title: Blood_TakenInPhaseWithRespectToMelatonin_at18:00_Per3_4\4genotype_Subject_BB0272_R_T7

description: Blood take at 18:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:05_Per3_4\4genotype_Subject_BB0289_R_T6

status: Public on Jan 23 2014

type: RNA

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

description: Blood take at 16:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalised using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

molecule: total RNA

organism: Homo sapiens

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

tag: tissue

value: Blood

tag: sleep timing

value: In phase with respect to melatonin

tag: per3 genotype

tag: time sample taken

tag: day sample was taken in protocol

tag: time point

tag: subject


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:10_Per3_4\4genotype_Subject_BB0289_R_T4

description: Blood take at 08:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at14:00_Per3_4\4genotype_Subject_BB0272_R_T13

description: Blood take at 14:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)

value: Out of phase with respect to melatonin


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:01_Per3_4\4genotype_Subject_BB0289_R_T2

description: Blood take at 00:01 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:05_Per3_4\4genotype_Subject_BB0289_R_T7

description: Blood take at 20:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:00_Per3_4\4genotype_Subject_BB0272_R_T8

description: Blood take at 18:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)


title: IDC_492706_tumoral sample

status: Public on Apr 01 2014

type: genomic

city: Paris

first: Jaydutt

middle: D

last: Bhalshankar

address: 26 rue d'Ulm

department: INSERM UNIT 830

country: France

institute: Institut CURIE

description: Hybridized to SNP6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 to generate .CEL files for downstream analysis.

data_processing: CEL files and TXT files (generated by Affymetrix Genotyping Console 3.0.1) were processed by GAP (Popova T et al, Genome Biol, 2009) and Partek® GS software version 6.5 build 6.10.1020

label: biotin

molecule: genomic DNA

source_name: IDC tumoral sample

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor fragments using a standard phenol/chloroform procedure. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: breast cancer

tag: tissue subtype

value: Invasive Ductal Carcinoma (IDC)

tag: tumor grade

value: ND


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:00_Per3_4\4genotype_Subject_BB0272_R_T14


title: IDC_488469_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:00_Per3_4\4genotype_Subject_BB0272_R_T10

description: Blood take at 02:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at06:00_Per3_4\4genotype_Subject_BB0272_R_T4

description: Blood take at 06:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:05_Per3_4\4genotype_Subject_BB0289_R_T5

description: Blood take at 12:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0289)


title: IMPC_MP34_tumoral sample

description: Hybridized to SNP6.0

source_name: IMPC tumoral sample

value: Invasive Micropapillary Carcinoma (IMPC)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:00_Per3_4\4genotype_Subject_BB0272_R_T6

description: Blood take at 14:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:12_Per3_4\4genotype_Subject_BB0272_R_T3

description: Blood take at 02:12 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:55_Per3_4\4genotype_Subject_BB0272_R_T2

description: Blood take at 21:55 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:00_Per3_4\4genotype_Subject_BB0272_R_T5

description: Blood take at 10:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0272)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:00_Per3_4\4genotype_Subject_BB0272_R_T1


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at  01:20_Per3_4\4genotype_Subject_BB0264_R_T9

description: Blood take at   01:20 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at05:20_Per3_4\4genotype_Subject_BB0264_R_T10

description: Blood take at 05:20 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at_Per3_4\4genotype_Subject_BB0264_R_T7

description: Blood take at NA when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at13:20_Per3_4\4genotype_Subject_BB0264_R_T5

description: Blood take at 13:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at07:55_Per3_5\5genotype_Subject_BB0246_R_T11

description: Blood take at 07:55 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:20_Per3_4\4genotype_Subject_BB0264_R_T8

description: Blood take at 21:20 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at17:20_Per3_4\4genotype_Subject_BB0264_R_T6

description: Blood take at 17:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at01:18_Per3_4\4genotype_Subject_BB0264_R_T2

description: Blood take at 01:18 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at13:15_Per3_4\4genotype_Subject_BB0264_R_T12

description: Blood take at 13:15 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at15:52_Per3_5\5genotype_Subject_BB0246_R_T13

description: Blood take at 15:52 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:20_Per3_4\4genotype_Subject_BB0264_R_T1

description: Blood take at 21:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at11:47_Per3_5\5genotype_Subject_BB0246_R_T12

description: Blood take at 11:47 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at23:55_Per3_5\5genotype_Subject_BB0246_R_T9

description: Blood take at 23:55 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at17:25_Per3_4\4genotype_Subject_BB0264_R_T13

description: Blood take at 17:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:55_Per3_5\5genotype_Subject_BB0246_R_T7

description: Blood take at 19:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:55_Per3_5\5genotype_Subject_BB0246_R_T8

description: Blood take at 19:55 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenInPhaseWithRespectToMelatonin_at09:20_Per3_4\4genotype_Subject_BB0264_R_T4

description: Blood take at 09:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at15:55_Per3_5\5genotype_Subject_BB0246_R_T6

description: Blood take at 15:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: IDC_469625_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenInPhaseWithRespectToMelatonin_at05:20_Per3_4\4genotype_Subject_BB0264_R_T3

description: Blood take at 05:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at11:55_Per3_5\5genotype_Subject_BB0246_R_T5

description: Blood take at 11:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at03:55_Per3_5\5genotype_Subject_BB0246_R_T10

description: Blood take at 03:55 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at09:20_Per3_4\4genotype_Subject_BB0264_R_T11

description: Blood take at 09:20 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:55_Per3_5\5genotype_Subject_BB0246_R_T14


title: Blood_TakenInPhaseWithRespectToMelatonin_at07:58_Per3_5\5genotype_Subject_BB0246_R_T4

description: Blood take at 07:58 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: Blood_TakenInPhaseWithRespectToMelatonin_at03:55_Per3_5\5genotype_Subject_BB0246_R_T3

description: Blood take at 03:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:45_Per3_4\4genotype_Subject_BB0239_R_T9

description: Blood take at 00:45 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:45_Per3_4\4genotype_Subject_BB0239_R_T13

description: Blood take at 16:45 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at12:41_Per3_4\4genotype_Subject_BB0239_R_T12

description: Blood take at 12:41 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:55_Per3_5\5genotype_Subject_BB0246_R_T1


title: Blood_TakenInPhaseWithRespectToMelatonin_at23:51_Per3_5\5genotype_Subject_BB0246_R_T2

description: Blood take at 23:51 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0246)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:47_Per3_4\4genotype_Subject_BB0239_R_T6

description: Blood take at 16:47 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:45_Per3_4\4genotype_Subject_BB0239_R_T5

description: Blood take at 12:45 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:45_Per3_4\4genotype_Subject_BB0239_R_T10

description: Blood take at 04:45 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:45_Per3_4\4genotype_Subject_BB0239_R_T7

description: Blood take at 20:45 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:48_Per3_4\4genotype_Subject_BB0239_R_T3

description: Blood take at 04:48 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:45_Per3_4\4genotype_Subject_BB0239_R_T4

description: Blood take at 08:45 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:43_Per3_4\4genotype_Subject_BB0239_R_T2

description: Blood take at 00:43 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0239)


title: IMPC_MP30_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:49_Per3_4\4genotype_Subject_BB0239_R_T14

description: Blood take at 20:49 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:25_Per3_5\5genotype_Subject_BB0236_R_T11

description: Blood take at 06:25 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:25_Per3_5\5genotype_Subject_BB0236_R_T14

description: Blood take at 18:25 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at10:20_Per3_5\5genotype_Subject_BB0236_R_T12

description: Blood take at 10:20 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:25_Per3_5\5genotype_Subject_BB0236_R_T7

description: Blood take at 18:25 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:45_Per3_4\4genotype_Subject_BB0239_R_T11

description: Blood take at 08:45 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:22_Per3_4\4genotype_Subject_BB0264_R_T14

description: Blood take at 21:22 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0264)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:45_Per3_4\4genotype_Subject_BB0239_R_T1


