title: Monocyte sample 204

status: Public on Oct 07 2017

type: RNA

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description:
sample 204
9967453001_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using log2-quantile normalization with the lumi package in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human peripheral monocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Blood was drawn into three 8 mL Cell Preparation Tubes (CPT) containing sodium citrate. Peripheral blood mononuclear cells (PBMCs) were then isolated through centrifugation within 6 hours of collection. PBMCs were washed with phosphate buffered saline, and then monocytes were isolated through Rosette separation (RosetteSep®; Stem Cell Technologies) according to the manufacturer instructions.

tag: arbitrary subject id

tag: timepoint

tag: hiv status

tag: age

tag: Sex

value: male

tag: gnf

tag: hand severity

tag: race

value: white

tag: bmi

tag: smoke

tag: alcohol

tag: education

tag: stripe

value: D

tag: arrayid


title: Monocyte sample 196

description:
sample 196
9965581144_H

value: H


title: Monocyte sample 192

description:
sample 192
9965581144_D


title: Monocyte sample 203

description:
sample 203
9967453001_C

value: C


title: Monocyte sample 191

description:
sample 191
9965581144_C


title: Monocyte sample 188

description:
sample 188
9965581143_L

value: black

value: L


title: Monocyte sample 190

description:
sample 190
9965581144_B

value: B


title: Monocyte sample 183

description:
sample 183
9965581143_G

value: hisp

value: G


title: Monocyte sample 187

description:
sample 187
9965581143_K

value: K


title: Monocyte sample 179

description:
sample 179
9965581143_C


title: Monocyte sample 184

description:
sample 184
9965581143_H


title: Monocyte sample 189

description:
sample 189
9965581144_A

value: A


title: Monocyte sample 182

description:
sample 182
9965581143_F

value: F


title: Monocyte sample 180

description:
sample 180
9965581143_D


title: Monocyte sample 186

description:
sample 186
9965581143_J

value: J


title: Monocyte sample 176

description:
sample 176
9965581139_L


title: Monocyte sample 181

description:
sample 181
9965581143_E

value: E


title: Monocyte sample 175

description:
sample 175
9965581139_K


title: Monocyte sample 169

description:
sample 169
9965581139_E


title: Monocyte sample 167

description:
sample 167
9965581139_C


title: Monocyte sample 168

description:
sample 168
9965581139_D


title: Monocyte sample 173

description:
sample 173
9965581139_I

value: I


title: Monocyte sample 172

description:
sample 172
9965581139_H


title: Monocyte sample 170

description:
sample 170
9965581139_F


title: Monocyte sample 171

description:
sample 171
9965581139_G


title: Monocyte sample 162

description:
sample 162
9965581138_J


title: Monocyte sample 177

description:
sample 177
9965581143_A


title: Monocyte sample 166

description:
sample 166
9965581139_B


title: Monocyte sample 178

description:
sample 178
9965581143_B


title: Monocyte sample 163

description:
sample 163
9965581138_K


title: Monocyte sample 174

description:
sample 174
9965581139_J


title: Monocyte sample 154

description:
sample 154
9965581138_B


title: Monocyte sample 156

description:
sample 156
9965581138_D


title: Monocyte sample 165

description:
sample 165
9965581139_A


title: Monocyte sample 160

description:
sample 160
9965581138_H


title: Monocyte sample 161

description:
sample 161
9965581138_I


title: Monocyte sample 185

description:
sample 185
9965581143_I


title: Monocyte sample 155

description:
sample 155
9965581138_C


title: Monocyte sample 159

description:
sample 159
9965581138_G


title: Monocyte sample 153

description:
sample 153
9965581138_A


title: Monocyte sample 158

description:
sample 158
9965581138_F


title: Monocyte sample 157

description:
sample 157
9965581138_E

value: other


title: Monocyte sample 149

description:
sample 149
9965581133_D

value: male


title: Monocyte sample 152

description:
sample 152
9965581133_G


title: Monocyte sample 147

description:
sample 147
9965581133_B


title: Monocyte sample 144

description:
sample 144
9965581132_K


title: Monocyte sample 140

description:
sample 140
9965581132_G


title: Monocyte sample 139

description:
sample 139
9965581132_F


title: Monocyte sample 142

description:
sample 142
9965581132_I


title: Monocyte sample 151

description:
sample 151
9965581133_F

value: white


title: Monocyte sample 148

description:
sample 148
9965581133_C


title: Monocyte sample 150

description:
sample 150
9965581133_E


title: Monocyte sample 145

description:
sample 145
9965581132_L


title: Monocyte sample 143

description:
sample 143
9965581132_J


title: Monocyte sample 146

description:
sample 146
9965581133_A


title: Monocyte sample 141

description:
sample 141
9965581132_H


title: Monocyte sample 135

description:
sample 135
9965581132_B


title: Monocyte sample 130

description:
sample 130
9965581131_I


title: Monocyte sample 136

description:
sample 136
9965581132_C


title: Monocyte sample 129

description:
sample 129
9965581131_H


title: Monocyte sample 138

description:
sample 138
9965581132_E


title: Monocyte sample 126

description:
sample 126
9965581131_E


title: Monocyte sample 122

description:
sample 122
9965581131_A


title: Monocyte sample 127

description:
sample 127
9965581131_F


title: Monocyte sample 125

description:
sample 125
9965581131_D

value: D


title: Monocyte sample 120

description:
sample 120
9256320023_H

value: H


title: Monocyte sample 128

description:
sample 128
9965581131_G


title: Monocyte sample 133

description:
sample 133
9965581131_L


title: Monocyte sample 115

description:
sample 115
9256320023_C

value: C


title: Monocyte sample 131

description:
sample 131
9965581131_J


title: Monocyte sample 119

description:
sample 119
9256320023_G


title: Monocyte sample 118

description:
sample 118
9256320023_F


title: Monocyte sample 132

description:
sample 132
9965581131_K


title: Monocyte sample 121

description:
sample 121
9256320023_J

value: black


title: Monocyte sample 124

description:
sample 124
9965581131_C


title: Monocyte sample 123

description:
sample 123
9965581131_B


title: Monocyte sample 134

description:
sample 134
9965581132_A


title: Monocyte sample 114

description:
sample 114
9231092129_K


title: Monocyte sample 117

description:
sample 117
9256320023_E


title: Monocyte sample 110

description:
sample 110
9231092129_F


title: Monocyte sample 116

description:
sample 116
9256320023_D


title: Monocyte sample 111

description:
sample 111
9231092129_G


title: Monocyte sample 112

description:
sample 112
9231092129_I


title: Monocyte sample 113

description:
sample 113
9231092129_J


title: Monocyte sample 108

description:
sample 108
9231092129_D


title: Monocyte sample 106

description:
sample 106
9231092129_A


title: Monocyte sample 164

description:
sample 164
9965581138_L

value: L


title: Monocyte sample 109

description:
sample 109
9231092129_E


title: Monocyte sample 94

description:
sample 94
8473515041_L


title: Monocyte sample 99

description:
sample 99
8473515044_E


title: Monocyte sample 103

description:
sample 103
8473515044_I


title: Monocyte sample 101

description:
sample 101
8473515044_G


title: Monocyte sample 91

description:
sample 91
8473515041_I


title: Monocyte sample 105

description:
sample 105
8473515044_L


title: Monocyte sample 104

description:
sample 104
8473515044_K


title: Monocyte sample 84

description:
sample 84
8473515041_A


title: Monocyte sample 89

description:
sample 89
8473515041_G


title: Monocyte sample 85

description:
sample 85
8473515041_B

value: B


title: Monocyte sample 102

description:
sample 102
8473515044_H


title: Monocyte sample 93

description:
sample 93
8473515041_K


title: Monocyte sample 100

description:
sample 100
8473515044_F


title: Monocyte sample 95

description:
sample 95
8473515044_A

value: hisp


title: Monocyte sample 96

description:
sample 96
8473515044_B


title: Monocyte sample 83

description:
sample 83
8292044074_L


title: Monocyte sample 87

description:
sample 87
8473515041_E


title: Monocyte sample 88

description:
sample 88
8473515041_F


title: Monocyte sample 92

description:
sample 92
8473515041_J


title: Monocyte sample 98

description:
sample 98
8473515044_D


title: Monocyte sample 97

description:
sample 97
8473515044_C


title: Monocyte sample 90

description:
sample 90
8473515041_H


title: Monocyte sample 82

description:
sample 82
8292044074_K


title: Monocyte sample 86

description:
sample 86
8473515041_C


title: Monocyte sample 107

description:
sample 107
9231092129_B


title: Monocyte sample 137

description:
sample 137
9965581132_D


title: Monocyte sample 77

description:
sample 77
8292044074_F


title: Monocyte sample 81

description:
sample 81
8292044074_J


title: Monocyte sample 79

description:
sample 79
8292044074_H


title: Monocyte sample 80

description:
sample 80
8292044074_I


title: Monocyte sample 71

description:
sample 71
8292044073_K


title: Monocyte sample 73

description:
sample 73
8292044074_B


title: Monocyte sample 78

description:
sample 78
8292044074_G

