title: Gastric cancer  tissue samples (FFPE)_157

description:
A pool of DNA from blood of normal individuals
T157_47_55_output_fused
T157


title: microRNA profile of case NPC94

status: Public on May 10 2012

type: RNA

city: Guangzhou

first: Rongrong

last: wei

address: 651 Dongfeng East Road

department: cancer center

country: China

institute: Sun-Yat Sen university

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes

hyb_protocol: The labeled RNAs were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: quantile normalization across multiple arrays, log 2 transformation of expression levels

molecule: total RNA

organism: Homo sapiens

source_name: Naspharyngeal Carcinoma

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647(Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: survival time (month), status (1-death, 0-survival)

tag: metastasis (1-yes, 0-no)

tag: gender (1-male, 0-female)

tag: age (1 - greater than or equal to 50y, 0 - less than 50y)

tag: max diameter of lymph nodes (1 - greater than or equal to 10mm, 0 - less than 10mm)

tag: disease state

value: Naspharyngeal Carcinoma

tag: tissue

value: Naspharyngeal Carcinoma tissue


title: microRNA profile of case NPC90


title: Gastric cancer  tissue samples (FFPE)_149

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
A pool of DNA from blood of normal individuals
T149_26_55_output_fused
T149

hyb_protocol: As described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Bluefuse software version 3.4 (BlueGnome, Cambridge, UK) was used for automatic feature extraction. Spots were excluded when the quality flag was below 1 or the confidence value was below 0.1. Log2 tumor to normal ratio was calculated for each clone and median block normalization was used to normalize the data.

molecule: genomic DNA

source_name: Gastric cancer

label_protocol: Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: Gastric cancer

tag: lymph node status

value: positive

tag: survival (years)

tag: comort

value: death due to cancer/recurrence

source_name: female reference DNA

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE)_146

description:
A pool of DNA from blood of normal individuals
T146_23_55_output_fused
T146

value: negative

value: alive

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE)_152

description:
A pool of DNA from blood of normal individuals
T152_33_55_output_fused
T152

value: death due to other reason


title: microRNA profile of case NPC77


title: microRNA profile of case NPC89


title: microRNA profile of case NPC84


title: microRNA profile of case NPC93


title: microRNA profile of case NPC71


title: Gastric cancer  tissue samples (FFPE)_155

description:
A pool of DNA from blood of normal individuals
T155_80_55_output_fused
T155


title: Gastric cancer  tissue samples (FFPE)_153

description:
A pool of DNA from blood of normal individuals
T153_53_55_output_fused
T153


title: Gastric cancer  tissue samples (FFPE)_145

description:
A pool of DNA from blood of normal individuals
T145_12_58_output_fused
T145


title: Gastric cancer  tissue samples (FFPE)_144

description:
A pool of DNA from blood of normal individuals
T144_89_55_output_fused
T144


title: microRNA profile of case NPC70


title: Gastric cancer  tissue samples (FFPE)_142

description:
A pool of DNA from blood of normal individuals
T142_87_55_output_fused
T142


title: microRNA profile of case NPC69


title: microRNA profile of case NPC68


title: microRNA profile of case NPC67


title: Gastric cancer  tissue samples (FFPE)_151

description:
A pool of DNA from blood of normal individuals
T151_34_55_output_fused
T151


title: Gastric cancer  tissue samples (FFPE)_141

description:
A pool of DNA from blood of normal individuals
T141_86_55_output_fused
T141


title: Gastric cancer  tissue samples (FFPE)_139

description:
A pool of DNA from blood of normal individuals
T139_74_55_output_fused
T139


title: Gastric cancer  tissue samples (FFPE)_140

description:
A pool of DNA from blood of normal individuals
T140_28_55_output_fused
T140


title: microRNA profile of case NPC73


title: Gastric cancer  tissue samples (FFPE)_138

description:
A pool of DNA from blood of normal individuals
T138_76_55_output_fused
T138


title: microRNA profile of case NPC65


title: 86 Tumour

status: Public on May 11 2012

city: Umea

first: Matilda

last: Rentoft

address: NUS

department: Medical Biosciences

country: Sweden

institute: Umea University

hyb_protocol: Hybridization were performed according to manufacturers protocol (WG-DASL) (illumina)

scan_protocol: Arrays were scanned with a BeadArray Reader (Illumina) and data was extracted using GenomeStudio software (Illumina).

data_processing: Data were normalized using Cubiq spline. No background correction were done.

label: Cy3 + Cy5

source_name: Tongue, FFPE

label_protocol: Labeling were performed according to manufacturers protocol (WG-DASL) (illumina)

extract_protocol: RNA were extracted using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol

tag: gender

value: Man

tag: age

tag: tnm

tag: quality (ctdiff)

tag: detected genes (p<0.05)


title: microRNA profile of case NPC63


title: microRNA profile of case NPC64


title: microRNA profile of case NPC61


title: microRNA profile of case NPC62


title: Gastric cancer  tissue samples (FFPE)_133

description:
A pool of DNA from blood of normal individuals
T133_54_55_output_fused
T133


title: Gastric cancer  tissue samples (FFPE)_135

description:
A pool of DNA from blood of normal individuals
T135_39_55_output_fused
T135


title: Gastric cancer  tissue samples (FFPE)_137

description:
A pool of DNA from blood of normal individuals
T137_37_55_output_fused
T137


title: Gastric cancer  tissue samples (FFPE)_136

description:
A pool of DNA from blood of normal individuals
T136_45_55_output_fused
T136


title: Gastric cancer  tissue samples (FFPE)_129

description:
A pool of DNA from blood of normal individuals
T129_84_55_output_fused
T129


title: microRNA profile of case NPC52

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes


title: Gastric cancer  tissue samples (FFPE)_131

description:
A pool of DNA from blood of normal individuals
T131_30_55_output_fused
T131


title: Gastric cancer  tissue samples (FFPE)_132

description:
A pool of DNA from blood of normal individuals
T132_82_55_output_fused
T132


title: microRNA profile of case NPC50


title: microRNA profile of case NPC60


title: Gastric cancer  tissue samples (FFPE)_134

description:
A pool of DNA from blood of normal individuals
T134_29_55_output_fused
T134


title: Gastric cancer  tissue samples (FFPE)_125

description:
A pool of DNA from blood of normal individuals
T125_41_55_output_fused
T125

value: operation mortality


title: Gastric cancer  tissue samples (FFPE)_124

description:
A pool of DNA from blood of normal individuals
T124_90_55_output_fused
T124


title: Gastric cancer  tissue samples (FFPE)_123

description:
A pool of DNA from blood of normal individuals
T123_36_55_output_fused
T123


title: microRNA profile of case NPC57


title: Gastric cancer  tissue samples (FFPE)_105

description:
A pool of DNA from blood of normal individuals
T105_52_37_output_fused
T105


title: Gastric cancer  tissue samples (FFPE)_103

description:
A pool of DNA from blood of normal individuals
T103_49_37_output_fused
T103


title: Gastric cancer  tissue samples (FFPE)_109

description:
A pool of DNA from blood of normal individuals
T109_54_37_output_fused
T109


title: Gastric cancer  tissue samples (FFPE)_128

description:
A pool of DNA from blood of normal individuals
T128_31_55_output_fused
T128


title: microRNA profile of case NPC54


title: Gastric cancer  tissue samples (FFPE)_127

description:
A pool of DNA from blood of normal individuals
T127_61_55_output_fused
T127


title: Gastric cancer  tissue samples (FFPE)_100

description:
A pool of DNA from blood of normal individuals
T100_71_37_output_fused
T100


title: microRNA profile of case NPC48


title: Gastric cancer  tissue samples (FFPE)_107

description:
A pool of DNA from blood of normal individuals
T107_53_37_output_fused
T107


title: microRNA profile of case NPC49


title: Gastric cancer  tissue samples (FFPE)_130

description:
A pool of DNA from blood of normal individuals
T130_85_55_output_fused
T130


title: Gastric cancer  tissue samples (FFPE)_126

description:
A pool of DNA from blood of normal individuals
T126_35_55_output_fused
T126


title: Gastric cancer  tissue samples (FFPE)_99

description:
A pool of DNA from blood of normal individuals
T99_14_37_output_fused
T99


title: Gastric cancer  tissue samples (FFPE)_120

description:
A pool of DNA from blood of normal individuals
T120_75_55_output_fused
T120


title: Gastric cancer  tissue samples (FFPE)_121

description:
A pool of DNA from blood of normal individuals
T121_38_55_output_fused
T121


title: Gastric cancer  tissue samples (FFPE)_122

description:
A pool of DNA from blood of normal individuals
T122_88_55_output_fused
T122


title: Gastric cancer  tissue samples (FFPE)_119

description:
A pool of DNA from blood of normal individuals
T119_48_55_output_fused
T119


title: Gastric cancer  tissue samples (FFPE)_97

description:
A pool of DNA from blood of normal individuals
T97_51_37_output_fused
T97


title: microRNA profile of case NPC47

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes


title: Gastric cancer  tissue samples (FFPE)_118

description:
A pool of DNA from blood of normal individuals
T118_49_55_output_fused
T118


title: microRNA profile of case NPC45


title: Gastric cancer  tissue samples (FFPE)_96

description:
A pool of DNA from blood of normal individuals
T96_67_37_output_fused
T96


title: microRNA profile of case NPC43


title: Gastric cancer  tissue samples (FFPE)_117

description:
A pool of DNA from blood of normal individuals
T117_77_55_output_fused
T117


title: Gastric cancer  tissue samples (FFPE)_114

description:
A pool of DNA from blood of normal individuals
T114_68_55_output_fused
T114


title: Gastric cancer  tissue samples (FFPE)_113

description:
A pool of DNA from blood of normal individuals
T113_46_55_output_fused
T113