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:27_Per3_5\5genotype_Subject_BB0236_R_T5

description: Blood take at 10:27 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:25_Per3_5\5genotype_Subject_BB0236_R_T9

description: Blood take at 22:25 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:20_Per3_5\5genotype_Subject_BB0236_R_T2

description: Blood take at 22:20 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0236)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:45_Per3_5\5genotype_Subject_BB0219_R_T7

description: Blood take at 18:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:45_Per3_5\5genotype_Subject_BB0219_R_T9

description: Blood take at 22:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:25_Per3_5\5genotype_Subject_BB0236_R_T6

description: Blood take at 14:25 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:25_Per3_5\5genotype_Subject_BB0236_R_T10

description: Blood take at 02:25 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:45_Per3_5\5genotype_Subject_BB0219_R_T8

description: Blood take at 18:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:25_Per3_5\5genotype_Subject_BB0236_R_T3

description: Blood take at 02:25 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:25_Per3_5\5genotype_Subject_BB0236_R_T8


title: IMPC_MP05_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at14:30_Per3_5\5genotype_Subject_BB0236_R_T13

description: Blood take at 14:30 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0236)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:45_Per3_5\5genotype_Subject_BB0219_R_T11

description: Blood take at 06:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0219)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:45_Per3_5\5genotype_Subject_BB0219_R_T10

description: Blood take at 02:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:45_Per3_5\5genotype_Subject_BB0219_R_T5

description: Blood take at 10:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:45_Per3_5\5genotype_Subject_BB0219_R_T6

description: Blood take at 14:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:55_Per3_5\5genotype_Subject_BB0219_R_T3

description: Blood take at 02:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at06:58_Per3_5\5genotype_Subject_BB0219_R_T4

description: Blood take at 06:58 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:40_Per3_5\5genotype_Subject_BB0219_R_T2

description: Blood take at 22:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0219)


title: IMPC_MP19_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:45_Per3_5\5genotype_Subject_BB0219_R_T1


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:10_Per3_4\4genotype_Subject_BB0148_R_T14

description: Blood take at 21:10 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at13:10_Per3_4\4genotype_Subject_BB0148_R_T12

description: Blood take at 13:10 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at09:10_Per3_4\4genotype_Subject_BB0148_R_T11

description: Blood take at 09:10 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at17:10_Per3_4\4genotype_Subject_BB0148_R_T13

description: Blood take at 17:10 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:45_Per3_5\5genotype_Subject_BB0141_R_T10

description: Blood take at 02:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0141)


title: IDC_518119_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenInPhaseWithRespectToMelatonin_at09:10_Per3_4\4genotype_Subject_BB0148_R_T4

description: Blood take at 09:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:45_Per3_5\5genotype_Subject_BB0141_R_T9

description: Blood take at 22:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0141)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at05:10_Per3_4\4genotype_Subject_BB0148_R_T10

description: Blood take at 05:10 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:51_Per3_5\5genotype_Subject_BB0141_R_T5

description: Blood take at 10:51 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:10_Per3_4\4genotype_Subject_BB0148_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at01:05_Per3_4\4genotype_Subject_BB0148_R_T9

description: Blood take at 01:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0148)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:45_Per3_5\5genotype_Subject_BB0141_R_T7

description: Blood take at 18:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenInPhaseWithRespectToMelatonin_at06:46_Per3_5\5genotype_Subject_BB0141_R_T4

description: Blood take at 06:46 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenInPhaseWithRespectToMelatonin_at17:10_Per3_4\4genotype_Subject_BB0148_R_T6

description: Blood take at 17:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:45_Per3_5\5genotype_Subject_BB0141_R_T3

description: Blood take at 02:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:10_Per3_4\4genotype_Subject_BB0148_R_T7

description: Blood take at 21:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:45_Per3_5\5genotype_Subject_BB0141_R_T6

description: Blood take at 14:45 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:00_Per3_5\5genotype_Subject_BB0135_R_T14

description: Blood take at 20:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:17_Per3_4\4genotype_Subject_BB0148_R_T1

description: Blood take at 21:17 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenInPhaseWithRespectToMelatonin_at01:05_Per3_4\4genotype_Subject_BB0148_R_T2

description: Blood take at 01:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:48_Per3_5\5genotype_Subject_BB0141_R_T8

description: Blood take at 18:48 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0141)


title: Blood_TakenInPhaseWithRespectToMelatonin_at05:10_Per3_4\4genotype_Subject_BB0148_R_T3

description: Blood take at 05:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0148)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:45_Per3_5\5genotype_Subject_BB0141_R_T11

description: Blood take at 06:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0141)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:45_Per3_5\5genotype_Subject_BB0141_R_T1


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:00_Per3_5\5genotype_Subject_BB0135_R_T13

description: Blood take at 16:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:00_Per3_5\5genotype_Subject_BB0135_R_T11

description: Blood take at 08:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at11:55_Per3_5\5genotype_Subject_BB0135_R_T12

description: Blood take at 11:55 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:00_Per3_5\5genotype_Subject_BB0135_R_T10

description: Blood take at 04:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: IDC_439455_tumoral sample

description: Hybridized to SNP6.0


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:00_Per3_5\5genotype_Subject_BB0135_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:00_Per3_5\5genotype_Subject_BB0135_R_T9

description: Blood take at 00:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0135)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:47_Per3_4\4genotype_Subject_BB0239_R_T8

description: Blood take at 20:47 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0239)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:00_Per3_5\5genotype_Subject_BB0135_R_T6

description: Blood take at 16:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:02_Per3_5\5genotype_Subject_BB0135_R_T1

description: Blood take at 20:02 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:01_Per3_5\5genotype_Subject_BB0135_R_T2

description: Blood take at 00:01 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:00_Per3_5\5genotype_Subject_BB0135_R_T3

description: Blood take at 04:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:02_Per3_5\5genotype_Subject_BB0135_R_T5

description: Blood take at 12:02 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:00_Per3_5\5genotype_Subject_BB0135_R_T7

description: Blood take at 20:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:00_Per3_5\5genotype_Subject_BB0135_R_T4

description: Blood take at 08:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0135)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:25_Per3_4\4genotype_Subject_BB0121_R_T13

description: Blood take at 16:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0121)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:25_Per3_4\4genotype_Subject_BB0121_R_T14

description: Blood take at 20:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0121)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:26_Per3_4\4genotype_Subject_BB0121_R_T9

description: Blood take at 00:26 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:25_Per3_4\4genotype_Subject_BB0121_R_T6

description: Blood take at 16:25 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:25_Per3_4\4genotype_Subject_BB0121_R_T10

description: Blood take at 04:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at17:20_Per3_4\4genotype_Subject_BB0104_R_T6

description: Blood take at 17:20 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:25_Per3_4\4genotype_Subject_BB0121_R_T1

description: Blood take at 20:25 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:25_Per3_4\4genotype_Subject_BB0121_R_T5

description: Blood take at 12:25 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:25_Per3_4\4genotype_Subject_BB0121_R_T8


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:42_Per3_4\4genotype_Subject_BB0104_R_T2

description: Blood take at 00:42 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:41_Per3_4\4genotype_Subject_BB0104_R_T4

description: Blood take at 08:41 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:25_Per3_4\4genotype_Subject_BB0121_R_T4

description: Blood take at 08:25 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:33_Per3_4\4genotype_Subject_BB0121_R_T2

description: Blood take at 00:33 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:25_Per3_4\4genotype_Subject_BB0121_R_T3

description: Blood take at 04:25 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0121)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:25_Per3_4\4genotype_Subject_BB0121_R_T7