value: G


title: Monocyte sample 75

description:
sample 75
8292044074_D


title: Monocyte sample 76

description:
sample 76
8292044074_E


title: Monocyte sample 74

description:
sample 74
8292044074_C


title: Monocyte sample 70

description:
sample 70
8292044073_J


title: Monocyte sample 68

description:
sample 68
8292044073_H


title: Monocyte sample 72

description:
sample 72
8292044073_L


title: Monocyte sample 65

description:
sample 65
8292044073_E


title: Monocyte sample 63

description:
sample 63
8292044073_C


title: Monocyte sample 67

description:
sample 67
8292044073_G


title: Monocyte sample 62

description:
sample 62
8292044073_B


title: Monocyte sample 66

description:
sample 66
8292044073_F


title: Monocyte sample 64

description:
sample 64
8292044073_D


title: Monocyte sample 54

description:
sample 54
8292044059_F


title: Monocyte sample 48

description:
sample 48
7649540069_L


title: Monocyte sample 58

description:
sample 58
8292044059_J


title: Monocyte sample 52

description:
sample 52
8292044059_D


title: Monocyte sample 56

description:
sample 56
8292044059_H


title: Monocyte sample 50

description:
sample 50
8292044059_B


title: Monocyte sample 60

description:
sample 60
8292044059_L


title: Monocyte sample 59

description:
sample 59
8292044059_K

value: K


title: Monocyte sample 61

description:
sample 61
8292044073_A

value: A


title: Monocyte sample 38

description:
sample 38
7649540069_B


title: Monocyte sample 47

description:
sample 47
7649540069_K


title: Monocyte sample 53

description:
sample 53
8292044059_E


title: Monocyte sample 55

description:
sample 55
8292044059_G


title: Monocyte sample 69

description:
sample 69
8292044073_I


title: Monocyte sample 37

description:
sample 37
7649540069_A


title: Monocyte sample 40

description:
sample 40
7649540069_D


title: Monocyte sample 51

description:
sample 51
8292044059_C


title: Monocyte sample 49

description:
sample 49
8292044059_A


title: Monocyte sample 33

description:
sample 33
7602346090_I


title: Monocyte sample 43

description:
sample 43
7649540069_G


title: Monocyte sample 35

description:
sample 35
7602346090_K


title: Monocyte sample 57

description:
sample 57
8292044059_I


title: Monocyte sample 34

description:
sample 34
7602346090_J


title: Monocyte sample 42

description:
sample 42
7649540069_F

value: F


title: Monocyte sample 46

description:
sample 46
7649540069_J

value: J


title: Monocyte sample 41

description:
sample 41
7649540069_E

value: E


title: Monocyte sample 44

description:
sample 44
7649540069_H


title: Monocyte sample 45

description:
sample 45
7649540069_I

value: I


title: Monocyte sample 39

description:
sample 39
7649540069_C


title: Monocyte sample 31

description:
sample 31
7602346090_G


title: Monocyte sample 32

description:
sample 32
7602346090_H


title: Monocyte sample 27

description:
sample 27
7602346090_B


title: Monocyte sample 19

description:
sample 19
7602346077_E


title: Monocyte sample 29

description:
sample 29
7602346090_D


title: Monocyte sample 17

description:
sample 17
7602346077_C


title: Monocyte sample 25

description:
sample 25
7602346077_L


title: Monocyte sample 23

description:
sample 23
7602346077_I


title: Monocyte sample 21

description:
sample 21
7602346077_G


title: Monocyte sample 15

description:
sample 15
7602346077_A


title: Monocyte sample 13

description:
sample 13
7602346063_J


title: Monocyte sample 9

description:
sample 9
7602346063_E


title: Monocyte sample 11

description:
sample 11
7602346063_G


title: Monocyte sample 8

description:
sample 8
7602346063_D


title: Monocyte sample 26

description:
sample 26
7602346090_A


title: Monocyte sample 7

description:
sample 7
7602346063_C


title: Monocyte sample 22

description:
sample 22
7602346077_H


title: Monocyte sample 5

description:
sample 5
7602346012_L


title: Monocyte sample 12

description:
sample 12
7602346063_H


title: Monocyte sample 14

description:
sample 14
7602346063_L


title: Monocyte sample 18

description:
sample 18
7602346077_D


title: Monocyte sample 4

description:
sample 4
7602346012_K


title: Monocyte sample 16

description:
sample 16
7602346077_B


title: Monocyte sample 30

description:
sample 30
7602346090_F


title: Monocyte sample 36

description:
sample 36
7602346090_L


title: Monocyte sample 10

description:
sample 10
7602346063_F


title: Monocyte sample 6

description:
sample 6
7602346063_B


title: Monocyte sample 24

description:
sample 24
7602346077_J


title: Monocyte sample 28

description:
sample 28
7602346090_C


title: Monocyte sample 20

description:
sample 20
7602346077_F


title: Monocyte sample 2

description:
sample 2
7602346012_H


title: Monocyte sample 1

description:
sample 1
7602346012_E


title: Monocyte sample 3

description:
sample 3
7602346012_J


title: SNUINT91

status: Public on Oct 05 2017

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

description:
Gene expression data from Non tumor
SNU_N_10

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio

source_name: Non tumor

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser

tag: tissue

value: liver


title: SNUINT94

description:
Gene expression data from Non tumor
SNU_N_2


title: SNUINT86

description:
Gene expression data from Non tumor
SNU_N_30


title: SNUINT89

description:
Gene expression data from Non tumor
SNU_N_69


title: SNUINT85

description:
Gene expression data from Non tumor
SNU_N_16


title: SNUINT83

description:
Gene expression data from Non tumor
SNU_N_63


title: SNUINT92

description:
Gene expression data from Non tumor
SNU_N_39


title: SNUINT84

description:
Gene expression data from Non tumor
SNU_N_11


title: SNUINT78

description:
Gene expression data from Non tumor
SNU_N_42


title: SNUINT82

description:
Gene expression data from Non tumor
SNU_N_1


title: SNUINT87

description:
Gene expression data from Non tumor
SNU_N_68


title: SNUINT69

description:
Gene expression data from Non tumor
SNU_N_43


title: SNUINT81

description:
Gene expression data from Non tumor
SNU_N_41


title: SNUINT71

description:
Gene expression data from Non tumor
SNU_N_29


title: SNUINT73

description:
Gene expression data from Non tumor
SNU_N_44


title: SNUINT66

description:
Gene expression data from Non tumor
SNU_N_4


title: SNUINT80

description:
Gene expression data from Non tumor
SNU_N_38


title: SNUINT70

description:
Gene expression data from Non tumor
SNU_N_6


title: SNUINT68

description:
Gene expression data from Non tumor
SNU_N_5


title: SNUINT72

description:
Gene expression data from Non tumor
SNU_N_25


title: SNUINT79

description:
Gene expression data from Non tumor
SNU_N_14


title: SNUINT67

description:
Gene expression data from Non tumor
SNU_N_20


title: SNUINT93

description:
Gene expression data from Non tumor
SNU_N_8


title: SNUINT74

description:
Gene expression data from Non tumor
SNU_N_7


title: SNUINT88

description:
Gene expression data from Non tumor
SNU_N_12


title: SNUINT76

description:
Gene expression data from Non tumor
SNU_N_21


title: SNUINT77

description:
Gene expression data from Non tumor
SNU_N_9


title: SNUINT65

description:
Gene expression data from Non tumor
SNU_N_67


title: SNUINT63

description:
Gene expression data from hepatocellular carcinoma
SNU_T_64

source_name: Hepatocellular carcinoma

value: Hepatocellular carcinoma


title: SNUINT75

description:
Gene expression data from Non tumor
SNU_N_13


title: SNUINT90

description:
Gene expression data from Non tumor
SNU_N_70


title: SNUINT64

description:
Gene expression data from hepatocellular carcinoma
SNU_T_65


title: SNUINT62

description:
Gene expression data from hepatocellular carcinoma
SNU_T_63


title: SNUINT56

description:
Gene expression data from hepatocellular carcinoma
SNU_T_56


title: SNUINT59

description:
Gene expression data from hepatocellular carcinoma
SNU_T_59


title: SNUINT54

description:
Gene expression data from hepatocellular carcinoma
SNU_T_54


title: SNUINT61

description:
Gene expression data from hepatocellular carcinoma
SNU_T_62


title: SNUINT52

description:
Gene expression data from hepatocellular carcinoma
SNU_T_52


title: SNUINT49

description:
Gene expression data from hepatocellular carcinoma
SNU_T_49


title: SNUINT43

description:
Gene expression data from hepatocellular carcinoma
SNU_T_43


title: SNUINT47

description:
Gene expression data from hepatocellular carcinoma
SNU_T_47


title: SNUINT39

description:
Gene expression data from hepatocellular carcinoma
SNU_T_39


title: SNUINT55

description:
Gene expression data from hepatocellular carcinoma
SNU_T_55


title: SNUINT38

description:
Gene expression data from hepatocellular carcinoma
SNU_T_38


title: SNUINT37

description:
Gene expression data from hepatocellular carcinoma
SNU_T_37


title: SNUINT60

description:
Gene expression data from hepatocellular carcinoma
SNU_T_61


title: SNUINT41

description:
Gene expression data from hepatocellular carcinoma
SNU_T_41


title: SNUINT57

description:
Gene expression data from hepatocellular carcinoma
SNU_T_57


title: SNUINT35

description:
Gene expression data from hepatocellular carcinoma
SNU_T_35


title: SNUINT51

description:
Gene expression data from hepatocellular carcinoma
SNU_T_51


title: SNUINT53

description:
Gene expression data from hepatocellular carcinoma
SNU_T_53


title: SNUINT58

description:
Gene expression data from hepatocellular carcinoma
SNU_T_58


title: SNUINT40

description:
Gene expression data from hepatocellular carcinoma
SNU_T_40


title: SNUINT36

description:
Gene expression data from hepatocellular carcinoma
SNU_T_36


title: SNUINT42

description:
Gene expression data from hepatocellular carcinoma
SNU_T_42


title: SNUINT46

description:
Gene expression data from hepatocellular carcinoma
SNU_T_46


title: SNUINT45

description:
Gene expression data from hepatocellular carcinoma
SNU_T_45


title: SNUINT34

description:
Gene expression data from hepatocellular carcinoma
SNU_T_34


title: SNUINT33

description:
Gene expression data from hepatocellular carcinoma
SNU_T_33


title: SNUINT48

description:
Gene expression data from hepatocellular carcinoma
SNU_T_48


title: SNUINT44

description:
Gene expression data from hepatocellular carcinoma
SNU_T_44


title: SNUINT50

description:
Gene expression data from hepatocellular carcinoma
SNU_T_50


title: SNUINT32

description:
Gene expression data from hepatocellular carcinoma
SNU_T_32


title: SNUINT28

description:
Gene expression data from hepatocellular carcinoma
SNU_T_28


title: SNUINT30

description:
Gene expression data from hepatocellular carcinoma
SNU_T_30


title: SNUINT22

description:
Gene expression data from hepatocellular carcinoma
SNU_T_22


title: SNUINT24

description:
Gene expression data from hepatocellular carcinoma
SNU_T_24


title: SNUINT29

description:
Gene expression data from hepatocellular carcinoma
SNU_T_29


title: SNUINT27

description:
Gene expression data from hepatocellular carcinoma
SNU_T_27


title: SNUINT23

description:
Gene expression data from hepatocellular carcinoma
SNU_T_23


title: SNUINT21

description:
Gene expression data from hepatocellular carcinoma
SNU_T_21


title: SNUINT26

description:
Gene expression data from hepatocellular carcinoma
SNU_T_26


title: SNUINT16

description:
Gene expression data from hepatocellular carcinoma
SNU_T_16


title: SNUINT13

description:
Gene expression data from hepatocellular carcinoma
SNU_T_13


title: SNUINT31

description:
Gene expression data from hepatocellular carcinoma
SNU_T_31


title: SNUINT17

description:
Gene expression data from hepatocellular carcinoma
SNU_T_17


title: SNUINT6

description:
Gene expression data from hepatocellular carcinoma
SNU_T_6


title: SNUINT15

description:
Gene expression data from hepatocellular carcinoma
SNU_T_15


title: SNUINT8

description:
Gene expression data from hepatocellular carcinoma
SNU_T_8


title: SNUINT5

description:
Gene expression data from hepatocellular carcinoma
SNU_T_5


title: SNUINT11

description:
Gene expression data from hepatocellular carcinoma
SNU_T_11


title: SNUINT20

description:
Gene expression data from hepatocellular carcinoma
SNU_T_20


title: SNUINT19

description:
Gene expression data from hepatocellular carcinoma
SNU_T_19


title: SNUINT10

description:
Gene expression data from hepatocellular carcinoma
SNU_T_10


title: SNUINT7

description:
Gene expression data from hepatocellular carcinoma
SNU_T_7


title: SNUINT9

description:
Gene expression data from hepatocellular carcinoma
SNU_T_9


title: SNUINT12

description:
Gene expression data from hepatocellular carcinoma
SNU_T_12


title: SNUINT14

description:
Gene expression data from hepatocellular carcinoma
SNU_T_14


title: SNUINT3

description:
Gene expression data from hepatocellular carcinoma
SNU_T_3


title: A2780_RT_2

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

description: miRNA expression resistant under epimiRNAtic reactivation treatment A2780 ovarian cancer cell line

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized onto Human miRNA Microarray v2, 8x15K (G4470B) for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent Technologies) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were washed according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were dried out using a centrifuge at 1000 rpm for 2 min.

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Image (.tiff file) provided by the scanner was analyzed using Feature Extraction software version 10 (Agilent Technologies). Data from the arrays were normalized based on the VSN method. After normalization, were considered for further analysis only those probes present in at least one sample for microRNA microarrays and at least 50% of all the samples for mRNA microarray; both experiments with average expression over the 20th percentile of all average expressions and that change across the experiment (i.e. with coefficient of variation (CV)>5 % across all samples)

source_name: Resistant under epigenetic reactivation treatment A2780 lung cancer cell line

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: Total RNA was extracted by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment as recommended by Agilent

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. Resistant variants were treated with epigenetic reactivation drugs 5Aza-2deoxycytidine (5Aza-dC) and Trichostatin A (TSA) (Sigma-Aldrich, Spain)

tag: cell line

value: Ovarian

tag: chemoterapy drug

value: cisplatin

tag: phenotype


title: A2780_RT_1

value: Resistant under epigenetic reactivation treatment


title: A2780_S_1

description: miRNA expression rene expression sensitive cisplatin A2780 ovarian cancer cell line

source_name: Sensitive cisplatin A2780 lung cancer cell line

value: Sensitive


title: A2780_R_1

description: miRNA expression resistant cisplatin A2780 ovarian cancer cell line

source_name: Resistant cisplatin A2780 lung cancer cell line

value: Resistant


title: A2780_R_2


title: A2780_S_2

description: miRNA expression sensitive cisplatin A2780 ovarian cancer cell line


title: SNUINT18

description:
Gene expression data from hepatocellular carcinoma
SNU_T_18


title: OVCAR3_S_1

description: miRNA expression sensitive cisplatin OVCAR3 ovarian cancer cell line

source_name: Sensitive cisplatin OVCAR3 lung cancer cell line


title: OVCAR3_S_2


title: OVCAR3_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment OVCAR3 ovarian cancer cell line

source_name: Resistant under epigenetic reactivation treatment OVCAR3 lung cancer cell line


title: OVCAR3_R_2

description: miRNA expression resistant cisplatin OVCAR3 ovarian cancer cell line

source_name: Resistant cisplatin OVCAR3 lung cancer cell line


title: H460_RT_1

description: miRNA expression resistant under epimiRNAtic reactivation treatment H2460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H2460 lung cancer cell line

value: Lung


title: H460_S_2

description: miRNA expression sensitive cisplatin H460 lung cancer cell line

source_name: Sensitive cisplatin H460 lung cancer cell line


title: H23_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment H23 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H23 lung cancer cell line


title: H460_S_1


title: OVCAR3_R_1


title: H23_R_1

description: miRNA expression resistant cisplatin H23 lung cancer cell line

source_name: Resistant cisplatin H23 lung cancer cell line


title: H23_RT_1


title: H23_S_2

description: miRNA expression sensitive cisplatin H23 lung cancer cell line

source_name: Sensitive cisplatin H23 lung cancer cell line


title: H23_R_2


title: SNUINT2

description:
Gene expression data from hepatocellular carcinoma
SNU_T_2


title: H23_S_1


title: H460_R_2

description: miRNA expression resistant cisplatin H460 lung cancer cell line

source_name: Resistant cisplatin H460 lung cancer cell line


title: H460_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment H460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H460 lung cancer cell line


title: H460_R_1


title: OVCAR3_RT_1


title: SNUINT1

description:
Gene expression data from hepatocellular carcinoma
SNU_T_1


title: SNUINT25

description:
Gene expression data from hepatocellular carcinoma
SNU_T_25


title: Liver_CON group at 9 d, rep 6

city: Helsinki

first: Nanbing

last: Qin

address: Koetilantie 5

department: Department of Agricultural Sciences

country: Finland

institute: University of Helsinki

description: Gene expression data from liver in CON group at 9 d, cow 528

hyb_protocol: Protocols were according to Affymetrix GeneChip Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 3 using Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 with Affymetrix GeneChip Command Console, version 2.0.

data_processing: Primary analyses were done with Affymetrix GeneChip Expression Console, version 1.1. The data were analyzed with R/Bioconductor and Chipster software packages using RMA as normalization method.

organism: Bos taurus

source_name: Liver biopsy in CON group at 9 d, cow 528

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Liver samples collected with biopsy at -8 d, 1 d, and 9 d and were stored in protective solution at -20°C before total RNA extraction.

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to manufacturer’s instructions.

treatment_protocol: Approximately 3-5 mg of liver was homogenized using TissueRuptor-homogenizer.