title: Gastric cancer  tissue samples (FFPE)_115

description:
A pool of DNA from blood of normal individuals
T115_66_55_output_fused
T115


title: Gastric cancer  tissue samples (FFPE)_116

description:
A pool of DNA from blood of normal individuals
T116_64_55_output_fused
T116


title: microRNA profile of case NPC42


title: microRNA profile of case NPC39


title: microRNA profile of case NPC41


title: Gastric cancer  tissue samples (FFPE)_112

description:
A pool of DNA from blood of normal individuals
T112_62_55_output_fused
T112


title: Gastric cancer  tissue samples (FFPE)_111

description:
A pool of DNA from blood of normal individuals
T111_67_55_output_fused
T111


title: Gastric cancer  tissue samples (FFPE)_94

description:
A pool of DNA from blood of normal individuals
T94_44_37_output_fused
T94


title: microRNA profile of case NPC37


title: Gastric cancer  tissue samples (FFPE)_92

description:
A pool of DNA from blood of normal individuals
T92_42_37_output_fused
T92


title: Gastric cancer  tissue samples (FFPE)_93

description:
A pool of DNA from blood of normal individuals
T93_13_37_output_fused
T93


title: Gastric cancer  tissue samples (FFPE)_91

description:
A pool of DNA from blood of normal individuals
T91_73_37_output_fused
T91


title: Gastric cancer  tissue samples (FFPE)_89

description:
A pool of DNA from blood of normal individuals
T89_41_37_output_fused
T89


title: microRNA profile of case NPC36


title: microRNA profile of case NPC35


title: microRNA profile of case NPC32


title: Gastric cancer  tissue samples (FFPE)_87

description:
A pool of DNA from blood of normal individuals
T87_38_37_output_fused
T87


title: MCF7_JMJD6-OE-C2_rep3

city: Singapore

first: Yi Fang

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: MCF7 Set C_JMJD6 Over-expressed clone 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: CHP and CEL data were generated using GCOS. Raw data were MAS5-normalized and log transformed using Genespring GX11.5 for further analysis.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix manual).

growth_protocol: Cells were cultured in DMEM 10% fetal bovine serum (FBS) or RPMI-1640 10% FBS for MCF-7 and MDA-MB231 respectively.

extract_protocol: Trizol RNA extraction according to manufacturer's protocol (Invitrogen)

treatment_protocol: siRNA was transfected into MCF-7 / MDA-MB231 for 48 hours prior to RNA extraction.

tag: cell line

tag: jmjd6 expression

value: Over-expressed


title: MCF7_Vector_rep2

description: MCF7 Set B_Empty vector control

value: Control (empty vector)


title: MCF7_JMJD6-OE-C7_rep3

description: MCF7 Set C_JMJD6 Over-expressed clone 7


title: MCF7_JMJD6-OE-C3_rep3

description: MCF7 Set C_JMJD6 Over-expressed clone 3


title: MCF7_Vector_rep3

description: MCF7 Set C_Empty vector control


title: microRNA profile of case NPC28

tag: survival time (month), status (1-death, 0-survival)


title: microRNA profile of case NPC29

tag: metastasis (1-yes, 0-no)


title: MCF7_JMJD6-OE-C7_rep2

description: MCF7 Set B_JMJD6 Over-expressed clone 7


title: Gastric cancer  tissue samples (FFPE)_66

description:
A pool of DNA from blood of normal individuals
T66_29_37_output_fused
T66


title: microRNA profile of case NPC25

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes

tag: gender (1-male, 0-female)


title: Gastric cancer  tissue samples (FFPE)_72

description:
A pool of DNA from blood of normal individuals
T72_32_37_output_fused
T72


title: microRNA profile of case NPC24

tag: age (1 - greater than or equal to 50y, 0 - less than 50y)


title: microRNA profile of case NPC23

tag: max diameter of lymph nodes (1 - greater than or equal to 10mm, 0 - less than 10mm)


title: microRNA profile of case NPC16

tag: disease state


title: Gastric cancer  tissue samples (FFPE)_74

description:
A pool of DNA from blood of normal individuals
T74_74_37_output_fused
T74

tag: tissue


title: Gastric cancer  tissue samples (FFPE)_86

description:
A pool of DNA from blood of normal individuals
T86_37_37_output_fused
T86

tag: lymph node status


title: Gastric cancer  tissue samples (FFPE)_81

description:
A pool of DNA from blood of normal individuals
T81_35_37_output_fused
T81

tag: survival (years)


title: Gastric cancer  tissue samples (FFPE)_84

description:
A pool of DNA from blood of normal individuals
T84_36_37_output_fused
T84

tag: comort


title: MCF7_JMJD6-OE-C2_rep1

description: MCF7 Set A_JMJD6 Over-expressed clone 2


title: Gastric cancer  tissue samples (FFPE)_77

description:
A pool of DNA from blood of normal individuals
T77_33_37_output_fused
T77


title: microRNA profile of case NPC14


title: MCF7_JMJD6-OE-C7_rep1

description: MCF7 Set A_JMJD6 Over-expressed clone 7


title: Gastric cancer  tissue samples (FFPE)_65

description:
A pool of DNA from blood of normal individuals
T65_64_37_output_fused
T65


title: MCF7_JMJD6 siRNA A_ rep2

description: MCF7 Set C_JMJD6 Knock-down by siRNA A

source_name: MCF7_JMJD6 siRNA A

value: Knock-down


title: MCF7_JMJD6 siRNA C_ rep2

description: MCF7 Set B_JMJD6 Knock-down by siRNA C

source_name: MCF7_JMJD6 siRNA C


title: microRNA profile of case NPC13


title: Gastric cancer  tissue samples (FFPE)_64

description:
A pool of DNA from blood of normal individuals
T64_27_37_output_fused
T64


title: MCF7_scrambled siRNA A_ rep2

description: MCF7 Set C_Scrambled siRNA Control to siRNA A

source_name: MCF7_scrambled siRNA A

value: Control (scrambled siRNA)


title: MCF7_scrambled siRNA C_ rep1

description: MCF7 Set A_Scrambled siRNA Control to siRNA C

source_name: MCF7_scrambled siRNA C


title: MCF7_scrambled siRNA A_ rep1

description: MCF7 Set A_Scrambled siRNA Control to siRNA A


title: MCF7_JMJD6-OE-C3_rep1

description: MCF7 Set A_JMJD6 Over-expressed clone 3


title: microRNA profile of case NPC12


title: microRNA profile of case NPC11


title: MCF7_JMJD6 siRNA C_ rep1

description: MCF7 Set A_JMJD6 Knock-down by siRNA C


title: Gastric cancer  tissue samples (FFPE)_59

description:
A pool of DNA from blood of normal individuals
T59_26_37_output_fused
T59


title: MCF7_Vector_rep1

description: MCF7 Set A_Empty vector control


title: Gastric cancer  tissue samples (FFPE)_34

description:
A pool of DNA from blood of normal individuals
T34_20_37_output_fused
T34


title: Gastric cancer  tissue samples (FFPE)_35

description:
A pool of DNA from blood of normal individuals
T35_21_37_output_fused
T35


title: MB231_scrambled siRNA A_ rep2

description: MB231 Set B_Scrambled siRNA Control to siRNA A

source_name: MB231_scrambled siRNA A


title: MCF7_scrambled siRNA C_ rep2

description: MCF7 Set B_Scrambled siRNA Control to siRNA C


title: MCF7_JMJD6 siRNA A_ rep1

description: MCF7 Set A_JMJD6 Knock-down by siRNA A


title: MCF7_JMJD6-OE-C3_rep2

description: MCF7 Set B_JMJD6 Over-expressed clone 3


title: MB231_JMJD6 siRNA C_ rep2

description: MB231 Set B_JMJD6 Knock-down by siRNA C

source_name: MB231_JMJD6 siRNA C


title: MB231_scrambled siRNA C_ rep2

description: MB231 Set B_Scrambled siRNA Control to siRNA C

source_name: MB231_scrambled siRNA C


title: MB231_JMJD6 siRNA A_ rep2

description: MB231 Set B_JMJD6 Knock-down by siRNA A

source_name: MB231_JMJD6 siRNA A


title: MCF7_JMJD6-OE-C2_rep2

description: MCF7 Set B_JMJD6 Over-expressed clone 2


title: microRNA profile of case NPC9

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes


title: microRNA profile of case NPC7


title: Gastric cancer  tissue samples (FFPE)_29

description:
A pool of DNA from blood of normal individuals
T29_16_37_output_fused
T29


title: Gastric cancer  tissue samples (FFPE)_33

description:
A pool of DNA from blood of normal individuals
T33_19_37_output_fused
T33


title: microRNA profile of case NPC4


title: microRNA profile of case NPC3


title: Gastric cancer  tissue samples (FFPE)_27

description:
A pool of DNA from blood of normal individuals
T27_63_37_output_fused
T27


title: microRNA profile of case NPC2


title: Gastric cancer  tissue samples (FFPE)_108

description:
A pool of DNA from blood of normal individuals
T108_72_28_output_fused
T108


title: Gastric cancer  tissue samples (FFPE)_110

description:
A pool of DNA from blood of normal individuals
T110_90_24_output_fused
T110


title: Gastric cancer  tissue samples (FFPE)_26

description:
A pool of DNA from blood of normal individuals
T26_62_37_output_fused
T26


title: Gastric cancer  tissue samples (FFPE)_24

description:
A pool of DNA from blood of normal individuals
T24_61_37_output_fused
T24


title: Gastric cancer  tissue samples (FFPE)_17

description:
A pool of DNA from blood of normal individuals
T17_75_37_output_fused
T17


title: MB231_scrambled siRNA A_ rep1

description: MB231 Set A_Scrambled siRNA Control to siRNA A


title: Gastric cancer  tissue samples (FFPE)_13

description:
A pool of DNA from blood of normal individuals
T13_60_37_output_fused
T13


