title: P270 pheochromocytoma

description: sample: P270


title: P263 pheochromocytoma

status: Public on Feb 14 2010

type: RNA

city: San Antonio

first: Patricia

middle: L.

last: Dahia

state: TX

address: 7703 Floyd Curl Dr MC7880

department: Medicine/Cel&Struct Biology

country: USA

institute: UTHSCSA

description: sample: P263

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0 and dChip.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: flash-frozen tumor specimen

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Trizol as described in Monti S et al. Blood. 2005 Mar 1;105(5):1851-61.

tag: tumor type

value: pheochromocytoma

tag: genetic class

value: SPOR

tag: tumor location

value: adrenal


title: P262 pheochromocytoma

description: sample: P262

value: unknown


title: P260 pheochromocytoma

description: sample: P260


title: Adipose tissue 181 SFA Final

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 181

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Twenty moderately overweight subjects, both males and females aged between 45-60 years, participated in this study. All subjects gave written informed consent to participate in the study and the study protocol was approved by the Medical Ethical Committee of Wageningen University, the Netherlands.

extract_protocol: Adipose tissue was rinsed with ice-cold phosphate-buffered saline to remove blood and immediately frozen in liquid nitrogen. Total RNA was isolated from adipose tissue using Trizol reagent (Invitrogen, Breda, NL) and purified using the Qiagen RNeasy Micro kit (Qiagen, Venlo, NL). RNA  integrity was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, NL).

treatment_protocol: Subjects consumed a diet containing high SFA or high MUFA for 8 weeks. Subcutaneous adipose tissue samples were obtained by needle biopsy from the periumbilical area under local anesthesia both before and after the diet intervention, before and after the intervention.

tag: individual

tag: tissue

value: Adipose

tag: gender

value: Male

tag: age

value: between 40-65 yrs


title: P236 pheochromocytoma

description: sample: P236


title: P266 pheochromocytoma

description: sample: P266


title: Adipose tissue 122 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 122

value: Female


title: Adipose tissue 179 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 179


title: Adipose tissue 169 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 169


title: Adipose tissue 170 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 170


title: Adipose tissue 103 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 103


title: Adipose tissue 114 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 114


title: Adipose tissue 119 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 119


title: Adipose tissue 113 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 113


title: Adipose tissue 101 MUFA Baseline

source_name: Subcutaneous adipose tissue, monounsaturated fatty acid rich diet, baseline, individual 101


title: P230 pheochromocytoma

description: sample: P230


title: Adipose tissue 181 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 181


title: Sorted Lgr5 high vs. low cells colour switch 1

status: Public on Feb 01 2010

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal, background information, and default 2 channel normalization were performed using Feature Extraction (V.9.5.3, Agilent Technologies).

organism: Mus musculus

source_name: sorted pyloric stomach cells expressing Lgr5 at a high level

label_protocol: 150 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

extract_protocol: RNA was isolated using Trizol (Invitrogen)

treatment_protocol: For the pyloric stem cell signature we used cells from Lgr5-EGFP-ires-CreERT2 knock-in mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhigh) and the other expressing GFP at low levels (GFPlow).

tag: mouse model

value: Lgr5-EGFP-ires-CreERT2 knock-in mice

value: pyloric stomach

source_name: sorted pyloric stomach cells expressing Lgr5 at a low level


title: Adipose tissue 185 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 185


title: Adipose tissue 179 SFA Baseline

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, baseline, individual 179


title: Adipose tissue 185 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 185


title: P246 pheochromocytoma

description: sample: P246

source_name: flash-frozen tumor specimen


title: Sorted Lgr5 high vs. low cells colour switch 2


title: Total blood mRNA profile from 14 pooled individuals (7 males + 7 females) after EPO treatment

status: Public on Jan 01 2010

type: SAGE

anchor: NlaIII

city: Montpellier

first: David

last: Piquemal

address: 1682, rue de la Valsière

country: France

institute: ACOBIOM

description:
The SAGE librairies were constructed by pooling blood samples from 14 athletes (7 males, 7 females) 1 week after injection with darbepoetin alpha (Amgen Europe B.V., Holland, 0.72 ± 0.01 g/kg injections per week, 4 weeks).
unpurified blood cells from 7 males + 7 females, pooled after RNA extraction

data_processing: Skuld-Tech (Montpellier, France) platform.

molecule: polyA RNA

source_name: total blood - after EPO treatment

extract_protocol: TRIzol

treatment_protocol: no

tag: tissue = unpurified blood cells


title: Sample M548

status: Public on Jan 28 2010

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Affymetrix standard hybridization protocol.

scan_protocol: Affymetrix standard scan protocol.

label_protocol: Affymetrix standard label protocol.

growth_protocol: NIDDK/NIH core lab growth protocol.

extract_protocol: TRIzol reagent.

treatment_protocol: None.

tag: strain

value: C57BL6  X 129sv mixed

value: liver

tag: genotype

value: WT


title: Adipose tissue 129 SFA Final

source_name: Subcutaneous adipose tissue, saturated fatty acid rich diet, after 8 wks intervention, individual 129


title: guthrie blood_G51

status: Public on Dec 12 2009

type: genomic

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

description:
DNA (bisulfite modified).
G51_guthrie blood

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93. Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers.

scan_protocol: Arrays were imaged using a BeadArray Reader scanner (Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93).

data_processing: Illumina BeadStudio Methylation software (version 3.2.0) was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: (β) = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.

molecule: genomic DNA

source_name: guthrie blood

label_protocol: DNA was sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA).