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:25_Per3_4\4genotype_Subject_BB0121_R_T11

description: Blood take at 08:25 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0121)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:40_Per3_4\4genotype_Subject_BB0104_R_T7

description: Blood take at 20:40 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at17:00_Per3_4\4genotype_Subject_BB0102_R_T13

description: Blood take at 17:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:42_Per3_4\4genotype_Subject_BB0104_R_T1

description: Blood take at 20:42 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:55_Per3_4\4genotype_Subject_BB0102_R_T9

description: Blood take at 00:55 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:00_Per3_4\4genotype_Subject_BB0102_R_T8

description: Blood take at 21:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at05:00_Per3_4\4genotype_Subject_BB0102_R_T10

description: Blood take at 05:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at13:00_Per3_4\4genotype_Subject_BB0102_R_T12

description: Blood take at 13:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:02_Per3_4\4genotype_Subject_BB0102_R_T14

description: Blood take at 21:02 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at09:00_Per3_4\4genotype_Subject_BB0102_R_T11

description: Blood take at 09:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:57_Per3_4\4genotype_Subject_BB0102_R_T5

description: Blood take at 12:57 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at05:00_Per3_4\4genotype_Subject_BB0102_R_T3

description: Blood take at 05:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:40_Per3_4\4genotype_Subject_BB0104_R_T3

description: Blood take at 04:40 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0104)


title: Blood_TakenInPhaseWithRespectToMelatonin_at09:00_Per3_4\4genotype_Subject_BB0102_R_T4

description: Blood take at 09:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:00_Per3_4\4genotype_Subject_BB0102_R_T7

description: Blood take at 21:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at01:00_Per3_4\4genotype_Subject_BB0102_R_T2

description: Blood take at 01:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenInPhaseWithRespectToMelatonin_at17:10_Per3_4\4genotype_Subject_BB0102_R_T6

description: Blood take at 17:10 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0102)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:41_Per3_5\5genotype_Subject_BB0100_R_T13

description: Blood take at 16:41 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:45_Per3_5\5genotype_Subject_BB0100_R_T14

description: Blood take at 20:45 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:40_Per3_5\5genotype_Subject_BB0100_R_T10

description: Blood take at 04:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:40_Per3_5\5genotype_Subject_BB0100_R_T7

description: Blood take at 20:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:41_Per3_5\5genotype_Subject_BB0100_R_T6

description: Blood take at 16:41 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:00_Per3_4\4genotype_Subject_BB0102_R_T1


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:35_Per3_5\5genotype_Subject_BB0100_R_T2

description: Blood take at 00:35 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:40_Per3_5\5genotype_Subject_BB0100_R_T4

description: Blood take at 08:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at12:35_Per3_5\5genotype_Subject_BB0100_R_T12

description: Blood take at 12:35 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:40_Per3_5\5genotype_Subject_BB0100_R_T8

description: Blood take at 20:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:42_Per3_5\5genotype_Subject_BB0100_R_T1

description: Blood take at 20:42 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at15:00_Per3_5\5genotype_Subject_BB0098_R_T13

description: Blood take at 15:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at15:00_Per3_5\5genotype_Subject_BB0098_R_T6

description: Blood take at 15:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at07:00_Per3_5\5genotype_Subject_BB0098_R_T4

description: Blood take at 07:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:00_Per3_5\5genotype_Subject_BB0098_R_T7

description: Blood take at 19:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at11:04_Per3_5\5genotype_Subject_BB0098_R_T5

description: Blood take at 11:04 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:40_Per3_5\5genotype_Subject_BB0100_R_T5

description: Blood take at 12:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at07:00_Per3_5\5genotype_Subject_BB0098_R_T11

description: Blood take at 07:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0098)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:40_Per3_5\5genotype_Subject_BB0100_R_T9

description: Blood take at 00:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:48_Per3_5\5genotype_Subject_BB0100_R_T11

description: Blood take at 08:48 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0100)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:40_Per3_5\5genotype_Subject_BB0100_R_T3

description: Blood take at 04:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0100)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at03:00_Per3_5\5genotype_Subject_BB0098_R_T10

description: Blood take at 03:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0098)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at23:00_Per3_5\5genotype_Subject_BB0098_R_T9

description: Blood take at 23:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0098)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:00_Per3_5\5genotype_Subject_BB0098_R_T8

description: Blood take at 19:00 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at03:00_Per3_5\5genotype_Subject_BB0098_R_T3

description: Blood take at 03:00 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:30_Per3_5\5genotype_Subject_BB0080_R_T13

description: Blood take at 16:30 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:30_Per3_5\5genotype_Subject_BB0080_R_T14

description: Blood take at 20:30 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:55_Per3_5\5genotype_Subject_BB0098_R_T2

description: Blood take at 22:55 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0098)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:30_Per3_5\5genotype_Subject_BB0080_R_T5

description: Blood take at 12:30 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:40_Per3_5\5genotype_Subject_BB0080_R_T6

description: Blood take at 16:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:31_Per3_5\5genotype_Subject_BB0080_R_T9

description: Blood take at 00:31 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:40_Per3_5\5genotype_Subject_BB0141_R_T2

description: Blood take at 22:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0141)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:30_Per3_5\5genotype_Subject_BB0080_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:30_Per3_5\5genotype_Subject_BB0080_R_T10

description: Blood take at 04:30 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:33_Per3_5\5genotype_Subject_BB0080_R_T11

description: Blood take at 08:33 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:30_Per3_5\5genotype_Subject_BB0080_R_T3

description: Blood take at 04:30 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:30_Per3_5\5genotype_Subject_BB0080_R_T7

description: Blood take at 20:30 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at12:25_Per3_5\5genotype_Subject_BB0080_R_T12

description: Blood take at 12:25 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:47_Per3_5\5genotype_Subject_BB0080_R_T2

description: Blood take at 00:47 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:05_Per3_4\4genotype_Subject_BB0072_R_T14

description: Blood take at 20:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at16:05_Per3_4\4genotype_Subject_BB0072_R_T6

description: Blood take at 16:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:47_Per3_5\5genotype_Subject_BB0080_R_T4

description: Blood take at 08:47 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0080)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:30_Per3_5\5genotype_Subject_BB0080_R_T1


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:06_Per3_4\4genotype_Subject_BB0072_R_T1

description: Blood take at 20:06 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at20:05_Per3_4\4genotype_Subject_BB0072_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at12:00_Per3_4\4genotype_Subject_BB0072_R_T12

description: Blood take at 12:00 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at12:05_Per3_4\4genotype_Subject_BB0072_R_T5

description: Blood take at 12:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at08:05_Per3_4\4genotype_Subject_BB0072_R_T11

description: Blood take at 08:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at16:05_Per3_4\4genotype_Subject_BB0072_R_T13

description: Blood take at 16:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at08:09_Per3_4\4genotype_Subject_BB0072_R_T4

description: Blood take at 08:09 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at04:05_Per3_4\4genotype_Subject_BB0072_R_T10

description: Blood take at 04:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at20:05_Per3_4\4genotype_Subject_BB0072_R_T7

description: Blood take at 20:05 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at09:10_Per3_5\5genotype_Subject_BB0061_R_T4

description: Blood take at 09:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:10_Per3_5\5genotype_Subject_BB0061_R_T1

description: Blood take at 21:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at00:05_Per3_4\4genotype_Subject_BB0072_R_T9

description: Blood take at 00:05 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at17:10_Per3_5\5genotype_Subject_BB0061_R_T13

description: Blood take at 17:10 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at09:10_Per3_5\5genotype_Subject_BB0061_R_T11

description: Blood take at 09:10 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at05:10_Per3_5\5genotype_Subject_BB0061_R_T10

description: Blood take at 05:10 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at17:10_Per3_5\5genotype_Subject_BB0061_R_T6

description: Blood take at 17:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at05:10_Per3_5\5genotype_Subject_BB0061_R_T3

description: Blood take at 05:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at00:00_Per3_4\4genotype_Subject_BB0072_R_T2

description: Blood take at 00:00 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenInPhaseWithRespectToMelatonin_at01:05_Per3_5\5genotype_Subject_BB0061_R_T2

description: Blood take at 01:05 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at13:05_Per3_5\5genotype_Subject_BB0061_R_T12