title: MB231_scrambled siRNA C_ rep1

description: MB231 Set A_Scrambled siRNA Control to siRNA C


title: Gastric cancer  tissue samples (FFPE)_7

description:
A pool of DNA from blood of normal individuals
T07_57_37_output_fused
T07


title: Gastric cancer  tissue samples (FFPE)_106

description:
A pool of DNA from blood of normal individuals
T106_61_28_output_fused
T106


title: Gastric cancer  tissue samples (FFPE)_104

description:
A pool of DNA from blood of normal individuals
T104_37_28_output_fused
T104


title: MB231_JMJD6 siRNA A_ rep1

description: MB231 Set A_JMJD6 Knock-down by siRNA A


title: Gastric cancer  tissue samples (FFPE)_102

description:
A pool of DNA from blood of normal individuals
T102_89_24_output_fused
T102


title: Gastric cancer  tissue samples (FFPE)_5

description:
A pool of DNA from blood of normal individuals
T05_11_37_output_fused
T05


title: Gastric cancer  tissue samples (FFPE)_101

description:
A pool of DNA from blood of normal individuals
T101_85_24_output_fused
T101


title: VE-Cadherin+/CD45+ cells from Tie-2 Etv2 Embryos Yolk sac (YS) rep2

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Stem Cell Biology

country: Japan

institute: Riken Center for Developmental Biology

hyb_protocol: We used Agilent Hybridization Oven, and followed manufacturer's protocol. http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf

scan_protocol: We used Agilent Microarray Scanner, and followed manufacturer's protocol. http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf

data_processing:
We used Agilent Feature Extraction 10.7 for quantification, and GeneSpring GX11.5.1 for data analysis.
1. Data Transformation: Set measurements less than 1 to 1
2. Per Chip: Normalize to 75 percentile
3. Per Gene: Normalize to median

organism: Mus musculus

source_name: YS from Tie-2-Etv2(Etv2 Tg turned ON by Tie-2 Cre Tg) embryo

label_protocol:
We used Agilent Low Input Quick Amp Labeling Kit, and followed manufacturer's protocol.
http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_One-color_v6.5.pdf

growth_protocol: FACS sort only, no treatment afterwards

extract_protocol: We used Qiagen RNA microelute Kit.

treatment_protocol: FACS sort only, no treatment afterwards

tag: cell type

tag: strain

value: mixed (B6/CBA and others)

tag: genotype/variation

value: yolk sac


title: Gastric cancer  tissue samples (FFPE)_98

description:
A pool of DNA from blood of normal individuals
T98_55_28_output_fused
T98


title: VE-Cadherin+/CD45+ cells from Tie-2 Etv2 Embryos Yolk sac (YS) rep1


title: MB231_JMJD6 siRNA C_ rep1

description: MB231 Set A_JMJD6 Knock-down by siRNA C


title: Gastric cancer  tissue samples (FFPE)_90

description:
A pool of DNA from blood of normal individuals
T90_83_24_output_fused
T90


title: Gastric cancer  tissue samples (FFPE)_88

description:
A pool of DNA from blood of normal individuals
T88_79_28_output_fused
T88


title: VE-Cadherin+/CD45+ cells from E10.5 Control Embryos (Yolk sac (YS))

source_name: Control YS from E10.5 embryo

value: Control


title: Gastric cancer  tissue samples (FFPE)_95

description:
A pool of DNA from blood of normal individuals
T95_36_28_output_fused
T95

value: Gastric cancer


title: ssDNA in S phase compared to G1 phase at timepoint 240 minutes

city: Houston

first: Sara

middle: Chloe

last: Di Rienzi

state: TX

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

country: USA

institute: Baylor College of Medicine

hyb_protocol: Hybridizations were performed using the recommendations of Agilent.

scan_protocol: Scans were performed using GenePix 4 as recommended by the vendor (Axon Instruments).

data_processing:
Data were normalized to reflect the actual percent single-stranded DNA (ssDNA) present in the sample (described in detail in Feng et al., 2007). To do so, the overall % ssDNA value observed in the microarray data were adjusted to match the % ssDNA detected by slot blot hybridization of nondenatured compared to denatured sample DNA.

% ssDNA of samples was determined by slot blotting. Normalization steps were implemented as a script in Mathematica 6 (Wolfram Research) with slot blot hybridization values of % ssDNA as user input. Normalized data were smoothed by lowess smoothing with a window size of 6 kb, except where windows contained genomic sequencing gaps predicted to be larger than 750 bp according to Kellis et al. (2004). See Feng et al., 2009, for details.

organism: Lachancea waltii

source_name: ssDNA in S phase at timepoint 240

label_protocol: 5 ug of DNA were digested with EcoRI in a total volume of 300 μl at 37 °C for 3 hours and ethanol precipitated. Digested DNA was labeled following the protocol described by Jonathan R. Pollack (http://cmgm.stanford.edu/pbrown/protocols/4_genomic.html) except that 5 ug of DNA were used and never denatured.

growth_protocol: Cells were grown in rich medium to an OD660 of 0.4 and hydroxyurea was added at a final concentration of 200 mM. 300 mL samples were harvested at different timepoints and arrested with 6 ml of 10% sodium azide and 48 ml of 0.5 M EDTA.

extract_protocol: DNA was extracted using the method described by Feng et al. (2007). In this method, yeast nuclei are isolated and carefully removed so to preserve ssDNA regions of the genome. DNA is then separated on a cesium-chloride gradient (1.308g CsCl per 1 g of 10 mM Tris, 100 mM EDTA, pH 7.5) and fractionated. Fractions containing genomic DNA are pooled and ethanol precipitated.

tag: cell cycle phase

value: S

tag: timepoint

value: 240 min

source_name: ssDNA in G1 phase at timepoint 240

growth_protocol: Cells growing logarithmically in rich medium were transferred into medium low in ammonium sulfate and incubated for 20 hours.


title: ssDNA in S phase compared to G1 phase at timepoint 180 minutes

source_name: ssDNA in S phase at timepoint 180

value: 180 min

source_name: ssDNA in G1 phase at timepoint 180


title: ssDNA in S phase compared to G1 phase at timepoint 180 minutes (dye swap)


title: ssDNA in S phase compared to G1 phase at timepoint 240 minutes (dye swap)


title: HEK293T-transfected [4572356067_F]

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

country: India

institute: IGIB

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Average Normalization using Illumina Beadstudio

label: Streptavidin Cy3

source_name: Human embryonic kidney cell line transfected with 4 micrograms of cloned miR-128 in 1 well of 6-well plate

label_protocol: As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol.The RNA was resuspended in diethyl pyrocarbonate-treated water, quantified by UV absorbance at 260/280 nm and immediately used for RNA amplification and labeling by Illumina TotalPrep RNA amplification kit

tag: cell line

value: human embryonic kidney


title: Gastric cancer  tissue samples (FFPE)_85

description:
A pool of DNA from blood of normal individuals
T85_64_28_output_fused
T85

source_name: Gastric cancer

value: negative

value: alive

source_name: female reference DNA


title: ssDNA in S phase compared to G1 phase at timepoint 120 minutes (dye swap)

source_name: ssDNA in G1 phase at timepoint 120

value: 120 min

source_name: ssDNA in S phase at timepoint 120


title: HEK293T-transfected [4572356067_E]

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: Gastric cancer  tissue samples (FFPE)_82

description:
A pool of DNA from blood of normal individuals
T82_65_28_output_fused
T82

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: HEK293T-control [4572356067_C]

source_name: Human embryonic kidney cell line


title: HEK293T-transfected [4572356067_D]


title: Gastric cancer  tissue samples (FFPE)_83

description:
A pool of DNA from blood of normal individuals
T83_82_24_output_fused
T83

value: positive

value: death due to other reason

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: liver_UVH2O2_rep8

city: Gothenburg

first: Marija

last: Cvijovic

address: Chalmers Tvärgata 3

institute: Chalmers Univeristy of Technology

hyb_protocol: Prehybridization was performed at room temperature for 15min with a prehybridization buffer (25ml 2× MES hybridization buffer and 1% BSA in 50ml DEPC H2O). Fragmented cRNA (6µg/array) was dissolved in hybridization buffer (final concentration 5× SSPE [Ambion], 20% formamide, 0.5 mg BSA/ml, 0.1× TE, 0.1mg human Cot-1 DNA [Invitrogen], 0.01% Tween 20). Samples were denatured for 3min at 95°C and hybridized to the biochips at 45°C for 16h, followed by a first washing step at 25°C with 6× SSPE and a second washing step at 45°C with 0.5× SSPE. Fluorescence staining was achieved by incubating the arrays with 5µg/ml streptavidin R-phycoerythrin conjugate (SAPE; Invitrogen) diluted in 6× SSPE containing 2mg BSA/ml at 25°C for 15min. Signal amplification was performed using biotinylated a-streptavidin antibodies (Vector Laboratories), followed by an additional incubation with SAPE.

scan_protocol: Signals were detected using the internal CCD camera system of the RT analyzer (Febit) instrument and quantified using the Geniom Wizard software. Integration times were between 390 and 620?ms, determined automatically by the instrument software.

data_processing:
All statistical calculations were done in R-2.12.2 (www.r-project.org) (1). Comparison of pre- and post normalized arrays was verified with Box and MA plots.  For data analysis limma package was used (2). Data were normalized using ‘quantile’ method , multiple linear models of arrays are fitted with lmFit. Moderated t-statistics and adjusted p-values of differential expression were calculated using the empirical Bayes model. For further analysis Volcano plots of log-fold changes versus log-odds of differential expression were created.
Six different exposures were done: (1) regular tap-water (in duplicates), (2) active carbon, (3,4) two Ozone samples with 5 and 15mg each, (5) Ozone with Biofilm and (6) UV treated hydrogen peroxide. First, tap-water duplicates were compared and due to expected similarity were treated as one sample. All groups are compared pairwise with the Henriksdal reference effluent.