value: guthrie blood

tag: pathogenicity

value: normal

value: male


title: guthrie blood_G9

description:
DNA (bisulfite modified).
G9_guthrie blood


title: guthrie blood_G6

description:
DNA (bisulfite modified).
G6_guthrie blood


title: guthrie blood_G7

description:
DNA (bisulfite modified).
G7_guthrie blood

value: female


title: Sample M539

value: sphingosine-1-phosphate (S1P) lyase knock-out


title: Sample M537


title: Sample M559


title: P233 pheochromocytoma

description: sample: P233

value: pheochromocytoma

value: VHL


title: Sample M558


title: Sample M535


title: guthrie blood_G5

description:
DNA (bisulfite modified).
G5_guthrie blood


title: guthrie blood_G48

description:
DNA (bisulfite modified).
G48_guthrie blood


title: guthrie blood_G49

description:
DNA (bisulfite modified).
G49_guthrie blood


title: guthrie blood_G46

description:
DNA (bisulfite modified).
G46_guthrie blood


title: guthrie blood_G47

description:
DNA (bisulfite modified).
G47_guthrie blood


title: guthrie blood_G8

description:
DNA (bisulfite modified).
G8_guthrie blood


title: guthrie blood_G50

description:
DNA (bisulfite modified).
G50_guthrie blood


title: guthrie blood_G42

description:
DNA (bisulfite modified).
G42_guthrie blood


title: guthrie blood_G43

description:
DNA (bisulfite modified).
G43_guthrie blood


title: guthrie blood_G41

description:
DNA (bisulfite modified).
G41_guthrie blood


title: guthrie blood_G44

description:
DNA (bisulfite modified).
G44_guthrie blood


title: guthrie blood_G39

description:
DNA (bisulfite modified).
G39_guthrie blood


title: guthrie blood_G4

description:
DNA (bisulfite modified).
G4_guthrie blood


title: guthrie blood_G37

description:
DNA (bisulfite modified).
G37_guthrie blood


title: guthrie blood_G45

description:
DNA (bisulfite modified).
G45_guthrie blood


title: guthrie blood_G36

description:
DNA (bisulfite modified).
G36_guthrie blood


title: guthrie blood_G34

description:
DNA (bisulfite modified).
G34_guthrie blood


title: guthrie blood_G35

description:
DNA (bisulfite modified).
G35_guthrie blood


title: guthrie blood_G33

description:
DNA (bisulfite modified).
G33_guthrie blood


title: guthrie blood_G30

description:
DNA (bisulfite modified).
G30_guthrie blood


title: guthrie blood_G26

description:
DNA (bisulfite modified).
G26_guthrie blood


title: guthrie blood_G31

description:
DNA (bisulfite modified).
G31_guthrie blood


title: guthrie blood_G32

description:
DNA (bisulfite modified).
G32_guthrie blood


title: guthrie blood_G27

description:
DNA (bisulfite modified).
G27_guthrie blood


title: guthrie blood_G28

description:
DNA (bisulfite modified).
G28_guthrie blood


title: guthrie blood_G23

description:
DNA (bisulfite modified).
G23_guthrie blood


title: guthrie blood_G25

description:
DNA (bisulfite modified).
G25_guthrie blood


title: guthrie blood_G24

description:
DNA (bisulfite modified).
G24_guthrie blood


title: guthrie blood_G29

description:
DNA (bisulfite modified).
G29_guthrie blood


title: guthrie blood_G40

description:
DNA (bisulfite modified).
G40_guthrie blood


title: guthrie blood_G3

description:
DNA (bisulfite modified).
G3_guthrie blood


title: guthrie blood_G21

description:
DNA (bisulfite modified).
G21_guthrie blood


title: guthrie blood_G22

description:
DNA (bisulfite modified).
G22_guthrie blood


title: guthrie blood_G20

description:
DNA (bisulfite modified).
G20_guthrie blood


title: guthrie blood_G17

description:
DNA (bisulfite modified).
G17_guthrie blood


title: guthrie blood_G19

description:
DNA (bisulfite modified).
G19_guthrie blood


title: guthrie blood_G16

description:
DNA (bisulfite modified).
G16_guthrie blood


title: guthrie blood_G15

description:
DNA (bisulfite modified).
G15_guthrie blood


title: guthrie blood_G14

description:
DNA (bisulfite modified).
G14_guthrie blood


title: guthrie blood_G11

description:
DNA (bisulfite modified).
G11_guthrie blood


title: guthrie blood_G10

description:
DNA (bisulfite modified).
G10_guthrie blood


title: guthrie blood_G12

description:
DNA (bisulfite modified).
G12_guthrie blood


title: guthrie blood_G13

description:
DNA (bisulfite modified).
G13_guthrie blood


title: guthrie blood_G2

description:
DNA (bisulfite modified).
G2_guthrie blood


title: brain_autopsy2

description:
DNA (bisulfite modified).
autopsy2_brain

source_name: brain

value: brain


title: guthrie blood_G1

description:
DNA (bisulfite modified).
G1_guthrie blood


title: guthrie blood_G18

description:
DNA (bisulfite modified).
G18_guthrie blood


title: brain_autopsy1

description:
DNA (bisulfite modified).
autopsy1_brain


title: brain_9A17

description:
DNA (bisulfite modified).
9A17_brain


title: brain_84A28

description:
DNA (bisulfite modified).
84A28_brain


title: brain_85A37

description:
DNA (bisulfite modified).
85A37_brain


title: brain_99A30

description:
DNA (bisulfite modified).
99A30_brain


title: brain_79A23

description:
DNA (bisulfite modified).
79A23_brain


title: brain_73A30

description:
DNA (bisulfite modified).
73A30_brain


title: head and neck_59240L

description:
DNA (bisulfite modified).
59240L_Head and Neck

source_name: head and neck

value: head and neck


title: head and neck_59375U

description:
DNA (bisulfite modified).
59375U_Head and Neck


title: head and neck_59167U

description:
DNA (bisulfite modified).
59167U_Head and Neck


title: head and neck_59303U

description:
DNA (bisulfite modified).
59303U_Head and Neck


title: head and neck_59036T

description:
DNA (bisulfite modified).
59036T_Head and Neck


title: head and neck_58926U

description:
DNA (bisulfite modified).
58926U_Head and Neck


title: head and neck_59167L

description:
DNA (bisulfite modified).
59167L_Head and Neck


title: head and neck_59167T

description:
DNA (bisulfite modified).
59167T_Head and Neck


title: head and neck_58926T

description:
DNA (bisulfite modified).
58926T_Head and Neck


title: brain_36A30

description:
DNA (bisulfite modified).
36A30_brain


title: head and neck_58926L

description:
DNA (bisulfite modified).
58926L_Head and Neck


title: brain_28A24

description:
DNA (bisulfite modified).
28A24_brain


title: brain_45A5

description:
DNA (bisulfite modified).
45A5_brain


title: placenta_ JP 7

description:
DNA (bisulfite modified).
JP 7_Placenta

source_name: placenta

value: placenta


title: head and neck_58862L

description:
DNA (bisulfite modified).
58862L_Head and Neck


title: placenta_ JP 31

description:
DNA (bisulfite modified).
JP 31_Placenta


title: placenta_ JP 32

description:
DNA (bisulfite modified).
JP 32_Placenta


title: placenta_ AL 89

description:
DNA (bisulfite modified).
AL 89_Placenta


title: placenta_ JP 18

description:
DNA (bisulfite modified).
JP 18_Placenta


title: placenta_ JP 20

description:
DNA (bisulfite modified).
JP 20_Placenta


title: placenta_ AL 99

description:
DNA (bisulfite modified).
AL 99_Placenta


title: placenta_ JP 15

description:
DNA (bisulfite modified).
JP 15_Placenta


title: placenta_ AL 69

description:
DNA (bisulfite modified).
AL 69_Placenta


title: placenta_ AL 86

description:
DNA (bisulfite modified).
AL 86_Placenta


title: placenta_ AL 59

description:
DNA (bisulfite modified).
AL 59_Placenta


title: pleura_69442

description:
DNA (bisulfite modified).
69442_pleura

source_name: pleura

value: pleura


title: pleura_66433

description:
DNA (bisulfite modified).
66433_pleura


title: placenta_ JP 26

description:
DNA (bisulfite modified).
JP 26_Placenta


title: placenta_ AL 43

description:
DNA (bisulfite modified).
AL 43_Placenta


title: placenta_ AL 22

description:
DNA (bisulfite modified).
AL 22_Placenta


title: placenta_ AL 2

description:
DNA (bisulfite modified).
AL 2_Placenta


title: placenta_ AL 47

description:
DNA (bisulfite modified).
AL 47_Placenta


title: placenta_ AL 82

description:
DNA (bisulfite modified).
AL 82_Placenta


title: pleura_61460

description:
DNA (bisulfite modified).
61460_pleura


title: pleura_51934

description:
DNA (bisulfite modified).
51934_pleura


title: pleura_78467

description:
DNA (bisulfite modified).
78467_pleura


title: pleura_72650

description:
DNA (bisulfite modified).
72650_pleura


title: placenta_ AL 140

description:
DNA (bisulfite modified).
AL 140_Placenta


title: pleura_65555

description:
DNA (bisulfite modified).
65555_pleura


title: pleura_93972

description:
DNA (bisulfite modified).
93972_pleura


title: pleura_64658

description:
DNA (bisulfite modified).
64658_pleura


title: pleura_51072

description:
DNA (bisulfite modified).
51072_pleura


title: placenta_ AL 45

description:
DNA (bisulfite modified).
AL 45_Placenta


title: pleura_46239

description:
DNA (bisulfite modified).
46239_pleura


title: kidney_10018

description:
DNA (bisulfite modified).
10018_kidney

source_name: kidney

value: kidney


title: pleura_58902

description:
DNA (bisulfite modified).
58902_pleura