tag: diet

value: CON

tag: time point

value: 9 d


title: Liver_CON group at 9 d, rep 2

description: Gene expression data from liver in CON group at 9 d, cow 477

source_name: Liver biopsy in CON group at 9 d, cow 477


title: Liver_CON group at 9 d, rep 5

description: Gene expression data from liver in CON group at 9 d, cow 527

source_name: Liver biopsy in CON group at 9 d, cow 527


title: Liver_HIGH group at 9 d, rep 4

description: Gene expression data from liver in HIGH group at 9 d, cow 460

source_name: Liver biopsy in HIGH group at 9 d, cow 460

value: HIGH


title: Liver_HIGH group at 9 d, rep 2

description: Gene expression data from liver in HIGH group at 9 d, cow 432

source_name: Liver biopsy in HIGH group at 9 d, cow 432


title: Liver_CON group at 9 d, rep 4

description: Gene expression data from liver in CON group at 9 d, cow 510

source_name: Liver biopsy in CON group at 9 d, cow 510


title: Liver_HIGH group at 9 d, rep 5

description: Gene expression data from liver in HIGH group at 9 d, cow 462

source_name: Liver biopsy in HIGH group at 9 d, cow 462


title: Liver_HIGH group at 9 d, rep 3

description: Gene expression data from liver in HIGH group at 9 d, cow 439

source_name: Liver biopsy in HIGH group at 9 d, cow 439


title: Liver_HIGH group at 9 d, rep 6

description: Gene expression data from liver in HIGH group at 9 d, cow 529

source_name: Liver biopsy in HIGH group at 9 d, cow 529


title: Liver_CON group at 1 d, rep 2

description: Gene expression data from liver in CON group at 1 d, cow 477

source_name: Liver biopsy in CON group at 1 d, cow 477

value: 1 d


title: Liver_HIGH group at 1 d, rep 5

description: Gene expression data from liver in HIGH group at 1 d, cow 462

source_name: Liver biopsy in HIGH group at 1 d, cow 462


title: Liver_HIGH group at 1 d, rep 4

description: Gene expression data from liver in HIGH group at 1 d, cow 460

source_name: Liver biopsy in HIGH group at 1 d, cow 460


title: Liver_HIGH group at 1 d, rep 3

description: Gene expression data from liver in HIGH group at 1 d, cow 439

source_name: Liver biopsy in HIGH group at 1 d, cow 439


title: Liver_CON group at 9 d, rep 1

description: Gene expression data from liver in CON group at 9 d, cow 445

source_name: Liver biopsy in CON group at 9 d, cow 445


title: Liver_CON group at 1 d, rep 4

description: Gene expression data from liver in CON group at 1 d, cow 510

source_name: Liver biopsy in CON group at 1 d, cow 510


title: Liver_HIGH group at -8 d, rep 3

description: Gene expression data from liver in HIGH group at -8 d, cow 460

source_name: Liver biopsy in HIGH group at -8 d, cow 460


title: Liver_HIGH group at 9 d, rep 1

description: Gene expression data from liver in HIGH group at 9 d, cow 512

source_name: Liver biopsy in HIGH group at 9 d, cow 512


title: Liver_CON group at 1 d, rep 1

description: Gene expression data from liver in CON group at 1 d, cow 445

source_name: Liver biopsy in CON group at 1 d, cow 445


title: Liver_HIGH group at -8 d, rep 4

description: Gene expression data from liver in HIGH group at -8 d, cow 462

source_name: Liver biopsy in HIGH group at -8 d, cow 462


title: Liver_HIGH group at 1 d, rep 1

description: Gene expression data from liver in HIGH group at 1 d, cow 512

source_name: Liver biopsy in HIGH group at 1 d, cow 512


title: Liver_CON group at 9 d, rep 3

description: Gene expression data from liver in CON group at 9 d, cow 483

source_name: Liver biopsy in CON group at 9 d, cow 483


title: Liver_HIGH group at 1 d, rep 6

description: Gene expression data from liver in HIGH group at 1 d, cow 529

source_name: Liver biopsy in HIGH group at 1 d, cow 529


title: WT_rep1 (II)

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

description: RNAs isolated from WT hKCs

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Control probes were excluded before data processing. Scanned signal intensity (gMedianSignal) was log2-transformed. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011b).

label: Cyanine 3-CTP

source_name: WT hKC

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Human epidermal keratinocytes (Cascade) were maintained in Keratinocyte Growth GOLD Medium (LONZA).

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

treatment_protocol: For siRNA transfection, we used ON-TARGETplus SMARTpool siRNA (Thermo) with Lipofectamine RNAiMax (Invitrogen) according to the manufacturers’ instructions.

tag: cell type

value: Human epidermal keratinocytes (hKCs)

tag: genotype/variation

value: WT


title: WT_rep2 (II)

description: RNAs isolated from WT hKCs


title: Liver_CON group at 1 d, rep 3

description: Gene expression data from liver in CON group at 1 d, cow 483

source_name: Liver biopsy in CON group at 1 d, cow 483


title: KD_rep1 (II)

description: RNAs isolated from ZIP10-KD hKCs

source_name: ZIP10-KD hKCs


title: Liver_HIGH group at 1 d, rep 2

description: Gene expression data from liver in HIGH group at 1 d, cow 432

source_name: Liver biopsy in HIGH group at 1 d, cow 432


title: Liver_HIGH group at -8 d, rep 5

description: Gene expression data from liver in HIGH group at -8 d, cow 529

source_name: Liver biopsy in HIGH group at -8 d, cow 529


title: KD_rep2 (II)

description: RNAs isolated from ZIP10-KD hKCs


title: Liver_HIGH group at -8 d, rep 2

description: Gene expression data from liver in HIGH group at -8 d, cow 439

source_name: Liver biopsy in HIGH group at -8 d, cow 439


title: Liver_CON group at -8 d, rep 2

description: Gene expression data from liver in CON group at -8 d, cow 477

source_name: Liver biopsy in CON group at -8 d, cow 477


title: Liver_CON group at -8 d, rep 3

description: Gene expression data from liver in CON group at -8 d, cow 483

source_name: Liver biopsy in CON group at -8 d, cow 483


title: Liver_HIGH group at -8 d, rep 1

description: Gene expression data from liver in HIGH group at -8 d, cow 432

source_name: Liver biopsy in HIGH group at -8 d, cow 432


title: Liver_CON group at -8 d, rep 5

description: Gene expression data from liver in CON group at -8 d, cow 528

source_name: Liver biopsy in CON group at -8 d, cow 528


title: Liver_CON group at -8 d, rep 4

description: Gene expression data from liver in CON group at -8 d, cow 527

source_name: Liver biopsy in CON group at -8 d, cow 527


title: Liver_CON group at -8 d, rep 1

description: Gene expression data from liver in CON group at -8 d, cow 445

source_name: Liver biopsy in CON group at -8 d, cow 445


title: Sample-11-REDD1 Knockout Exercise

city: SAN DIEGO

first: Alexey

middle: M

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

description: Gene expression data from plantaris of exercised mouse

hyb_protocol: Following fragmentation, 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45 degrees C on GeneChip Mouse Gene 2.0 ST Arrays.  The staining and washing of the arrays were conducted using an Affymetrix Fluidics 450 Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Sofware and GeneChip Scanner 3000 7G according to manufacturer's instructions.

data_processing: Raw data files were imported into Partek's Genomic Software.  The Robust Microarray Average method was used for data processing which included background correction, quantile normalization, and median polish corrections.  Signals for probes were Log2 transformed.

organism: Mus musculus

source_name: Plantaris from exercised REDD1 knockout mouse

label_protocol: 300 ng of total RNA was labeled according to the Whole Transcript Sense Target Labeling Assay protocol using Affymetrix's GeneChip WT PLUS Reagent kit (cat. #902281)

growth_protocol: Mice were bred and housed in a temperature (25 degree C) and light controlled environment (12hr:12hr light:dark) on corn cob bedding.  Mice were provided rodent chow (Harlan-Teklad 2018) and water ad libitum.  All mice were deprived of food for 3 hr prior to acute exercise

extract_protocol: Total RNA from plantaris was extracted in 500 ul of Tri Reagent (Zymo) and isolated using a Zymo RNA Miniprep kit (cat. #R2071) with on column Dnase treatment according to the manufacturer's instructions

treatment_protocol: All mice were anesthetized with 2-3% isoflurane and the plantaris was extracted, frozen in liquid nitrogen, and stored at -80 degree C until analysis

value: plantaris

tag: genotype

value: REDD1 Knockout

tag: gender

value: male

tag: age

value: 12 weeks


title: Sample-12-REDD1 Knockout Exercise


title: Sample-7-REDD1 Knockout Sedentary

description: Gene expression data from plantaris of sedentary mouse

source_name: Plantaris from sedentary REDD1 knockout mouse


title: SNUINT4

description:
Gene expression data from hepatocellular carcinoma
SNU_T_4

source_name: Hepatocellular carcinoma

value: Hepatocellular carcinoma


title: Sample-8-REDD1 Knockout Sedentary


title: Sample-10-REDD1 Knockout Exercise


title: Sample-9-REDD1 Knockout Sedentary


title: Sample-5-Wild Type Exercise

source_name: Plantaris from exercised wild type mouse

value: Wild Type


title: OsFBK1 knock-down 14-day-old seedling, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of roots of OsFBK1-KD 14-day-old Pusa Basmati-1 seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using Expression Console 1.4.1.46 (Affymetrix).

label: Biotin

organism: Oryza sativa Indica Group

source_name: 14-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each line were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown for fourteen days on half-strength MS basal at 28±1oC.

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

tag: cultivar

value: Pusa Basmati 1

value: root


title: OsFBK1 over-expression 14-day-old seedling, Biological replicate 1

description: Gene expression data of roots of OsFBK1-OE 14-day-old Pusa Basmati-1 seedling


title: Sample-6-Wild Type Exercise


title: Vector control 14-day old-seedling, Biological replicate 1

description: Gene expression data of roots of Vector control 14-day-old Pusa Basmati-1 seedling

value: Vector control


title: Sample-4-Wild Type Exercise


title: Sample-2-Wild Type Sedentary

source_name: Plantaris from sedentary wild type mouse


title: OsFBK1 knock-down 14-day-old seedling, Biological replicate 2


title: OsFBK1 over-expression 14-day-old seedling, Biological replicate 2


title: Vector control 14-day old-seedling, Biological replicate 2


title: Wild type Pusa Basmati-1 14-day-old seedling, Biological replicate 1

description: Gene expression data of roots of Wild-type 14-day-old Pusa Basmati-1 seedling

value: Wild-type


title: Sample-3-Wild Type Sedentary


title: TL-OM1_THZ1_3

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: Array signals were normalized using RMA (http://rmaexpress.bmbolstad.com/).  Differential gene expression was determined using a moderated t-test in the “limma” package (http://bioinf.wehi.edu.au/limma/) from Bioconductor (www.bioconductor.org).

