title: Patient 120 mucosa control sample

value: Con Patient 120

value: M


title: Patient 109 mucosa control sample

status: Public on Nov 28 2017

type: RNA

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

country: USA

institute: NCI

hyb_protocol: cRNA was hybridized to the Human 4 × 44 K array platform from Agilent Technologies (G4112F) as recommended by the manufacturer.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed using the Agilent feature extraction software (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol.

molecule: total RNA

organism: Homo sapiens

source_name: mucosa

label_protocol: 600ng of total RNA was amplified and transcribed into fluorescence labeled cRNA following the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5339).

extract_protocol: Using the Qiagen AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany) according to manufactures recommendation, RNA was isolated from FFPE samples. Using TRIZOL (cat. no. 15596-018, Life Technologies, Rockeville, MD, USA) RNA was extracted from RNAlater biopsies. All samples underwent strict quality assessment, nucleic acid quantity, and purity was determined using the NanoDrop spectrophotometer ND1000 (Thermo Fisher Scientific Inc., Waltham, MA, USA), quality and integrity was assessed by a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: During index rectoscopy several biopsies of tumor and normal mucosa were taken and either directly buffered in 4% formalin, stored overnight and embedded in paraffin the next day or immediately transferred into RNAlater (Qiagen, Hilden, Germany). Tissue in RNAlater was stored over night at 4 °C to allow saturation of the entire biopsy and stored at −20 °C until RNA isolation.

tag: patient

value: Con Patient 109

tag: age

tag: gender

value: F

tag: tissue

value: mucosa

tag: kras mutation

tag: preoperative radiochemotherapy (rct)

value: 5-FU + RT

tag: depth of invasion before rct

tag: lymph node metastasis before rct

tag: metastasis before rct

tag: depth of invasion after rct

tag: lymph node metastasis after rct

tag: metastasis after rct

tag: cancer recurrance after surgery

tag: disease free time (month)

tag: death due to tumor

tag: survival time (month)