title: kidney_10019

description:
DNA (bisulfite modified).
10019_kidney


title: kidney_10020

description:
DNA (bisulfite modified).
10020_kidney


title: pleura_20089

description:
DNA (bisulfite modified).
20089_pleura


title: pleura_15221

description:
DNA (bisulfite modified).
15221_pleura


title: pleura_25287

description:
DNA (bisulfite modified).
25287_pleura


title: bladder_10016

description:
DNA (bisulfite modified).
10016_Bladder

source_name: bladder

value: bladder


title: kidney_10017

description:
DNA (bisulfite modified).
10017_kidney


title: pleura_14074

description:
DNA (bisulfite modified).
14074_pleura


title: bladder_10014

description:
DNA (bisulfite modified).
10014_Bladder


title: kidney_10015

description:
DNA (bisulfite modified).
10015_kidney


title: pleura_48620

description:
DNA (bisulfite modified).
48620_pleura


title: small intestine_10012

description:
DNA (bisulfite modified).
10012_Small Intestine

source_name: small Intestine

value: small Intestine


title: bladder_10006

description:
DNA (bisulfite modified).
10006_Bladder


title: lung_10013

description:
DNA (bisulfite modified).
10013_lung

source_name: lung

value: lung


title: small intestine_10011

description:
DNA (bisulfite modified).
10011_Small Intestine


title: bladder_10009

description:
DNA (bisulfite modified).
10009_Bladder


title: kidney_10007

description:
DNA (bisulfite modified).
10007_kidney


title: lung_10008

description:
DNA (bisulfite modified).
10008_lung


title: small intestine_10010

description:
DNA (bisulfite modified).
10010_Small Intestine


title: small intestine_10005

description:
DNA (bisulfite modified).
10005_Small Intestine


title: bladder_10002

description:
DNA (bisulfite modified).
10002_Bladder


title: blood_4708

description:
DNA (bisulfite modified).
4708_blood

source_name: blood

value: blood


title: pleura_6012

description:
DNA (bisulfite modified).
6012_pleura


title: lung_10001

description:
DNA (bisulfite modified).
10001_lung


title: small intestine_10003

description:
DNA (bisulfite modified).
10003_Small Intestine


title: blood_3757

description:
DNA (bisulfite modified).
3757_blood


title: blood_3692

description:
DNA (bisulfite modified).
3692_blood


title: lung_10004

description:
DNA (bisulfite modified).
10004_lung


title: blood_3676

description:
DNA (bisulfite modified).
3676_blood


title: blood_3620

description:
DNA (bisulfite modified).
3620_blood


title: blood_3612

description:
DNA (bisulfite modified).
3612_blood


title: blood_3385

description:
DNA (bisulfite modified).
3385_blood


title: blood_3572

description:
DNA (bisulfite modified).
3572_blood


title: blood_3503

description:
DNA (bisulfite modified).
3503_blood


title: Brain_3518

description:
DNA (bisulfite modified).
3518_Brain


title: blood_3338

description:
DNA (bisulfite modified).
3338_blood


title: blood_3036

description:
DNA (bisulfite modified).
3036_blood


title: blood_2982

description:
DNA (bisulfite modified).
2982_blood


title: blood_3146

description:
DNA (bisulfite modified).
3146_blood


title: blood_3155

description:
DNA (bisulfite modified).
3155_blood


title: blood_3336

description:
DNA (bisulfite modified).
3336_blood


title: blood_2980

description:
DNA (bisulfite modified).
2980_blood


title: blood_2567

description:
DNA (bisulfite modified).
2567_blood


title: blood_2509

description:
DNA (bisulfite modified).
2509_blood


title: blood_3374

description:
DNA (bisulfite modified).
3374_blood


title: blood_2824

description:
DNA (bisulfite modified).
2824_blood


title: blood_3389

description:
DNA (bisulfite modified).
3389_blood


title: blood_2292

description:
DNA (bisulfite modified).
2292_blood


title: blood_2391

description:
DNA (bisulfite modified).
2391_blood


title: blood_1610

description:
DNA (bisulfite modified).
1610_blood


title: blood_2922

description:
DNA (bisulfite modified).
2922_blood


title: blood_1269

description:
DNA (bisulfite modified).
1269_blood


title: lung_986

description:
DNA (bisulfite modified).
986_lung


title: lung_924

description:
DNA (bisulfite modified).
924_lung


title: lung_901

description:
DNA (bisulfite modified).
901_lung


title: lung_900

description:
DNA (bisulfite modified).
900_lung


title: blood_3132

description:
DNA (bisulfite modified).
3132_blood


title: lung_889

description:
DNA (bisulfite modified).
889_lung


title: lung_778

description:
DNA (bisulfite modified).
778_lung


title: blood_1200

description:
DNA (bisulfite modified).
1200_blood


title: blood_2404

description:
DNA (bisulfite modified).
2404_blood


title: lung_759

description:
DNA (bisulfite modified).
759_lung


title: lung_723

description:
DNA (bisulfite modified).
723_lung


title: blood_714

description:
DNA (bisulfite modified).
714_blood


title: lung_307

description:
DNA (bisulfite modified).
307_lung


title: lung_621

description:
DNA (bisulfite modified).
621_lung


title: lung_554

description:
DNA (bisulfite modified).
554_lung


title: lung_587

description:
DNA (bisulfite modified).
587_lung


title: lung_528

description:
DNA (bisulfite modified).
528_lung


title: lung_286

description:
DNA (bisulfite modified).
286_lung


title: lung_244

description:
DNA (bisulfite modified).
244_lung


title: lung_245

description:
DNA (bisulfite modified).
245_lung


title: lung_268

description:
DNA (bisulfite modified).
268_lung


title: lung_234

description:
DNA (bisulfite modified).
234_lung


title: lung_224

description:
DNA (bisulfite modified).
224_lung


title: lung_226

description:
DNA (bisulfite modified).
226_lung


title: lung_205

description:
DNA (bisulfite modified).
205_lung


title: lung_130

description:
DNA (bisulfite modified).
130_lung


title: lung_202

description:
DNA (bisulfite modified).
202_lung


title: lung_146

description:
DNA (bisulfite modified).
146_lung


title: lung_140

description:
DNA (bisulfite modified).
140_lung


title: lung_127

description:
DNA (bisulfite modified).
127_lung


title: lung_145

description:
DNA (bisulfite modified).
145_lung


title: lung_233

description:
DNA (bisulfite modified).
233_lung


title: lung_204

description:
DNA (bisulfite modified).
204_lung


title: lung_119

description:
DNA (bisulfite modified).
119_lung


title: lung_116

description:
DNA (bisulfite modified).
116_lung


title: lung_115

description:
DNA (bisulfite modified).
115_lung


title: lung_141

description:
DNA (bisulfite modified).
141_lung


title: lung_615

description:
DNA (bisulfite modified).
615_lung


title: lung_113

description:
DNA (bisulfite modified).
113_lung


title: lung_71

description:
DNA (bisulfite modified).
71_lung


title: lung_100

description:
DNA (bisulfite modified).
100_lung


title: lung_77

description:
DNA (bisulfite modified).
77_lung


title: lung_211

description:
DNA (bisulfite modified).
211_lung


title: lung_68

description:
DNA (bisulfite modified).
68_lung


title: lung_46

description:
DNA (bisulfite modified).
46_lung


title: guthrie blood_36

description:
DNA (bisulfite modified).
36_guthrie blood


title: guthrie blood_35

description:
DNA (bisulfite modified).
35_guthrie blood


title: guthrie blood_34

description:
DNA (bisulfite modified).
34_guthrie blood


title: lung_56

description:
DNA (bisulfite modified).
56_lung


title: lung_44

description:
DNA (bisulfite modified).
44_lung


title: lung_24

description:
DNA (bisulfite modified).
24_lung


title: guthrie blood_31

description:
DNA (bisulfite modified).
31_guthrie blood


title: lung_23

description:
DNA (bisulfite modified).
23_lung


title: lung_21

description:
DNA (bisulfite modified).
21_lung


title: lung_15

description:
DNA (bisulfite modified).
15_lung


title: cervical_8

description:
DNA (bisulfite modified).
8_cervical

source_name: cervix

value: cervix


title: cervical_14

description:
DNA (bisulfite modified).
14_cervical


title: lung_13

description:
DNA (bisulfite modified).
13_lung


title: cervical_13

description:
DNA (bisulfite modified).
13_cervical


title: guthrie blood_32

description:
DNA (bisulfite modified).
32_guthrie blood

value: guthrie blood


title: non-tumor pleura_93972

status: Public on Jul 28 2009

description: no additional information

scan_protocol: Arrays were imaged using a BeadArray Reader scanner (Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.)

data_processing: Illumina BeadStudio Methylation software (version 3.2.0) was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level (β) = (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. The β-value provides a continuous measure of levels of DNA methylation in samples, ranging from 0 in the case of completely unmethylated sites to 1 in completely methylated sites. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.

source_name: non-malignant pulmonary tissue

extract_protocol: DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)