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol: Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).

treatment_protocol: TL-Om1 cells were treated with control DMSO or THZ1 (100 nM) for 6 hours in biological triplicates.

value: adult T-cell leukemia/lymphoma (ATL) cell line

tag: treated with

value: THZ1 for 6 hrs


title: A2780_RT_1

description: Gene expression resistant under epigenetic reactivation treatment A2780 ovarian cancer cell line

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were dried out using a centrifuge.

scan_protocol: Arrays were scanned at 5 um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

data_processing: Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies). Data from the arrays were normalized based on the VSN method. After normalization, were considered for further analysis only those probes present in at least one sample for microRNA microarrays and at least 50% of all the samples for mRNA microarray; both experiments with average expression over the 20th percentile of all average expressions and that change across the experiment (i.e. with coefficient of variation (CV)>5 % across all samples)

source_name: Resistant under epigenetic reactivation treatment A2780 lung cancer cell line

label_protocol: One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. Briefly, 1 ug of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP

value: Ovarian

value: cisplatin


title: Sample-1-Wild Type Sedentary


title: TL-OM1_DMSO_3

value: control DMSO  for 6 hrs


title: TL-OM1_THZ1_1


title: Wild type Pusa Basmati-1 14-day-old seedling, Biological replicate 2

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 45oC on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.


title: A2780_RT_2

value: Resistant under epigenetic reactivation treatment


title: TL-OM1_THZ1_2


title: A2780_S_2

description: Gene expression sensitive cisplatin A2780 ovarian cancer cell line

source_name: Sensitive cisplatin A2780 lung cancer cell line

value: Sensitive


title: TL-OM1_DMSO_2


title: A2780_R_1

description: Gene expression resistant cisplatin A2780 ovarian cancer cell line

source_name: Resistant cisplatin A2780 lung cancer cell line

value: Resistant


title: OVCAR3_R_2

description: Gene expression resistant cisplatin OVCAR3 ovarian cancer cell line

source_name: Resistant cisplatin OVCAR3 lung cancer cell line


title: A2780_S_1

description: Gene expression rene expression sensitive cisplatin A2780 ovarian cancer cell line


title: OVCAR3_RT_2

description: Gene expression resistant under epigenetic reactivation treatment OVCAR3 ovarian cancer cell line

source_name: Resistant under epigenetic reactivation treatment OVCAR3 lung cancer cell line


title: OVCAR3_S_2

description: Gene expression sensitive cisplatin OVCAR3 ovarian cancer cell line

source_name: Sensitive cisplatin OVCAR3 lung cancer cell line


title: H23_RT_2

description: Gene expression resistant under epigenetic reactivation treatment H23 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H23 lung cancer cell line

value: Lung


title: OVCAR3_S_1


title: H460_S_2

description: Gene expression sensitive cisplatin H460 lung cancer cell line

source_name: Sensitive cisplatin H460 lung cancer cell line


title: H460_R_1

description: Gene expression resistant cisplatin H460 lung cancer cell line

source_name: Resistant cisplatin H460 lung cancer cell line


title: TL-OM1_DMSO_1


title: H460_RT_2

description: Gene expression resistant under epigenetic reactivation treatment H460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H460 lung cancer cell line


title: H460_RT_1

description: Gene expression resistant under epigenetic reactivation treatment H2460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H2460 lung cancer cell line


title: OVCAR3_RT_1


title: H460_S_1


title: H23_R_2

description: Gene expression resistant cisplatin H23 lung cancer cell line

source_name: Resistant cisplatin H23 lung cancer cell line


title: H23_RT_1


title: H23_S_2

description: Gene expression sensitive cisplatin H23 lung cancer cell line

source_name: Sensitive cisplatin H23 lung cancer cell line


title: OVCAR3_R_1


title: 7785_Donor 3

city: Houston

first: Cliona

last: Rooney

state: Texas

address: 1102 Bates Street

institute: Baylor College of Medicine

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7785_12.RCC

hyb_protocol: Hybridization protocol: Depending on sample quality, either 100ng or 300 nanograms of total RNA were hybridized  with the NanoString Technologies nCounter GX Human Immunology Kit V2 containing 594  unique pairs of 35-50bp reporter probes and biotin-labeled capture probes, including internal  reference controls. Overnight hybridization occurred for 16.8 hours at 65°C.                 Wash protocol:  Removal of excess probes with magnetic bead purification was performed on the nCounter  Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA  structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end  to remove excess capture probes. Once unbound probes were washed away, the tripartite  structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned  by an electric current (negative to positive), and immobilized. Photobleaching and flurophore  degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer  (software v3.0.1.4) and scanned at 555 fields of view (FOV). An epi-fluorescent microscope and  CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality  control metrics were recorded using the nSolver Analysis Software v3.0.22.

data_processing: The raw data was analyzed with the nSolver Analysis Software 3.0 program to generate the normalized data. The median values of negative controls were used for background subtraction and the geometric mean was used for normalization. The normalized output excluded lanes/samples flagged in normalization.

source_name: donor 3

label_protocol: No label is used in Nanostring

extract_protocol: Qiagen MRNeasy Micro Kit

tag: subject status

value: Healthy human donor

value: peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: GD2-CAR-modified T-cells


title: H23_R_1


title: 7547_Donor 4

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7547_04.RCC

source_name: donor 4


title: 7544_Donor 1

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7544_01.RCC

source_name: donor 1


title: 7548_Donor 5

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7548_05.RCC

source_name: donor 5


title: 7551_Donor 2

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7551_07.RCC

source_name: donor 2

value: GD2-CAR.C7R-modified T-cells


title: 7545_Donor 2

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7545_02.RCC


title: 7550_Donor 1

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7550_06.RCC


title: 7555_Donor 4

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7555_11.RCC


title: 7552_Donor 3

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7552_08.RCC


title: 7554_Donor 5

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7554_10.RCC


title: 7553_Donor 6

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7553_09.RCC

source_name: donor 6


title: 7546_Donor 3

description:
T-cells have been isolated from co-culture by magnetic bead separation
20170404_mtb-HF-112140-NSXHIm2_HF7546_03.RCC


title: H23_S_1


title: H460_R_2

description: Gene expression resistant cisplatin H460 lung cancer cell line


title: Bhadua

status: Public on Oct 04 2017

city: Nagoya

first: Takeshi

last: Kuroha

address: Chikusa-ku Furo-cho

country: Japan

institute: Bioscience and Biotechnology Center,  Nagoya University

hyb_protocol: 825 ng of each Cy-3-labeled cRNAs were used for hybridization.

scan_protocol: Using Agilent scanner model G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent)

organism: Oryza sativa

source_name: Basal node to 1 cm above shoot apical meristem, 8 hour submergence, 6 week-old samples.

label_protocol: 400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).

growth_protocol: Plants were grown until eight-leaf-stage in the field.

extract_protocol: RNAs were extracted from basal node to 1 cm above shoot apical meristem by RNeasy mini kit (Qiagen).

treatment_protocol: Plants were completely submerged for 6 hours.

tag: line name

value: Parental line, Bhadua


title: RIL_114

value: Recombinant inbred line #114 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_111

value: Recombinant inbred line #111 (T65 x Bhadua)


title: RIL_109

value: Recombinant inbred line #109 (T65 x Bhadua)


title: RIL_118

value: Recombinant inbred line #118 (T65 x Bhadua)


title: RIL_116

value: Recombinant inbred line #116 (T65 x Bhadua)


title: RIL_106

value: Recombinant inbred line #106 (T65 x Bhadua)


title: T65

value: Parental line, T65


title: RIL_77

value: Recombinant inbred line #77 (T65 x Bhadua)


title: RIL_79

value: Recombinant inbred line #79 (T65 x Bhadua)


title: RIL_104

value: Recombinant inbred line #104 (T65 x Bhadua)


title: RIL_94

value: Recombinant inbred line #94 (T65 x Bhadua)


title: RIL_96

value: Recombinant inbred line #96 (T65 x Bhadua)


title: RIL_93

value: Recombinant inbred line #93 (T65 x Bhadua)


title: RIL_98

value: Recombinant inbred line #98 (T65 x Bhadua)


title: RIL_87

value: Recombinant inbred line #87 (T65 x Bhadua)


title: RIL_112

value: Recombinant inbred line #112 (T65 x Bhadua)


title: RIL_72

value: Recombinant inbred line #72 (T65 x Bhadua)


title: RIL_82

value: Recombinant inbred line #82 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_83

value: Recombinant inbred line #83 (T65 x Bhadua)


title: RIL_90

value: Recombinant inbred line #90 (T65 x Bhadua)


title: RIL_80

value: Recombinant inbred line #80 (T65 x Bhadua)


title: RIL_92

value: Recombinant inbred line #92 (T65 x Bhadua)


title: A2780_R_2

description: Gene expression resistant cisplatin A2780 ovarian cancer cell line

source_name: Resistant cisplatin A2780 lung cancer cell line

value: Ovarian

value: cisplatin

value: Resistant


title: RIL_71

value: Recombinant inbred line #71 (T65 x Bhadua)


title: RIL_74

value: Recombinant inbred line #74 (T65 x Bhadua)


title: RIL_81

value: Recombinant inbred line #81 (T65 x Bhadua)


title: RIL_91

value: Recombinant inbred line #91 (T65 x Bhadua)


title: N27_MPP+_rep3

type: genomic

city: Pune

first: Santosh

middle: Chandrakant

last: Narwade

state: Maharashtra

address: Ganeshkhind Road

department: Department of Zoology

institute: University of Pune

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with MPP+ _rep3

hyb_protocol: Genomic DNA (2 µg) was sheared into 1.5-2 kb fragments by sonication and the fragments were denatured by heating at 95OC and hybridized on to a Rat GE 4x44K v3 Microarray slides (Agilent Technologies, CA, USA) each with 4x44K arrays, containing 44,000 probes of 22,583 genes.

scan_protocol: Scanned with ScanArray Express at 5 m resolution at 543 nm. Scanarray software was used for data acquisition, mean or median intensity calculation of each spot and normalization.