label: Biotin

organism: Oncorhynchus mykiss

source_name: liver

label_protocol: Biotinylated anti - sense RNA (aRNA) was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The aRNA samples (20 µg) were vacuum dried in a vacuum centrifuge, dissolved in 10 µl water and fragmented according to the manufacturer's protocol.

extract_protocol: Homogenization of the frozen liver tissue was carried out using Tissuelyser (Qiagen, Hilden, Germany) and hepatic total RNA was extracted and purified using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity and quality were assessed by spectrophotometric measurements with the Nanodrop 1000 (NanoDrop Technologies, Wilmington, DE). To ensure that no degradation had occurred, the isolated RNA was analyzed using Experion automated electrophoresis (Bio-Rad, Hercules, CA).

tag: gender

value: Male

tag: age

value: Juvenile

value: liver

tag: exposure

value: UVtreated hydrogen peroxide


title: HEK293T-control [4572356067_B]


title: liver_UVH2O2_rep7


title: Gr-1+/Mac-1+ (Gr) cells from Vav-Etv2 bone marrow rep2

source_name: Gr-1+/Mac-1+(Gr) cells from 6 weeks old Vav-Etv2(Etv2 Tg turned ON by Vav-iCre Tg) mice

value: 6 weeks

value: mixed (B6/CBA and others)

value: bone marrow


title: Gr-1+/Mac-1+ (Gr) cells from Vav-Etv2 bone marrow rep1


title: Density transfer data for 9% HL ("arrest")

data_processing:
Data were normalized in two steps (for details, see Alvino et al., 2007). In the first step, the overall ratio of HL (replicated) DNA signal to HH (unreplicated) DNA signal as reported from the microarray scan was adjusted to reflect the actual ratio of HL to HH DNA that was present in the original sample. This correction factor was obtained from slot blot hybridization of the source HL and HH DNA with total genomic DNA as probe, revealing the actual proportion of HL and HH DNA in the sample. This correction is necessary to allow meaningful comparison of replication profiles constructed for different timed samples within an experiment. In the second normalization step, the data were adjusted to account for the proportion of cells in the culture that were actually progressing through the cell cycle (i.e., eliminating the contribution of non-cycling cells). The proportion of cycling cells was determined from the plateau of kinetic curves of replication obtained by slot blot hybridization of the timed S phase samples with genomic DNA as probe.

Normalization steps were implemented as a script in Mathematica 6 (Wolfram Research) with slot blot hybridization values of the HL/HH ratio and the percent of cycling cells as user input.  Normalized data were smoothed by lowess smoothing with a window size of 20 kb, except where windows contained genomic sequencing gaps predicted to be larger than 750 bp according to Kellis et al. (2004). See Feng et al., 2009 for details.

source_name: 9% Heavy-Light DNA

label_protocol: 1 ug of sample was labeled following the protocol by Jonathan R. Pollack (http://cmgm.stanford.edu/pbrown/protocols/4_genomic.html) using 15 mg of random hexamers as primers and 50 units Klenow fragment.

growth_protocol: Cells were grown for 8 generations at 23C in minimal medium with heavy carbon and nitrogen (13C, 15N). When cells reached an OD660 of 0.4, they were transferred to hydroxyurea (100 mM) in medium containing light carbon and nitrogen and incubated for 2 hours. Afterwards, the cells were washed free of the hydroxyurea and resuspended in light medium. Following timed samples were collected. The percent HL of each sample was determined (see extraction protocol).

extract_protocol: 300 ml samples of the cells were collected and arrested with 48 ml frozen 0.5 M EDTA and 6 ml 10% sodium azide. DNA was prepared using Rose and Winston (1990) and digested with PvuII overnight. Heavy-heavy (HH) labeled DNA and heavy-light (HL) DNA were separated by centrifugation in cesium chloride (CsCl) (1.308g CsCl per 1 g of 10 mM Tris, 100 mM EDTA, pH 7.5). Fractions containing HL (as determined by slot blotting) were pooled and ethanol precipitated.

tag: genotype

value: wild type

tag: dna molecule

value: replicated

source_name: 91% Heavy-Heavy DNA

extract_protocol: 300 ml samples of the cells were collected and arrested with 48 ml frozen 0.5 M EDTA and 6 ml 10% sodium azide. DNA was prepared using Rose and Winston (1990) and digested with PvuII overnight. Heavy-heavy (HH) labeled DNA and heavy-light (HL) DNA were separated by centrifugation in cesium chloride (CsCl) (1.308g CsCl per 1 g of 10 mM Tris, 100 mM EDTA, pH 7.5). Fractions containing HH (as determined by slot blotting) were pooled and ethanol precipitated.

value: unreplicated


title: microRNA profile of case NPC10

description: Sample was used for hybridization on each miRNA microarray chip containing 917 probes

source_name: Naspharyngeal Carcinoma

tag: survival time (month), status (1-death, 0-survival)

tag: metastasis (1-yes, 0-no)

tag: gender (1-male, 0-female)

tag: age (1 - greater than or equal to 50y, 0 - less than 50y)

tag: max diameter of lymph nodes (1 - greater than or equal to 10mm, 0 - less than 10mm)

value: Naspharyngeal Carcinoma

value: Naspharyngeal Carcinoma tissue


title: ssDNA in S phase compared to G1 phase at timepoint 120 minutes

value: S

value: 120 min


title: Density transfer data for 9% HL ("arrest") (dye swap)


title: Density transfer data for 45% HL (dye swap)

source_name: 55% Heavy-Heavy DNA

source_name: 45% Heavy-Light DNA


title: Gr-1+/Mac-1+(Gr) cells from Control bone marrow rep1

source_name: Gr-1+/Mac-1+(Gr) cells from 6 weeks old control mice

value: Control

tag: tissue


title: Gastric cancer  tissue samples (FFPE)_80

description:
A pool of DNA from blood of normal individuals
T80_84_28_output_fused
T80

value: Gastric cancer

tag: lymph node status

value: positive

tag: survival (years)

tag: comort

value: death due to cancer/recurrence

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Density transfer data for 25% HL (dye swap)

source_name: 75% Heavy-Heavy DNA

tag: strain

source_name: 25% Heavy-Light DNA


title: KSL cells from Vav-Etv2 bone marrow rep1

source_name: KSL cells from 6 weeks Vav-Etv2(Etv2 Tg turned ON by Vav-iCre Tg)

tag: cell type

value: KSL

tag: genotype/variation


title: Density transfer data for 45% HL


title: VE-Cadherin+/CD45+(P4) cells from Tie-2 Etv2 YS rep2

data_processing: We used Agilent Feature Extraction 10.7 for quantification, and GeneSpring GX11.5.1 for data analysis. 1. Data Transformation: Set measurements less than 1 to 1 2. Per Chip: Normalize to 75 percentile 3. Per Gene: Normalize to median

source_name: Mouse Embryos (E11.5); Tie-2-Etv2(Etv2 Tg turned ON by Tie-2 Cre Tg);YS VE-Cadherin+/CD45+(P4) cells.

value: yolk sac


title: Gr-1+/Mac-1+(Gr) cells from Control bone marrow rep2

value: 6 weeks


title: KSL cells from Vav-Etv2 bone marrow rep2

value: mixed (B6/CBA and others)


title: KSL cells from control bone marrow rep2

source_name: KSL cells from 6 weeks control mice

value: bone marrow


title: HEK293T-control [4572356067_A]

tag: cell line

value: human embryonic kidney


title: KSL cells from control bone marrow rep1

tag: age


title: Gastric cancer  tissue samples (FFPE)_78

description:
A pool of DNA from blood of normal individuals
T78_81_24_output_fused
T78

source_name: Gastric cancer

value: death due to other reason

source_name: female reference DNA


title: Gastric cancer  tissue samples (FFPE)_76

description:
A pool of DNA from blood of normal individuals
T76_87_28_output_fused
T76

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: Density transfer data for 25% HL

value: wild type

value: replicated

value: unreplicated


title: Gastric cancer  tissue samples (FFPE)_73

description:
A pool of DNA from blood of normal individuals
T73_76_28_output_fused
T73


title: liver_UVH2O2_rep5

tag: gender

value: Male

value: Juvenile

value: liver

tag: exposure

value: UVtreated hydrogen peroxide


title: Gastric cancer  tissue samples (FFPE)_75

description:
A pool of DNA from blood of normal individuals
T75_86_28_output_fused
T75

value: Gastric cancer

value: negative


title: liver_UVH2O2_rep3


title: VE-Cadherin+/CD45+(P4) cells from Tie-2 Etv2 YS rep1


title: liver_UVH2O2_rep6


title: liver_UVH2O2_rep2


title: VE-Cadherin+/CD45+(P4) cells from Control YS rep1

source_name: Mouse Embryos (E11.5); Control;YS VE-Cadherin+/CD45+(P4) cells.