tag: disease state

value: control


title: non-tumor pleura_72650

description: no additional information

value: male


title: non-tumor pleura_14074

description: no additional information

value: female


title: non-tumor pleura_20089

description: no additional information


title: pleural mesothelioma_9438

description: no additional information

source_name: pleural mesothelioma

value: pleural mesothelioma


title: non-tumor pleura_78467

description: no additional information


title: non-tumor pleura_46239

description: no additional information


title: non-tumor pleura_25287

description: no additional information


title: non-tumor pleura_58902

description: no additional information


title: non-tumor pleura_61460

description: no additional information


title: non-tumor pleura_51934

description: no additional information


title: non-tumor pleura_66433

description: no additional information


title: non-tumor pleura_48620

description: no additional information


title: non-tumor pleura_51072

description: no additional information


title: non-tumor pleura_64658

description: no additional information


title: non-tumor pleura_69442

description: no additional information


title: pleural mesothelioma_9426

description: no additional information


title: non-tumor pleura_65555

description: no additional information


title: pleural mesothelioma_9403

description: no additional information


title: pleural mesothelioma_9407

description: no additional information


title: pleural mesothelioma_9412

description: no additional information


title: pleural mesothelioma_9406

description: no additional information


title: pleural mesothelioma_9431

description: no additional information


title: pleural mesothelioma_9389

description: no additional information


title: non-tumor pleura_15221

description: no additional information


title: pleural mesothelioma_9384

description: no additional information


title: pleural mesothelioma_9382

description: no additional information


title: pleural mesothelioma_9386

description: no additional information


title: pleural mesothelioma_9388

description: no additional information


title: pleural mesothelioma_9370

description: no additional information


title: pleural mesothelioma_9372

description: no additional information


title: pleural mesothelioma_9336

description: no additional information


title: pleural mesothelioma_9363

description: no additional information


title: pleural mesothelioma_9369

description: no additional information


title: pleural mesothelioma_9308

description: no additional information


title: pleural mesothelioma_9278

description: no additional information


title: pleural mesothelioma_9284

description: no additional information


title: pleural mesothelioma_9282

description: no additional information


title: pleural mesothelioma_9301

description: no additional information


title: pleural mesothelioma_9307

description: no additional information


title: pleural mesothelioma_9303

description: no additional information


title: pleural mesothelioma_9264

description: no additional information


title: pleural mesothelioma_9294

description: no additional information


title: pleural mesothelioma_9296

description: no additional information


title: pleural mesothelioma_9300

description: no additional information


title: pleural mesothelioma_9327

description: no additional information


title: pleural mesothelioma_9310

description: no additional information


title: pleural mesothelioma_9281

description: no additional information


title: pleural mesothelioma_9290

description: no additional information


title: pleural mesothelioma_9253

description: no additional information


title: pleural mesothelioma_9247

description: no additional information


title: pleural mesothelioma_9244

description: no additional information


title: pleural mesothelioma_9248

description: no additional information


title: pleural mesothelioma_9245

description: no additional information


title: pleural mesothelioma_9224

description: no additional information


title: pleural mesothelioma_9225

description: no additional information


title: pleural mesothelioma_9223

description: no additional information


title: pleural mesothelioma_9215

description: no additional information


title: pleural mesothelioma_9206

description: no additional information


title: pleural mesothelioma_9198

description: no additional information


title: pleural mesothelioma_9197

description: no additional information


title: pleural mesothelioma_9236

description: no additional information


title: pleural mesothelioma_9189

description: no additional information


title: pleural mesothelioma_9181

description: no additional information


title: pleural mesothelioma_9184

description: no additional information


title: pleural mesothelioma_9174

description: no additional information


title: pleural mesothelioma_9062

description: no additional information


title: pleural mesothelioma_9134

description: no additional information


title: pleural mesothelioma_9114

description: no additional information


title: pleural mesothelioma_9162

description: no additional information


title: pleural mesothelioma_9172

description: no additional information


title: pleural mesothelioma_9098

description: no additional information


title: pleural mesothelioma_9095

description: no additional information


title: pleural mesothelioma_9061

description: no additional information


title: pleural mesothelioma_9068

description: no additional information


title: pleural mesothelioma_9101

description: no additional information


title: pleural mesothelioma_9107

description: no additional information


title: pleural mesothelioma_9112

description: no additional information


title: pleural mesothelioma_9105

description: no additional information


title: pleural mesothelioma_9056

description: no additional information


title: lung_622

description:
DNA (bisulfite modified).
622_lung

value: normal


title: pleural mesothelioma_9054

description: no additional information


title: pleural mesothelioma_9188

description: no additional information


title: pleural mesothelioma_9177

description: no additional information


title: pleural mesothelioma_9159

description: no additional information


title: pleural mesothelioma_9139

description: no additional information


title: pleural mesothelioma_9044

description: no additional information


title: pleural mesothelioma_9100

description: no additional information


title: pleural mesothelioma_9042

description: no additional information


title: pleural mesothelioma_9041

description: no additional information


title: pleural mesothelioma_9026

description: no additional information


title: pleural mesothelioma_9033

description: no additional information


title: pleural mesothelioma_9039

description: no additional information


title: pleural mesothelioma_9037

description: no additional information


title: pleural mesothelioma_9027

description: no additional information


title: pleural mesothelioma_9014

description: no additional information


title: pleural mesothelioma_9024

description: no additional information


title: pleural mesothelioma_9004

description: no additional information


title: pleural mesothelioma_9011

description: no additional information


title: pleural mesothelioma_9008

description: no additional information


title: non-tumor pleura_6012

description: no additional information


title: pleural mesothelioma_73

description: no additional information


title: pleural mesothelioma_9023

description: no additional information


title: pleural mesothelioma_9005

description: no additional information


title: pleural mesothelioma_9013

description: no additional information


title: pleural mesothelioma_71

description: no additional information


title: pleural mesothelioma_72

description: no additional information


title: pleural mesothelioma_67

description: no additional information


title: pleural mesothelioma_9034

description: no additional information


title: pleural mesothelioma_66

description: no additional information


title: pleural mesothelioma_9017

description: no additional information


title: pleural mesothelioma_61

description: no additional information


title: pleural mesothelioma_62

description: no additional information


title: pleural mesothelioma_64

description: no additional information


title: pleural mesothelioma_9022

description: no additional information


title: pleural mesothelioma_9019

description: no additional information


title: pleural mesothelioma_63

description: no additional information


title: pleural mesothelioma_58

description: no additional information


title: pleural mesothelioma_57

description: no additional information


title: pleural mesothelioma_60

description: no additional information


title: pleural mesothelioma_69

description: no additional information


title: pleural mesothelioma_59

description: no additional information


title: pleural mesothelioma_55

description: no additional information


title: pleural mesothelioma_53

description: no additional information


title: pleural mesothelioma_52

description: no additional information


title: pleural mesothelioma_56

description: no additional information


title: pleural mesothelioma_54

description: no additional information


title: pleural mesothelioma_50

description: no additional information


title: pleural mesothelioma_51

description: no additional information


title: pleural mesothelioma_47

description: no additional information


title: pleural mesothelioma_46

description: no additional information


title: pleural mesothelioma_49

description: no additional information


title: pleural mesothelioma_44

description: no additional information


title: pleural mesothelioma_45

description: no additional information


title: pleural mesothelioma_48

description: no additional information


title: pleural mesothelioma_42

description: no additional information


title: pleural mesothelioma_43

description: no additional information


title: pleural mesothelioma_40

description: no additional information


title: pleural mesothelioma_41

description: no additional information


title: pleural mesothelioma_38

description: no additional information


title: pleural mesothelioma_37

description: no additional information


title: pleural mesothelioma_39

description: no additional information


title: pleural mesothelioma_36

description: no additional information


title: pleural mesothelioma_35

description: no additional information


title: pleural mesothelioma_34

description: no additional information


title: pleural mesothelioma_32

description: no additional information


title: pleural mesothelioma_33

description: no additional information


title: pleural mesothelioma_29

description: no additional information


title: pleural mesothelioma_27

description: no additional information


title: pleural mesothelioma_24

description: no additional information


title: pleural mesothelioma_25

description: no additional information


title: pleural mesothelioma_30

description: no additional information


title: pleural mesothelioma_23

description: no additional information


title: pleural mesothelioma_22

description: no additional information


title: pleural mesothelioma_19

description: no additional information


title: pleural mesothelioma_21

description: no additional information


title: pleural mesothelioma_20

description: no additional information


title: pleural mesothelioma_16

description: no additional information


title: pleural mesothelioma_14