data_processing: For normalization of microarray data, LOWESS normalization was used as the default parameter for the array scanning apparatus. The microarray slides were provided with spots containing negative controls and positive controls, which provides a background signal. The fluorescence values from these spots were considered to be representatives of non-specific binding of the DNA to the slides and these values were used to determine the true positives in the data. These values were together termed as control values. The control values from each individual array were used to normalize the fluorescence for all the genes of that array in order to provide a uniform scale for comparison of genes between arrays. Assuming an error of 20 % in the ability to detect true positives, signals which were higher than 20% of the control value were considered a true positive. The normalization was performed by dividing the fluorescence values with the cutoff value of the respective arrays. For comparison of the genes between arrays the normalized values of fluorescence were used. The signal intensities were normalized considering signal to noise ratio of 1. This gave a quantifiable positive value in the form of fold intensity which was then compared within the replicates. All the spots which were identified as true positives in all three arrays were used for further analysis.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: N27_MPP+ treated cells_rep3

label_protocol: After hybridization at 42OC for 16 h, the slides were washed, blocked and then incubated in anti-5-methylcytosine antibody (1h at 25OC). Slides were then washed and incubated in cy3 labeled anti-mouse IgG (1h at 25OC)

growth_protocol: Rat dopaminergic neural cell line at standard condition in medium

extract_protocol: Genomic DNA was isolated from cells of different experimental groups, subjected to proteinase K digestion in the presence of 1% SDS, followed by phenol: chloroform extraction, RNase A treatment and precipitation using NaCl and ethanol.

treatment_protocol: Rat dopaminergic neural cells treated with treated with MPP+ at sublethal dose.

value: Rat Dopaminergic Neural Cell Line

tag: treatment

value: MPP


title: RIL_113

value: Recombinant inbred line #113 (T65 x Bhadua)

tag: tissue


title: RIL_108

value: Recombinant inbred line #108 (T65 x Bhadua)


title: N27_MPP+_rep2

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with MPP+ _rep2

source_name: N27_MPP+ treated cells_rep2

tag: cell line


title: N27_MPP+_rep1

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with MPP+ _rep1

source_name: N27_MPP+ treated cells_rep1


title: N27_Mn_rep2

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with Mn _rep2

source_name: N27_Mn treated cells_rep2

treatment_protocol: Rat dopaminergic neural cells treated with treated Mn at sublethal dose.

value: Mn


title: N27_Control_rep3

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line_rep3

source_name: N27_Control cells_rep3

treatment_protocol: Rat dopaminergic neural cells were used as control for other treatments.

value: control


title: N27_Mn_rep3

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with Mn _rep3

source_name: N27_Mn treated cells_rep3


title: N27_Control_rep2

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line_rep2

source_name: N27_Control cells_rep2


title: N27_Mn_rep1

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line treated with Mn _rep1

source_name: N27_Mn treated cells_rep1


title: N27_Control_rep1

description: Genome wide DNA methylation analysis of rat dopaminergic neural cell line_rep1

source_name: N27_Control cells_rep1


title: RIL_70

value: Recombinant inbred line #70 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_66

value: Recombinant inbred line #66 (T65 x Bhadua)


title: RIL_69

value: Recombinant inbred line #69 (T65 x Bhadua)


title: RIL_62

value: Recombinant inbred line #62 (T65 x Bhadua)


title: RIL_64

value: Recombinant inbred line #64 (T65 x Bhadua)


title: RIL_65

value: Recombinant inbred line #65 (T65 x Bhadua)


title: RIL_51

value: Recombinant inbred line #51 (T65 x Bhadua)


title: RIL_63

value: Recombinant inbred line #63 (T65 x Bhadua)


title: RIL_60

value: Recombinant inbred line #60 (T65 x Bhadua)


title: RIL_57

value: Recombinant inbred line #57 (T65 x Bhadua)


title: RIL_56

value: Recombinant inbred line #56 (T65 x Bhadua)


title: RIL_58

value: Recombinant inbred line #58 (T65 x Bhadua)


title: RIL_49

value: Recombinant inbred line #49 (T65 x Bhadua)


title: RIL_61

value: Recombinant inbred line #61 (T65 x Bhadua)


title: RIL_46

value: Recombinant inbred line #46 (T65 x Bhadua)


title: RIL_48

value: Recombinant inbred line #48 (T65 x Bhadua)


title: RIL_54

value: Recombinant inbred line #54 (T65 x Bhadua)


title: RIL_45

value: Recombinant inbred line #45 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_55

value: Recombinant inbred line #55 (T65 x Bhadua)


title: RIL_59

value: Recombinant inbred line #59 (T65 x Bhadua)


title: RIL_38

value: Recombinant inbred line #38 (T65 x Bhadua)


title: RIL_50

value: Recombinant inbred line #50 (T65 x Bhadua)


title: RIL_40

value: Recombinant inbred line #40 (T65 x Bhadua)


title: RIL_37

value: Recombinant inbred line #37 (T65 x Bhadua)


title: RIL_34

value: Recombinant inbred line #34 (T65 x Bhadua)


title: RIL_36

value: Recombinant inbred line #36 (T65 x Bhadua)


title: RIL_42

value: Recombinant inbred line #42 (T65 x Bhadua)


title: RIL_41

value: Recombinant inbred line #41 (T65 x Bhadua)


title: RIL_29

value: Recombinant inbred line #29 (T65 x Bhadua)


title: RIL_43

value: Recombinant inbred line #43 (T65 x Bhadua)


title: RIL_31

value: Recombinant inbred line #31 (T65 x Bhadua)


title: RIL_33

value: Recombinant inbred line #33 (T65 x Bhadua)


title: RIL_26

value: Recombinant inbred line #26 (T65 x Bhadua)


title: RIL_27

value: Recombinant inbred line #27 (T65 x Bhadua)


title: RIL_28

value: Recombinant inbred line #28 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_24

value: Recombinant inbred line #24 (T65 x Bhadua)


title: D24d2

first: Zhiqiang

last: Wang

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Performed by Expression Analysis (Durham, NC) using Illumina HT12v4.0 BeadArrays

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated by GenomeStudio with quantile normalization subtract background.

source_name: Cell line

growth_protocol: Cells were cultured in growth medium (RPMI supplemented with 10% FCS and 1% Normocin) and plated at no more than 75% confluence for treatment with each drug.  After treatment with drug or control for 24 hr, cells were washed with sterile PBS and then trypsinized. Collected cells were then washed twice with sterile PBS and spun. Supernatant was aspirated, and cell pellet flash frozen in liquid nitrogen.

extract_protocol: Frozen pellets were shipped to Expression Analysis (Durham, NC) for RNA isolation and analysis.

value: Control, DMSO


title: RIL_18

value: Recombinant inbred line #18 (T65 x Bhadua)


title: RIL_22

value: Recombinant inbred line #22 (T65 x Bhadua)


title: RIL_23

value: Recombinant inbred line #23 (T65 x Bhadua)


title: RIL_17

value: Recombinant inbred line #17 (T65 x Bhadua)


title: RIL_13

value: Recombinant inbred line #13 (T65 x Bhadua)


title: RIL_16

value: Recombinant inbred line #16 (T65 x Bhadua)


title: RIL_20

value: Recombinant inbred line #20 (T65 x Bhadua)


title: C24d2

scan_protocol: Performed by Expression Analysis (Durham, NC) using Illumina HT12v4.0 BeadArrays


title: D24d1

label_protocol: Performed by Expression Analysis (Durham, NC)


title: RIL_19

value: Recombinant inbred line #19 (T65 x Bhadua)


title: D24b1

value: Ganetespib, 125 nM


title: D24a1

value: SN38, 1 uM


title: RIL_15

value: Recombinant inbred line #15 (T65 x Bhadua)


title: D24b2


title: C24b2


title: C24a1


title: D24a2


title: RIL_10

value: Recombinant inbred line #10 (T65 x Bhadua)


title: RIL_47

value: Recombinant inbred line #47 (T65 x Bhadua)


title: C24a2


title: C24d1


title: C24b1


title: RIL_5

value: Recombinant inbred line #5 (T65 x Bhadua)


title: B24b1


title: A24a2


title: B24d1


title: RIL_9

value: Recombinant inbred line #9 (T65 x Bhadua)

value: Basal node to 1 cm above shoot apical meristem


title: RIL_6

value: Recombinant inbred line #6 (T65 x Bhadua)


title: B24a1


title: RIL_2

value: Recombinant inbred line #2 (T65 x Bhadua)


title: A24d1

value: Control, DMSO


title: A24a1


title: RIL_3

value: Recombinant inbred line #3 (T65 x Bhadua)


title: RIL_25

value: Recombinant inbred line #25 (T65 x Bhadua)


title: RIL_7

value: Recombinant inbred line #7 (T65 x Bhadua)


title: RIL_4

value: Recombinant inbred line #4 (T65 x Bhadua)


title: A24b1


title: INM-rep1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

description: SAMPLE 7

hyb_protocol: Hybridization of 2µg labelled cDNA per sample was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 20 µm/pixel resolution and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47)

source_name: INM

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2µg amplified cDNA was Cy3-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: Mice were grown under standard conditions. RNA was isolated directly after FACS sorting. Cells were not grown in vitro.

extract_protocol: Qiagen Rneasy micro kit

treatment_protocol: All groups: pregnant mice were injected with tamoxifen at embryonic day E15.5 (0.1mg/g body weight). Lungs were harvested for FACS sorting of RFP-positive cells at E18.5. Cells were stained with Acta2 and PDGFRalpha. RFP,Acta2-positive populations comprise airway and vascular smooth musle cell group. RFP, PDGFRalpha-positive populations comprise alveolar myofibroblast progenitors. RFP,Acta2-low, PDGFRalpha-low populations comprise intermediate non-differentiated progenitors for smooth muscle cells or alveolar myofibroblasts.