description: Blood take at 13:05 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at01:10_Per3_5\5genotype_Subject_BB0061_R_T9

description: Blood take at 01:10 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at04:06_Per3_4\4genotype_Subject_BB0072_R_T3

description: Blood take at 04:06 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0072)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:11_Per3_5\5genotype_Subject_BB0061_R_T8

description: Blood take at 21:11 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at21:10_Per3_5\5genotype_Subject_BB0061_R_T14

description: Blood take at 21:10 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0061)


title: Blood_TakenInPhaseWithRespectToMelatonin_at21:10_Per3_5\5genotype_Subject_BB0061_R_T7


title: Blood_TakenInPhaseWithRespectToMelatonin_at13:10_Per3_5\5genotype_Subject_BB0061_R_T5

description: Blood take at 13:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0061)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at15:35_Per3_4\4genotype_Subject_BB0041_R_T13

description: Blood take at 15:35 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at15:35_Per3_4\4genotype_Subject_BB0041_R_T6

description: Blood take at 15:35 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:35_Per3_4\4genotype_Subject_BB0041_R_T7

description: Blood take at 19:35 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at03:35_Per3_4\4genotype_Subject_BB0041_R_T10

description: Blood take at 03:35 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:35_Per3_4\4genotype_Subject_BB0041_R_T14

description: Blood take at 19:35 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at07:35_Per3_4\4genotype_Subject_BB0041_R_T11

description: Blood take at 07:35 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at23:36_Per3_4\4genotype_Subject_BB0041_R_T9

description: Blood take at 23:36 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at23:32_Per3_4\4genotype_Subject_BB0041_R_T2

description: Blood take at 23:32 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at07:35_Per3_4\4genotype_Subject_BB0041_R_T4

description: Blood take at 07:35 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:35_Per3_4\4genotype_Subject_BB0041_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at11:34_Per3_4\4genotype_Subject_BB0041_R_T12

description: Blood take at 11:34 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:35_Per3_4\4genotype_Subject_BB0041_R_T1


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:50_Per3_4\4genotype_Subject_BB0040_R_T10

description: Blood take at 02:50 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:50_Per3_4\4genotype_Subject_BB0040_R_T6

description: Blood take at 14:50 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:50_Per3_4\4genotype_Subject_BB0040_R_T7

description: Blood take at 18:50 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at10:45_Per3_4\4genotype_Subject_BB0040_R_T12

description: Blood take at 10:45 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at11:35_Per3_4\4genotype_Subject_BB0041_R_T5

description: Blood take at 11:35 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenInPhaseWithRespectToMelatonin_at06:50_Per3_4\4genotype_Subject_BB0040_R_T4

description: Blood take at 06:50 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at03:35_Per3_4\4genotype_Subject_BB0041_R_T3

description: Blood take at 03:35 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0041)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:50_Per3_4\4genotype_Subject_BB0040_R_T8

description: Blood take at 18:50 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at14:55_Per3_4\4genotype_Subject_BB0040_R_T13

description: Blood take at 14:55 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:50_Per3_4\4genotype_Subject_BB0040_R_T9

description: Blood take at 22:50 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:50_Per3_4\4genotype_Subject_BB0040_R_T5

description: Blood take at 10:50 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:52_Per3_4\4genotype_Subject_BB0040_R_T3

description: Blood take at 02:52 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:57_Per3_4\4genotype_Subject_BB0040_R_T14

description: Blood take at 18:57 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:50_Per3_4\4genotype_Subject_BB0040_R_T1


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:45_Per3_4\4genotype_Subject_BB0040_R_T2

description: Blood take at 22:45 when  in phase with respect to melatonin  4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:40_Per3_5\5genotype_Subject_BB0028_R_T14

description: Blood take at 19:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:50_Per3_4\4genotype_Subject_BB0040_R_T11

description: Blood take at 06:50 when  out of phase with respect to melatonin   4\4 genotype subject (Subject BB0040)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at15:40_Per3_5\5genotype_Subject_BB0028_R_T13

description: Blood take at 15:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at11:35_Per3_5\5genotype_Subject_BB0028_R_T12

description: Blood take at 11:35 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:40_Per3_5\5genotype_Subject_BB0028_R_T7

description: Blood take at 19:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at03:40_Per3_5\5genotype_Subject_BB0028_R_T10

description: Blood take at 03:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenInPhaseWithRespectToMelatonin_at15:40_Per3_5\5genotype_Subject_BB0028_R_T6

description: Blood take at 15:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at19:40_Per3_5\5genotype_Subject_BB0028_R_T8


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at23:40_Per3_5\5genotype_Subject_BB0028_R_T9

description: Blood take at 23:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenInPhaseWithRespectToMelatonin_at03:40_Per3_5\5genotype_Subject_BB0028_R_T3

description: Blood take at 03:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: Blood_TakenInPhaseWithRespectToMelatonin_at23:35_Per3_5\5genotype_Subject_BB0028_R_T2

description: Blood take at 23:35 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at07:40_Per3_5\5genotype_Subject_BB0028_R_T11

description: Blood take at 07:40 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0028)


title: Blood_TakenInPhaseWithRespectToMelatonin_at07:44_Per3_5\5genotype_Subject_BB0028_R_T4

description: Blood take at 07:44 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at02:15_Per3_5\5genotype_Subject_BB0012_R_T9

description: Blood take at 02:15 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at10:15_Per3_5\5genotype_Subject_BB0012_R_T11

description: Blood take at 10:15 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at06:15_Per3_5\5genotype_Subject_BB0012_R_T10

description: Blood take at 06:15 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at14:11_Per3_5\5genotype_Subject_BB0012_R_T12

description: Blood take at 14:11 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at10:15_Per3_5\5genotype_Subject_BB0012_R_T4

description: Blood take at 10:15 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at18:15_Per3_5\5genotype_Subject_BB0012_R_T13

description: Blood take at 18:15 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:15_Per3_5\5genotype_Subject_BB0012_R_T14

description: Blood take at 22:15 when  out of phase with respect to melatonin   5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at02:10_Per3_5\5genotype_Subject_BB0012_R_T2

description: Blood take at 02:10 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at14:15_Per3_5\5genotype_Subject_BB0012_R_T5

description: Blood take at 14:15 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenOutofPhaseWithRespectToMelatonin_at22:15_Per3_5\5genotype_Subject_BB0012_R_T8


title: Blood_TakenInPhaseWithRespectToMelatonin_at18:18_Per3_5\5genotype_Subject_BB0012_R_T6

description: Blood take at 18:18 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at06:15_Per3_5\5genotype_Subject_BB0012_R_T3

description: Blood take at 06:15 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:15_Per3_5\5genotype_Subject_BB0012_R_T7

description: Blood take at 22:15 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0012)


title: Blood_TakenInPhaseWithRespectToMelatonin_at22:15_Per3_5\5genotype_Subject_BB0012_R_T1

description: Blood take at 22:15 when  in phase with respect to melatonin from a Per3  5\5 genotype subject (Subject BB0012)


title: SARSmus,PBS, Lung, 1dpi(inf), 03-2

status: Public on Oct 01 2013

city: Shinnjuku-ku

first: Naoko

last: Iwata-Yoshikawa

state: Tokyo

address: 1-23-1 Toyama

department: Pathology

country: Japan

institute: National institute of infectious diseases

description: Gene expression of lung in mouse at 1 day after SARS-CoV challenge

hyb_protocol: After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60°C for 30 min.  These samples were hybridized onto the Whole Mouse Genome Microarray 44k probes × 4 arrays/ slide (Agilent) at 65°C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM).  Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing: The image files were analyzed by using of Feature Extraction software (Agilent) and automatically exported with flag information.

organism: Mus musculus

source_name: SARSmus, PBS, Lung, 1dpi(inf), 03-2

label_protocol: Three hundred nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 300 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter.  cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.

extract_protocol: Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: Mouse lungs treated with RNAlater (ABI) were stored at -80°C until use.