description: no additional information


title: pleural mesothelioma_12

description: no additional information


title: pleural mesothelioma_17

description: no additional information


title: pleural mesothelioma_18

description: no additional information


title: pleural mesothelioma_15

description: no additional information


title: pleural mesothelioma_13

description: no additional information


title: pleural mesothelioma_10

description: no additional information


title: pleural mesothelioma_7

description: no additional information


title: pleural mesothelioma_9

description: no additional information


title: pleural mesothelioma_31

description: no additional information


title: pleural mesothelioma_8

description: no additional information


title: pleural mesothelioma_5

description: no additional information


title: pleural mesothelioma_4

description: no additional information


title: pleural mesothelioma_11

description: no additional information


title: pleural mesothelioma_6

description: no additional information


title: lung adenocarcinoma_1022

description: no additional information

source_name: lung adenocarcinoma

value: lung adenocarcinoma


title: lung adenocarcinoma_1064

description: no additional information


title: pleural mesothelioma_1

description: no additional information


title: lung adenocarcinoma_1030

description: no additional information


title: pleural mesothelioma_3

description: no additional information


title: pleural mesothelioma_2

description: no additional information


title: lung adenocarcinoma_1039

description: no additional information


title: lung adenocarcinoma_994

description: no additional information


title: lung adenocarcinoma_1019

description: no additional information


title: lung adenocarcinoma_889

description: no additional information


title: lung adenocarcinoma_986

description: no additional information


title: lung adenocarcinoma_981

description: no additional information


title: lung adenocarcinoma_642

description: no additional information


title: lung adenocarcinoma_670

description: no additional information


title: lung adenocarcinoma_676

description: no additional information


title: lung adenocarcinoma_652

description: no additional information


title: lung adenocarcinoma_625

description: no additional information


title: lung adenocarcinoma_623

description: no additional information


title: lung adenocarcinoma_628

description: no additional information


title: lung adenocarcinoma_607

description: no additional information


title: lung adenocarcinoma_622

description: no additional information


title: lung adenocarcinoma_596

description: no additional information


title: lung adenocarcinoma_621

description: no additional information


title: lung adenocarcinoma_624

description: no additional information


title: pleural mesothelioma_26

description: no additional information


title: lung adenocarcinoma_490

description: no additional information


title: lung adenocarcinoma_615

description: no additional information


title: lung adenocarcinoma_636

description: no additional information


title: lung adenocarcinoma_957

description: no additional information


title: lung adenocarcinoma_287

description: no additional information


title: lung adenocarcinoma_268

description: no additional information


title: lung adenocarcinoma_374

description: no additional information


title: lung adenocarcinoma_319

description: no additional information


title: lung adenocarcinoma_412

description: no additional information


title: lung adenocarcinoma_778

description: no additional information


title: lung adenocarcinoma_299

description: no additional information


title: lung adenocarcinoma_316

description: no additional information


title: lung adenocarcinoma_217

description: no additional information


title: lung adenocarcinoma_211

description: no additional information


title: lung adenocarcinoma_204

description: no additional information


title: lung adenocarcinoma_145

description: no additional information


title: lung adenocarcinoma_202

description: no additional information


title: lung adenocarcinoma_146

description: no additional information


title: lung adenocarcinoma_245

description: no additional information


title: lung adenocarcinoma_127

description: no additional information


title: lung adenocarcinoma_142

description: no additional information


title: lung adenocarcinoma_128

description: no additional information


title: lung adenocarcinoma_100

description: no additional information


title: lung adenocarcinoma_122

description: no additional information


title: lung adenocarcinoma_141

description: no additional information


title: lung adenocarcinoma_46

description: no additional information


title: lung adenocarcinoma_119

description: no additional information


title: lung adenocarcinoma_58

description: no additional information


title: lung adenocarcinoma_45

description: no additional information


title: lung adenocarcinoma_226

description: no additional information


title: lung adenocarcinoma_135

description: no additional information


title: lung adenocarcinoma_205

description: no additional information


title: lung adenocarcinoma_30

description: no additional information


title: normal lung_10013

description: no additional information


title: lung adenocarcinoma_15

description: no additional information


title: normal lung_10004

description: no additional information


title: normal lung_10001

description: no additional information


title: normal lung_10008

description: no additional information


title: lung adenocarcinoma_12

description: no additional information


title: non-tumor lung_924

description: no additional information


title: non-tumor lung_986

description: no additional information


title: lung adenocarcinoma_68

description: no additional information


title: non-tumor lung_759

description: no additional information


title: non-tumor lung_889

description: no additional information


title: non-tumor lung_723

description: no additional information


title: non-tumor lung_778

description: no additional information


title: non-tumor lung_621

description: no additional information


title: non-tumor lung_622

description: no additional information


title: non-tumor lung_528

description: no additional information


title: non-tumor lung_615

description: no additional information


title: non-tumor lung_554

description: no additional information


title: non-tumor lung_244

description: no additional information


title: non-tumor lung_226

description: no additional information


title: non-tumor lung_307

description: no additional information


title: non-tumor lung_233

description: no additional information


title: non-tumor lung_245

description: no additional information


title: non-tumor lung_901

description: no additional information


title: non-tumor lung_234

description: no additional information


title: non-tumor lung_900

description: no additional information


title: non-tumor lung_587

description: no additional information


title: non-tumor lung_268

description: no additional information


title: non-tumor lung_224

description: no additional information


title: non-tumor lung_204

description: no additional information


title: non-tumor lung_202

description: no additional information


title: non-tumor lung_146

description: no additional information


title: non-tumor lung_141

description: no additional information


title: non-tumor lung_142

description: no additional information


title: non-tumor lung_205

description: no additional information


title: non-tumor lung_140

description: no additional information


title: non-tumor lung_286

description: no additional information


title: non-tumor lung_127

description: no additional information


title: non-tumor lung_119

description: no additional information


title: non-tumor lung_211

description: no additional information


title: non-tumor lung_100

description: no additional information


title: non-tumor lung_113

description: no additional information


title: non-tumor lung_116

description: no additional information


title: non-tumor lung_115

description: no additional information


title: non-tumor lung_46

description: no additional information


title: non-tumor lung_56

description: no additional information


title: non-tumor lung_77

description: no additional information


title: non-tumor lung_68

description: no additional information


title: non-tumor lung_24

description: no additional information


title: non-tumor lung_23

description: no additional information


title: non-tumor lung_44

description: no additional information


title: non-tumor lung_21

description: no additional information


title: non-tumor lung_15

description: no additional information

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93. Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers. ^SAMPLE = GSM415954 Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93. Bisulfite-converted DNAs are biotinylated and hybridized to query oligos, and washed. The hybridized oligos are then extended and ligated to create amplifiable templates with methylation-specific primers. The PCR that follows uses fluorescently labeled universal PCR primers.


title: non-tumor lung_71

description: no additional information


title: Patient 6 Subcutaneous Lean

status: Public on Apr 03 2009

city: Quebec

first: Katherine

last: Cianflone

state: Quebec

address: 2725 Ste Foy

country: Canada

institute: Laval University

description: 10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences). The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences). The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).

label: Biotin labelled cRNA

source_name: adipose tissue

label_protocol: cRNA was synthesized by in vitro transcription and hybridisation as previously described. Briefly, 10 ug of high quality total RNA was converted to cDNA and then to biotin-labelled cRNA (10 mM Biotin-11-UTP, Perkin-Elmer) by linear amplification (iExpress Assay reagent kit, GE Healthcare Bio-Sciences, Montreal, Quebec).

extract_protocol: Adipose tissue was collected at the beginning of the operation (within 30 minutes) into sterile 50 mL conical tubes and immediately flash- frozen in liquid nitrogen. Subcutaneous adipose tissue was collected from the subcutaneous abdominal wall and omental adipose tissue was collected from the greater omentum which is representative of intra-abdominal adipose depots drained by the portal vein. RNA was extracted from tissues using Qiagen spin columns (Qiagen, Mississauga, Canada) following manufacturer’s protocol for fatty tissue with the addition of two RNase free DNase treatments (Qiagen) between RW1 washes. RNA quality was assessed by spectrometry (260/280 ratio) with ratios of 1.9 – 2.0. As well, RNA quality was assessed by chromatography.

tag: patient

value: Subcutaneous adipose tissue

tag: surgery

value: Coronary artery bypass graft

value: 44 years

value: Male

tag: body mass index

tag: body size category

value: lean


title: Patient 23 Subcutaneous Obese

hyb_protocol: 10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences).

scan_protocol: The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences).

data_processing: The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).

value: Gastric bypass

value: 32 years

value: 58 BMI

value: obese


title: Patient 19 Subcutaneous Obese

value: 45 years

value: Female

value: 62 BMI


title: non-tumor lung_13

description: no additional information

hyb_protocol: Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.