title: Patient 110 mucosa control sample

value: Con Patient 110

value: WT

value: 5-FU + Oxaliplatin + RT


title: Patient 106 mucosa control sample

value: Con Patient 106


title: Patient 105 mucosa control sample

value: Con Patient 105


title: Patient 107 mucosa control sample

value: Con Patient 107


title: Patient 112 mucosa control sample

value: Con Patient 112


title: Patient 102 mucosa control sample

value: Con Patient 102


title: Patient 103 mucosa control sample

value: Con Patient 103


title: Patient 104 mucosa control sample

value: Con Patient 104


title: Patient 99 mucosa control sample

value: Con Patient 99


title: Patient 101 mucosa control sample

value: Con Patient 101


title: Patient 95 mucosa control sample

value: Con Patient 95

value: M


title: Patient 97 mucosa control sample

value: Con Patient 97

value: F


title: Patient 124 mucosa control sample

value: Con Patient 124

value: mucosa


title: Patient 111 mucosa control sample

value: Con Patient 111

value: WT


title: Patient 135 mucosa control sample

value: Con Patient 135

value: 5-FU + Oxaliplatin + RT


title: Patient 108 mucosa control sample

value: Con Patient 108


title: Patient 96 mucosa control sample

value: Con Patient 96

value: 5-FU + RT


title: Patient 92 mucosa control sample

value: Con Patient 92


title: Patient 100 mucosa control sample

value: Con Patient 100


title: Patient 86 mucosa control sample

value: Con Patient 86


title: Patient 88 mucosa control sample

value: Con Patient 88


title: Patient 93 mucosa control sample

value: Con Patient 93


title: Patient 84 mucosa control sample

value: Con Patient 84

value: M


title: Patient 90 mucosa control sample

value: Con Patient 90

value: F


title: Patient 91 mucosa control sample

value: Con Patient 91

value: mucosa


title: Patient 89 mucosa control sample

value: Con Patient 89


title: Patient 98 mucosa control sample

value: Con Patient 98

value: WT


title: Patient 82 mucosa control sample

value: Con Patient 82


title: Patient 85 mucosa control sample

value: Con Patient 85


title: Patient 94 mucosa control sample

value: Con Patient 94

value: 5-FU + Oxaliplatin + RT


title: Patient 80 mucosa control sample

value: Con Patient 80

value: 5-FU + RT


title: Patient 76 mucosa control sample

value: Con Patient 76


title: Patient 87 mucosa control sample

value: Con Patient 87


title: Patient 72 mucosa control sample

value: Con Patient 72


title: Patient 75 mucosa control sample

value: Con Patient 75

value: M


title: Patient 77 mucosa control sample

value: Con Patient 77


title: Patient 81 mucosa control sample

value: Con Patient 81


title: Patient 74 mucosa control sample

value: Con Patient 74

value: mucosa


title: Patient 71 mucosa control sample

value: Con Patient 71


title: Patient 73 mucosa control sample

value: Con Patient 73

value: WT


title: Patient 78 mucosa control sample

value: Con Patient 78

value: F


title: Patient 70 mucosa control sample

value: Con Patient 70

value: 5-FU + Oxaliplatin + RT


title: Patient 68 mucosa control sample

value: Con Patient 68

value: 5-FU + RT


title: Patient 69 mucosa control sample

value: Con Patient 69


title: Patient 67 mucosa control sample

value: Con Patient 67


title: Patient 63 mucosa control sample

value: Con Patient 63


title: Patient 65 mucosa control sample

value: Con Patient 65

value: M


title: Patient 55 mucosa control sample

value: Con Patient 55


title: Patient 54 mucosa control sample

value: Con Patient 54


title: Patient 56 mucosa control sample

value: Con Patient 56

value: mucosa


title: Patient 62 mucosa control sample

value: Con Patient 62


title: Patient 66 mucosa control sample

value: Con Patient 66


title: Patient 64 mucosa control sample

value: Con Patient 64


title: Patient 58 mucosa control sample

value: Con Patient 58


title: Patient 57 mucosa control sample

value: Con Patient 57

value: F


title: Patient 53 mucosa control sample

value: Con Patient 53

value: WT


title: Patient 61 mucosa control sample

value: Con Patient 61

value: 5-FU + Oxaliplatin + RT


title: Patient 59 mucosa control sample

value: Con Patient 59


title: Patient 49 mucosa control sample

value: Con Patient 49

value: 5-FU + RT


title: Patient 60 mucosa control sample

value: Con Patient 60

value: M


title: Patient 130 mucosa control sample

value: Con Patient 130


title: Patient 51 mucosa control sample

value: Con Patient 51

value: mucosa


title: Patient 52 mucosa control sample

value: Con Patient 52


title: Patient 47 mucosa control sample

value: Con Patient 47


title: Patient 45 mucosa control sample

value: Con Patient 45


title: Patient 48 mucosa control sample

value: Con Patient 48


title: Patient 44 mucosa control sample

value: Con Patient 44

value: F


title: Patient 46 mucosa control sample

value: Con Patient 46


title: Patient 43 mucosa control sample

value: Con Patient 43

value: WT


title: Patient 50 mucosa control sample

value: Con Patient 50


title: Patient 41 mucosa control sample

value: Con Patient 41


title: Patient 42 mucosa control sample

value: Con Patient 42

value: 5-FU + RT


title: Patient 113 mucosa control sample

value: Con Patient 113

value: 5-FU + Oxaliplatin + RT


title: Patient 40 mucosa control sample

value: Con Patient 40

value: M


title: Patient 38 mucosa control sample

value: Con Patient 38

value: mucosa


title: Patient 30 mucosa control sample

value: Con Patient 30


title: Patient 34 mucosa control sample

value: Con Patient 34


title: Patient 23 mucosa control sample

value: Con Patient 23


title: Patient 28 mucosa control sample

value: Con Patient 28


title: Patient 22 mucosa control sample

value: Con Patient 22


title: Patient 37 mucosa control sample

value: Con Patient 37

value: F


title: Patient 79 mucosa control sample

value: Con Patient 79

value: WT


title: Patient 21 mucosa control sample

value: Con Patient 21


title: Patient 18 mucosa control sample

value: Con Patient 18

value: 5-FU + RT


title: Patient 39 mucosa control sample

value: Con Patient 39


title: Patient 26 mucosa control sample

value: Con Patient 26

value: 5-FU + Oxaliplatin + RT


title: Patient 24 mucosa control sample

value: Con Patient 24


title: Patient 31 mucosa control sample

value: Con Patient 31

value: mucosa


title: Patient 32 mucosa control sample

value: Con Patient 32

value: M


title: Patient 33 mucosa control sample

value: Con Patient 33


title: Patient 20 mucosa control sample

value: Con Patient 20


title: Patient 25 mucosa control sample

value: Con Patient 25


title: Patient 19 mucosa control sample

value: Con Patient 19


title: Patient 16 mucosa control sample

value: Con Patient 16

value: F


title: Patient 15 mucosa control sample

value: Con Patient 15


title: Patient 13 mucosa control sample

value: Con Patient 13

value: WT


title: Patient 36 mucosa control sample

value: Con Patient 36

value: 5-FU + RT


title: Patient 17 mucosa control sample

value: Con Patient 17


title: Patient 14 mucosa control sample

value: Con Patient 14

value: 5-FU + Oxaliplatin + RT


title: Patient 29 mucosa control sample

value: Con Patient 29

value: mucosa


title: Patient 27 mucosa control sample

value: Con Patient 27

value: M


title: Patient 35 mucosa control sample

value: Con Patient 35


title: Patient 83 mucosa control sample

value: Con Patient 83


title: Patient 12 mucosa control sample

value: Con Patient 12


title: Patient 11 mucosa control sample

value: Con Patient 11


title: Patient 8 mucosa control sample

value: Con Patient 8


title: Patient 2 mucosa control sample

value: Con Patient 2


title: Patient 7 mucosa control sample

value: Con Patient 7


title: Patient 200 tumor sample

source_name: rectal tumor

value: Tum Patient 200

value: F

value: rectal tumor

value: WT


title: Patient 5 mucosa control sample

value: Con Patient 5

value: 5-FU + RT


title: Patient 1 mucosa control sample

value: Con Patient 1

value: 5-FU + Oxaliplatin + RT


title: Patient 4 mucosa control sample

value: Con Patient 4

value: mucosa


title: Patient 197 tumor sample

value: Tum Patient 197

value: M


title: Patient 10 mucosa control sample

value: Con Patient 10


title: Patient 6 mucosa control sample

value: Con Patient 6


title: Patient 201 tumor sample

value: Tum Patient 201


title: Patient 189 tumor sample

value: Tum Patient 189


title: Patient 188 tumor sample

value: Tum Patient 188


title: Patient 199 tumor sample

value: Tum Patient 199


title: Patient 193 tumor sample

value: Tum Patient 193


title: Patient 3 mucosa control sample

value: Con Patient 3


title: Patient 196 tumor sample

value: Tum Patient 196

value: rectal tumor

value: WT

value: 5-FU + Oxaliplatin + Cetuximab + RT


title: Patient 195 tumor sample

value: Tum Patient 195

value: 5-FU + Oxaliplatin + RT


title: Patient 191 tumor sample

value: Tum Patient 191

value: F


title: Patient 203 tumor sample

value: Tum Patient 203

value: 5-FU + RT


title: Patient 187 tumor sample

value: Tum Patient 187


title: Patient 192 tumor sample

value: Tum Patient 192

value: M


title: Patient 202 tumor sample

value: Tum Patient 202


title: Patient 198 tumor sample

value: Tum Patient 198


title: Patient 194 tumor sample

value: Tum Patient 194


title: Patient 186 tumor sample

value: Tum Patient 186


title: Patient 190 tumor sample

value: Tum Patient 190


title: Patient 185 tumor sample

value: Tum Patient 185

value: rectal tumor


title: Patient 184 tumor sample

value: Tum Patient 184

value: WT


title: Patient 183 tumor sample

value: Tum Patient 183


title: Patient 166 tumor sample

value: Tum Patient 166

value: 5-FU + Oxaliplatin + RT


title: Patient 179 tumor sample

value: Tum Patient 179

value: F


title: Patient 171 tumor sample

value: Tum Patient 171

value: 5-FU + RT


title: Patient 176 tumor sample

value: Tum Patient 176

value: M


title: Patient 169 tumor sample

value: Tum Patient 169


title: Patient 172 tumor sample

value: Tum Patient 172


title: Patient 182 tumor sample

value: Tum Patient 182


title: Patient 167 tumor sample

value: Tum Patient 167


title: Patient 170 tumor sample

value: Tum Patient 170


title: Patient 160 tumor sample

value: Tum Patient 160

value: rectal tumor


title: Patient 163 tumor sample

value: Tum Patient 163

value: WT


title: Patient 181 tumor sample

value: Tum Patient 181


title: Patient 173 tumor sample

value: Tum Patient 173

value: 5-FU + Oxaliplatin + RT


title: Patient 165 tumor sample

value: Tum Patient 165


title: Patient 168 tumor sample

value: Tum Patient 168


title: Patient 174 tumor sample

value: Tum Patient 174


title: Patient 158 tumor sample

value: Tum Patient 158

value: F

value: 5-FU + RT


title: Patient 164 tumor sample

value: Tum Patient 164

value: M


title: Patient 162 tumor sample

value: Tum Patient 162


title: Patient 175 tumor sample

value: Tum Patient 175


title: Patient 178 tumor sample

value: Tum Patient 178


title: Patient 159 tumor sample

value: Tum Patient 159

value: rectal tumor


title: Patient 161 tumor sample

value: Tum Patient 161


title: Patient 180 tumor sample

value: Tum Patient 180


title: Patient 157 tumor sample

value: Tum Patient 157


title: Patient 156 tumor sample

value: Tum Patient 156

value: WT

value: 5-FU + Oxaliplatin + RT


title: Patient 155 tumor sample

value: Tum Patient 155


title: Patient 148 tumor sample

value: Tum Patient 148


title: Patient 153 tumor sample

value: Tum Patient 153

value: F


title: Patient 154 tumor sample

value: Tum Patient 154

value: 5-FU + RT


title: Patient 139 tumor sample

value: Tum Patient 139


title: Patient 152 tumor sample

value: Tum Patient 152


title: Patient 143 tumor sample

value: Tum Patient 143

value: M


title: Patient 146 tumor sample

value: Tum Patient 146

value: rectal tumor


title: Patient 144 tumor sample

value: Tum Patient 144


title: Patient 145 tumor sample

value: Tum Patient 145


title: Patient 142 tumor sample

value: Tum Patient 142


title: Patient 151 tumor sample

value: Tum Patient 151

value: WT


title: Patient 138 tumor sample

value: Tum Patient 138


title: Patient 137 tumor sample

value: Tum Patient 137


title: Patient 134 tumor sample

value: Tum Patient 134

value: 5-FU + Oxaliplatin + Cetuximab + RT


title: Patient 140 tumor sample

value: Tum Patient 140

value: F

value: 5-FU + Oxaliplatin + RT


title: Patient 141 tumor sample

value: Tum Patient 141

value: 5-FU + RT


title: Patient 147 tumor sample

value: Tum Patient 147


title: Patient 127 tumor sample

value: Tum Patient 127

value: M


title: Patient 150 tumor sample

value: Tum Patient 150

value: rectal tumor


title: Patient 130 tumor sample

value: Tum Patient 130


title: Patient 131 tumor sample

value: Tum Patient 131


title: Patient 9 mucosa control sample

value: Con Patient 9

value: mucosa

value: WT


title: Patient 149 tumor sample

value: Tum Patient 149


title: Patient 135 tumor sample

value: Tum Patient 135


title: Patient 125 tumor sample

value: Tum Patient 125


title: Patient 133 tumor sample

value: Tum Patient 133

value: F

value: 5-FU + Oxaliplatin + Cetuximab + RT


title: Patient 136 tumor sample

value: Tum Patient 136

value: 5-FU + RT


title: Patient 132 tumor sample

value: Tum Patient 132


title: Patient 129 tumor sample

value: Tum Patient 129

value: M

value: 5-FU + Oxaliplatin + RT


title: Patient 126 tumor sample

value: Tum Patient 126

value: rectal tumor


title: Patient 128 tumor sample

value: Tum Patient 128


title: Patient 123 tumor sample

value: Tum Patient 123


title: Patient 124 tumor sample

value: Tum Patient 124

value: WT


title: Patient 121 tumor sample

value: Tum Patient 121


title: Patient 115 tumor sample

value: Tum Patient 115


title: Patient 177 tumor sample

value: Tum Patient 177


title: Patient 102 tumor sample

value: Tum Patient 102


title: Patient 113 tumor sample

value: Tum Patient 113

value: F


title: Patient 99 tumor sample

value: Tum Patient 99

value: 5-FU + RT


title: Patient 117 tumor sample

value: Tum Patient 117


title: Patient 103 tumor sample

value: Tum Patient 103


title: Patient 116 tumor sample

value: Tum Patient 116


title: Patient 120 tumor sample

value: Tum Patient 120

value: M

value: 5-FU + Oxaliplatin + RT


title: Patient 104 tumor sample

value: Tum Patient 104

value: rectal tumor


title: Patient 97 tumor sample

value: Tum Patient 97

value: WT


title: Patient 95 tumor sample

value: Tum Patient 95


title: Patient 100 tumor sample

value: Tum Patient 100


title: Patient 119 tumor sample

value: Tum Patient 119


title: Patient 111 tumor sample

value: Tum Patient 111


title: Patient 112 tumor sample

value: Tum Patient 112

value: F


title: Patient 106 tumor sample

value: Tum Patient 106

value: 5-FU + RT