value: Control


title: Gastric cancer  tissue samples (FFPE)_71

description:
A pool of DNA from blood of normal individuals
T71_83_28_output_fused
T71

value: positive

value: death due to cancer/recurrence

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE)_70

description:
A pool of DNA from blood of normal individuals
T70_60_28_output_fused
T70


title: Density transfer data for 15% HL (dye swap)

source_name: 85% Heavy-Heavy DNA

tag: genotype

tag: dna molecule

source_name: 15% Heavy-Light DNA


title: liver_MBBR_rep7

source_name: liver

value: ozone and biofilm


title: Gastric cancer  tissue samples (FFPE)_69

description:
A pool of DNA from blood of normal individuals
T69_59_28_output_fused
T69


title: liver_UVH2O2_rep1


title: VE-Cadherin+/CD45+(P4) cells from Control YS rep2

value: mixed (B6/CBA and others)

value: yolk sac


title: liver_MBBR_rep6


title: Gastric cancer  tissue samples (FFPE)_79

description:
A pool of DNA from blood of normal individuals
T79_87_24_output_fused
T79

value: alive

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: VE-Cadherin+/CD45-(P3) cells from Tie-2 Etv2 YS rep2

source_name: Mouse Embryos (E11.5); Tie-2-Etv2(Etv2 Tg turned ON by Tie-2 Cre Tg) YS; VE-Cadherin+/CD45-(P3) cells


title: VE-Cadherin+/CD45-(P3) cells from Control YS rep2

source_name: Mouse Embryos (E11.5); Control YS; VE-Cadherin+/CD45-(P3) cells


title: VE-Cadherin+/CD45-(P3) cells from Tie-2 Etv2 YS rep1


title: liver_UVH2O2_rep4


title: VE-Cadherin+/CD45-(P3) cells from Control YS rep1


title: Density transfer data for 15% HL

value: wild type

value: replicated


title: VE-Cadherin+/CD45+(P4) cells from Tie-2 Etv2 Embryo proper(Emb) rep2

source_name: Mouse Embryos (E11.5); Tie-2-Etv2(Etv2 Tg turned ON by Tie-2 Cre Tg); Emb; VE-Cadherin+/CD45+(P4) cells

value: embryo proper


title: liver_MBBR_rep5

value: Male

value: Juvenile


title: Gastric cancer  tissue samples (FFPE)_67

description:
A pool of DNA from blood of normal individuals
T67_58_28_output_fused
T67


title: VE-Cadherin+/CD45+(P4) cells from Tie-2 Etv2 Embryo proper(Emb) rep1


title: Gastric cancer  tissue samples (FFPE)_63

description:
A pool of DNA from blood of normal individuals
T63_63_28_output_fused
T63


title: liver_MBBR_rep8

value: liver


title: Gastric cancer  tissue samples (FFPE)_62

description:
A pool of DNA from blood of normal individuals
T62_68_28_output_fused
T62

value: Gastric cancer


title: VE-Cadherin+/CD45+(P4) cells from Control Embryo proper(Emb) rep2

source_name: Mouse Embryos (E11.5); Control; Emb; VE-Cadherin+/CD45+(P4) cells


title: liver_MBBR_rep3


title: Gastric cancer  tissue samples (FFPE)_60

description:
A pool of DNA from blood of normal individuals
T60_57_28_output_fused
T60

value: negative

value: death due to other reason


title: liver_MBBR_rep2


title: liver_ozone15_rep8

value: active ozone 15 mg


title: Gastric cancer  tissue samples (FFPE)_179

description:
A pool of DNA from blood of normal individuals
T179_73_47_output_fused
T179

value: positive

value: death due to cancer/recurrence


title: liver_MBBR_rep4

value: ozone and biofilm


title: Gastric cancer  tissue samples (FFPE)_61

description:
A pool of DNA from blood of normal individuals
T61_75_24_output_fused
T61


title: VE-Cadherin+/CD45+(P4) cells from Control Embryo proper(Emb) rep1

value: mixed (B6/CBA and others)

value: Control


title: liver_ozone15_rep7


title: liver_ozone15_rep6


title: Gastric cancer  tissue samples (FFPE)_57

description:
A pool of DNA from blood of normal individuals
T57_43_28_output_fused
T57


title: VE-Cadherin+/CD45-(P3) cells from Tie-2 Embryo proper(Emb) rep1

source_name: Mouse Embryos (E11.5); Tie-2-Etv2(Etv2 Tg turned ON by Tie-2 Cre Tg) Emb


title: Gastric cancer  tissue samples (FFPE)_58

description:
A pool of DNA from blood of normal individuals
T58_74_24_output_fused
T58


title: Gastric cancer  tissue samples (FFPE)_178

description:
A pool of DNA from blood of normal individuals
T178_67_47_output_fused
T178

value: alive

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: VE-Cadherin+/CD45-(P3) cells from control Embryo proper(Emb) rep2

source_name: Mouse Embryos (E11.5); VE-Cadherin+/CD45-(P3) cells; control Emb


title: Gastric cancer  tissue samples (FFPE)_56

description:
A pool of DNA from blood of normal individuals
T56_42_28_output_fused
T56


title: Gastric cancer  tissue samples (FFPE)_54

description:
A pool of DNA from blood of normal individuals
T54_49_28_output_fused
T54


title: liver_ozone15_rep5


title: Gastric cancer  tissue samples (FFPE)_55

description:
A pool of DNA from blood of normal individuals
T55_54_28_output_fused
T55


title: Gastric cancer  tissue samples (FFPE)_174

description:
A pool of DNA from blood of normal individuals
T174_72_47_output_fused
T174


title: VE-Cadherin+/CD45-(P3) cells from control Embryo proper(Emb) rep1


title: Gastric cancer  tissue samples (FFPE)_168

description:
A pool of DNA from blood of normal individuals
T168_71_47_output_fused
T168


title: Gastric cancer  tissue samples (FFPE)_154

description:
A pool of DNA from blood of normal individuals
T154_66_47_output_fused
T154

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: liver_MBBR_rep1


title: Gastric cancer  tissue samples (FFPE)_159

description:
A pool of DNA from blood of normal individuals
T159_74_47_output_fused
T159


title: Gastric cancer  tissue samples (FFPE)_150

description:
A pool of DNA from blood of normal individuals
T150_68_47_output_fused
T150


title: Gastric cancer  tissue samples (FFPE)_169

description:
A pool of DNA from blood of normal individuals
T169_70_47_output_fused
T169

value: operation mortality


title: liver_ozone15_rep1


title: Gastric cancer  tissue samples (FFPE)_50

description:
A pool of DNA from blood of normal individuals
T50_52_28_output_fused
T50


title: liver_ozone15_rep3


title: Gastric cancer  tissue samples (FFPE)_49

description:
A pool of DNA from blood of normal individuals
T49_47_28_output_fused
T49


title: Gastric cancer  tissue samples (FFPE)_51

description:
A pool of DNA from blood of normal individuals
T51_48_28_output_fused
T51


title: Gastric cancer  tissue samples (FFPE)_165

description:
A pool of DNA from blood of normal individuals
T165_75_47_output_fused
T165


title: liver_ozone15_rep4


title: liver_ozone15_rep2


title: Gastric cancer  tissue samples (FFPE)_148

description:
A pool of DNA from blood of normal individuals
T148_76_47_output_fused
T148


title: liver_ozone5_rep6

value: active ozone 5 mg


title: liver_ozone5_rep7

value: Male


title: VE-Cadherin+/CD45-(P3) cells from Tie-2 Embryo proper(Emb) rep2

value: embryo proper


title: liver_ozone5_rep8

value: Juvenile

value: liver


title: Gastric cancer  tissue samples (FFPE)_147

description:
A pool of DNA from blood of normal individuals
T147_69_47_output_fused
T147

value: Gastric cancer


title: Gastric cancer  tissue samples (FFPE)_52

description:
A pool of DNA from blood of normal individuals
T52_41_28_output_fused
T52

value: negative

value: death due to other reason


title: Gastric cancer  tissue samples (FFPE)_48

description:
A pool of DNA from blood of normal individuals
T48_72_24_output_fused
T48

value: positive


title: Gastric cancer  tissue samples (FFPE)_47

description:
A pool of DNA from blood of normal individuals
T47_39_28_output_fused
T47


title: liver_ozone5_rep5


title: CD25+CD49f+ T cells, biological rep4

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). Genechips were washed ans stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray data were processed and normalized using RMA.

source_name: CD25+CD49f+ T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Valencia, CA), as per the manufacturer’s protocol.

value: T cells

value: Female


title: liver_ozone5_rep4


title: Gastric cancer  tissue samples (FFPE)_143

description:
A pool of DNA from blood of normal individuals
T143_77_47_output_fused
T143

value: death due to cancer/recurrence


title: Gastric cancer  tissue samples (FFPE)_46

description:
A pool of DNA from blood of normal individuals
T46_51_28_output_fused
T46


title: Gastric cancer  tissue samples (FFPE)_45

description:
A pool of DNA from blood of normal individuals
T45_56_28_output_fused
T45


title: Gastric cancer  tissue samples (FFPE)_43

description:
A pool of DNA from blood of normal individuals
T43_67_28_output_fused
T43


title: liver_ozone5_rep3


title: Gastric cancer  tissue samples (FFPE)_44

description:
A pool of DNA from blood of normal individuals
T44_68_24_output_fused
T44


title: CD25+CD49f+ T cells, biological rep1


title: CD25+CD49f+ T cells, biological rep2


title: liver_ozone5_rep1


title: liver_ozone5_rep2


title: CD25+CD49f+ T cells, biological rep3


title: Gastric cancer  tissue samples (FFPE)_42

description:
A pool of DNA from blood of normal individuals
T42_46_28_output_fused
T42


title: CD25+CD49f- T cells, biological rep5

source_name: CD25+CD49f- T cells


title: Gastric cancer  tissue samples (FFPE)_68

description:
A pool of DNA from blood of normal individuals
T68_66_28_output_fused
T68


title: CD25+CD49f- T cells, biological rep3


title: CD25+CD49f- T cells, biological rep4


title: Gastric cancer  tissue samples (FFPE)_53

description:
A pool of DNA from blood of normal individuals
T53_53_28_output_fused
T53


title: 42_B45_MP3bis

city: paris

first: toullec

last: aurore

address: 41 boulevard de la chapelle

country: France

institute: Inserm U965

description:
Lot I
Sample name: MA30

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data were processed with the apt-probeset-summarize program from the Affymetrix Power Tools (v1.10.2) for background correction and normalization. RMA algorithm with full quantile normalization  was applied using the array design library files V1 release 4 and normalised values expressed on a log base 2 scale. Transcripts and genes were annotated with the Affymetrix release 29 annotation file based on the human genome version 18 assembly.  Data analysis was performed with the R Bioconductor LIMMA package.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cancer cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM,  supplemented with 10% FBS (DMEM-10%FBS) and 100 µg/µl sodium pyruvate in the presence of antibiotics (100 units/ml penicillin, 100 µg/ml streptomycin, 500 µg/ml geneticin G418,)