tag: strain

value: BALB/c

value: lung

tag: treatment

value: Naïve


title: Blood_TakenInPhaseWithRespectToMelatonin_at19:40_Per3_5\5genotype_Subject_BB0028_R_T1

description: Blood take at 19:40 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: SARSmus,PBS, Lung, 1dpi(inf), 02-2

source_name: SARSmus, PBS, Lung, 1dpi(inf), 02-2


title: PDAC patient 17

status: Public on Aug 12 2013

city: Jaen

first: Octavio

last: Caba

state: Jaen

address: Paraje de las Lagunillas

department: Health Sciences

country: Spain

institute: University of Jaen

description: Gene expression data from peripheral blood before treatment of PDAC patient 17

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner

data_processing: Raw data was preprocessed using the RMA method. For transcript probe set definition the custom CDF package from the brainarray group (hugene10stv1enstcdf version 13, defining probe sets for transcripts from Ensembl core database version 58) was used

source_name: Peripheral blood before treatment of PDAC patient 17

label_protocol: RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station

extract_protocol: Total RNA was extracted from peripheral blood samples using the PAXgene Blood RNA Kit (PreAnalytix). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 7.

tag: gender

value: Female

tag: age

tag: disease state

value: PDAC

tag: pathological staging

value: III

tag: cell type

value: PBMC


title: Blood_TakenInPhaseWithRespectToMelatonin_at11:44_Per3_5\5genotype_Subject_BB0028_R_T5

description: Blood take at 11:44 when  in phase with respect to melatonin  5\5 genotype subject (Subject BB0028)


title: PDAC patient 16

description: Gene expression data from peripheral blood before treatment of PDAC patient 16

source_name: Peripheral blood before treatment of PDAC patient 16

value: IV


title: mTR-/-G4 islets (Sample c)

city: Baltimore

first: Nini

last: Guo

address: 725 North Wolfe St. PCTB605

country: USA

institute: Johns Hopkins University

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Partek GS, customized to Partek defaults, using all extended probesets mps option
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.na31.mm9.probeset_extended.mps

source_name: Isolated mouse pancreatic islets from mTR-/-G4 mice

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter random primers for cDNA synthesis, and Invitrogen SuperScript II reverse transcriptase (www.affymetrix.com, GeneChip Expression Analysis, Technicam Manual).

growth_protocol: Mice were kept on a 12-hour light/dark cycle, food ad lib

extract_protocol: Total RNA was extracted by QIAGEN RNeasy kit.

treatment_protocol: Pancreatic islets were purified by collagenase digestion.

tag: Sex

value: Male

value: 15 month

tag: genotype


title: mTR-/-G4 islets (Sample b)


title: WT_T0_2

status: Public on Sep 12 2013

city: Sydney

first: xiuquan

last: ma

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: RNA from cells, vector

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

source_name: 3T3-L1 cells, vector, 0hr

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturer's instructions.

growth_protocol: 3T3-L1 cells expressing ISL1 or not were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% newborn calf serum or fetal calf serum, 2 mM L-glutamine, 100 units/liter penicillin, and 100 ug/liter streptomycin at 37 °C in 10% CO2.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit (Qiagen) according to manufacturer's instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: 3T3-L1 cells expressing ISL1 or not were grown to confluence at 37 °C in 10% CO2. Two days after reaching 100% confluence, 3T3-L1 fibroblast cells were treated by differentiation medium containing 10% fetal calf serum, 350 nmol/l insulin, 0.5 mmol/l isobutylmethylxanthine, 250 nmol/l dexamethasone, 400 nmol/l biotin for different times as indicated. 0h means just prior to the differentiation induction.

tag: cell line

tag: construct

value: pMIG vector


title: ISL1_T0_2

description: RNA from cells, ISL1

source_name: 3T3-L1 cells, ISL1, 0hr


title: PDAC patient 13

description: Gene expression data from peripheral blood before treatment of PDAC patient 13

source_name: Peripheral blood before treatment of PDAC patient 13


title: WT_T0_1

description: RNA from cells, vector


title: Wildtype islets (Sample b)

source_name: Isolated mouse pancreatic islets from wildtype mice

value: wildtype(WT)


title: mTR-/-G4 islets (Sample a)


title: PDAC patient 15

description: Gene expression data from peripheral blood before treatment of PDAC patient 15

source_name: Peripheral blood before treatment of PDAC patient 15


title: Wildtype islets (Sample c)


title: ISL1_T0_1

description: RNA from cells, ISL1


title: WT_T0_3

description: RNA from cells, vector


title: PDAC patient 11

description: Gene expression data from peripheral blood before treatment of PDAC patient 11

source_name: Peripheral blood before treatment of PDAC patient 11


title: PDAC patient 12

description: Gene expression data from peripheral blood before treatment of PDAC patient 12

source_name: Peripheral blood before treatment of PDAC patient 12


title: PDAC patient 10

description: Gene expression data from peripheral blood before treatment of PDAC patient 10

source_name: Peripheral blood before treatment of PDAC patient 10


title: PDAC patient 8

description: Gene expression data from peripheral blood before treatment of PDAC patient 8

source_name: Peripheral blood before treatment of PDAC patient 8


title: PDAC patient 18

description: Gene expression data from peripheral blood before treatment of PDAC patient 18

source_name: Peripheral blood before treatment of PDAC patient 18


title: ISL1_T0_3

description: RNA from cells, ISL1


title: PDAC patient 9

description: Gene expression data from peripheral blood before treatment of PDAC patient 9

source_name: Peripheral blood before treatment of PDAC patient 9


title: PDAC patient 14

description: Gene expression data from peripheral blood before treatment of PDAC patient 14

source_name: Peripheral blood before treatment of PDAC patient 14


title: PDAC patient 6

description: Gene expression data from peripheral blood before treatment of PDAC patient 6

source_name: Peripheral blood before treatment of PDAC patient 6


title: Wildtype islets (Sample a)


title: PDAC patient 3

description: Gene expression data from peripheral blood before treatment of PDAC patient 3

source_name: Peripheral blood before treatment of PDAC patient 3


title: PDAC patient 4

description: Gene expression data from peripheral blood before treatment of PDAC patient 4

source_name: Peripheral blood before treatment of PDAC patient 4


title: PDAC patient 2

description: Gene expression data from peripheral blood before treatment of PDAC patient 2

source_name: Peripheral blood before treatment of PDAC patient 2


title: PDAC patient 5

description: Gene expression data from peripheral blood before treatment of PDAC patient 5

source_name: Peripheral blood before treatment of PDAC patient 5


title: PDAC patient 7

description: Gene expression data from peripheral blood before treatment of PDAC patient 7

source_name: Peripheral blood before treatment of PDAC patient 7


title: PDAC patient 1

description: Gene expression data from peripheral blood before treatment of PDAC patient 1

source_name: Peripheral blood before treatment of PDAC patient 1


title: 11696.s1

status: Public on Apr 15 2013

city: Atlanta

first: Pankaj

last: Chopra

state: GA

address: 615 Michael St. NE, Ste. 375

department: Human Genetics

institute: Emory University

hyb_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

scan_protocol: Using an Illumina HiScan

data_processing: Raw signal intensities were quantile normalized separately and imputed values calculated for missing values (see unmethylated and methylated signal intensities in GSE-linked supplementary file). The beta value was calculated as: (signal b)/(signal a + signal b + 100)

label: Cy5 and Cy3

source_name: Peripheral blood, control

extract_protocol: Standard DNA extraction protocol

value: male

tag: tissue

value: blood

tag: phenotype

value: Control


title: XX_FX4

source_name: Peripheral blood, Case

label_protocol: Contained within the Illumina Infinium HumanMethylation450 BeadChips protocol

value: Case


title: 11312.s1


title: XX_FX3


title: XX_FX2


title: 11366.s1


title: XX_FX1


title: 11318.s1


title: 11597.s1


title: 11296.s1


title: XX_FX_BLOOD_1


title: XX_FX_BLOOD_4_77


title: XX_FX6


title: 11251.s1


title: 11218.s1


title: 11546.s1


title: 11298.s1


title: XX_FX_BLOOD_11_63


title: 11599.s1


title: 11018.s1


title: XX_FX5


title: 11561.s1


title: 11245.s1


title: 11381.s1


title: 11511.s1


title: 13358.s1


title: 11270.s1


title: 11557.s1


title: 11077.s1


title: 11452.s1


title: 11428.s1


title: 11459.s1


title: 11484.s1


title: 11325.s1


title: 11417.s1


title: 11201.s1


title: 11089.s1


title: 11216.s1


title: 11415.s1


title: 11156.s1


title: 11057.s1


title: Vestibular Schwannoma [352]

status: Public on Mar 01 2013

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

institute: Hospital Universitari Germans Trias i Pujol

hyb_protocol: Hybridization, washing, staining and scanning of Affymetrix Human Gene ST 1.0 arrays were performed following the manufacturer's recommendations