title: Patient 122 tumor sample

value: Tum Patient 122


title: Patient 107 tumor sample

value: Tum Patient 107


title: Patient 108 tumor sample

value: Tum Patient 108


title: Patient 109 tumor sample

value: Tum Patient 109


title: Patient 98 tumor sample

value: Tum Patient 98

value: M


title: Patient 110 tumor sample

value: Tum Patient 110

value: rectal tumor

value: 5-FU + Oxaliplatin + RT


title: Patient 118 tumor sample

value: Tum Patient 118

value: WT


title: Patient 96 tumor sample

value: Tum Patient 96


title: Patient 94 tumor sample

value: Tum Patient 94


title: Patient 105 tumor sample

value: Tum Patient 105


title: Patient 114 tumor sample

value: Tum Patient 114

value: F


title: Patient 101 tumor sample

value: Tum Patient 101

value: 5-FU + RT


title: Patient 93 tumor sample

value: Tum Patient 93


title: Patient 88 tumor sample

value: Tum Patient 88


title: Patient 89 tumor sample

value: Tum Patient 89


title: Patient 85 tumor sample

value: Tum Patient 85


title: Patient 90 tumor sample

value: Tum Patient 90


title: Patient 92 tumor sample

value: Tum Patient 92

value: M


title: Patient 91 tumor sample

value: Tum Patient 91

value: rectal tumor

value: 5-FU + Oxaliplatin + RT


title: Patient 83 tumor sample

value: Tum Patient 83

value: WT


title: Patient 86 tumor sample

value: Tum Patient 86


title: Patient 80 tumor sample

value: Tum Patient 80


title: Patient 84 tumor sample

value: Tum Patient 84


title: Patient 71 tumor sample

value: Tum Patient 71


title: Patient 79 tumor sample

value: Tum Patient 79

value: F

value: 5-FU + RT


title: Patient 74 tumor sample

value: Tum Patient 74


title: Patient 81 tumor sample

value: Tum Patient 81


title: Patient 77 tumor sample

value: Tum Patient 77


title: Patient 72 tumor sample

value: Tum Patient 72


title: Patient 73 tumor sample

value: Tum Patient 73

value: M


title: Patient 70 tumor sample

value: Tum Patient 70

value: rectal tumor


title: Patient 82 tumor sample

value: Tum Patient 82


title: Patient 67 tumor sample

value: Tum Patient 67

value: WT


title: Patient 75 tumor sample

value: Tum Patient 75

value: 5-FU + Oxaliplatin + RT


title: Patient 69 tumor sample

value: Tum Patient 69


title: Patient 68 tumor sample

value: Tum Patient 68


title: Patient 76 tumor sample

value: Tum Patient 76


title: Patient 78 tumor sample

value: Tum Patient 78

value: F

value: 5-FU + RT


title: Patient 87 tumor sample

value: Tum Patient 87


title: Patient 66 tumor sample

value: Tum Patient 66


title: Patient 65 tumor sample

value: Tum Patient 65


title: Patient 62 tumor sample

value: Tum Patient 62

value: M


title: Patient 63 tumor sample

value: Tum Patient 63

value: rectal tumor


title: Patient 59 tumor sample

value: Tum Patient 59


title: Patient 56 tumor sample

value: Tum Patient 56

value: WT


title: Patient 60 tumor sample

value: Tum Patient 60

value: 5-FU + Oxaliplatin + RT


title: Patient 61 tumor sample

value: Tum Patient 61


title: Patient 55 tumor sample

value: Tum Patient 55


title: Patient 52 tumor sample

value: Tum Patient 52


title: Patient 51 tumor sample

value: Tum Patient 51


title: Patient 54 tumor sample

value: Tum Patient 54

value: 5-FU + RT


title: Patient 47 tumor sample

value: Tum Patient 47


title: Patient 50 tumor sample

value: Tum Patient 50


title: Patient 64 tumor sample

value: Tum Patient 64


title: Patient 49 tumor sample

value: Tum Patient 49

value: F


title: Patient 57 tumor sample

value: Tum Patient 57

value: rectal tumor


title: Patient 43 tumor sample

value: Tum Patient 43

value: M


title: Patient 48 tumor sample

value: Tum Patient 48


title: Patient 44 tumor sample

value: Tum Patient 44

value: 5-FU + Oxaliplatin + RT


title: Patient 58 tumor sample

value: Tum Patient 58


title: Patient 45 tumor sample

value: Tum Patient 45


title: Patient 46 tumor sample

value: Tum Patient 46


title: Patient 41 tumor sample

value: Tum Patient 41

value: WT


title: Patient 38 tumor sample

value: Tum Patient 38


title: Patient 53 tumor sample

value: Tum Patient 53

value: 5-FU + RT


title: Patient 40 tumor sample

value: Tum Patient 40


title: Patient 35 tumor sample

value: Tum Patient 35


title: Patient 39 tumor sample

value: Tum Patient 39


title: Patient 36 tumor sample

value: Tum Patient 36

value: rectal tumor


title: Patient 34 tumor sample

value: Tum Patient 34

value: F


title: Patient 32 tumor sample

value: Tum Patient 32

value: M


title: Patient 33 tumor sample

value: Tum Patient 33


title: Patient 37 tumor sample

value: Tum Patient 37

value: 5-FU + Oxaliplatin + RT


title: Patient 29 tumor sample

value: Tum Patient 29


title: Patient 25 tumor sample

value: Tum Patient 25


title: Patient 31 tumor sample

value: Tum Patient 31


title: Patient 28 tumor sample

value: Tum Patient 28


title: Patient 27 tumor sample

value: Tum Patient 27

value: WT

value: 5-FU + RT


title: Patient 20 tumor sample

value: Tum Patient 20


title: Patient 30 tumor sample

value: Tum Patient 30


title: Patient 24 tumor sample

value: Tum Patient 24

value: rectal tumor


title: Patient 23 tumor sample

value: Tum Patient 23


title: Patient 26 tumor sample

value: Tum Patient 26


title: Patient 21 tumor sample

value: Tum Patient 21

value: F


title: Patient 22 tumor sample

value: Tum Patient 22

value: M


title: Patient 17 tumor sample

value: Tum Patient 17


title: Patient 18 tumor sample

value: Tum Patient 18


title: Patient 19 tumor sample

value: Tum Patient 19


title: Rag2 KO spleen, biological replicate 2

city: Seoul

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

country: South Korea

institute: Konkuk University

description: Gene Expression BeadChip array analysis

hyb_protocol: Hybridized to the Illumina Expression Beadchip

scan_protocol: Scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Data data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label: Biotin

organism: Mus musculus

source_name: Rag2 KO mouse Spleen

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: The experimental mice were maintained on a congenic C57Bl/6J background and were allowed to eat standard mouse chow (Cargill Agri Purina, Inc., Seongnam-Si, Korea) and drink on an ad libitum basis.

extract_protocol: Total RNA was isolated from mouse spleen tissue using the miRNeasy mini kit (Qiagen, Valencia, CA, USA) following the manufacturer's protocol.

treatment_protocol: Rag2 KO group was deficient of Rag2 gene and possessed severe immuno deficiency status.

tag: background strain

tag: mutation status

value: Rag2 KO


title: Patient 16 tumor sample

tag: patient

value: Tum Patient 16

tag: age


title: Wild type spleen, biological replicate 1

description: Gene Expression BeadChip array analysis

source_name: Wild type mouse Spleen

value: Wild type


title: Wild type spleen, biological replicate 3

description: Gene Expression BeadChip array analysis


title: Rag2 KO spleen, biological replicate 3

description: Gene Expression BeadChip array analysis


title: Wild type spleen, biological replicate 2

description: Gene Expression BeadChip array analysis


title: Patient 15 tumor sample

value: Tum Patient 15

tag: gender

tag: tissue

value: 5-FU + Oxaliplatin + RT


title: Patient 14 tumor sample

value: Tum Patient 14

tag: kras mutation

value: WT

tag: preoperative radiochemotherapy (rct)


title: Rag2 KO spleen, biological replicate 1

description: Gene Expression BeadChip array analysis


title: Patient 13 tumor sample

value: Tum Patient 13

value: rectal tumor

value: 5-FU + RT

tag: depth of invasion before rct

tag: lymph node metastasis before rct


title: siFOXK1 + Empty Vector + Vehicle_2

city: Higashi-ku

first: Hirokazu

last: Nakatsumi

state: Fukuoka

address: 3-1-1, Maidashi

department: Department of Molecular and Cellular Biology

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description: Expression changes of HeLa mRNA

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Analysis by RMA.

source_name: Human cell line

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was obtained using the WT Expression Kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: 1nM siRNA and 1 microgram/ml of expression vector were transfected into HeLa cells

tag: cell line

value: HeLa

tag: transfection

value: siFOXK1 and empty vector and vehicle


title: Patient 12 tumor sample

value: Tum Patient 12

tag: metastasis before rct

tag: depth of invasion after rct

tag: lymph node metastasis after rct

tag: metastasis after rct


title: siFOXK1 + RhebCA + Vehicle_2

description: Expression changes of HeLa mRNA

value: siFOXK1 and RhebCA and vehicle


title: siControl + RhebCA + Rapamycin_2

description: Expression changes of HeLa mRNA

value: siControl and RhebCA and Rapamycin


title: Patient 10 tumor sample

value: Tum Patient 10

value: M

tag: cancer recurrance after surgery

tag: disease free time (month)

tag: death due to tumor

tag: survival time (month)


title: Patient 11 tumor sample

tag: patient

value: Tum Patient 11

tag: age


title: Patient 7 tumor sample

value: Tum Patient 7

tag: gender

tag: tissue


title: Patient 5 tumor sample

value: Tum Patient 5

value: F

tag: kras mutation

tag: preoperative radiochemotherapy (rct)


title: Patient 8 tumor sample

value: Tum Patient 8

tag: depth of invasion before rct

tag: lymph node metastasis before rct


title: siControl + RhebCA + Rapamycin_1

description: Expression changes of HeLa mRNA

tag: cell line

tag: transfection


title: siFOXK1 + RhebCA + Vehicle_1

description: Expression changes of HeLa mRNA


title: siControl + Empty Vector + Vehicle_2

description: Expression changes of HeLa mRNA

value: siControl and empty vector


title: Patient 6 tumor sample

value: Tum Patient 6

value: 5-FU + Oxaliplatin + RT

tag: metastasis before rct

tag: depth of invasion after rct


title: siControl + RhebCA + Vehicle_1

description: Expression changes of HeLa mRNA

value: siControl and RhebCA and vehicle


title: FOXK1_Overexpression_2

description: Expression changes of HeLa mRNA after transfection for 24hrs

treatment_protocol: 1 microgram/ml of expression vector were transfected into HeLa cells

value: FOXK1 overexpression


title: siControl + Empty Vector + Vehicle_1

description: Expression changes of HeLa mRNA

value: HeLa


title: siFOXK1 + Empty Vector + Vehicle_1

description: Expression changes of HeLa mRNA

value: siFOXK1 and empty vector and vehicle


title: Patient 9 tumor sample

value: Tum Patient 9

value: rectal tumor

value: WT

tag: lymph node metastasis after rct

tag: metastasis after rct


title: MNASE WT NAKED DNA

type: SRA

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

library_source: genomic

data_processing:
Reads were mapped using GEM mapper version build 539 with default parameters
unambigous mapped reads were analyzed with DANPOS 2.1.2
Genome_build: Genome_build: sarCer2

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast

extract_protocol:
500 ml of yeast culture growing exponentially were cross-linked by the addition of formaldehyde to a final concentration of 1 %, followed by 15 minutes of incubation at room temperature. For quenching, glycine was added to 2 % and the sample incubated for 5 minutes at room temperature. Cells were washed three times with cold distilled water. Then, they were resuspended in 10 ml of Buffer Z2 (1 M Sorbitol; 50 mM Tris-HCl pH 7.4; 10 mM β-mercaptoethanol). Spheroplasts were prepared by adding 50 μl of Zymolyase 100T (20 μg/ml). Samples were incubated at 30 ºC during approximately 30 minutes until the optical density at 600 nm was around 10 % of the initial. After washing two times the spheroplasts with cold washing buffer I (1 M sorbitol; 20 mM Tris-HCl pH 8; 1 mM EDTA; 150 mM NaCl), they were resuspended in 1,5 ml of buffer II (20 mM Tris-HCl pH 8; 1 mM EDTA; 150 mM NaCl; 0.1 mM PMSF; 0.2 % Triton X-100). Spheroplasts were separated in 5 tubes with 3 ml of MNase buffer (15 mM Tris-HCl pH 8; 50 mM NaCl; 1.4 mM CaCl2; 0.2 mM EGTA; 0.2 mM EDTA) and different amounts of microccocal nuclease ranging from 500 to 10 mU. Samples were incubated for 30 minutes at 37 ºC, and reactions were stopped by adding 100 μl of stop buffer (0.4 M EDTA; 0.3 M Tris-HCl pH 8) and 150 μl of 10 % SDS. Subsequently, the samples were treated with 75 μl of proteinase K (20 mg/ml) for 30 minutes at 37 ºC, and then at 65 ºC for at least 1 hour. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated, resupended in double-distilled water and treated with 170 µg/ml RNase A for 30 minutes at room temperature. Digested DNA was resolved in 2 % agarose gels. One of the digestions was chosen, with the following criteria: 1) the trinucleosome band was visible, indicating that there was negligible overdigestion; 2) the mononucleosome band was the most intense (see Fig. 1). The band corresponding to mononucleosomes was purified using Quiagen Gel Extraction kit. DNAs were analyzed by real-time quantitative PCR or ultrasequencing.
The naked DNA was prepared by treating the cells exactly as before up to the point of the RNase treatment, with the only difference that no MNase was added. From there, naked DNA was divided into four different tubes with MNase buffer and different ammounts of MNase ranging from 15 to 1 mU. The digestion with a range of fragments similar to that of the chosen chromatin sample (see Fig. 1) was electrophoresed in parallel with the chromatin sample. A slice of gel containing those naked DNA fragments with a similar size to the mononucleosome was cut and the DNA purified

tag: background strain

tag: genotype

value: wildtype


title: MNASE DST1D mutant rep 1

value: DST1 mutant


title: siControl + RhebCA + Vehicle_2

description: Expression changes of HeLa mRNA


title: FOXK1_Overexpression_1


title: Patient 3 tumor sample

value: Tum Patient 3

value: M

value: 5-FU + RT

tag: cancer recurrance after surgery

tag: disease free time (month)

tag: death due to tumor

tag: survival time (month)


title: Empty Vector_2

value: empty vector


title: Patient 4 tumor sample

tag: patient

value: Tum Patient 4

tag: age

tag: gender

tag: tissue


title: Patient 1 tumor sample

value: Tum Patient 1

value: F

tag: kras mutation

tag: preoperative radiochemotherapy (rct)

tag: depth of invasion before rct

tag: lymph node metastasis before rct


title: MNASE DST1D mutant rep 2


title: Patient 2 tumor sample

value: Tum Patient 2

tag: metastasis before rct

tag: depth of invasion after rct


title: Empty Vector_1

tag: cell line

tag: transfection


title: Blood-NS_081_D01

status: Public on Nov 27 2017

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

description: Gene expression data from whole blood

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000.

data_processing: The data were normalized using RMA methods.