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) by direct lyses on the 10cm culture dish with 600 μl RLT Buffer following manufacture’s instructions. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix) starting from 300 ng of total RNAs.

treatment_protocol: Human MDA-MB-231 breast cancer cells (ATCC, Molsheim, France) were used to generate stable transfected clones overexpressing VEGF165, VEGF189 or control vector (referred to as 42ctl8, 13ctl3 and PCIctl3, respectively) as previously described (Am J Pathol. 2008 Jan;172(1):167-78. Epub 2007 Dec 13.).

tag: cell line origin

value: lung metastasis

value: VEGF165 overexpression


title: CD25+CD49f- T cells, biological rep2


title: liver_activcarbon_rep7

value: active carbon


title: Gastric cancer  tissue samples (FFPE)_9

description:
A pool of DNA from blood of normal individuals
T09_27_47_output_fused
T09

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE)_41

description:
A pool of DNA from blood of normal individuals
T41_45_28_output_fused
T41


title: 42_B45_MP3

description:
Lot I
Sample name: MA29


title: Gastric cancer  tissue samples (FFPE)_40

description:
A pool of DNA from blood of normal individuals
T40_67_24_output_fused
T40

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: liver_activcarbon_rep6


title: 13_B31_MP9

description:
Lot I
Sample name: MA28

value: VEGF189 overexpression


title: Gastric cancer  tissue samples (FFPE)_39

description:
A pool of DNA from blood of normal individuals
T39_65_24_output_fused
T39


title: PCI_B9_MP2

description:
Lot I
Sample name: MA26

value: Control


title: 13_B31_MP3

description:
Lot I
Sample name: MA27


title: Gastric cancer  tissue samples (FFPE)_38

description:
A pool of DNA from blood of normal individuals
T38_44_28_output_fused
T38

value: alive


title: CD25-CD49f+ T cells, biological rep7

source_name: CD25-CD49f+ T cells


title: Gastric cancer  tissue samples (FFPE)_37

description:
A pool of DNA from blood of normal individuals
T37_75_28_output_fused
T37


title: CD25-CD49f+ T cells, biological rep6


title: liver_activcarbon_rep8

value: Male

value: Juvenile


title: liver_activcarbon_rep5

value: liver


title: CD25+CD49f- T cells, biological rep1


title: liver_activcarbon_rep3


title: CD25-CD49f+ T cells, biological rep4


title: 42_Ctl_8_23

description:
Lot I
Sample name: MA23

value: breast cancer


title: Gastric cancer  tissue samples (FFPE)_36

description:
A pool of DNA from blood of normal individuals
T36_78_28_output_fused
T36

value: Gastric cancer

value: death due to other reason


title: liver_activcarbon_rep4


title: CD25-CD49f+ T cells, biological rep5

value: T cells


title: PCI_B9_MP9

description:
Lot I
Sample name: MA25


title: liver_conventional_rep8

value: conventional


title: liver_activcarbon_rep1


title: liver_activcarbon_rep2


title: 42_Ctl_8_17

description:
Lot I
Sample name: MA17


title: Gastric cancer  tissue samples (FFPE)_30

description:
A pool of DNA from blood of normal individuals
T30_82_28_output_fused
T30

value: negative


title: liver_conventional_rep7


title: Gastric cancer  tissue samples (FFPE)_28

description:
A pool of DNA from blood of normal individuals
T28_55_24_output_fused
T28

value: positive

value: death due to cancer/recurrence


title: Gastric cancer  tissue samples (FFPE)_32

description:
A pool of DNA from blood of normal individuals
T32_73_28_output_fused
T32


title: CD25-CD49f+ T cells, biological rep2

value: Female


title: liver_conventional_rep6


title: Gastric cancer  tissue samples (FFPE)_31

description:
A pool of DNA from blood of normal individuals
T31_56_24_output_fused
T31

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE)_25

description:
A pool of DNA from blood of normal individuals
T25_35_28_output_fused
T25

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: liver_conventional_rep4


title: Gastric cancer  tissue samples (FFPE)_23

description:
A pool of DNA from blood of normal individuals
T23_54_24_output_fused
T23


title: 42_Ctl_8_11

description:
Lot I
Sample name: MA11

value: VEGF165 overexpression


title: CD25-CD49f- T cells, biological rep6

source_name: CD25-CD49f- T cells


title: liver_conventional_rep5


title: CD25-CD49f+ T cells, biological rep1


title: 13_Ctl_3_21

description:
Lot I
Sample name: MA21

value: VEGF189 overexpression


title: 42_Ctl_8_05

description:
Lot I
Sample name: MA05


title: liver_conventional_rep3


title: 13_Ctl_3_03

description:
Lot I
Sample name: MA03


title: 13_Ctl_3_09

description:
Lot I
Sample name: MA09


title: 13_Ctl_3_15

description:
Lot I
Sample name: MA15


title: Gastric cancer  tissue samples (FFPE)_22

description:
A pool of DNA from blood of normal individuals
T22_53_24_output_fused
T22

value: alive


title: CD25-CD49f- T cells, biological rep7


title: CD25-CD49f- T cells, biological rep4


title: CD25-CD49f- T cells, biological rep3


title: PCI_Ctl_3_19

description:
Lot I
Sample name: MA19

value: Control


title: liver_conventional_rep1

value: Male

value: Juvenile


title: liver_conventional_rep2

value: liver


title: Gastric cancer  tissue samples (FFPE)_21

description:
A pool of DNA from blood of normal individuals
T21_52_24_output_fused
T21

value: Gastric cancer


title: Gastric cancer  tissue samples (FFPE)_20

description:
A pool of DNA from blood of normal individuals
T20_45_24_output_fused
T20


title: Gastric cancer  tissue samples (FFPE)_19

description:
A pool of DNA from blood of normal individuals
T19_44_24_output_fused
T19


title: PCI_Ctl_3_13

description:
Lot I
Sample name: MA13

value: breast cancer


title: Gastric cancer  tissue samples (FFPE)_18

description:
A pool of DNA from blood of normal individuals
T18_43_24_output_fused
T18


title: CD25-CD49f- T cells, biological rep1

value: T cells


title: PCI_Ctl_3_07

description:
Lot I
Sample name: MA07


title: CD25-CD49f- T cells, biological rep2


title: Gastric cancer  tissue samples (FFPE)_16

description:
A pool of DNA from blood of normal individuals
T16_42_24_output_fused
T16


title: Gastric cancer  tissue samples (FFPE)_15

description:
A pool of DNA from blood of normal individuals
T15_33_28_output_fused
T15

value: death due to other reason


title: liver_Tap water_rep14

value: tap water


title: liver_Tap water_rep15


title: liver_Tap water_rep16


title: PCI_Ctl_3_01

description:
Lot I
Sample name: MA01


title: HPCa51T_PSA-ve/PSA+ve cells_rep2

city: Smithville

first: Dean

middle: G

last: Tang

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

description: The current array analysis was carried out to study the changes in the gene expression profile of PSA-negative cells compared to PSA-positive cells isolated from HPCa51T(patient#) prostate tumor

hyb_protocol: Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

scan_protocol: Scanning and data acquisition were performed using Agilent scanner and feature extraction protocol GE2-v5_91 (available at www.agilent.com).

data_processing: The data was acquired using Agilent's feature extraction protocol GE2-v5_91 with inbuilt Lowess normalization feature and Logratio algorithms, for details visit www.agilent.com

source_name: HPCa51T PSA positive(+ve) cells

extract_protocol: Total RNA was extracted from PSA+ HPCa51T prostate tumor cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

tag: hpca51t psa-positive cells

value: PSA-positive cells selected from patient HPCa51T's prostate tumor using a PSA-GFP expression vector

source_name: HPCa51T PSA negative(-ve) cells

label_protocol: labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

tag: hpca51t psa-negative cells

value: PSA-negative cells selected from patient HPCa51T's prostate tumor using a PSA-GFP expression vector


title: HPCa49T_PSA-ve/PSA+ve cells_rep3

description: The current array analysis was carried out to study the changes in the gene expression profile of PSA-negative cells compared to PSA-positive cells isolated from HPCa49T(patient#) prostate tumor

source_name: HPCa49T PSA positive(+ve) cells

label_protocol: abeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

extract_protocol: Total RNA was extracted from PSA+ HPCa49T prostate tumor cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

tag: hpca49t psa-positive cells

value: PSA-positive cells selected from patient HPCa49T's prostate tumor using a PSA-GFP expression vector

source_name: HPCa49T PSA negative(-ve) cells

tag: hpca49t psa-negative cells

value: PSA-negative cells selected from patient HPCa49T's prostate tumor using a PSA-GFP expression vector


title: 6 h auxin-treated seedlings vs control: replicate 2

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

institute: Tokyo University of Agriculture & Technology

description: Biological replicate 2 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio (treated/control).