value: control

value: male


title: Patient 21 Subcutaneous Obese

value: 52 years

value: 61 BMI


title: Patient 20 Subcutaneous Obese

value: 48 years

value: 43 BMI


title: Patient 6 Omental Lean

value: Omental adipose tissue

value: Coronary artery bypass graft


title: Patient 14 Subcutaneous Obese

value: Subcutaneous adipose tissue

value: 37 years

value: Male

value: 78 BMI


title: Patient 17 Subcutaneous Obese

value: Gastric bypass

value: 31 years

value: 45 BMI


title: Patient 15 Subcutaneous Obese

value: 54 years

value: Female

value: obese


title: Patient 22 Subcutaneous Obese

value: 29 years

value: 41 BMI


title: Patient 18 Subcutaneous Obese

value: 53 years

value: 40 BMI


title: Patient 10 Subcutaneous Obese

value: 46 years


title: Patient 22 Omental Obese

value: Omental adipose tissue


title: Patient 19 Omental Obese

value: 45 years

value: 62 BMI


title: Patient 5 Subcutaneous Lean

value: Subcutaneous adipose tissue

value: Hernia surgery

value: 64 years

value: lean


title: Patient 24 Omental Obese

value: Gastric bypass

value: 40 years

value: 63 BMI


title: Patient 17 Omental Obese

value: 31 years

value: Female

value: 45 BMI


title: Patient 14 Omental Obese

value: 37 years

value: Male

value: 78 BMI

value: obese


title: Patient 18 Omental Obese

value: Omental adipose tissue

value: 53 years

value: 40 BMI


title: Patient 20 Omental Obese

value: 48 years

value: 43 BMI


title: Patient 15 Omental Obese

value: 54 years


title: Patient 3 Subcutaneous Lean

value: Subcutaneous adipose tissue

value: Hysterectomy

value: 34 years

value: lean


title: Patient 5 Omental Lean

value: Hernia surgery

value: 64 years


title: Patient 10 Omental Obese

value: Gastric bypass

value: 46 years

value: Female


title: Patient 4 Subcutaneous Lean


title: Patient 1 Omental Lean

value: Valve surgery

value: 68 years

value: Male


title: Patient 21 Omental Obese

value: Omental adipose tissue

value: 52 years

value: 61 BMI

value: obese


title: Patient 23 Omental Obese

value: 32 years

value: 58 BMI


title: Sugarcane-LL_Brix_I9xI1-11m_R

status: Public on Feb 12 2009

city: São Paulo

first: Milton

middle: Yutaka

last: Nishiyama Jr

state: São Paulo

address: Av. Professor Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Universidade de São Paulo - USP

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: low brix internodes 1 (commercial varieties - Progeny 2) (R)
Pool of low brix internodes 9 vs pool of low brix internodes 1 (commercial varieties - Progeny 2)

hyb_protocol: micro_Manual Hyb; Manual Hybridization of microarrays

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Generation III Scanner and image intensity data were extracted with ArrayVision software.

data_processing: Default lowess normalization

organism: Saccharum hybrid cultivar (mixed)

source_name: low brix internodes 9 (In9-LB)

label_protocol: Micro_First Strand_dT. Cyscribe First strand cDNA labeling kit, Amersham Biosciences. Using OLIGO-dT primers only.

extract_protocol: Trizol

value: internode 9 pool from seven progeny 2 (F1) plants with eleven months old and low brix content

source_name: low brix internodes 1 (In1-LB)

value: internode 1 pool from seven progeny 2 (F1) plants with eleven months old and low brix content


title: Sugarcane-LL_Brix_I9xI1-11m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: low brix internodes 1 (commercial varieties - Progeny 2) (L)
Pool of low brix internodes 9 vs pool of low brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-LL_Brix_I1xI9-11m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: low brix internodes 9 (commercial varieties - Progeny 2) (L)
Pool of low brix internodes 1 vs pool of low brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-LL_Brix_I9xI1-7m_R

value: internode 9 pool from seven progeny 2 (F1) plants with seven months old and low brix content

value: internode 1 pool from seven progeny 2 (F1) plants with seven months old and low brix content


title: Sugarcane-LL_Brix_I1xI9-11m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: low brix internodes 9 (commercial varieties - Progeny 2) (R)
Pool of low brix internodes 1 vs pool of low brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-HH_Brix_I9xI1-11m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: high brix internodes 1 (commercial varieties - Progeny 2) (R)
Pool of high brix internodes 9 vs pool of high brix internodes 1 (commercial varieties - Progeny 2)

source_name: high brix internodes 9 (In9-HB)

value: internode 9 pool from seven progeny 2 (F1) plants with eleven months old and high brix content

source_name: high brix internodes 1 (In1-HB)

value: internode 1 pool from seven progeny 2 (F1) plants with eleven months old and high brix content


title: Sugarcane-LL_Brix_I9xI1-7m_L


title: Sugarcane-LL_Brix_I1xI9-7m_L


title: Sugarcane-HH_Brix_I1xI9-11m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: high brix internodes 9 (commercial varieties - Progeny 2) (R)
Pool of high brix internodes 1 vs pool of high brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-LL_Brix_I1xI9-7m_R


title: Sugarcane-HH_Brix_I9xI1-11m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: high brix internodes 1 (commercial varieties - Progeny 2) (L)
Pool of high brix internodes 9 vs pool of high brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-HH_Brix_I1xI9-11m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: high brix internodes 9 (commercial varieties - Progeny 2) (L)
Pool of high brix internodes 1 vs pool of high brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-HH_Brix_I9xI1-7m_L

value: internode 9 pool from seven progeny 2 (F1) plants with seven months old and high brix content

value: internode 1 pool from seven progeny 2 (F1) plants with seven months old and high brix content


title: Sugarcane-HH_Brix_I1xI9-7m_L


title: Sugarcane-LH_Brix_I9-11m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: high brix internodes 9 (commercial varieties - Progeny 2) (L)
Pool of low brix internodes 9 vs pool of high brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-LH_Brix_I9-11m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: high brix internodes 9 (commercial varieties - Progeny 2) (R)
Pool of low brix internodes 9 vs pool of high brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I5-11m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 5; ch2: low brix internodes 5 (commercial varieties - Progeny 2) (L)
Pool of high brix internodes 5 vs pool of low brix internodes 5 (commercial varieties - Progeny 2)

source_name: high brix internodes 5 (In5-HB)

value: internode 5 pool from seven progeny 2 (F1) plants with eleven months old and high brix content

source_name: low brix internodes 5 (In5-LB)

value: internode 5 pool from seven progeny 2 (F1) plants with eleven months old and low brix content


title: Sugarcane-HH_Brix_I9xI1-7m_R


title: Sugarcane-HL_Brix_I9-7m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: low brix internodes 9 (commercial varieties - Progeny 2) (L)
Pool of high brix internodes 9 vs pool of low brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I9-7m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: low brix internodes 9 (commercial varieties - Progeny 2) (R)
Pool of high brix internodes 9 vs pool of low brix internodes 9 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I9-11m_R


title: Sugarcane-LH_Brix_I5-11m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 5; ch2: high brix internodes 5 (commercial varieties - Progeny 2) (L)
Pool of low brix internodes 5 vs pool of high brix internodes 5 (commercial varieties - Progeny 2)


title: Sugarcane-LH_Brix_I5-11m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 5; ch2: high brix internodes 5 (commercial varieties - Progeny 2) (R)
Pool of low brix internodes 5 vs pool of high brix internodes 5 (commercial varieties - Progeny 2)


title: Sugarcane-LH_Brix_I9-7m_R


title: Sugarcane-HL_Brix_I5-11m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 5; ch2: low brix internodes 5 (commercial varieties - Progeny 2) (R)
Pool of high brix internodes 5 vs pool of low brix internodes 5 (commercial varieties - Progeny 2)


title: Sugarcane-HH_Brix_I1xI9-7m_R


title: Sugarcane-LH_Brix_I5-7m_R

value: internode 5 pool from seven progeny 2 (F1) plants with seven months old and low brix content

value: internode 5 pool from seven progeny 2 (F1) plants with seven months old and high brix content


title: Sugarcane-LH_Brix_I5-7m_L


title: Sugarcane-HL_Brix_I5-7m_L


title: Sugarcane-HL_Brix_I9-11m_L


title: Sugarcane-LH_Brix_I1-11m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: high brix internodes 1 (commercial varieties - Progeny 2) (R)
Pool of low brix internodes 1 vs pool of high brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I5-7m_R


title: Sugarcane-LH_Brix_I1-11m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: high brix internodes 1 (commercial varieties - Progeny 2) (L)
Pool of low brix internodes 1 vs pool of high brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-LH_Brix_I9-7m_L


title: Sugarcane-HL_Brix_I1-7m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: low brix internodes 1 (commercial varieties - Progeny 2) (L)
Pool of high brix internodes 1 vs pool of low brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I1-11m_L


title: Sugarcane-LH_Brix_I9-10m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: high brix internodes 9 (Saccharum genotypes - Progeny 1) (R)
Pool of low brix internodes 9 vs pool of high brix internodes 9 (Saccharum genotypes Progeny 1)

value: internode 9 pool from eight progeny 1 (F3) plants with ten months old and low brix content

value: internode 9 pool from eight progeny 1 (F3) plants with ten months old and high brix content


title: Sugarcane-HL_Brix_I1-11m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: low brix internodes 1 (commercial varieties - Progeny 2) (R)
Pool of high brix internodes 1 vs pool of low brix internodes 1 (commercial varieties - Progeny 2)