label: biotin

source_name: Patient 81, Day1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from PAXgene tubes according to the manufacturer’s instructions. In brief, total RNA was isolated using the PAXgene blood RNA kit (PreAnalytix, Hilden, Germany). The residual genomic DNA was digested using the RNase-Free DNase set (Qiagen Valencia, CA, USA).

tag: time point

tag: survival

value: Non Survivor


title: Blood-NS_081_D03

description: Gene expression data from whole blood

source_name: Patient 81, Day3


title: Blood-NS_067_D01

description: Gene expression data from whole blood

source_name: Patient 67, Day1

value: H


title: Blood-NS_077_D01

description: Gene expression data from whole blood

source_name: Patient 77, Day1


title: Blood-NS_068_D03

description: Gene expression data from whole blood

source_name: Patient 68, Day3


title: Blood-NS_078_D01

description: Gene expression data from whole blood

source_name: Patient 78, Day1


title: Blood-NS_062_D03

description: Gene expression data from whole blood

source_name: Patient 62, Day3


title: Blood-NS_077_D02

description: Gene expression data from whole blood

source_name: Patient 77, Day2


title: Blood-NS_035_D03

description: Gene expression data from whole blood

source_name: Patient 35, Day3


title: Blood-NS_078_D03

description: Gene expression data from whole blood

source_name: Patient 78, Day3


title: Blood-NS_067_D03

description: Gene expression data from whole blood

source_name: Patient 67, Day3


title: Blood-NS_212_D01

description: Gene expression data from whole blood

source_name: Patient 212, Day1


title: Blood-NS_062_D01

description: Gene expression data from whole blood

source_name: Patient 62, Day1


title: Blood-NS_035_D01

description: Gene expression data from whole blood

source_name: Patient 35, Day1


title: Blood-NS_068_D01

description: Gene expression data from whole blood

source_name: Patient 68, Day1


title: Blood-NS_036_D01

description: Gene expression data from whole blood

source_name: Patient 36, Day1


title: Blood-NS_201_D02

description: Gene expression data from whole blood

source_name: Patient 201, Day2


title: Blood-NS_036_D03

description: Gene expression data from whole blood

source_name: Patient 36, Day3


title: Blood-NS_212_D02

description: Gene expression data from whole blood

source_name: Patient 212, Day2


title: Blood-NS_216_D03

description: Gene expression data from whole blood

source_name: Patient 216, Day3


title: Blood-NS_201_D01

description: Gene expression data from whole blood

source_name: Patient 201, Day1


title: Blood-NS_198_D01

description: Gene expression data from whole blood

source_name: Patient 198, Day1


title: Blood-NS_216_D01

description: Gene expression data from whole blood

source_name: Patient 216, Day1


title: Patient 42 tumor sample

source_name: rectal tumor

value: Tum Patient 42

tag: lymph node metastasis after rct

tag: metastasis after rct

tag: cancer recurrance after surgery

tag: disease free time (month)