organism: Arabidopsis thaliana

source_name: 6 h auxin-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and equilibrated for 1 h at 22 °C in 20 ml deionized water, and then transferred to 20 ml of deionized water containing 20 µM auxin and 0.0125% dimethyl sulfoxide, and then incubated under light. Plants were collected at 0 (control) and 6 h, and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

value: Col. 0

value: day 14

tag: tissue

value: seedling

tag: agent

value: auxin

source_name: control seedlings

value: control


title: liver_Tap water_rep10

source_name: liver

value: Male


title: HPCa49T_PSA-ve/PSA+ve cells_rep2


title: liver_Tap water_rep13

value: Juvenile


title: liver_Tap water_rep12

value: liver


title: Pdx02

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: Biological replicate 2 of 3, Pdx1 adenovirus

hyb_protocol: Cy5-labeled samples were hybridized with n equimolar amount of rat reference RNA labeled with Cy3 to a DNA chip containing the version 3 rat microarray (Operon Biotechnologies) printed with 27,649 spots corresponding to 27,095 annotated genes   After hybridization, slides were washed sequentially.  Details of hybridization and washing protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

scan_protocol: Scanned on a Gene Pix 5000 scanner in the Duke University Microarray Core facility.

data_processing: The data were processed using GenePix Pro 5 software and uploaded to the Duke Institute for Genome Sciences and Policy Express Data Repository (http://data.genome.duke.edu/schislerMCB2008)  Data were normalized using per-chip and per-spot intensity-dependent LOWESS normalization with a threshold of 0.01.

organism: Rattus norvegicus

source_name: Rat reference

label_protocol: 500 ng of total RNA from three to five independent groups of AdCMV-Nkx6.1-, AdCMV-Pdx1-, and AdCMV-bGAL-treated islets were used for two rounds of amplification and labeled with Cy5.  Details of amplification and labeling protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

growth_protocol: Pancreatic islets were harvested from male Sprague-Dawley rats weighing approximately 250 g under a protocol approved by the Duke University Institutional Animal Care and Use Committee. Approximately 200 rat islets per condition were cultured in 2 ml of RPMI medium (10% fetal calf serum, 8 mM glucose).

extract_protocol: Total RNA was prepared from rat islets and was purified using the RNeasy microkit (Qiagen)  in accordance with the manufacturer‚Äôs instructions which included DNase treatment to eliminate genomic contamination. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer.

treatment_protocol: Islet pools were treated with viruses at a concentration of 5E9 particles/ml medium for 18 h. Virus-containing medium was replaced with fresh culture medium, and islets were cultured for an additional 60 h, with fresh medium daily

tag: reference

value: pool of rat RNA (Stratagene)

source_name: Isolated pancreatic islets of langerhans

value: Sprague-Dawley

value: male

tag: adenovirus


title: 6 h auxin-treated seedlings vs control: replicate1

description: Biological replicate 1 of 2

tag: strain


title: Pdx03

description: Biological replicate 3 of 3, Pdx1 adenovirus


title: liver_Tap water_rep11


title: Gastric cancer  tissue samples (FFPE)_10

description:
A pool of DNA from blood of normal individuals
T10_77_28_output_fused
T10

source_name: Gastric cancer

value: Gastric cancer

tag: lymph node status

value: positive

tag: survival (years)

tag: comort

value: death due to cancer/recurrence

source_name: female reference DNA

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE)_14

description:
A pool of DNA from blood of normal individuals
T14_32_28_output_fused
T14

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: HPCa47T_PSA-ve/PSA+ve cells_rep3

description: The current array analysis was carried out to study the changes in the gene expression profile of PSA-negative cells compared to PSA-positive cells isolated from HPCa47T(patient#) prostate tumor

source_name: HPCa47T PSA positive(+ve) cells

extract_protocol: Total RNA was extracted from PSA+ HPCa47T prostate tumor cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

tag: hpca47t psa-positive cells

value: PSA-positive cells selected from patient HPCa47T's prostate tumor using a PSA-GFP expression vector

source_name: HPCa47T PSA negative(-ve) cells

tag: hpca47t psa-negative cells

value: PSA-negative cells selected from patient HPCa46T's prostate tumor using a PSA-GFP expression vector


title: HPCa51T_PSA-ve/PSA+ve cells_rep3

value: PSA-positive cells selected from patient HPCa51T's prostate tumor using a PSA-GFP expression vector

value: PSA-negative cells selected from patient HPCa51T's prostate tumor using a PSA-GFP expression vector


title: Gastric cancer  tissue samples (FFPE)_8

description:
A pool of DNA from blood of normal individuals
T08_50_28_output_fused
T08


title: HPCa51T_PSA-ve/PSA+ve cells_rep1


title: liver_Tap water_rep9

tag: gender

tag: age

tag: exposure

value: tap water


title: liver_Tap water_rep8


title: Gastric cancer  tissue samples (FFPE)_11

description:
A pool of DNA from blood of normal individuals
T11_77_24_output_fused
T11

value: negative

value: death due to other reason


title: HPCa49T_PSA-ve/PSA+ve cells_rep1

value: PSA-positive cells selected from patient HPCa49T's prostate tumor using a PSA-GFP expression vector

value: PSA-negative cells selected from patient HPCa49T's prostate tumor using a PSA-GFP expression vector


title: Nkx05, 2

description: Biological replicate 5 of 5, NKx6.1 adenovirus

value: pool of rat RNA (Stratagene)


title: HPCa47T_PSA-ve/PSA+ve cells_rep2

value: PSA-negative cells selected from patient HPCa47T's prostate tumor using a PSA-GFP expression vector


title: Gastric cancer  tissue samples (FFPE)_12

description:
A pool of DNA from blood of normal individuals
T12_86_24_output_fused
T12


title: Nkx04, 2

description: Biological replicate 4 of 5, NKx6.1 adenovirus

value: Sprague-Dawley

value: male


title: liver_Tap water_rep7

value: Male

value: Juvenile

value: liver


title: Pdx01

description: Biological replicate 1 of 3, Pdx1 adenovirus


title: Nkx03, 2

description: Biological replicate 3 of 5, NKx6.1 adenovirus


title: Gastric cancer  tissue samples (FFPE)_4

description:
A pool of DNA from blood of normal individuals
T04_76_24_output_fused
T04

value: Gastric cancer

value: positive

value: reference:Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE)_6

description:
A pool of DNA from blood of normal individuals
T06_41_24_output_fused
T06

value: death due to cancer/recurrence

value: reference:Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE)_2

description:
A pool of DNA from blood of normal individuals
T02_39_24_output_fused
T02


title: Gastric cancer  tissue samples (FFPE)_3

description:
A pool of DNA from blood of normal individuals
T03_40_24_output_fused
T03


title: Gastric cancer  tissue samples (FFPE)_1

description:
A pool of DNA from blood of normal individuals
T01_38_24_output_fused
T01


title: HPCa46T_PSA-ve/PSA+ve cells_rep1

description: The current array analysis was carried out to study the changes in the gene expression profile of PSA-negative cells compared to PSA-positive cells isolated from HPCa46T(patient#) prostate tumor

source_name: HPCa46T PSA positive(+ve) cells

extract_protocol: Total RNA was extracted from PSA+ HPCa46T prostate tumor cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

tag: hpca46t psa-positive cells

value: PSA-positive cells selected from patient HPCa46T's prostate tumor using a PSA-GFP expression vector

source_name: HPCa46T PSA negative(-ve) cells

tag: hpca46t psa-negative cells

value: PSA-negative cells selected from patient HPCa46T's prostate tumor using a PSA-GFP expression vector


title: Nkx01, 2

description: Biological replicate 1 of 5, NKx6.1 adenovirus


title: liver_Tap water_rep5

value: tap water


title: HPCa47T_PSA-ve/PSA+ve cells_rep1

value: PSA-positive cells selected from patient HPCa47T's prostate tumor using a PSA-GFP expression vector

extract_protocol: Total RNA was extracted from PSA+ HPCa47T prostate tumor  cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.


title: liver_Tap water_rep4


title: liver_Tap water_rep6


title: Nkx02, 2

description: Biological replicate 2 of 5, NKx6.1 adenovirus


title: bGAL05, 2

description: Biological replicate 5 of 5, control (bGAL) adenovirus

value: AdCMV-bGAL


title: bGAL04, 2

description: Biological replicate 4 of 5, control (bGAL) adenovirus

value: pool of rat RNA (Stratagene)


title: bGAL02, 2

description: Biological replicate 2 of 5, control (bGAL) adenovirus


title: liver_Tap water_rep3


title: liver_Tap water_rep1

hyb_protocol: Prehybridization was performed at room temperature for 15min with a prehybridization buffer (25ml 2× MES hybridization buffer and 1% BSA in 50ml DEPC H2O). Fragmented cRNA (6µg/array) was dissolved in hybridization buffer (final concentration 5× SSPE [Ambion], 20% formamide, 0.5mg BSA/ml, 0.1× TE, 0.1mg human Cot-1 DNA [Invitrogen], 0.01% Tween 20). Samples were denatured for 3min at 95°C and hybridized to the biochips at 45°C for 16h, followed by a first washing step at 25°C with 6× SSPE and a second washing step at 45°C with 0.5× SSPE. Fluorescence staining was achieved by incubating the arrays with 5µg/ml streptavidin R-phycoerythrin conjugate (SAPE; Invitrogen) diluted in 6× SSPE containing 2mg BSA/ml at 25°C for 15min. Signal amplification was performed using biotinylated α-streptavidin antibodies (Vector Laboratories), followed by an additional incubation with SAPE.

scan_protocol: Signals were detected using the internal CCD camera system of the RT analyzer (Febit) instrument and quantified using the Geniom Wizard software. Integration times were between 390 and 620 ms, determined automatically by the instrument software.

label_protocol: Biotinylated anti - sense RNA (aRNA) was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The aRNA samples (20 μg) were vacuum dried in a vacuum centrifuge, dissolved in 10 μl water and fragmented according to the manufacturer's protocol.