value: tamoxifen at E15.5 (0.1mg/g b.w.)

value: lung

tag: harvested at

value: intermediate undifferentiated progenitor cells (INM)

tag: sma expression level

value: low

tag: pdgfralpha level


title: IS Sample 1

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from cultured human mesenchymal stem cells treated with 1:4 (dye:medium) dilution of Isovue

hyb_protocol: Hybridization and staining to the HumanHT-12 v4 Expression BeadChip (Illumina, San Diego, CA) was performed using 750ng of biotin-antisense RNA (aRNA) product following protocols outlined in the Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: Scanning of the BeadChip was performed using the iScan Microarray Scanner (Illumina, San Diego, CA).

data_processing: Gene expression data were imported into Illumina’s Genome Studio. They were imported with cubic spline normalization. Quality control was performed in Genome Studio. The Partek Report Plug-in from Illumina’s Genome Studio was used to export the gene expression data for import into Partek’s Genomics Suite (version 6.14.0828).

source_name: MSC_Treated with 1:4 (dye:medium) dilution of Isovue

label_protocol: RNA was then amplified and labeled using the TargetAmp-Nano Labeling Kit (Epicenter, Madison, WI) which enables amplification and target preparation compatible with the Direct Hybridization Assay (Illumina, San Diego, CA). Amplification was performed with 500 ng of total RNA input following procedures described in the TargetAmp-Nano Labeling Kit user guide.

growth_protocol: Human umbilical cord derived MSCs (CPJ45) were isolated and characterized in our laboratory . MSCs were seeded onto 0.1% gelatin-coated culture plates and propagated in the growth medium containing high glucose DMEM, supplemented with 10% of fetal bovine serum, and 5.6% of antibiotic solution (0.1% gentamicin, 0.2% streptomycin, and 0.12% penicillin). Cells were incubated at 37°C in an atmosphere of 5% CO2 in a humidified incubator.

extract_protocol: RNA was isolated from frozen cell pellets using the E.Z.N.A. Total RNA Kit I (Omega, Norcross, GA).  RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and stored at -80°C.

treatment_protocol: MSCs (1×106 cells) were cultured in 75 cm2 flasks in GM overnight. Cells were treated with 1:4 (dye:medium) of either Omnipaqe or Isovue for 24h.

value: Treated (one part of Isovue:Four parts of medium)


title: INM-rep3

description: SAMPLE 9


title: IS Sample 3

value: Human umbilical cord derived MSCs (CPJ45)


title: IS Sample 2


title: RIL_12

value: Recombinant inbred line #12 (T65 x Bhadua)


title: INM-rep2

description: SAMPLE 8


title: OP Sample 3

description: Gene expression data from cultured human mesenchymal stem cells treated with 1:4 (dye:medium) dilution of Omnipaque

source_name: MSC_Treated with 1:4 (dye:medium) dilution of Omnipaque

value: Treated (one part of Omnipaque:Four parts of medium)


title: RIL_8

value: Recombinant inbred line #8 (T65 x Bhadua)


title: MYF-rep3

description: SAMPLE 6

source_name: MYF

value: progenitors for alveolar miofibroblasts (MYF)

value: high


title: OP Sample 2


title: MYF-rep2

description: SAMPLE 5


title: B24d2


title: B24b2

value: Ganetespib, 125 nM


title: MYF-rep1

description: SAMPLE 4


title: SMC-rep2

description: SAMPLE 2

source_name: SMC

value: airway and vascular smooth muscle cells (SMCs)


title: OP Sample 1


title: B24a2

value: SN38, 1 uM


title: A24d2

value: Control, DMSO


title: SMC-rep3

description: SAMPLE 3


title: RIL_1

source_name: Basal node to 1 cm above shoot apical meristem, 8 hour submergence, 6 week-old samples.

value: Recombinant inbred line #1 (T65 x Bhadua)


title: Control Sample 1

description: Gene expression data from cultured human mesenchymal stem cells

value: Untreated (Control)


title: Muscle, Vitamin A restricted rep.2

status: Public on Oct 03 2017

city: Tsukuba

first: Masayuki

last: Hayashi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Metabolism and Nutrition

institute: National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science

hyb_protocol: Following fragmentation, 1.5 ug of aRNA were hybridized for 16 hr at 45 degrees C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data was normalized and calculated model-based expression values with Distribution Free Weighted (DFW) method (Chen et al., 2007).

source_name: Steer muscle, Vitamin A restricted.

label_protocol: Biotinylated aRNA were prepared from 100 ng total RNA according to the Genechip 3' IVT express kit user manual Rev. 6 (2009, Affymetrix).

growth_protocol: 13 to 14 month of age Japanese Black steers fattended to 20 to 21 month of age. Steers were sufficiently fed to give a daily weight gain of 1.0 kg/day.

extract_protocol: Trizol (Thermo Fisher Scientific) extraction of total RNA was performed according to the manufacturer's instructions. The extracted RNA  samples were purified by RNeasy mini kit (Qiagen) according to manufacture's instructions.

treatment_protocol: Vitamin A supplemented group was orally supplemented with 296.8 IU/kg BW vitamin A every week. Vitamin A restricted group restricted VA supplementation.

tag: breed

value: Japanese Black

value: castrated male

value: longissimus thoracis muscle

value: 595 days


title: Muscle, Vitamin A supplemented rep.1

source_name: Steer muscle, Vitamin A supplemented.

value: 600 days


title: Control Sample 2

value: Human umbilical cord derived MSCs (CPJ45)


title: Muscle, Vitamin A restricted rep.3

value: 611 days


title: Control Sample 3


title: Muscle, Vitamin A supplemented rep.2

value: 612 days


title: A24b2


title: Muscle, Vitamin A supplemented rep.3

value: 618 days


title: Cyclosporin A_replicate2

city: Memphis

first: Gadiparthi

middle: N

last: Rao

state: TN

address: 71 S Manassas Street, #309 TSRB

department: Physiology

institute: UTHSC

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Aortic smooth muscle cell

growth_protocol: Human aortic smooth muscle were quiesced for 24 hours.

treatment_protocol: After 24 hours of Quiescence, cells were treated with thrombin (0.5 units/ml) for 2 hours and 8 hours cells in presence or absence of cyclosporin A.

value: smooth muscle cell

value: cyclosporin A


title: Muscle, Vitamin A restricted rep.1

value: 589 days


title: Control_replicate2


title: Cyclosporin A + Thrombin 2 hour_replicate 2

value: cyclosporin A and thrombin (0.5 units/ml) for 2 hours


title: Cyclosporin A_replicate3


title: Cyclosporin A + Thrombin 8 hour_replicate 3

value: cyclosporin A and thrombin (0.5 units/ml) for 8 hours


title: Thrombin 8 hour_replicate 3

value: thrombin (0.5 units/ml) for 8 hours


title: SMC-rep1

description: SAMPLE 1

value: tamoxifen at E15.5 (0.1mg/g b.w.)

value: lung

tag: cell type

value: airway and vascular smooth muscle cells (SMCs)

value: high

value: low


title: Cyclosporin A + Thrombin 2 hour_replicate 3


title: Cyclosporin A + Thrombin 8 hour_replicate 1


title: Thrombin 2 hour_replicate 2

value: thrombin (0.5 units/ml) for 2 hours


title: Thrombin 8 hour_replicate 1


title: Thrombin 2 hour_replicate 3


title: Cyclosporin A + Thrombin 2 hour_replicate 1


title: Thrombin 8 hour_replicate 2


title: Cyclosporin A_replicate1


title: Thrombin 2 hour_replicate 1


title: Cyclosporin A + Thrombin 8 hour_replicate 2


title: Control_replicate3


title: CS22695 Replicate 1

city: Iizuka

first: Kazumasa

last: Shirai

state: Fukuoka

address: 680-4 Kawazu

department: Frontier Research Academy for Young Researchers

institute: Kyushu Institute of Technology

description: Gene expression of CS22695

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2505 BDNA microarray scanner (Agilent Technologies)

data_processing: Data analysis was performed by Feature Extraction and Image Analysis software (Agilent Technologies)

organism: Arabidopsis thaliana

source_name: Aerial parts of seedling

label_protocol: labeling were performed using the Agilent Low RNA Input Linear Amplification Kit (Agilent Technology), according to the manufacturer’s protocol.