title: Blood-NS_198_D03

description: Gene expression data from whole blood

source_name: Patient 198, Day3

tag: age


title: Blood-NS_179_D01

description: Gene expression data from whole blood

source_name: Patient 179, Day1

tag: gender


title: Blood-NS_179_D02

description: Gene expression data from whole blood

source_name: Patient 179, Day2


title: Blood-NS_018_D02

description: Gene expression data from whole blood

source_name: Patient 18, Day2


title: Blood-NS_123_D01

description: Gene expression data from whole blood

source_name: Patient 123, Day1


title: Blood-SV_093_D03

description: Gene expression data from whole blood

source_name: Patient 93, Day3

value: Survivor


title: Blood-NS_123_D02

description: Gene expression data from whole blood

source_name: Patient 123, Day2


title: Blood-SV_095_D01

description: Gene expression data from whole blood

source_name: Patient 95, Day1


title: Blood-NS_168_D01

description: Gene expression data from whole blood

source_name: Patient 168, Day1


title: Blood-NS_168_D02

description: Gene expression data from whole blood

source_name: Patient 168, Day2


title: Blood-SV_095_D03

description: Gene expression data from whole blood

source_name: Patient 95, Day3


title: Blood-NS_102_D01

description: Gene expression data from whole blood

source_name: Patient 102, Day1


title: Blood-SV_086_D01

description: Gene expression data from whole blood

source_name: Patient 86, Day1


title: Blood-SV_074_D02

description: Gene expression data from whole blood

source_name: Patient 74, Day2


title: Blood-SV_069_D03

description: Gene expression data from whole blood

source_name: Patient 69, Day3


title: Blood-SV_070_D01

description: Gene expression data from whole blood

source_name: Patient 70, Day1


title: Blood-SV_093_D01

description: Gene expression data from whole blood

source_name: Patient 93, Day1


title: Blood-SV_080_D03

description: Gene expression data from whole blood

source_name: Patient 80, Day3


title: Blood-SV_074_D01

description: Gene expression data from whole blood

source_name: Patient 74, Day1


title: Blood-SV_069_D01

description: Gene expression data from whole blood

source_name: Patient 69, Day1


title: Blood-SV_046_D03

description: Gene expression data from whole blood

source_name: Patient 46, Day3


title: Blood-SV_072_D01

description: Gene expression data from whole blood

source_name: Patient 72, Day1


title: Blood-SV_080_D01

description: Gene expression data from whole blood

source_name: Patient 80, Day1


title: Blood-NS_102_D02

description: Gene expression data from whole blood

source_name: Patient 102, Day2


title: Blood-SV_070_D02

description: Gene expression data from whole blood

source_name: Patient 70, Day2


title: Blood-SV_054_D01

description: Gene expression data from whole blood

source_name: Patient 54, Day1


title: Blood-SV_046_D01

description: Gene expression data from whole blood

source_name: Patient 46, Day1


title: Blood-SV_054_D03

description: Gene expression data from whole blood

source_name: Patient 54, Day3


title: Blood-SV_044_D01

description: Gene expression data from whole blood

source_name: Patient 44, Day1


title: Blood-NS_018_D01

description: Gene expression data from whole blood

source_name: Patient 18, Day1


title: Blood-SV_044_D03

description: Gene expression data from whole blood

source_name: Patient 44, Day3


title: Blood-SV_043_D01

description: Gene expression data from whole blood

source_name: Patient 43, Day1


title: Blood-SV_086_D02

description: Gene expression data from whole blood

source_name: Patient 86, Day2


title: Blood-SV_248_D01

description: Gene expression data from whole blood

source_name: Patient 248, Day1


title: Blood-SV_248_D02

description: Gene expression data from whole blood

source_name: Patient 248, Day2


title: Blood-SV_027_D02

description: Gene expression data from whole blood

source_name: Patient 27, Day2


title: Blood-SV_033_D03

description: Gene expression data from whole blood

source_name: Patient 33, Day3


title: Blood-SV_033_D01

description: Gene expression data from whole blood

source_name: Patient 33, Day1


title: Blood-SV_032_D03

description: Gene expression data from whole blood

source_name: Patient 32, Day3


title: Blood-SV_032_D01

description: Gene expression data from whole blood

source_name: Patient 32, Day1


title: Blood-SV_019_D02

description: Gene expression data from whole blood

source_name: Patient 19, Day2


title: Blood-SV_021_D01

description: Gene expression data from whole blood

source_name: Patient 21, Day1


title: Blood-SV_213_D02

description: Gene expression data from whole blood

source_name: Patient 213, Day2


title: Blood-SV_021_D03

description: Gene expression data from whole blood

source_name: Patient 21, Day3


title: Blood-SV_215_D02

description: Gene expression data from whole blood

source_name: Patient 215, Day2


title: Blood-SV_209_D03

description: Gene expression data from whole blood

source_name: Patient 209, Day3


title: Blood-SV_209_D01

description: Gene expression data from whole blood

source_name: Patient 209, Day1


title: Blood-SV_027_D01

description: Gene expression data from whole blood

source_name: Patient 27, Day1


title: Blood-SV_043_D03

description: Gene expression data from whole blood

source_name: Patient 43, Day3


title: Blood-SV_175_D03

description: Gene expression data from whole blood

source_name: Patient 175, Day3


title: Blood-SV_211_D03

description: Gene expression data from whole blood

source_name: Patient 211, Day3


title: Blood-SV_211_D01

description: Gene expression data from whole blood

source_name: Patient 211, Day1


title: Blood-SV_183_D01

description: Gene expression data from whole blood

source_name: Patient 183, Day1


title: Blood-SV_019_D01

description: Gene expression data from whole blood

source_name: Patient 19, Day1


title: Blood-SV_072_D03

description: Gene expression data from whole blood

source_name: Patient 72, Day3


title: Blood-SV_213_D01

description: Gene expression data from whole blood

source_name: Patient 213, Day1


title: Blood-SV_175_D01

description: Gene expression data from whole blood

source_name: Patient 175, Day1


title: Blood-SV_215_D01

description: Gene expression data from whole blood

source_name: Patient 215, Day1


title: Blood-SV_016_D02

description: Gene expression data from whole blood

source_name: Patient 16, Day2


title: Blood-SV_016_D01

description: Gene expression data from whole blood

source_name: Patient 16, Day1


title: Blood-SV_153_D01

description: Gene expression data from whole blood

source_name: Patient 153, Day1


title: Blood-SV_183_D02

description: Gene expression data from whole blood

source_name: Patient 183, Day2


title: Blood-SV_151_D01

description: Gene expression data from whole blood

source_name: Patient 151, Day1


title: Blood-SV_142_D01

description: Gene expression data from whole blood

source_name: Patient 142, Day1


title: Blood-SV_135_D03

description: Gene expression data from whole blood

source_name: Patient 135, Day3


title: Blood-SV_115_D01

description: Gene expression data from whole blood

source_name: Patient 115, Day1


title: Blood-SV_153_D03

description: Gene expression data from whole blood

source_name: Patient 153, Day3


title: Blood-SV_151_D03

description: Gene expression data from whole blood

source_name: Patient 151, Day3


title: Blood-PC_534_D00

description: Gene expression data from whole blood

source_name: Control 534


title: Blood-SV_119_D02

description: Gene expression data from whole blood

source_name: Patient 119, Day2


title: Blood-SV_124_D01

description: Gene expression data from whole blood

source_name: Patient 124, Day1


title: Blood-SV_119_D01

description: Gene expression data from whole blood

source_name: Patient 119, Day1


title: Blood-PC_517_D00

description: Gene expression data from whole blood

source_name: Control 517


title: Blood-SV_121_D01

description: Gene expression data from whole blood

source_name: Patient 121, Day1


title: Blood-SV_121_D03

description: Gene expression data from whole blood

source_name: Patient 121, Day3


title: Blood-PC_511_D00

description: Gene expression data from whole blood

source_name: Control 511


title: Blood-SV_135_D01

description: Gene expression data from whole blood

source_name: Patient 135, Day1


title: Blood-PC_532_D00

description: Gene expression data from whole blood

source_name: Control 532


title: Blood-SV_108_D01

description: Gene expression data from whole blood

source_name: Patient 108, Day1


title: Blood-PC_537_D00

description: Gene expression data from whole blood

source_name: Control 537


title: Blood-PC_535_D00

description: Gene expression data from whole blood

source_name: Control 535


title: Blood-PC_530_D00

description: Gene expression data from whole blood

source_name: Control 530


title: Blood-PC_528_D00

description: Gene expression data from whole blood

source_name: Control 528


title: Blood-PC_523_D00

description: Gene expression data from whole blood

source_name: Control 523


title: Blood-SV_115_D03

description: Gene expression data from whole blood

source_name: Patient 115, Day3


title: Blood-CS_789_D00

description: Gene expression data from whole blood

source_name: Control 789


title: Blood-SV_108_D02

description: Gene expression data from whole blood

source_name: Patient 108, Day2


title: Blood-CS_742_D00

description: Gene expression data from whole blood

source_name: Control 742


title: Blood-PC_513_D00

description: Gene expression data from whole blood

source_name: Control 513


title: Blood-CS_628_D00

description: Gene expression data from whole blood

source_name: Control 628


title: Blood-CS_598_D00

description: Gene expression data from whole blood

source_name: Control 598


title: Blood-CS_793_D00

description: Gene expression data from whole blood

source_name: Control 793


title: Blood-CS_535_D00

description: Gene expression data from whole blood


title: Blood-CS_529_D00

description: Gene expression data from whole blood

source_name: Control 529


title: Blood-SV_124_D03

description: Gene expression data from whole blood

source_name: Patient 124, Day3


title: Blood-CS_530_D00

description: Gene expression data from whole blood


title: Blood-CS_500_D00

description: Gene expression data from whole blood

source_name: Control 500


title: Blood-CS_526_D00

description: Gene expression data from whole blood

source_name: Control 526


title: T_inhib2

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

hyb_protocol: retrotranscribed RNA was  hybridized on HT12 Human bead chips (Illumina), as per manufacturer’s instructions

scan_protocol: Bead array scanner (Illumina) was used, as per manufacturer’s instructions

data_processing:
idat files were imported and analyzed with R/Bioconductor packages (e.g. lumi, limma)
raw intensities were normalized using neqc (background correction using negative control probes + quantile normalization using negative and positive control probes). Raw log2 intensities and neqc normalized values accompany this submission.

source_name: inhibitor (MiR500a suppressed)

label_protocol: total RNA from cells transfected with Pre-miR-500a-5p, miR-500a-5p inhibitor, or control miR-125a-5p inhibitor was reverse-transcribed using Ambion Illumina Total Prep

growth_protocol: cells were grown in standard medium (10% FBS,  1% Pen/Step, 1% Na pyruvate, and 1% glutamine)

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Pre-miR mature microRNA (Pre-miR-500a-5p) sequence (Applied Biosystems) and knock-down (miR-500a-5p inhibitor) locked nucleic acid (LNA) (Exiqon) were used for overexpression and inhibition of miR-500a-5p, respectively. miR-125a-5p LNA was used as negative control.

tag: cell type

value: Breast cancer cell line


title: T_control1

source_name: control


title: T_inhib1


title: T_mimic3

source_name: mimic (MiR500a overexpressed)


title: T_mimic2


title: T_control3


title: Blood-CS_553_D00

description: Gene expression data from whole blood

source_name: Control 553


title: M_mimic4


title: M_inhib2


title: M_control3


title: T_mimic1


title: M_inhib1


title: M_control4


title: T_control2


title: Blood-PC_538_D00

description: Gene expression data from whole blood

source_name: Control 538


title: T_inhib3


title: M_control1


title: M_control2


title: M_mimic1


title: M_mimic3


title: M_mimic2


title: M_inhib4


title: M_inhib3


title: CAKUT Patient 19

city: Belgrade

first: Aleksandra

last: Stankovic

address: Mike Petrovica Alasa 12

department: Department of Health and Environment

country: Serbia

institute: VINCA Institute of Nuclear Sciences, University of Belgrade

hyb_protocol: Illumina® Direct Hybridization Assay protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and normalised using quantile normalisation using GenomeStudio software 2011.1 (Illumina)

source_name: Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT) Patient

label_protocol: TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre)

extract_protocol: TRI Reagent® Solution (Ambion) protocol

tag: tissue

value: Ureter


title: CAKUT Patient 17


title: CAKUT Patient 18


title: Blood-SV_142_D03

description: Gene expression data from whole blood

source_name: Patient 142, Day3


title: v4_C_t1

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Human Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V19 was used for annotation.

label_protocol: 200 ng of total RNA is reverse transcribed  following the Gene chip® WT-Amp Plus kit (Affymetrix). Briefly, the resulting double stranded cDNA is used to produce single stranded RNA using T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

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

treatment_protocol: Rectal biopsies were collected before and after a dietary intervention with casein, soy protein or maltodextrin (placebo),

value: rectal mucosa


title: CAKUT Patient 12


title: CAKUT Patient 15


title: v21_A_t1


title: v18_C_t1


title: CAKUT Patient 10


title: v27_B_t4


title: v4_C_t4


title: v15_B_t4


title: CAKUT Patient 16


title: v15_B_t1


title: v34_B_t1


title: CAKUT Patient 14


title: CAKUT Patient 8


title: v13_C_t1


title: CAKUT Patient 9


title: v12_B_t1


title: CAKUT Patient 6


title: v40_C_t4


title: CAKUT Patient 13


title: CAKUT Patient 11


title: v33_B_t4


title: v33_B_t1


title: CAKUT Patient 7


title: v30_A_t1


title: CAKUT Patient 3


title: v22_B_t4


title: CAKUT Patient 2


title: v3_A_t4


title: v30_A_t4


title: v34_B_t4


title: v38_B_t4


title: CAKUT Patient 4


title: CAKUT Patient 1


title: Healthy Control 4

source_name: Healthy Control


title: Healthy Control 6


title: v7_B_t1


title: Healthy Control 5


title: v27_B_t1


title: Healthy Control 7


title: v40_C_t1


title: v39_C_t4


title: Healthy Control 3


title: v22_B_t1


title: v31_A_t1


title: v19_C_t1


title: v9_A_t4


title: v41_B_t4


title: v42_C_t1


title: v3_A_t1


title: v14_A_t1


title: v19_C_t4


title: Healthy Control 2


title: Healthy Control 1


title: v37_A_t4


title: v32_A_t4


title: v2_B_t4


title: v32_A_t1


title: v26_C_t4


title: v9_A_t1


title: v12_B_t4


title: v41_B_t1


title: v42_C_t4


title: v39_C_t1


title: v35_C_t4


title: v25_A_t4


title: v31_A_t4


title: v29_C_t1


title: v37_A_t1


title: v26_C_t1


title: v29_C_t4


title: v35_C_t1


title: v23_C_t4


title: v20_B_t4


title: v25_A_t1


title: v38_B_t1


title: v24_A_t4


title: v14_A_t4


title: v13_C_t4


title: v24_A_t1


title: v20_B_t1


title: v18_C_t4


title: v21_A_t4


title: v11_C_t1


title: v23_C_t1


title: v7_B_t4


title: v11_C_t4


title: v2_B_t1


title: LF3h, technical rep2

status: Public on Nov 26 2017

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: duodenum mucosa of mice at 3 h after a LF meal ingestion.

hyb_protocol: Fifteen micrograms of fragmented cRNA was hybridised for 16 h at 45°C with constant rotation. After hybridisation, chips were processed by using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE)(Molecular Probes), followed by amplification with a biotinylated anti-streptavidin antibody (Vector Laboratories), and by a second round of SAPE.

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 G7 (Affymetrix) enabled for High-Resolution Scanning. Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4).

data_processing: The background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA. Gene expression profiles were determined with Affymetrix GeneChip® MOE 430 v2.0 .

growth_protocol: C57BL6 mice (12 wk-old) were purchased from the Charles River Canada Inc. and were acclimated for two wk. LF diet (Research Diet # 12450B: 10% calories from fat, 70% from carbohydrate, and 20% from protein; 3.85 kcal/g) and tap water were served ad libitum. The last day of the acclimatization, the body weight paired mice were randomly distributed into seven groups and fasted for 12 h during darkness of the light cycle. On the experimental day, one group of 20 fasted mice was euthanized by cervical dislocation, exsanguinated by cardiac puncture, and opened via ventral abdominal incision. The other mice were fed ad libitum with a HF (Research Diet # 12492: 60% calories from fat, 20% from carbohydrate, and 20% from protein; 5.24 kcal/g) or LF  meal until the end of experiment, and 20 mice per each group were sacrificed 30 min, 1 h and 3 h after the beginning of the meal. Both meals are open formula purified ingredient diet with a powder form.

treatment_protocol: Duodenum was opened vertically, flushed clean with saline, and the mucosa was removed by scrapping with a glass microscope slide. The samples were rapidly frozen in liquid nitrogen and stored at -80oC until RNA extraction.

value: male

tag: strain

value: Duedenum mucosa


title: CAKUT Patient 5


title: HF30min, technical rep1

description: duodenum mucosa of mice at 30 min after a HF meal ingestion.


title: LF1h, technical rep2

description: duodenum mucosa of mice at 1 h after a LF meal ingestion.


title: HF3h, technical rep1

description: duodenum mucosa of mice at 3 h after a HF meal ingestion.


title: HF30min, technical rep2

source_name: duodenum mucosa of mice at 30 min after a HF meal ingestion.


title: LF30min, technical rep1

description: duodenum mucosa of mice at 30 min after a LF meal ingestion.


title: H3K27-Control THP-1 Cell

type: genomic

city: Xiamen

first: Qi-Fan

last: Zheng

state: Fujian

address: South Xiang'an Road

department: Medical collage

country: China

institute: Xiamen University

description: comparison of control vs PMA treated THP-1 cells

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4μg of Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA). For array hybridization, ArrayStar Human RefSeq Promoter Array was used, which is a single array designs that includes 23,148 gene promoter regions (from about -1300bp to +500bp of the TSSs) totally covered by ~180,000 probes with approximately 210bp spacing, dependent on the sequence composition of the region.

scan_protocol: Microarrays were scanned using Agilent Scanner G2505C.

data_processing:
Raw data were extracted as txt files by Agilent Feature Extraction software (version 11.0.1.1).
We perform Median-centering, quantile normalization and linear smoothing in this analysis process by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample.

source_name: H3K27me3 ChIP DNA from THP-1 control cells

label_protocol: The purified DNA was quantified using a NanoDrop ND-1000. For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen ChIP-on-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labelled DNA was purified by isopropanol / ethanol precipitation.