title: Sugarcane-HL_Brix_I1-7m_R


title: Sugarcane-LH_Brix_I9-10m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 9; ch2: high brix internodes 9 (Saccharum genotypes - Progeny 1) (L)
Pool of low brix internodes 9 vs pool of high brix internodes 9 (Saccharum genotypes Progeny 1)


title: Sugarcane-HL_Brix_I9-10m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: low brix internodes 9 (Saccharum genotypes - Progeny 1) (R)
Pool of high brix internodes 9 vs pool of low brix internodes 9 (Saccharum genotypes -Progeny 1)


title: Sugarcane-LH_Brix_I1-7m_R


title: Sugarcane-LH_Brix_I1-7m_L


title: Sugarcane-HL_Brix_I9-10m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 9; ch2: low brix internodes 9 (Saccharum genotypes - Progeny 1) (L)
Pool of high brix internodes 9 vs pool of low brix internodes 9 (Saccharum genotypes -Progeny 1)


title: Sugarcane-LH_Brix_I5-10m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 5; ch2: high brix internodes 5 (Saccharum genotypes- Progeny 1) (R)
Pool of low brix internodes 5 vs pool of high brix internodes 5 (Saccharum genotypes -  Progeny 1)

value: internode 5 pool from eight progeny 1 (F3) plants with ten months old and low brix content

value: internode 5 pool from eight progeny 1 (F3) plants with ten months old and high brix content


title: Sugarcane-LH_Brix_I5-10m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 5; ch2: high brix internodes 5 (Saccharum genotypes- Progeny 1) (L)
Pool of low brix internodes 5 vs pool of high brix internodes 5 (Saccharum genotypes -  Progeny 1)


title: Sugarcane-HL_Brix_I5-10m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 5; ch2: low brix internodes 5 (Saccharum genotypes - Progeny 1) (R)
Pool of high brix internodes 5 vs pool of low brix internodes 5 (Saccharum genotypes -  Progeny 1)


title: Sugarcane-LH_Brix_I1-10m_L

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: high brix internodes 1 (Saccharum genotypes - Progeny 1) (L)
Pool of low brix internodes 1 vs pool of high brix internodes 1 (Saccharum genotypes - Progeny 1)

value: internode 1 pool from eight progeny 1 (F3) plants with ten months old and low brix content

value: internode 1 pool from eight progeny 1 (F3) plants with ten months old and high brix content


title: Sugarcane-HL_Brix_I5-10m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 5; ch2: low brix internodes 5 (Saccharum genotypes - Progeny 1) (L)
Pool of high brix internodes 5 vs pool of low brix internodes 5 (Saccharum genotypes -  Progeny 1)


title: Sugarcane-HL_Brix_I1-10m_R

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: low brix internodes 1 (Saccharum genotypes - Progeny 1) (R)
Pool of high brix internodes 1 vs pool of low brix internodes 1 (Saccharum genotypes -  Progeny 1)


title: Sugarcane-LH_Brix_I1-10m_R

description:
Sugarcane transcriptome - ch1: low brix internodes 1; ch2: high brix internodes 1 (Saccharum genotypes - Progeny 1) (R)
Pool of low brix internodes 1 vs pool of high brix internodes 1 (Saccharum genotypes - Progeny 1)


title: Sugarcane-HL_Brix_I1-10m_L

description:
Sugarcane transcriptome - ch1: high brix internodes 1; ch2: low brix internodes 1 (Saccharum genotypes - Progeny 1) (L)
Pool of high brix internodes 1 vs pool of low brix internodes 1 (Saccharum genotypes -  Progeny 1)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 8 (Technical replicate B)

status: Public on Jan 16 2009

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been utilized in these experiments (see data processing).

hyb_protocol: Ranges along 350 and 300 pico-moles and 2.7 and 3.0 µg of aRNA labeled with Cy3 and Cy5 were co-precipitated with the ammonium acetate and ethanol. Pellet was resuspended in 110 µl with the hybridization solution composed by SSC 5X, SDS 0.1%, Formamide 25% and salmon sperm purified DNA 100 ng/µl and carried out in an automatic hybridization station (ArrayBooster, Advalytix) at 48° C for 30 hours in the competitive hybridization. Microarray slides, before hybridization, have been blocked with the pre-hybridization solution (SSC 5X, SDS 0.1%, salmon sperm purified DNA 100 ng/ul and Denhardt's solution 5X) for 8 hours at 48° C. After the hybridization slides were washed at room temperature with 1X SSC 0.2% SDS for 4 minutes one time; 0.1X SSC 0.2% SDS for 4 minutes one time; 0.2X SSC for 3 minutes two times each with new solution and 0.1X SSC for 3 minutes one time. Slides were dried centrifuging 1 minute at 800 X g at 20° C.

scan_protocol: After stringent washings, fluorescence left in the microarray slides were read with the ScanArray LITE confocal laser scanner (PerkinElmer) with 5 µm resolution. Each slide was subjected to three consecutive scans at low, medium and high settings of laser and photomultiplier. This protocol allows for a wide dynamic range of detection spectrum of fluorescent spots in the microarray like proposed by Skibbe et al. (Bioinformatics. 2006;22(15):1863-1870) . Low, intermediate and high intensity scans images were quantified with ScanArray Express (PerkinElmer) software using the fixed circle method.

data_processing:
Data from each of three scan intensities (low, medium, high) were analyzed separately. Fluorescence intensity was determined with the ScanArray Express software (PerkinElmer) using fixed circle method and median spot intensity background subtracted was normalized in the MIDAW tool using sequentially global mean normalization and local mean normalization (LOWESS) methods. Lowess normalization was performed without distinguishing between different sub-arrays.
Normalized log2(patient_ch1/controls_ch2) values were filtered according to the median of the value calculated in the empty array position for the average of the Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD values.  Ch1% or Ch2% > BKG + 1 SD value is the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity. Processing for data filtering is here summarized:
1.	calculate average for Ch1% > BKG + 1 SD and Ch2% > BKG + 1 SD for each gene;
2.	calculate median of the average calculated in point 1 for the empty position (see table description for experiments filtering on supplementary data table);
3.	exclude normalized gene expression values presenting average calculated in point 1 under median calculated in point 2 for each experiment;
4.	generated expression matrix was loaded in to TIGR MeV software and filtered for missing values along experiments. Only genes presenting calculated value in all experiment but one were used to identify differentially expressed genes by SAM software;
5.	differentially expressed genes calculated at the point 4 for each scan type (high, medium and low) were integrated.

source_name: Left anterior descendent (LAD) coronary, plaque >75% stenosis

label_protocol:
Extracted total RNA was quantized by UV adsorption in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and analyzed for quality by capillary electrophoresis in an Agilent 2100 Bioanalyzer. All RNAs utilized in this study presented RIN at least 7.
				1ug of total RNA for each studied patient and for the control pool obtained by mixing equal aliquots of each control coronaries was linearly amplified with with the MessageAmp™ aRNA amplification kit (Ambion). 5ug of the amplified RNA (aRNA) have been dried for 12 hours using a Heto Lyolab 3000 freeze-dryer (Heto-Holten A/S) and coupled with Cy3 and Cy5 post-labeling dye (Amersham, GE Healthcare). Coupling was performed for 45 minutes at room temperature. Unincorporated dyes were eliminated using MEGAclear™ Kit (Ambion). Labeled aRNA was eluted in ultraPURE™ distilled water DNase, RNase Free (Gibco) and quantized in a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

extract_protocol:
Total RNA was extracted with TRIzol method (Invitrogen). The procedure was:
1. Homogenization of the coronary fragments, dimensionally homogeneous, by the IKA® Werke (GmbH & Co.) homogenizer;
2. Incubation, at room temperature, for 15 minutes;
3. Addition of 0.2ml/1ml Trizol and shake for 1 minute;
4. Leave in ice for 15 minutes and then centrifuge at 4º C for 20 minutes at 14,000 X g;
5 Transfer the supernatant to 1.5 ml microfuge non-stick tubes and add an equal volume of isopropanol to precipitate the RNA;
6. Incubate at -20º C for one hour and centrifuge at 4º C for 20 minutes at 14,000 X g;
7. Discard the supernatant and wash with ethanol 75% three times centrifuging every time for 15 minutes at 4º C at 14,000 X g;
8. Pellet was resuspended in ultraPURE™ distilled water DNase, RNase Free (Gibco).

treatment_protocol:
18 patients were recruited at the Cardio-Chirurgic Section of the University Hospital Borgo Trento (Verona, Italy) for heart transplantation or by-pass surgery. According to clinical diagnosis and angiography, patients were subdivided in atherosclerotic with at least 75% stenosis and non-atherosclerotic controls. Before and during heart transplantation, cases were subjected to standard oral medication with aspirin.
LAD coronaries were dissected from diseased hearts immediately after surgical removal, cleaned from fatty and cardiac muscle tissues and starved in RNAlater Solution (Ambion) for further microscopy and gene expression analysis. 5-μm-thick serial sections of paraffin included coronaries fragments were used for hematoxylin-eosin staining and microscopic analysis.
Visible plaques and LAD controls, adjacent to the segment utilized for histochemical analysis, were dissected from the entire coronary fragment and used separately for total RNA extraction with TRIzol (Invitrogen).

tag: patient number

tag: sex

value: M

tag: age (years)

value: LAD

tag: pathology

value: Ischemic

tag: comorbidities

tag: pharm. therapies

value: Diuretics, Anti-arrhythmics, Hypertension regulators

tag: plasma lipid/stenosis

source_name: Left anterior descendent (LAD) coronary, without plaque (Controls pool). Patients presented Dilated Cardiomyopathy.

tag: Pool derived from 10 LAD control coronaries without plaque. For description of patients pool composing see patients supplementary data table.