growth_protocol: 18-days-old seedlings were growing on 1% agar plates containing Murashige and Skoog (MS)

extract_protocol: Approximately 500 μg total RNA was extracted from each sample using TRIzol (Invitrogen)

tag: accession

value: Aerial parts of seedling


title: CS22693 Replicate 1

description: Gene expression of CS22693


title: CS22694 Replicate 2

description: Gene expression of CS22694


title: Control_replicate1

scan_protocol: Standard Illumina scanning protocol

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays


title: CS22695 Replicate 2

description: Gene expression of CS22695


title: CS22693 Replicate 2

description: Gene expression of CS22693


title: CS22694 Replicate 1

description: Gene expression of CS22694


title: CS22691 Replicate 2

description: Gene expression of CS22691


title: CS22692 Replicate 2

description: Gene expression of CS22692


title: CS22691 Replicate 1

description: Gene expression of CS22691


title: CS22690 Replicate 2

description: Gene expression of CS22690


title: CS22684 Replicate 2

description: Gene expression of CS22684


title: CS22686 Replicate 2

description: Gene expression of CS22686


title: CS22688 Replicate 2

description: Gene expression of CS22688


title: CS22689 Replicate 1

description: Gene expression of CS22689


title: CS22687 Replicate 1

description: Gene expression of CS22687


title: CS22687 Replicate 2

description: Gene expression of CS22687


title: CS22685 Replicate 1

description: Gene expression of CS22685


title: CS22688 Replicate 1

description: Gene expression of CS22688


title: CS22692 Replicate 1

description: Gene expression of CS22692


title: CS22690 Replicate 1

description: Gene expression of CS22690


title: CS22684 Replicate 1

description: Gene expression of CS22684


title: CS22685 Replicate 2

description: Gene expression of CS22685


title: CS22683 Replicate 2

description: Gene expression of CS22683


title: CS22683 Replicate 1

description: Gene expression of CS22683


title: CS22682 Replicate 1

description: Gene expression of CS22682


title: CS22681 Replicate 1

description: Gene expression of CS22681


title: CS22681 Replicate 2

description: Gene expression of CS22681


title: CS22689 Replicate 2

description: Gene expression of CS22689


title: CS22686 Replicate 1

description: Gene expression of CS22686


title: CS22679 Replicate 2

description: Gene expression of CS22679


title: CS22679 Replicate 1

description: Gene expression of CS22679


title: CS22682 Replicate 2

description: Gene expression of CS22682


title: CS22680 Replicate 1

description: Gene expression of CS22680


title: CS22678 Replicate 1

description: Gene expression of CS22678


title: CS22680 Replicate 2

description: Gene expression of CS22680


title: CS22678 Replicate 2

description: Gene expression of CS22678


title: CS22677 Replicate 2

description: Gene expression of CS22677


title: CS22676 Replicate 1

description: Gene expression of CS22676


title: CS22807 Replicate 1

description: Gene expression of CS22807


title: CS22677 Replicate 1

description: Gene expression of CS22677


title: CS22676 Replicate 2

description: Gene expression of CS22676


title: CS22754 Replicate 1

description: Gene expression of CS22754


title: CS22823 Replicate 2

description: Gene expression of CS22823


title: CS22823 Replicate 1

description: Gene expression of CS22823


title: CS22765 Replicate 2

description: Gene expression of CS22765


title: CS22807 Replicate 2

description: Gene expression of CS22807


title: CS22765 Replicate 1

description: Gene expression of CS22765


title: CS22760 Replicate 2

description: Gene expression of CS22760


title: CS22747 Replicate 2

description: Gene expression of CS22747


title: CS22760 Replicate 1

description: Gene expression of CS22760


title: CS22730 Replicate 1

description: Gene expression of CS22730


title: CS22698 Replicate 2

description: Gene expression of CS22698


title: CS22747 Replicate 1

description: Gene expression of CS22747


title: CS22712 Replicate 2

description: Gene expression of CS22712


title: CS22703 Replicate 2

description: Gene expression of CS22703


title: CS22756 Replicate 2

description: Gene expression of CS22756


title: CS22703 Replicate 1

description: Gene expression of CS22703


title: CS22654 Replicate 2

description: Gene expression of CS22654


title: CS22712 Replicate 1

description: Gene expression of CS22712


title: CS22756 Replicate 1

description: Gene expression of CS22756


title: CS22754 Replicate 2

description: Gene expression of CS22754


title: CS22698 Replicate 1

description: Gene expression of CS22698


title: CS22730 Replicate 2

description: Gene expression of CS22730


title: CS22654 Replicate 1

description: Gene expression of CS22654


title: CS22650 Replicate 2

description: Gene expression of CS22650


title: CS22643 Replicate 1

description: Gene expression of CS22643


title: CS22636 Replicate 1

description: Gene expression of CS22636


title: CS22634 Replicate 1

description: Gene expression of CS22634


title: CS22650 Replicate 1

description: Gene expression of CS22650


title: CS22652 Replicate 2

description: Gene expression of CS22652


title: CS22635 Replicate 1

description: Gene expression of CS22635


title: CS22652 Replicate 1

description: Gene expression of CS22652


title: CS22638 Replicate 1

description: Gene expression of CS22638


title: CS22643 Replicate 2

description: Gene expression of CS22643


title: CS22626 Replicate 1

description: Gene expression of CS22626


title: CS22638 Replicate 2

description: Gene expression of CS22638


title: PAO1 algRD54E biological rep 1

city: Aurora

first: Michael

middle: J

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

description: Gene expression from PAO1 algRD54E grown 16 hrs in LB

hyb_protocol: Hybridization was performed by the University of Colorado Genomics core according to the Affymetrix GeneChip P. aeruginosa genome array expression protocol.

scan_protocol: Scanning was performed by the University of Colorado Genomics core according to the Affymetrix GeneChip P. aeruginosa genome array expression protocol.

data_processing: Probe set summarization (.CHP) files were generated using the RMA (Robust Multi-chip Analysis) algorithm. Background-corrected perfect match intensities were computed for each perfect match cell on every GeneChip and base-2 logarithm of each background-corrected perfect match intensity was obtained. These background-corrected and log-transformed perfect match intensities were normalized using the quantile normalization method. Tukey's median polish was used to obtain estimates that serve as the log-scale expression measures associated with the particular probe set. These data were imported into Transcriptome Analysis Console (Affymetrix version 3.0.0) Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Signal estimates for each transcript cluster for each condition was calculated using Tukey's Bi-weight Average Algorithm. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. Finally, the mean value of the signal log ratios from each comparison file was calculated.  Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than of equal to 1 for down-regulated transcripts were kept in the final list of genes.

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa PAO1 algRD54E

label_protocol: Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

growth_protocol: Three independent replicates of P. aeruginosa strains PAO1, PAO1 algRD54E and PAO1 algRD54N were grown for 16 hrs in LB (10g tryptone, 5 g Yeast extract and 10g NaCl) shaking at 250 rpm at 37°C

extract_protocol: Total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.

treatment_protocol: Cells were treated with RNAprotect (Qiagen) after 16 hrs growth and frozen at -80°C.

tag: genotype/variation


title: CS22616 Replicate 1

description: Gene expression of CS22616


title: CS22635 Replicate 2

description: Gene expression of CS22635


title: CS22607 Replicate 1

description: Gene expression of CS22607


title: CS22626 Replicate 2

description: Gene expression of CS22626


title: CS22607 Replicate 2

description: Gene expression of CS22607


title: PAO1 algRD54E biological rep 3


title: CS22634 Replicate 2

description: Gene expression of CS22634


title: CS22636 Replicate 2

description: Gene expression of CS22636


title: CS22616 Replicate 2

description: Gene expression of CS22616


title: CS22615 Replicate 1

description: Gene expression of CS22615


title: CS22617 Replicate 1

description: Gene expression of CS22617


title: CS22615 Replicate 2

description: Gene expression of CS22615


title: PAO1 algRD54E biological rep 2


title: CS22602 Replicate 2

description: Gene expression of CS22602


title: PAO1_16_1 biological rep 3

description: Gene expression from PAO1 grown 16 hrs in LB

source_name: P. aeruginosa  PAO1

value: wild-type


title: CS22591 Replicate 2

description: Gene expression of CS22591


title: PAO1 algRD54N biological rep 3

description: Gene expression from PAO1 algRD54N grown 16 hrs in LB

source_name: P. aeruginosa PAO1 algRD54N


title: PAO1 algRD54N biological rep 2


title: PAO1 algRD54N biological rep 1


title: PAO1_16_1 biological rep 1


title: PAO1_16_1 biological rep 2


title: CS22590 Replicate 1

description: Gene expression of CS22590


title: CS22591 Replicate 1

description: Gene expression of CS22591


title: CS22617 Replicate 2

description: Gene expression of CS22617


title: CS22602 Replicate 1

description: Gene expression of CS22602


title: CS22574 Replicate 2

description: Gene expression of CS22574


title: CS22590 Replicate 2

description: Gene expression of CS22590


title: CS22570 Replicate 2

description: Gene expression of CS22570


title: SCC9_HNSCC_rep1

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
940CC0069-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: fRMA normalization and removal of date effect estimated with a limma linear model

source_name: HNSCC cell line SCC9

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: HNSCC (head and neck squamous cell carcinoma)


title: SCC15_HNSCC_rep1

description:
940CC0072-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SCC15


title: CS1380 Replicate 2

description: Gene expression of CS1380


title: SQ9G_HNSCC_rep2

description:
940CC0124-20090623-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SQ9G


title: CS22574 Replicate 1

description: Gene expression of CS22574


title: CS22567 Replicate 1

description: Gene expression of CS22567


title: CS22570 Replicate 1

description: Gene expression of CS22570


title: SQ9G_HNSCC_rep1

description:
940CC0078-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC15_HNSCC_rep2

description:
940CC0073-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: HSC3_HNSCC_rep2

description:
940CC0121-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line HSC3


title: SCC9_HNSCC_rep2

description:
940CC0114-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: CS1380 Replicate 1

description: Gene expression of CS1380


title: CS6907 Replicate 2

description: Gene expression of CS6907


title: CS6907 Replicate 1

description: Gene expression of CS6907


title: CS917 Replicate 1

description: Gene expression of CS917


title: CS22567 Replicate 2

description: Gene expression of CS22567


title: CS6918 Replicate 2

description: Gene expression of CS6918


title: CS917 Replicate 2

description: Gene expression of CS917


title: CS6902 Replicate 2

description: Gene expression of CS6902


title: CS6902 Replicate 1

description: Gene expression of CS6902


title: CS6891 Replicate 1

description: Gene expression of CS6891


title: UNC10_HNSCC_rep2

description:
940CC0123-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line UNC10


title: JSQ3_HNSCC_rep2

description:
940CC0077-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line JSQ3


title: HN5_HNSCC_rep2

description:
940CC0075-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line HN5


title: CS6897 Replicate 2

description: Gene expression of CS6897


title: CS6857 Replicate 1

description: Gene expression of CS6857


title: HSC3_HNSCC_rep1

description:
940CC0120-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.