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were kept at 37℃ with 5% CO2.

extract_protocol: For each immunoprecipitate (IP), cells were cross-linked with 1% formaldehyde for 10 min, washed in cold PBS buffer, resuspended in lysis buffer, and sonicated to obtain chromatin fragments between 200 bp and 1000 bp. Sonicated chromatin was resuspended in IP buffer and incubated overnight at 4°C with magnetic beads conjugated antibodies (H3K4me3 or H3K27me3). The IP was then washed with lysis buffer, LiCl buffer and TE buffer, eluted in elution buffer. The DNA was then recovered by reversing the crosslinks, and purified by QIAGEN Purification Kit. An un-enriched sample of DNA was treated in a similar manner to serve as input.

treatment_protocol: control

value: Monocytic leukemia

tag: agent

value: control

tag: chip antibody

source_name: Input DNA from THP-1 control cells


title: LF3h, technical rep1

source_name: duodenum mucosa of mice at 3 h after a LF meal ingestion.


title: si4B

status: Public on Nov 25 2017

city: Jinan

first: Han

last: Bo

address: #44, Wenhua Xi Rd

department: Department of Pathology

institute: Shandong University Medical School

description: MKN45  cells  siliencing CUL4B(si4B)

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 ?g of Cy3 labeled ds-cDNA in Agilent hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - Agilent  Technologies,Inc. Waldbronn, Germany). Following hybridization, washing was performed using the  Agilent Wash Buffer kit ( Agilent  Technologies,Inc. Waldbronn, Germany). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into Agilent software (version 2.5) for grid alignment and expression data analysis.

data_processing: All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the Agilent Gene Expression Analysis protocol ( Agilent  Technologies,Inc. Waldbronn, Germany). Briefly, ds-cDNA was incubated with 4 ?g RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the epicentreTargetAmp 1-round aRNA amplification kit  was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (  Agilent  Technologies,Inc. Waldbronn, Germany). One ?g ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: MKN45/NC cells were cultured in RPMI1640 medium and then transfected with control siRNA for 48hs as negative control. MKN45/si4B cells were cultured in RPMI1640 medium and then transfected with siRNA transiently knockdown CUL4B for 48 hs.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: developmental stage

value: poorly differentiated adenocarcinoma cells


title: LF1h, technical rep1

source_name: duodenum mucosa of mice at 1 h after a LF meal ingestion.


title: HF1h, technical rep1

description: duodenum mucosa of mice at 1 h after a HF meal ingestion.


title: HF3h, technical rep2

source_name: duodenum mucosa of mice at 3 h after a HF meal ingestion.


title: H3K27-PMA treated THP-1 Cell

source_name: H3K27me3 ChIP DNA from THP-1 PMA treated cells

treatment_protocol: 50 ng/ml PMA treatment for 72 h

value: PMA

source_name: Input DNA from THP-1 PMA treated cells


title: H3K4-PMA treated THP-1 Cell Replicate 3

source_name: H3K4me3 ChIP DNA from THP-1 PMA treated cells


title: Fasting, technical rep1

description: duodenum mucosa of mice after 12-h fasting.


title: NC

description: MKN45  cells transfected with negative control(NC)


title: HF1h, technical rep2

source_name: duodenum mucosa of mice at 1 h after a HF meal ingestion.


title: H3K4-PMA treated THP-1 Cell Replicate 2


title: H3K4-PMA treated THP-1 Cell Replicate 1


title: TW39

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

country: Singapore

institute: National University Health System, Singapore

hyb_protocol: Hybridization was performed according to NuGEN specifications.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000.

data_processing: Data processed with FRMA algorithm using R/Bioconductor system's frma and oligo packages.

source_name: tumor

label_protocol: Amplification and labeling of RNA samples were performed using the Ovation FFPE WTA system (NuGEN, USA).

extract_protocol: Total RNA was extracted using RecoverAll Total Nucleic Acid Isolation (ThermoFisher Scientific, USA) according to manufacturer's instructions.

tag: disease state

value: NKTL

tag: preparation

value: FFPE


title: H3K4-Control THP-1 Cell Replicate 1

source_name: H3K4me3 ChIP DNA from THP-1 control cells

tag: cell line


title: TW40


title: LF30min, technical rep2

source_name: duodenum mucosa of mice at 30 min after a LF meal ingestion.


title: Fasting, technical rep2

source_name: duodenum mucosa of mice after 12-h fasting.


title: TW38


title: H3K4-Control THP-1 Cell Replicate 3


title: TW37


title: TW22


title: TW27


title: TW23


title: TW26


title: TW33


title: TW9


title: TW29


title: TW34


title: TW19


title: TW35


title: TW14


title: TW7


title: TW24


title: H3K4-Control THP-1 Cell Replicate 2


title: TW11


title: T242


title: TW10


title: TNK10


title: TNK4


title: TW13


title: T241


title: TNK5


title: TW8


title: TNK9


title: T114


title: T202


title: TNK1


title: TNK3


title: TNK6


title: T35


title: MD11


title: T85


title: T72


title: T25


title: MD15


title: MD10


title: MD05


title: SGH2010


title: MD07


title: MD09


title: Cecum_FKO_Day22_rep5

first: Bruno

last: LAMAS

address: 27 rue Chaligny

department: CHU St Antoine

institute: Unité INSERM 1157/UMR 7203

description:
M40
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 22 days after C. rodentium infection

hyb_protocol: For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes and hybridized to the microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed and then dried immediately.

scan_protocol: After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies), with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing: The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE1_107_Sep09 protocol.

source_name: Cecum_Flore KO_Day22

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: female C57BL/6j mice and female Card9-/- mice on the background C57BL/6j were bred in specific-pathogen–free facilities. Germ-free Card9-/- and C57BL/6J mice were bred in germ-free isolators in the facilities.

extract_protocol: Total RNA was isolated from cecum samples using RNeasy® Mini Kit (Qiagen), according to the manufacturer's instructions. RNA integrity was checked onto a Bioanalyzer 2100 using RNA 6000 Nano chips (Agilent Technologies) and all of the samples showed a RIN score higher than 7.

treatment_protocol: Fresh stool samples from WT or Card9-/- mice (8 weeks old, males) were immediately transferred to an anaerobic chamber, in which the stool samples were suspended and diluted in LYHBHI medium supplemented with cellobiose (1 mg/ml), maltose (1 mg/ml) and cysteine (0.5 mg/ml). WT germ-free mice (4-5 weeks old, females) were randomly assigned to two groups and inoculated via oral gavage with 400 µl of fecal suspension (1:100) from the conventional wild-type (WT-->GF) or Card9-/- (Card9-/- -->GF) mice and maintained in separated isolators. three weks after the colonization, mice were infected by oral gavage with 0.5 mL of phosphate-buffered saline (PBS) containing approximately 1x10^9 CFU of C. rodentium strain DBS100. Mice were euthanized before (Day0), 4, 12 and 22 days after C. rodentium infection.

tag: strain background

tag: genotype/variation

value: germ free WT

value: female

value: 7 weeks

tag: inoculated with

value: 400 µl of fecal suspension (1:100) from Card9-/-

tag: time point

value: 22 days after C. rodentium infection

value: cecum


title: MD13


title: Cecum_FKO_Day22_rep2

description:
M37
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 22 days after C. rodentium infection


title: MD04


title: Cecum_FKO_Day22_rep4

description:
M39
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 22 days after C. rodentium infection


title: MD01


title: A1


title: Cecum_FKO_Day22_rep1

description:
M36
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 22 days after C. rodentium infection


title: K2


title: Cecum_FWT_Day22_rep3

description:
M35
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 22 days after C. rodentium infection

source_name: Cecum_Flore WT_Day22

value: 400 µl of fecal suspension (1:100) from WT


title: NKTL60


title: NKTL65


title: K1


title: Cecum_FWT_Day22_rep2

description:
M34
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 22 days after C. rodentium infection


title: Cecum_FKO_Day22_rep3

description:
M38
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 22 days after C. rodentium infection


title: MD02


title: NKTL69


title: Cecum_FKO_Day12_rep5

description:
M32
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 12 days after C. rodentium infection

source_name: Cecum_Flore KO_Day12

value: 5 weeks

value: 12 days after C. rodentium infection


title: Cecum_FKO_Day12_rep4

description:
M31
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 12 days after C. rodentium infection


title: NKTL53


title: Cecum_FWT_Day22_rep1

description:
M33
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 22 days after C. rodentium infection


title: Cecum_FKO_Day12_rep3

description:
M30
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 12 days after C. rodentium infection


title: T25

hyb_protocol: Arrays were hybridized, washed, and stained in GeneChip Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: Arrays were scanned using the GeneChip 3000 7G scanner according to manufacturer's protocols.

data_processing: Data processed using Affymetrix OncoScan Console (v1.3) software.

source_name: Tumor

label_protocol: MIP probe annealing and hybridization was performed according to manufacturer's protocols.

extract_protocol: Genomic DNAs were extracted according to manufacturer's protocols.

tag: disease


title: 1411-12

value: B cell lymphoma


title: T241


title: NKTL59


title: NKTL50


title: 1411-11


title: 1411-13


title: T202


title: NKTL36


title: NKTL40


title: NKTL52


title: 1411-08

value: T cell lymphoma


title: Cecum_FKO_Day12_rep2

description:
M29
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 12 days after C. rodentium infection


title: NKTL43


title: T242


title: NKTL24


title: Cecum_FKO_Day12_rep1

description:
M28
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 12 days after C. rodentium infection


title: Cecum_FWT_Day12_rep5

description:
M27
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 12 days after C. rodentium infection

source_name: Cecum_Flore WT_Day12


title: Cecum_FWT_Day12_rep3

description:
M25
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 12 days after C. rodentium infection


title: Cecum_FWT_Day12_rep2

description:
M24
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 12 days after C. rodentium infection


title: NKTL41


title: NKTL23A


title: A1


title: Cecum_FWT_Day12_rep1

description:
M23
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 12 days after C. rodentium infection


title: 1411-06

value: Normal B

value: Primary tissue


title: Cecum_FWT_Day12_rep4

description:
M26
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 12 days after C. rodentium infection


title: T114


title: MD15


title: MD11


title: 1411-05


title: NKTL27B


title: MD10


title: 1411-03

value: Normal T


title: MD05


title: 1411-04


title: 1411-01

value: Normal NK


title: NKTL17

value: NKTL


title: Cecum_FKO_Day4_rep4

description:
M20
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection

source_name: Cecum_Flore KO_Day4

value: 4 weeks

value: 4 days after C. rodentium infection


title: NKTL22

value: FFPE


title: Cecum_FKO_Day4_rep5

description:
M21
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection

value: germ free WT

value: female


title: 1405-12

value: Normal LN


title: Cecum_FKO_Day4_rep1

description:
M17
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection

value: 400 µl of fecal suspension (1:100) from Card9-/-

value: cecum


title: Cecum_FKO_Day4_rep2

description:
M18
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection


title: TW39


title: 1411-02


title: Cecum_FWT_Day4_rep4

description:
M14
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection

source_name: Cecum_Flore WT_Day4

value: 400 µl of fecal suspension (1:100) from WT


title: Cecum_FWT_Day4_rep6

description:
M16
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection


title: TW38


title: TW37


title: 1405-10

value: Normal Tonsil


title: 1405-11


title: Cecum_FWT_Day4_rep3

description:
M13
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection


title: 1405-09

value: B cell lymphoma


title: Cecum_FWT_Day4_rep5

description:
M15
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection


title: Cecum_FKO_Day4_rep3

description:
M19
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection


title: TW33


title: 1405-07

value: T cell lymphoma


title: TW34


title: TW29


title: 1405-08


title: 1405-05


title: TW27


title: Cecum_FWT_Day4_rep1

description:
M11
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection


title: 1405-06


title: TW22


title: 1405-04


title: TW13


title: TW7


title: 1405-03


title: 1411-10


title: 1405-02


title: TW26


title: Cecum_FKO_Day0_rep5

description:
M10
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota before C. rodentium infection