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Scanned images (DAT files) were transformed into intensities (CEL files) by GCOS (Affymetrix).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
RMA signal log2 converted from Expression Console Software 1.1.2800.29167. As samples were processes in two batches, ComBat method was used to remove batch effect. Only NM_ probes from RefSeq annotation were selected for analysis, since the amplification and labeling method is not intended for use with other types of RNAs such as miRNAs, tRNAs, etc. Olfactory receptor were removed to avoid the cross hybridization issues with these genes.

source_name: Vestibular Schwannoma

label_protocol: library preparation and amplification were performed following the distributor’s (Sigma-Aldrich) recommendations for whole transcriptome amplification (WTA2). Amplification was performed for 17 cycles, and amplified cDNA was purified and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo-Fischer). Some 8 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from a GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

extract_protocol: RNA was isolated using RNeasy® Mini Kit (QIAGEN) following instructions. Rnase-Free Dnase Set  (QIAGEN) was used to eliminate DNA contamitations.

treatment_protocol: Samples were frozen in liquid Nitrogen immediately after surgical resection, and then conserved at -80ºC until extraction

tag: group

value: Tumor

tag: batch


title: 11075.s1


title: 11383.s1


title: 11004.s1


title: 11498.s1


title: 11242.s1


title: 11108.s1


title: Vestibular Schwannoma [350]


title: 11378.s1


title: 11303.s1


title: 11299.s1


title: 11641.s1


title: 11252.s1


title: 11052.s1


title: 11194.s1


title: Vestibular Schwannoma [371]


title: Vestibular Schwannoma [369]


title: Vestibular Schwannoma [354]


title: 11094.s1


title: 11046.s1


title: 11429.s1


title: 11289.s1


title: Vestibular Schwannoma [399]


title: 11028.s1


title: Vestibular Schwannoma [374]


title: Vestibular Schwannoma [417]


title: Vestibular Schwannoma [407]


title: Vestibular Schwannoma [467]


title: Vestibular Schwannoma [458]


title: Vestibular Schwannoma [444]


title: Vestibular Schwannoma [471]


title: Vestibular Schwannoma [422]


title: Vestibular Schwannoma [373]


title: Vestibular Schwannoma [450]


title: Vestibular Schwannoma [447]


title: Vestibular Schwannoma [482]


title: Vestibular Schwannoma [474]


title: Vestibular Schwannoma [449]


title: Vestibular Schwannoma [488]


title: Vestibular Schwannoma [490]


title: Vestibular Schwannoma [437]


title: Vestibular Schwannoma [473]


title: Vestibular Schwannoma [491]


title: Vestibular Schwannoma [486]


title: Vestibular Schwannoma [505]


title: Vestibular Schwannoma [506]


title: Vestibular Schwannoma [507]


title: Human Schwann Cells [N_HSC]

description: commercial human adult normal RNA from Schwann Cells (ScienCell, HSC total RNA Catalog Number 1705

source_name: Human Schwann Cells


title: Vestibular Schwannoma [509]


title: Facial Nerve [N_434]

source_name: Facial Nerve


title: Vestibular Nerve [N_432]

source_name: Vestibular Nerve


title: 11197.s1


title: Cervical Nerve [N_504]

source_name: Cervical Nerve


title: VIII craneal nerve [N_483]

source_name: VIII craneal nerve


title: Vestibular Schwannoma [510]


title: Hipoglosal Nerve [N_504HIP]

source_name: Hipoglosal Nerve


title: Cervical Nerve [N_502]


title: 12582.s1


title: WT_T48_3

status: Public on Sep 05 2012

description:
XM_10.3
RNA from cells, vector

source_name: 3T3-L1 cells, vector, 48hr

value: differentiation medium

tag: time point


title: ISL1_T48_2

description:
XM_3.2
RNA from cells, ISL1

source_name: 3T3-L1 cells, ISL1, 48hr


title: WT_T48_1

description:
XM_10.1
RNA from cells, vector


title: Auricular Nerve [N_511]

source_name: Auricular Nerve


title: WT_T48_2

description:
XM_10.2
RNA from cells, vector


title: Auricular Nerve [N_518]


title: Gene expression data from PC1 high B1a cells, biological rep6

status: Public on Jul 09 2012

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

country: South Korea

institute: seoul national university

hyb_protocol: Five micrograms of labeled target from twenty-four submitted samples (received 2-10-09) was combined with 2X hybridization buffer, 3nM B2 control oligo (Affymetrix 900457), 20X spike in (Affymetrix 51214), and DMSO making a final volume of 100ul for the twenty-four individual hybridizations to the commercial Affymetrix GeneChip, mouse gene 1.0 ST containing the Mus musculus genome.  The hybridization cocktail, including the components listed above, was denatured for five minutes at 99◦C then transferred to a 45◦C heat block for an additional five minutes before transferring 80ul of the cocktail into the chip.  The hybridization was carried out at a constant temperature of 45◦C for approximately seventeen hours using the Affymetrix 640 oven 500k approved.

scan_protocol: Upon completion of the fluidics process, each sample was scanned using the Affymetrix GeneChip 3000 7Gplus scanner to create the image files (dat).  GeneChip Operating Software (GCOS v1.4) was then used to convert the image files to cel files

data_processing: Data were collected using GeneChip Operating Software (GCOS v1.4). The robust multiarray average (RMA) and quantile normalization were performed.

label_protocol: Total of 5 µg of double stranded cDNA was concentrated to 25 µL.  Each sample was combined with 5 µL fragmentation buffer mix (FL1) and 2 µL fragmentation enzyme mix (FL2).  DNA was digested at 37 °C for 30 minutes and enzyme was denatured at 95 °C for 2 minutes.  Fragmented ds cDNAs were biotin end-labeled using terminal transferase.  Each fragmented sample was combined with15 μl labeling buffer mix (FL3), 1.5 μl biotinylated nucleotides (FL4), 1.5 μl terminal transferase (FL5), incubated at 37 °C for 60 minutes, and heat inactivated.

extract_protocol: Antibody stained spleen cells were sorted using FACS Aria Cell-Sorting System (Beckton-Dickinson, Franklin Lake, NJ) and either 10^4 PC1 high cells or 10^4 PC1 low B1a cells were directly collected into RLT buffer (Qiagen, Valencia, CA). lysates were thawed in room temperature and genomic DNA was fragmented to by spinning the samples through Qiashredder columns for 2 minutes at 21,000 x g.  To RLT buffer sample was added to 100% ethanol and RNAs were extracted using Qiagen RNeasy 96-well system as described previously (Virtaneva et al., 2005).  As contaminating gDNA will interfere with the downstream Nugen Ribo-SPIA™ technology, each RNA sample were treated with 27 units of DNAse I (Qiagen, Valencia, CA) for 15 minutes at room temperature during extraction.  RNA yield was estimated using Nanodrop (NanoDrop Technologies, Wilmington, DE) and 2100 Bioanalyzer (Agilent Technologies, Santa Clare, CA).