title: bGAL03, 2

description: Biological replicate 3 of 5, control (bGAL) adenovirus


title: liver_Tap water_rep2


title: LNCaP PSA+ vs PSA- comparison_rep3

source_name: LNCaP PSA+ Cells

extract_protocol: Total RNA was extracted from LNCaP PSA+ cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cells positive for PSA (prostate specific antigen)

source_name: LNCaP PSA- Cells

extract_protocol: Total RNA was extracted from LNCaP PSA -ve cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

value: prostate cancer cells negative for PSA (prostate specific antigen)


title: LNCaP PSA+ vs PSA- comparison_rep1


title: zebrafish eye - D vs L (replicates 1,2,3)

city: San Marcos

first: Dana

middle: M

last: Garcia

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

description:
Contains three biological replicates:
rep1 = D1-3/L1-5 (ch1_Cy3/ch2_Cy5)
rep2 = D2-5/L2-3 (ch1_Cy5/ch2_Cy3)
rep3 = D3-5/L3-3 (ch1_Cy5/ch2_Cy3)

hyb_protocol: aRNA sample was fragmented using Ambion RNA fragmentation reagents and added to hybridization solution (Ocimum Biosolutions.) Hybridization performed under 40 mmX22mm lifterslip by addition of 240 ul of labeled solution to zebrafish 14K OciChip

scan_protocol: Scanned using Affymetrix 428 Array scanner and analyzed with GenePix Pro 3.0 software.

data_processing: Array normalization and statistical analysis was performed using limma:Linear Models for Microarray Data library module (version 2.2.0) of the R statistical package (version 2.2.0).   Signal intensities of less than 1000 in all time points are marked as null in the Matrix datasheet and were removed from the analysis. One-way ANOVA was performed on ratios of triplicate time points. Slide intensity dara were normalized using the global LOWESS method with the least squares method used for linear model fit.

organism: Danio rerio

source_name: Midnight

label_protocol: 1 ug of RNA was labeled using Amino-AllylmessageAMP II aRNA Amplification Kit (ambion) labled with Cy3/Cy5

extract_protocol:
Total RNA extracted using TRI-reagent and cleaned-up with RNeasy spin columns per manufacturer's instructions
Quality assessment: RNA quality was assesed using a Nanodrop spectophotometer,  glyoxal gel electophoresis, and the Agilent BioAnalyzer.

tag: tissue

value: eye

tag: genetic line

value: wildtype (zdr)

tag: light cycle

value: 12 hour light/dark

tag: time

value: Dark

tag: treatment

value: Midnight

source_name: Midday

value: Midday

value: Light


title: bGAL01, 2

description: Biological replicate 1 of 5, control (bGAL) adenovirus

tag: reference

tag: strain

value: Sprague-Dawley

value: male

tag: adenovirus


title: LNCaP PSA+ vs PSA- comparison_rep2


title: LAPC9 PSA-vsPSA+_rep3

description: The current array analysis was carried out to study the changes in the gene expression profile of PSA- LAPC9 cells compared to PSA+ LAPC9 cells isolated from LAPC9 xenograft tumors from mice.

source_name: LAPC9 PSA+ cells

extract_protocol: Total RNA was extracted from PSA+ LAPC9 cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

treatment_protocol: LAPC9 cells were transfected with GFP vector under PSA promoter through a lentivirus and the LAPC9 cells were sorted for PSA+ cells by flow cytometry from a LAPC9 tumor isolated from mice.

value: prostate cancer xenograft cells positive for PSA (prostate specific antigen)

source_name: LAPC9 PSA- cells

extract_protocol: Total RNA was extracted from PSA- LAPC9 cells using an RNAeasy RNA purification kit (Qiagen, Valencia, CA), including on-column DNase digestion to completely remove contaminating genomic DNA. RNA concentrations were determined in NanoDrop and the quality assessed using a Bioanalyzer.

treatment_protocol: LAPC9 cells were transfected with GFP vector under PSA promoter through a lentivirus and the LAPC9 cells were sorted for PSA- cells by flow cytometry from a LAPC9 tumor isolated from mice.

value: prostate cancer xenograft cells negative for PSA (prostate specific antigen)


title: MIAMI-3231-FCTX-CpG

status: Public on May 09 2012

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Human Brain Tissue: FCTX

hyb_protocol: Two bead types correspond to each CpG locus, one to the methylated (C) state, and the other to the unmethylated (T) state. After extension, the BeadChip was fluorescently stained.

scan_protocol: Illumina iScan laser confocal scanner to measure the intensities of unmethylated and methylated bead types for each locus.

data_processing: Genome Studio Methylation Module v3.2.0, no normalization

label: C-Bio and A-DNP

source_name: Human Brain Tissue: FCTX

label_protocol: 1ug of genomic DNA underwent bisulfite conversion using the WZ-96 DNA Methylation Kit according to the manufacturer’s protocol (Zymo Research Corp, Orange, CA). Incubation conditions used during conversion were as follows: (95°C for 30 seconds, 50°C for 1 hour) for 16 cycles, hold overnight at 4°C. Unmethylated cytosines were chemically deaminated to uracil in the presence of bisulfite, while methylated cytosines were refractory to the effects of bisulfite and remained as cytosines. Methylation was then detected as a C/T nucleotide polymorphism at each CpG site. After bisulfite conversion, each sample was whole-genome amplified, fragmented, and hybridized to the BeadChip. DNA molecules anneal to locus-specific DNA oligomers.

extract_protocol: Genomic DNA for the Infinium methylation assay was extracted using phenol-chloroform and ethanol precipitation. DNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and DNA extraction was repeated using a new tissue aliquot for samples with DNA concentration less than 50ng/ul, or with a 260/280 ratio less than 1.7.

value: frontal cortex

tag: age (y)

tag: pmi (hr)

tag: tissuebank

value: Miami


title: CD25-CD49f+ T cells, biological rep3

source_name: CD25-CD49f+ T cells

value: T cells

tag: gender

value: Female


title: CD25-CD49f- T cells, biological rep5

source_name: CD25-CD49f- T cells


title: UMARY-1573-FCTX-CpG

description: Human Brain Tissue: FCTX

value: female

value: UMARY


title: UMARY-5125-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-510-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3410-FCTX-CpG

description: Human Brain Tissue: FCTX


title: LAPC9 PSA-vsPSA+_rep2


title: UMARY-1539-FCTX-CpG

description: Human Brain Tissue: FCTX


title: LAPC9 PSA-vsPSA+_rep1


title: SH-99-54-FCTX-CpG

description: Human Brain Tissue: FCTX

value: SHRI


title: MIAMI-3799-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5173-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1672-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1323-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3638-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1790-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-44-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-95-21-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-02-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-29-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3772-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1111-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5111-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4643-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-4022-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1475-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3278-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-50-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-31-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-38-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-99-14-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-13-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-44-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-08-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-32-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-95-27-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-95-26-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-35-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-14-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-00-49-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-92-05-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-92-10-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-19-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-37-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-09-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-28-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-05-36-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-06-05-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-98-32-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-28-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-37-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-18-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-01-46-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-04-05-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-06-25-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-05-16-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-08-23-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-04-08-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-02-08-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-63-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-63-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-50-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-04-19-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-01-37-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-94-35-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-02-12-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-01-14-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-17-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-06-21-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-11-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-04-21-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-39-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1113-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1379-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-30-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-73-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-544-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5119-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3228-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1845-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-02-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1796-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1274-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1213-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1429-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5123-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3828-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1500-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3839-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1423-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1013-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3643-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-55-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-17-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5179-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-46-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-08-44-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1410-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-11-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-2843-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-1931-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1908-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5089-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-165-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-164-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-455-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1455-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-2852-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1277-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-257-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3216-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4898-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-288-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-72-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-96-22-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4722-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-433-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3860-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5114-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-00-38-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1744-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5077-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-07-04-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1743-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1670-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1609-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1279-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-878-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-772-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-01-31-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-818-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-814-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-675-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-105-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5082-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-662-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-72-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-650-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-794-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-634-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-689-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-15-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-630-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-616-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-671-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-02-06-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5120-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5116-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-497-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-03-66-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-2841-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5117-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-26-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-46-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-260-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-290-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-240-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-2112-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3651-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3296-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-388-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3797-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1442-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1322-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1266-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-08-04-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-229-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-305-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-05-10-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-06-66-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3751-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1027-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-143-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3747-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-3-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1039-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1378-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-00-34-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4848-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1428-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1843-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1841-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-251-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1831-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1823-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5171-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1674-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4976-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1794-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5088-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1818-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-5085-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-98-23-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4735-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4724-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4670-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4592-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4638-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1789-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4906-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-98-19-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-177-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4591-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4669-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4781-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4728-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-97-53-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4546-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4287-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1864-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-4228-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1861-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-4042-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1461-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1859-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-95-34-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1599-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-92-14-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1607-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1259-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1675-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1569-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1363-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-92-32-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1365-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1403-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1185-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1497-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1101-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1543-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1441-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1464-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1135-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1024-FCTX-CpG

description: Human Brain Tissue: FCTX


title: SH-95-02-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1406-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1038-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-1347-FCTX-CpG

description: Human Brain Tissue: FCTX


title: UMARY-164-CRBLM-CpG

description: Human Brain Tissue: CRBLM

source_name: Human Brain Tissue: CRBLM

value: cerebellum


title: UMARY-1500-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1423-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1362-FCTX-CpG

description: Human Brain Tissue: FCTX


title: MIAMI-3751-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-257-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1213-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-165-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5173-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1845-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1410-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: MIAMI-3799-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5082-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1672-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1539-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1908-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-143-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-4643-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-02-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-44-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-30-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-14-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1322-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-50-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1111-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-54-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5111-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-08-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-5089-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-29-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1113-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1796-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-39-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-13-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-35-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: UMARY-1323-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-96-32-CRBLM-CpG

description: Human Brain Tissue: CRBLM


title: SH-99-31-CRBLM-CpG

description: Human Brain Tissue: CRBLM