source_name: Cecum_Flore KO_Day0

value: before C. rodentium infection


title: Cecum_FKO_Day0_rep3

description:
M08
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota before C. rodentium infection


title: Cecum_FKO_Day0_rep1

description:
M06
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota before C. rodentium infection


title: Cecum_FKO_Day0_rep2

description:
M07
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota before C. rodentium infection


title: Cecum_FKO_Day4_rep6

description:
M22
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota 4 days after C. rodentium infection


title: Cecum_FWT_Day4_rep2

description:
M12
Gene expression in cecum from germ free WT mouse colonized with WT microbiota 4 days after C. rodentium infection


title: TNK10


title: Cecum_FWT_Day0_rep5

description:
M05
Gene expression in cecum from germ free WT mouse colonized with WT microbiota before C. rodentium infection

source_name: Cecum_Flore WT_Day0


title: TNK9


title: Cecum_FKO_Day0_rep4

description:
M09
Gene expression in cecum from germ free WT mouse colonized with Card9-/- microbiota before C. rodentium infection


title: Cecum_FWT_Day0_rep4

description:
M04
Gene expression in cecum from germ free WT mouse colonized with WT microbiota before C. rodentium infection


title: TNK6


title: TNK4


title: TNK3


title: TNK1


title: NKTL60


title: NKTL59


title: NKTL53


title: NKTL50


title: NKTL24

hyb_protocol: Hybridization was performed according to Affymetrix GeneChip Hybridization, Wash and Stain Kit (Affymetrix, CA, USA).

data_processing: Data processed with RMA algorithm using R/Bioconductor system's oligo package.

label_protocol: Amplification and labeling of RNA samples were performed using the Affymetrix FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, CA, USA).


title: Cecum_FWT_Day0_rep1

description:
M01
Gene expression in cecum from germ free WT mouse colonized with WT microbiota before C. rodentium infection


title: TNK10


title: Cecum_FWT_Day0_rep2

description:
M02
Gene expression in cecum from germ free WT mouse colonized with WT microbiota before C. rodentium infection


title: NKTL43


title: Cecum_FWT_Day0_rep3

description:
M03
Gene expression in cecum from germ free WT mouse colonized with WT microbiota before C. rodentium infection


title: TW22


title: NKTL41


title: NKTL59


title: TNK6


title: NKTL27A


title: NKTL40


title: NKTL36


title: TNK4


title: NKTL22


title: 1411-07


title: NKTL41


title: NKTL40


title: NKTL50


title: TNK9


title: NKTL23A


title: NKTL23A


title: NKTL52


title: NKTL60


title: NKTL24


title: ACC lesion #7b

status: Public on Nov 24 2017

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description:
Gene expression data from adenocortical lesion
Sample name: B_7

hyb_protocol: Performed according to Affymetrix protocol

data_processing:
Array design (PrimeView.cdf, rev01) and genomic annotation (PrimeView.na35.annot.csv) were downloaded from Affymetrix product support. CEL files were processed by JMP/Genomics software (v.7, SAS Institute, Cary NC) with the Affymetrix Import Engine AP using RMA background correction, transformation to log2 after adding 16 (shifting factor), and summarization by median polish.
Log2 RMA signal intensity calculated using JMP/Genomics software from cel files.  The RMA values are available in the file RMA_values.txt on the series record. The RMA values were further quantile normalized using JMP/Genomics software and the quantile normalized values were used for analysis.

source_name: adrenocortical carcinoma lesion

extract_protocol: RNA isolated from frozen ACC samples was extracted using Qiagen miRNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol:
Samples: Human ACC samples were acquired from consenting patients after surgery, under NIH protocol Natural History and Tissue Acquisition Study of Adrenocortical Carcinoma no. 14-C-0001 ClinicalTrials.gov Identifier NCT02015026.
Samples originating from different lesions from the same patient are labeled with the same letter (a thru I) in the column patient
5 normal adrenal tissue samples (written as NA* under the ACC_Num column) were obtained from CHTN Southern Division, Birmingham, AL; H295R cell line was obtained from ATCC Manassas, VA
Samples were frozen immediately after surgery

value: adrenocortical carcinoma

tag: study

tag: condition

value: tumor

tag: patient


title: ACC lesion #4b

description:
Gene expression data from adenocortical lesion
Sample name: B_4

scan_protocol: Performed according to Affymetrix protocol


title: ACC lesion #24newb

description:
Gene expression data from adenocortical lesion
Sample name: B_24_1

label_protocol: Performed according to Affymetrix protocol


title: ACC lesion #30newb

description:
Gene expression data from adenocortical lesion
Sample name: B_30_1

value: i


title: ACC lesion #25b

description:
Gene expression data from adenocortical lesion
Sample name: B_25


title: ACC lesion #26b

description:
Gene expression data from adenocortical lesion
Sample name: B_26


title: ACC lesion #29b

description:
Gene expression data from adenocortical lesion
Sample name: B_29


title: ACC lesion #8b

description:
Gene expression data from adenocortical lesion
Sample name: B_8


title: ACC lesion #27b

description:
Gene expression data from adenocortical lesion
Sample name: B_27


title: ACC lesion #24b

description:
Gene expression data from adenocortical lesion
Sample name: B_24


title: ACC lesion #32newb

description:
Gene expression data from adenocortical lesion
Sample name: B_31


title: ACC lesion #3b

description:
Gene expression data from adenocortical lesion
Sample name: B_32_1


title: ACC lesion #23b

description:
Gene expression data from adenocortical lesion
Sample name: B_23


title: ACC lesion #15newb

description:
Gene expression data from adenocortical lesion
Sample name: B_15_1


title: ACC lesion #5b

description:
Gene expression data from adenocortical lesion
Sample name: B_5


title: ACC lesion #31b

description:
Gene expression data from adenocortical lesion
Sample name: B_3


title: ACC lesion #12newb

description:
Gene expression data from adenocortical lesion
Sample name: B_12_1

value: h


title: ACC lesion #28b

description:
Gene expression data from adenocortical lesion
Sample name: B_28


title: ACC lesion #16b

description:
Gene expression data from adenocortical lesion
Sample name: B_16


title: ACC lesion #17b

description:
Gene expression data from adenocortical lesion
Sample name: B_17


title: MD04

value: NKTL


title: ACC lesion #22b

description:
Gene expression data from adenocortical lesion
Sample name: B_22


title: ACC lesion #13b

description:
Gene expression data from adenocortical lesion
Sample name: B_13


title: ACC lesion #12b

description:
Gene expression data from adenocortical lesion
Sample name: B_12


title: ACC lesion #18b

description:
Gene expression data from adenocortical lesion
Sample name: B_18


title: ACC lesion #11newb

description:
Gene expression data from adenocortical lesion
Sample name: B_11_1


title: ACC lesion #14b

description:
Gene expression data from adenocortical lesion
Sample name: B_14


title: ACC lesion #H295R

description:
Gene expression data from adenocortical lesion
Sample name: B_1

source_name: adrenocortical carcinoma lesion_cell line


title: AV-CON-3_smmc-7721

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

hyb_protocol: The pre-hybridization of HOA v6.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on HOA v6.1 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The Matrix value is normalized intensities. The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: SMMC-7721 cells were cultured in DMEM with 10% fetal bovine serum.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: The human lncRNA-PRAL were subcloned into GV314 (GeneChem Co., Ltd Shanghai, China) for overexpression.

tag: cell type

value: hepatocellular carcinoma


title: AV-PRAL-3_smmc-7721


title: Normal sample NA4

description:
Gene expression data from normal adrenal tissue
Sample name: A_NA4

source_name: normal adrenal tissue

tag: tissue

value: normal adrenal

value: normal


title: AV-PRAL-2_smmc-7721


title: Normal sample NA18

description:
Gene expression data from normal adrenal tissue
Sample name: A_NA18


title: ACC lesion #39

description:
Gene expression data from adenocortical lesion
Sample name: A_8

value: g


title: ACC lesion #21b

description:
Gene expression data from adenocortical lesion
Sample name: B_21


title: Normal sample NA1

description:
Gene expression data from normal adrenal tissue
Sample name: A_NA1


title: ACC lesion #38

description:
Gene expression data from adenocortical lesion
Sample name: A_7

value: f


title: ACC lesion #10b

description:
Gene expression data from adenocortical lesion
Sample name: B_10


title: ACC lesion #36

description:
Gene expression data from adenocortical lesion
Sample name: A_41


title: ACC lesion #34

description:
Gene expression data from adenocortical lesion
Sample name: A_38


title: ACC lesion #35

description:
Gene expression data from adenocortical lesion
Sample name: A_39


title: AV-PRAL-3_QSG-7701

growth_protocol: QSG-7701 cells were cultured in DMEM with 10% fetal bovine serum.

value: hepatocyte


title: AV-PRAL-2_QSG-7701


title: Normal sample NA19

description:
Gene expression data from normal adrenal tissue
Sample name: A_NA19


title: AV-PRAL-1_QSG-7701


title: AV-CON-3_QSG-7701


title: AV-PRAL-1_smmc-7721


title: Normal sample NA2

description:
Gene expression data from normal adrenal tissue
Sample name: A_NA2


title: AV-CON-2_smmc-7721


title: AV-CON-1_smmc-7721


title: ACC lesion #33

description:
Gene expression data from adenocortical lesion
Sample name: A_37

value: e


title: ACC lesion #29

description:
Gene expression data from adenocortical lesion
Sample name: A_33


title: ACC lesion #31

description:
Gene expression data from adenocortical lesion
Sample name: A_35

value: a


title: ACC lesion #28

description:
Gene expression data from adenocortical lesion
Sample name: A_32


title: ACC lesion #26

description:
Gene expression data from adenocortical lesion
Sample name: A_30


title: AV-CON-1_QSG-7701


title: ACC lesion #20

description:
Gene expression data from adenocortical lesion
Sample name: A_27


title: ACC lesion #32

description:
Gene expression data from adenocortical lesion
Sample name: A_36


title: ACC lesion #9

description:
Gene expression data from adenocortical lesion
Sample name: A_15

value: d


title: ACC lesion #27

description:
Gene expression data from adenocortical lesion
Sample name: A_31


title: ACC lesion #11

description:
Gene expression data from adenocortical lesion
Sample name: A_16


title: ACC lesion #22

description:
Gene expression data from adenocortical lesion
Sample name: A_28


title: ACC lesion #30

description:
Gene expression data from adenocortical lesion
Sample name: A_34


title: ACC lesion #13

description:
Gene expression data from adenocortical lesion
Sample name: A_17


title: ACC lesion #6

description:
Gene expression data from adenocortical lesion
Sample name: A_11

value: b


title: ACC lesion #25

description:
Gene expression data from adenocortical lesion
Sample name: A_29


title: ACC lesion #17

description:
Gene expression data from adenocortical lesion
Sample name: A_26


title: ACC lesion #15

description:
Gene expression data from adenocortical lesion
Sample name: A_22


title: ACC lesion #14

description:
Gene expression data from adenocortical lesion
Sample name: A_20


title: ACC lesion #41

description:
Gene expression data from adenocortical lesion
Sample name: A_9


title: ACC lesion #7

description:
Gene expression data from adenocortical lesion
Sample name: A_13

value: c


title: AV-CON-2_QSG-7701


title: ACC lesion #8

description:
Gene expression data from adenocortical lesion
Sample name: A_14


title: ACC lesion #37

description:
Gene expression data from adenocortical lesion
Sample name: A_6


title: RAW-264.7 FoxQ1, clone 7.3

status: Public on Nov 23 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of human mouse430_2-type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: RAW-264.7 macrophage/monocyte cell line