treatment_protocol: FACS sorting protocol: Stained cells were sorted for PC1low (CD19+CD5+CD23-PC1lo) and PC1hi (CD19+CD5+CD23-PC1hi)

tag: cells

value: Peritoneal B1a cells

tag: pc1 expression level

value: high


title: 11285.s1


title: Gene expression data from PC1 low B1a cells, biological rep5

tag: strain

value: low


title: ISL1_T48_1

description:
XM_3.1
RNA from cells, ISL1

tag: treatment


title: ISL1_T48_3

description:
XM_3.3
RNA from cells, ISL1


title: Gene expression data from PC1 low B1a cells, biological rep3


title: Gene expression data from PC1 low B1a cells, biological rep6


title: Gene expression data from PC1 low B1a cells, biological rep1


title: Gene expression data from PC1 low B1a cells, biological rep4


title: Gene expression data from PC1 high B1a cells, biological rep5


title: Gene expression data from PC1 low B1a cells, biological rep2


title: Gene expression data from PC1 high B1a cells, biological rep2


title: Gene expression data from PC1 high B1a cells, biological rep3


title: Gene expression data from PC1 high B1a cells, biological rep4


title: Gene expression data from PC1 high B1a cells, biological rep1


title: siIRF8 replicate 3

status: Public on Oct 15 2011

description: technical replicate 3 of 6

hyb_protocol: Chips were prehybridized in a sealed chamber immersed in a 42°C waterbath using established procedures.Chips were then washed twice for 2 min with agitation, first in ultra-pure water, then in isopropyl alcohol. After the last isopropyl alcohol wash, samples were quickly placed in a room-temperature centrifuge and spun dry (3000 rmp, 5 min). The chips were hybridized overnight in a sealed humidified slide chamber immersed in a light-protected 42°C waterbath, then washed, dried, and stored in the dark until scanned.

scan_protocol: Chips were scanned using an Axon 4000B scanner and GenePix 4.0 software. Photomultiplier tube voltage settings were adjusted to allow 1% saturation of signal in both channels.

data_processing: Image data were extracted, and extracted data were normalized with lowess smoothing function.

source_name: siIRF8 retro-viral transfected cells

label_protocol: Labeling RNA,(one for Cy3 and one for Cy5) using dUTP-Cy3 OR dUTP Cy5 by incubating reverse transcription reaction mixture at 42°C for 90 min, followed by degrading RNA and cleaning up labeled cDNA.

growth_protocol: cells were cultured in RPMI medium supplemented with 200 U/ml penicillin G and 10% FCS

extract_protocol: Isolate RNA using Trizol Reagent and clean up RNAs with Qiagen Rnase kit

treatment_protocol: siIRF8 vector and retroviral transfection were detailed in JEM 2006 203(1):63.

value: B cell lymphoma cell line derived from NFS congenic mice

source_name: control vector retro-viral transfected cells


title: siIRF8 replicate 1

description: technical replicate 1 of 6


title: siIRF8 replicate 6

description: technical replicate 6 of 6


title: siIRF8 replicate 4

description: technical replicate 4 of 6


title: siIRF8 replicate 2

description: technical replicate 2 of 6


title: siIRF8 replicate 5

description: technical replicate 5 of 6


title: IRF8 ChIP_VAL_promoter1

description: comaprison of ChIP DNA with input DNA

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction

source_name: IRF8 ChIP DNA from VAL

label_protocol: Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with klenow extension

growth_protocol: RPMI medium supplemented with 200 U/ml penicillin G and 10% FCS

extract_protocol: cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000).  Following immunoprecipitation with anti-mouse IRF8 antibody (Santa Cruz Biotechnology), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR.

treatment_protocol: no special treatment

tag: genotype/variation

value: IRF8 positive

tag: antibody

value: anti-mouse IRF8 (Santa Cruz Biotechnology)

source_name: Input control DNA from VAL

value: none (input)


title: IRF8 ChIP_ODH1_promoter1

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from ODH1

source_name: Input control DNA from ODH1


title: IRF8 ChIP_LY1_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from LY1

source_name: Input control DNA from LY1


title: PU1 ChIP_NFS202_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: PU1 ChIP DNA from NFS202

value: PU1 positive

source_name: Input control DNA from NFS202


title: IRF8 ChIP_MMS1_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from MMS1

value: IRF8 negative

source_name: Input control DNA from MMS1


title: 650nM MLN4924 after 24hr, replicate 3

status: Public on Jul 09 2011

city: Cambridge

first: Hugues

last: Bernard

state: MA

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

description: Gene expression data from treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133Plus 2.0 Array in an Affymetrix Model 640 hybridization oven . GeneChips were washed and stained on an Affymetrix FS450 station.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console software from Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Cell culture of Melanoma Cell Line - A375

label_protocol: Biotinylated cRNA were prepared using modified MesageAmp-based protocols (Ambion Inc) from 1.5ug total RNA.

growth_protocol: A375 cells were maintained at 37oC in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 100 U/ml penicillin/100 g/ml streptomycin (Invitrogen).

extract_protocol: Cells were precipitated, PBS washed, lysed using Qiagen RLT Buffer, and then RNA was extracted with Ambion MegaMax kit using King Fisher automated platform. All protocoles were executed following manufacturers recommendations.

treatment_protocol: 0.065% DMSO or 650nM MLN4924 were added to 2 million A375 cells and incubated for 1, 2, 4, 8, or 24 hours before recovery for RNA isolation and Gene Expression.

value: Melanoma Cell Line - A375

tag: time


title: 650nM MLN4924 after 24hr, replicate 2

description: Gene expression data from treated cells


title: IRF8 ChIP_VAL_promoter2

description: comaprison of ChIP DNA with input DNA


title: IRF8 ChIP_NFS205_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from NFS205

source_name: Input control DNA from NFS205


title: 650nM MLN4924 after 24hr, replicate 1

description: Gene expression data from treated cells


title: PU1 ChIP_NFS205_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: PU1 ChIP DNA from NFS205

value: PU1 negative


title: IRF8 ChIP_LY1_promoter1

description: comaprison of ChIP DNA with input DNA


title: PU1 ChIP_NFS205_promoter1

description: comaprison of ChIP DNA with input DNA


title: 650nM MLN4924 after 8hr, replicate 3

description: Gene expression data from treated cells


title: 650nM MLN4924 after 8hr, replicate 2

description: Gene expression data from treated cells


title: IRF8 ChIP_MPC11_promoter1

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from MPC11

source_name: Input control DNA from MPC11


title: IRF8 ChIP_MPC11_promoter2

description: comaprison of ChIP DNA with input DNA


title: 650nM MLN4924 after 8hr, replicate 1

description: Gene expression data from treated cells


title: 650nM MLN4924 after 4hr, replicate 3

description: Gene expression data from treated cells


title: PU1 ChIP_NFS201_promoter2

description: comaprison of ChIP DNA with input DNA

source_name: PU1 ChIP DNA from NFS201

source_name: Input control DNA from NFS201


title: 650nM MLN4924 after 4hr, replicate 1

description: Gene expression data from treated cells


title: IRF8 ChIP_ODH1_promoter2

description: comaprison of ChIP DNA with input DNA


title: IRF8 ChIP_MMS1_promoter1

description: comaprison of ChIP DNA with input DNA


title: PU1 ChIP_NFS202_promoter1

description: comaprison of ChIP DNA with input DNA


title: IRF8 ChIP_NFS202_promoter1

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from NFS202


title: IRF8 ChIP_NFS205_promoter1

description: comaprison of ChIP DNA with input DNA


title: PU1 ChIP_NFS201_promoter1

description: comaprison of ChIP DNA with input DNA


title: 650nM MLN4924 after 2hr, replicate 1

description: Gene expression data from treated cells


title: IRF8 ChIP_NFS201_promoter1

description: comaprison of ChIP DNA with input DNA

source_name: IRF8 ChIP DNA from NFS201


title: 650nM MLN4924 after 2hr, replicate 2

description: Gene expression data from treated cells


title: IRF8 ChIP_NFS202_promoter2

description: comaprison of ChIP DNA with input DNA


title: 650nM MLN4924 after 2hr, replicate 3

description: Gene expression data from treated cells


title: DMSO Control after 24hr, replicate 1

description: Gene expression data from treated cells

value: DMSO Control


title: 650nM MLN4924 after 1hr, replicate 3

description: Gene expression data from treated cells


title: DMSO Control after 24hr, replicate 3

description: Gene expression data from treated cells


title: 650nM MLN4924 after 1hr, replicate 1

description: Gene expression data from treated cells


title: 650nM MLN4924 after 1hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 24hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 4hr, replicate 3