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

growth_protocol: RAW-264.7 stable transfectants were propagated in DMEM+Glutamax medium (ThermoFisher Scientific) supplemented with 10% fetal bovine serum, 1% pen/strep and 6 µg/ml blasticidin S

extract_protocol: Isolation of total RNA from cells was performed using E.Z.N.A. total RNA Kit I (Omega bio-tek) according to manufacturer’s recommendation

treatment_protocol: No additional treatments

tag: transfection

value: mouse FoxQ1 expression construct


title: RAW-264.7 FoxQ1, clone 7.4


title: RAW-264.7 FoxQ1, clone 7.2


title: RAW-264.7 FoxQ1, clone 7.5


title: RAW-264.7 empty vector, clone 6

value: pEF6/V5-His TOPO vector


title: sample_208378-CP-saliva

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array at 50C for 17 hours according to the manufacturer's instructions.

scan_protocol: The array was washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
To achieve comprehensive CNV calling, we used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek.
primary data description: Genotype Call (SNP call): AA, AB, BB, and NoCall

source_name: Mother

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Oragene saliva kits were heated o/n (5pm - 9am) at 50C in an air oven. OG500 saliva kits collected from adults were extracted using Puregene chemistry on an AutopureLS automated DNA extractor. Saliva lysates were RNase a treated prior to extracting using either a 5.0ml or 2.5ml lysate protocol depending on collected saliva volume. OG575 saliva kits collected from children were extracted manually using same Puregene chemistry and RNase A treatment. Pelleted DNA was rehydrated in TE overnight and quantitated next day using Hoescht dye and FLX800 Flurometer.

tag: gender

value: Female

value: saliva


title: sample_208346-CP-saliva

source_name: Child


title: sample_208290-CP-saliva


title: sample_208347-CP-saliva

source_name: Father

value: Male


title: sample_208291-CP-saliva


title: sample_214278-CP-saliva


title: sample_214277-CP-saliva


title: sample_214276-CP-saliva


title: sample_208342-CP-saliva


title: sample_208340-CP-saliva


title: RAW-264.7 FoxQ1, clone 7.1


title: sample_208343-CP-saliva


title: ACC lesion #1

description:
Gene expression data from adenocortical lesion
Sample name: A_1

value: adrenocortical carcinoma

value: tumor


title: sample_208379-CP-saliva


title: RAW-264.7 empty vector, clone 5


title: sample_208380-CP-saliva


title: sample_208373-CP-saliva


title: sample_208372-CP-saliva


title: RAW-264.7 empty vector, clone 4


title: sample_208355-CP-saliva


title: sample_208341-CP-saliva


title: sample_208354-CP-saliva


title: sample_208356-CP-saliva


title: sample_208280-CP-saliva


title: sample_208357-CP-saliva


title: sample_208350-CP-saliva


title: sample_208359-CP-saliva


title: sample_208358-CP-saliva


title: sample_208349-CP-saliva


title: sample_208351-CP-saliva


title: sample_208282-CP-saliva


title: sample_208289-CP-saliva


title: sample_208288-CP-saliva


title: CEC Differentiation Wk 6

city: Taipa

first: Jung

middle: Woo

last: Park

state: Macau

department: Faculty of Health Sciences

institute: University of Macau

description:
200723220003_D_Grn.idat
non-replicate sample

hyb_protocol: Standard Illumina hybridization protocol

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

source_name: Differentiating cells

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

growth_protocol: E6 medium

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: E6 medium was replaced everyday until the harvested date

tag: time

value: 6 weeks

value: Differentiating cells


title: CEC Differentiation Wk 8

description:
200723220003_E_Grn.idat
non-replicate sample

value: 8 weeks


title: sample_248581-CP-saliva


title: CEC Differentiation Wk 4

description:
200723220003_C_Grn.idat
non-replicate sample

value: 4 weeks


title: CEC Differentiation Wk 2

description:
200723220003_B_Grn.idat
non-replicate sample

value: 2 weeks


title: sample_248583-CP-saliva


title: sample_217489-CP-saliva


title: sample_217485-CP-saliva


title: sample_217486-CP-saliva


title: sample_217488-CP-saliva


title: sample_219134-CP-saliva


title: sample_217479-CP-saliva


title: sample_208284-CP-saliva


title: sample_217490-CP-saliva


title: sample_208285-CP-saliva


title: H9 undifferentiated

description:
200723220003_A_Grn.idat
non-replicate sample

source_name: Embryonic stem cells

value: 0 weeks

value: Embryonic stem cells


title: sample_217480-CP-saliva


title: sample_217484-CP-saliva


title: sample_217481-CP-saliva


title: sample_231928-CP-saliva


title: sample_216860-CP-saliva


title: sample_216861-CP-saliva


title: sample_216853-CP-saliva


title: sample_216849-CP-saliva


title: sample_217476-CP-saliva


title: sample_216862-CP-saliva


title: sample_231930-CP-saliva


title: sample_216859-CP-saliva


title: sample_216856-CP-saliva


title: sample_216850-CP-saliva


title: sample_216857-CP-saliva


title: sample_247907-CP-saliva


title: sample_247909-CP-saliva


title: sample_247904-CP-saliva


title: sample_216848-CP-saliva


title: sample_221704-CP-saliva


title: sample_247905-CP-saliva


title: RAW-264.7 empty vector, clone 7


title: sample_221706-CP-saliva


title: sample_231931-CP-saliva


title: sample_247906-CP-saliva


title: ACC lesion #16

description:
Gene expression data from adenocortical lesion
Sample name: A_25


title: sample_221705-CP-saliva


title: sample_221712-CP-saliva


title: sample_221713-CP-saliva


title: sample_221714-CP-saliva


title: sample_221719-CP-saliva


title: sample_216205-CP-saliva


title: sample_221721-CP-saliva


title: sample_216204-CP-saliva


title: sample_216206-CP-saliva


title: sample_247908-CP-saliva


title: sample_216202-CP-saliva


title: sample_221720-CP-saliva


title: sample_216201-CP-saliva


title: sample_216199-CP-saliva


title: sample_216200-CP-saliva


title: sample_216203-CP-saliva


title: sample_216197-CP-saliva


title: sample_216191-CP-saliva


title: sample_216198-CP-saliva


title: sample_216196-CP-saliva


title: sample_216190-CP-saliva


title: sample_216195-CP-saliva


title: sample_216188-CP-saliva


title: sample_216187-CP-saliva


title: sample_216185-CP-saliva


title: sample_216184-CP-saliva


title: sample_216192-CP-saliva


title: sample_216189-CP-saliva


title: sample_216181-CP-saliva


title: sample_216182-CP-saliva


title: sample_216178-CP-saliva


title: sample_216180-CP-saliva


title: sample_216177-CP-saliva


title: sample_216179-CP-saliva


title: sample_216167-CP-saliva


title: sample_216166-CP-saliva


title: sample_217931-CP-saliva


title: sample_216168-CP-saliva


title: sample_217930-CP-saliva


title: sample_217932-CP-saliva


title: sample_211620-CP-saliva


title: sample_211622-CP-saliva


title: sample_208943-CP-saliva


title: sample_208938-CP-saliva


title: sample_208953-CP-saliva


title: sample_208952-CP-saliva


title: sample_216183-CP-saliva


title: sample_208941-CP-saliva


title: sample_211616-CP-saliva


title: sample_208930-CP-saliva


title: sample_208946-CP-saliva


title: sample_208936-CP-saliva


title: sample_199730-CP-saliva


title: sample_208937-CP-saliva


title: sample_199742-CP-saliva


title: sample_208948-CP-saliva


title: sample_199743-CP-saliva


title: sample_208932-CP-saliva


title: sample_211619-CP-saliva


title: sample_199721-CP-saliva


title: sample_208944-CP-saliva


title: sample_199736-CP-saliva


title: sample_199739-CP-saliva


title: sample_208939-CP-saliva


title: sample_218636-CP-saliva


title: sample_218639-CP-saliva


title: sample_218626-CP-saliva


title: sample_220176-CP-saliva


title: sample_220174-CP-saliva


title: sample_220173-CP-saliva


title: sample_216080-CP-saliva


title: sample_220170-CP-saliva


title: sample_248579-CP-saliva


title: sample_220172-CP-saliva


title: sample_220171-CP-saliva


title: sample_208951-CP-saliva


title: sample_215001-CP-saliva


title: sample_216081-CP-saliva


title: sample_215005-CP-saliva


title: sample_215011-CP-saliva


title: sample_212298-CP-saliva


title: sample_212299-CP-saliva


title: sample_199735-CP-saliva


title: sample_212297-CP-saliva


title: sample_199724-CP-saliva


title: sample_212304-CP-saliva


title: sample_212309-CP-saliva


title: sample_212303-CP-saliva


title: sample_212307-CP-saliva


title: sample_216074-CP-saliva


title: sample_212306-CP-saliva


title: sample_220175-CP-saliva


title: sample_216073-CP-saliva


title: sample_208588-CP-saliva


title: sample_216075-CP-saliva


title: sample_209044-CP-saliva


title: sample_220169-CP-saliva


title: sample_209043-CP-saliva


title: sample_216071-CP-saliva


title: sample_209040-CP-saliva


title: sample_209038-CP-saliva


title: sample_216070-CP-saliva


title: sample_209036-CP-saliva


title: sample_209039-CP-saliva


title: sample_202234-CP-saliva


title: sample_209037-CP-saliva


title: sample_212302-CP-saliva


title: sample_202235-CP-saliva


title: sample_200122-CP-saliva


title: sample_200119-CP-saliva


title: sample_200117-CP-saliva


title: sample_200118-CP-saliva


title: sample_200121-CP-saliva


title: sample_200120-CP-saliva


title: sample_198189-CP-saliva


title: sample_198191-CP-saliva


title: sample_200123-CP-saliva


title: sample_198190-CP-saliva


title: sample_198192-CP-saliva