description: Gene expression data from treated cells


title: DMSO Control after 8hr, replicate 3

description: Gene expression data from treated cells


title: DMSO Control after 8hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 8hr, replicate 1

description: Gene expression data from treated cells


title: DMSO Control after 1hr, replicate 1

description: Gene expression data from treated cells


title: DMSO Control after 1hr, replicate 3

description: Gene expression data from treated cells


title: DMSO Control after 4hr, replicate 1

description: Gene expression data from treated cells


title: DMSO Control after 4hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 2hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 1hr, replicate 2

description: Gene expression data from treated cells


title: DMSO Control after 2hr, replicate 1

description: Gene expression data from treated cells


title: DMSO Control after 2hr, replicate 3

description: Gene expression data from treated cells


title: IRF8 ChIP_NFS201_promoter2

description: comaprison of ChIP DNA with input DNA


title: whole-blood_0_pair-92

status: Public on Mar 01 2011

city: CA

first: James

middle: A.

last: Wingrove

state: CA

address: 2500 Faber Place

institute: CardioDx, Inc.

hyb_protocol: Labeled RNAs were hybridized using the Agilent protocol

scan_protocol: Agilent Feature Extraction Software (version 10.2.1.3) was used for background subtraction and LOWESS normalization.

data_processing: Agilent processed signal values were used;  values were scaled to a trimmed mean of 100 using an R script developed in-house at CardioDx.

label_protocol: 200 ng of each patient whole blood RNA was labeled with Cy3 using Agilent's Low RNA Input Linear Amplification Kit following the recommended protocol.

growth_protocol: Whole blood (2.5 ml) was collected via syringe prior to catheterization.

extract_protocol: RNA was extracted using a magnetic bead-based approach (Agencourt RNAdvance) on an automated platform (Hamilton Star)

treatment_protocol: Collected blood was aliquoted into PaxGene tubes, inverted 10X and then frozen at -20 C until further processing

tag: disease state

value: Control (0)

tag: pair

value: pair 92

tag: sex (gender)

value: Male

tag: date of birth

tag: smoking status

value: Current


title: whole-blood_0_pair-94

value: pair 94

value: Never


title: 650nM MLN4924 after 4hr, replicate 2

description: Gene expression data from treated cells

tag: cell line


title: whole-blood_0_pair-99

value: pair 99


title: whole-blood_0_pair-95

value: pair 95

value: Quit more than 2 months ago


title: whole-blood_0_pair-96

value: pair 96


title: whole-blood_0_pair-98

value: pair 98


title: whole-blood_1_pair-90

value: Case (1)

value: pair 90

value: Female


title: wt P12 vs wt ni [30 hpi]

status: Public on Apr 03 2012

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Features were extracted with an image analysis tool version A.10.5.1.1 using the GE2-V4_95_Feb07 protocol (Agilent Technologies).

hyb_protocol: Labeled samples was mixed and hybridized to the microarray according to the supplier`s protocol (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies) and recommended settings.

data_processing: The extracted MAGE-ML files was analyzed with the Rosetta Resolver Biosoftware, Build 7.2.2 SP 1.3.1 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: wt P12

label_protocol: RNA labeling was performed with the dual color Quick Amp Labeling Kit (Agilent Technologies) according the suppliers recommendation. In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 3-CTP.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 5x10e6 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer. The amount of RNA was determined by OD260/280 nm measurement using a NanoDrop 1000 spectrophotometer (Kisker, Steinfurt, Germany). The RNA size, integrity and the amount of total RNA were measured with a Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany) on a RNA Nano 6000 microfluidics kit.

treatment_protocol:
BMM were generated as described (Collins et al., J Cell Sci. 1997 Jan;110 ( Pt 2):191-200). In brief, monocytes were isolated from the femur and tibia of C57Bl/6 mice. These were plated in 10-cm dishes in RPMI medium containing 10% hi FCS and 30% L929 supernatant as source of M-CSF. After 7d in culture these cells were washed twice with PBS and replated ON in RPMI medium containing 10% hi FCS and 10% L929 supernatant.
H.pylori P12 Infection was carried out after 3h of serum starvation with MOI 50 for 6h in only RPMI, then the medium was replaced by RPMI medium containing 10% hi FCS, 10% L929 supernatant and gentamicin. Cells were analyzed at 30 h post infection.

tag: infection

value: H.pylori P12

tag: cell type

value: bone marrow derived macrophages (BMM)

value: wild type

source_name: wt ni

label_protocol: RNA labeling was performed with the dual color Quick Amp Labeling Kit (Agilent Technologies) according the suppliers recommendation. In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 5-CTP.

value: uninfected


title: whole-blood_1_pair-9

value: pair 9


title: whole-blood_1_pair-92

value: pair 92

value: Male


title: whole-blood_1_pair-94

value: pair 94


title: whole-blood_1_pair-98

value: Current


title: whole-blood_0_pair-9

value: Control (0)


title: whole-blood_1_pair-99

value: pair 99


title: whole-blood_1_pair-96


title: whole-blood_0_pair-89

value: pair 89

value: Quit more than 2 months ago


title: whole-blood_1_pair-89


title: whole-blood_1_pair-93

value: pair 93


title: whole-blood_1_pair-88

value: Case (1)

value: pair 88


title: whole-blood_1_pair-87

value: pair 87

value: Never


title: whole-blood_1_pair-95

value: pair 95


title: whole-blood_0_pair-90

value: pair 90

value: Female


title: whole-blood_0_pair-87


title: whole-blood_0_pair-93


title: whole-blood_1_pair-86

value: pair 86


title: whole-blood_0_pair-86


title: whole-blood_0_pair-88


title: wt ni vs wt P12 [30 hpi]

treatment_protocol: BMM were generated as described (Collins et al., J Cell Sci. 1997 Jan;110 ( Pt 2):191-200). In brief, monocytes were isolated from the femur and tibia of C57Bl/6 mice. These were plated in 10-cm dishes in RPMI medium containing 10% hi FCS and 30% L929 supernatant as source of M-CSF. After 7d in culture these cells were washed twice with PBS and replated ON in RPMI medium containing 10% hi FCS and 10% L929 supernatant.

value: uninfected

value: bone marrow derived macrophages (BMM)

value: wild type

value: H.pylori P12


title: whole-blood_0_pair-8

value: Control (0)

value: pair 8

value: Male

value: Current


title: whole-blood_0_pair-85

value: pair 85


title: whole-blood_1_pair-8

value: Case (1)


title: whole-blood_1_pair-83

value: pair 83

value: Quit more than 2 months ago


title: whole-blood_1_pair-85


title: whole-blood_0_pair-83

value: Never


title: whole-blood_0_pair-81

value: pair 81


title: whole-blood_0_pair-78

value: pair 78


title: whole-blood_1_pair-76

value: pair 76

value: Female


title: whole-blood_1_pair-81


title: whole-blood_0_pair-74

value: pair 74


title: whole-blood_1_pair-77

value: pair 77


title: whole-blood_0_pair-75

value: pair 75


title: whole-blood_1_pair-73

value: pair 73