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 7

tag: tissue

value: Stone Kidney


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 5 (Technical replicate)

value: Pulmonary arterial hypertension (PAH)

value: Diuretics, Anti-arrhythmics, Hypertension regulators, Statins


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 3

value: Cholecystectomy


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 3 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 8 Biological replicate (B)

tag: lad coronary plaque segment derived from patient 8 and different from which used for experiments 17 and 18 (ex17 and ex18) was used in this experiment.patient number


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 4

value: Diuretics, Hypertension regulators


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 2 (Biological replicate B)

tag: lad coronary plaque segment derived from patient 2 and different from which used for experiments 9 and 10 (ex9 and ex10) was used in this experiment. patient number

value: F

value: Diuretics, Anti-coagulants


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 6 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 2 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 8 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Low sacnning Patient 2 (A)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 2 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 6


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 5


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 8 (A)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 4 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 1 (Technical replicate A)

value: Hypothyroidism

value: Diuretics, Anti-arrhythmics, Anti-coagulants, Hypertension regulators


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 7 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 1 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 1 (Biological replicate B)

tag: lad coronary plaque segment derived from patient 1 and different from which used for experiments 1 and 2 (ex1 and ex2) was used in this experiment. patient number


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 8 Biological replicate (B)

tag: lad coronary plaque segment derived from patient 8 and different from which used for experiments 17 and 18 (ex17 and ex18) was used in this experiment. patient number


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 8 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 7


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 7 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Low scanning Patient 1 (A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 3 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 5


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 3


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 2 (A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 5 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 2 Biological replicate (B)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 1 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 6 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 4


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 1 Biological replicate B


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 2 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 8 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 6


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 2 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 4 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 1 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 1 (A)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 8 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression Medium scanning Patient 8 (A)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 7


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 2 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 2 biological replicate (B)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 8 A


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 5 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 2 (Technical replicate A)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 7 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 8 (Technical replicate B)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 3


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 4 technical replicate


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 5


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 3 (Technical replicate)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 6 (Techincal replicate)


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 8 Biological replicate (B)

source_name: Left anterior descendent (LAD) coronary, plaque >75% stenosis.


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 6


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 2


title: fra-2 pineal gland, mid-night, rep 3

status: Public on Jan 15 2009

middle: C.

last: Klein

address: 49 Convent Dr.

department: PDEGEN

institute: NICHD/NIH

description: in vivo pineal gland

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 18 hr at 45oC to an Affymetrix rat RAE230A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Rattus norvegicus

source_name: DN-Fra-2 pineal gland, mid-night

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Rats were kept on a 14 hr light:10 hr dark (14:10 LD) cycle. Pineals were taken at Zeitgeber time (ZT) 7 and ZT19.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was subjected to DNase treatment using Turbo DNA-free.

treatment_protocol: Pineal glands were stored at -80oC prior to RNA extraction.

tag: time

value: mid-night

tag: strain

value: Sprague-Dawley

tag: genotype/variation

value: transgenic line DN-Fra-2

tag: age

value: 2-3 months


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 1 (Biological replicate Ex1 and Ex2)

source_name: Left anterior descendent (LAD) coronary, plaque >75% stenosis (Biological replicate for patient 1)

value: M


title: fra-2 pineal gland, mid-night, rep 1

description: in vivo pineal gland


title: fra-2 pineal gland, mid-night, rep 2

description: in vivo pineal gland


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 1 (Technical replicate Ex1)

source_name: Left anterior descendent (LAD) coronary, plaque >75% stenosis (Technical replicate Ex1)

tag: patient number

value: LAD


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 4

tag: sex

value: Ischemic


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 1 (Ex 3 technical replicate)

tag: lad coronary plaque segment derived from patient 1 and different from which used for experiments 1 and 2 (ex1 and ex2) was used in this experiment. this is technical replicate for the ex3. patient number

tag: age (years)


title: fra-2 pineal gland mid-day rep 3

description: in vivo pineal gland

source_name: DN-Fra-2 pineal gland, mid-day

value: mid-day


title: pineal gland, mid-night, rep 3

description: in vivo pineal gland

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 18 hr at 45oC on an Affymetrix rat RG_U34A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

source_name: pineal gland, mid-night


title: pineal gland, mid-night, rep 1

description: in vivo pineal gland

value: wild type


title: fra-2 pineal gland, mid-day, rep 1

description: in vivo pineal gland


title: pineal gland, mid-day, rep 1

description: in vivo pineal gland

source_name: pineal gland, mid-day


title: fra-2 pineal gland, mid-day, rep 2

description: in vivo pineal gland


title: pineal gland, mid-night, rep 2

description: in vivo pineal gland


title: pineal gland, mid-day, rep 3

description: in vivo pineal gland


title: pineal gland, mid-night, rep 1

description: in vivo pineal gland


title: pineal gland, mid-day, rep 2

description: in vivo pineal gland


title: pineal gland, mid-night, rep 2

description: in vivo pineal gland


title: pineal gland, mid-day, rep 1

description: in vivo pineal gland


title: pineal gland, mid-day, rep 2

description: in vivo pineal gland


title: cultured pineal, forskolin, rep 1

description: cultured pineal gland

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45oC to an Affymetrix rat RAE230 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

source_name: cultured pineal, forskolin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Rats were kept on a 14 hr light:10 hr dark (14:10 LD) cycle.  Pineals were taken at Zeitgeber time (ZT) 7 and ZT19. Cultured pineal glands were kept in BGJb medium for 48 hours before being treated with a vehicle (norepinephrine (1 μM), dibutyryl cAMP (0.5 or 1 mM), or forskolin (10 μM)) for 6 hours.

treatment_protocol: Pineal glands and tissues were stored at -80oC prior to RNA extraction.

value: cultured pineal

tag: agent

value: forskolin


title: pineal gland, mid-night, rep 3

description: in vivo pineal gland


title: cultured pineal, forskolin, rep 3

description: cultured pineal gland


title: cultured pineal, norepinephrine, rep 2

description: cultured pineal gland

source_name: cultured pineal, norepinephrine

value: norepinephrine


title: cultured pineal, DBcAMP, rep 3

description: cultured pineal gland

source_name: cultured pineal, dibutyryl-cAMP

value: dibutyryl-cAMP


title: cultured pineal, forskolin, rep 2

description: cultured pineal gland


title: cultured pineal, control, rep 2

description: cultured pineal gland

source_name: cultured pineal, untreated

value: untreated


title: LAD coronary atherosclerotic plaque gene expression High scanning Patient 1

tag: pathology

tag: comorbidities

tag: pharm. therapies


title: cultured pineal, DBcAMP, rep 2

description: cultured pineal gland

tag: tissue


title: cultured pineal, control, rep 1

description: cultured pineal gland


title: heart, mid-day, rep 1

description: in vivo heart

source_name: heart, mid-day

value: heart


title: heart, mid-night, rep 2

description: in vivo heart

source_name: heart, mid-night


title: cultured pineal, norepinephrine, rep 3

description: cultured pineal gland


title: cultured pineal, control, rep 3

description: cultured pineal gland


title: cultured pineal, norepinephrine, rep 1

description: cultured pineal gland


title: liver, mid-night, rep 2

description: in vivo liver

source_name: liver, mid-night

value: liver


title: cultured pineal, DBcAMP, rep 1

description: cultured pineal gland


title: pineal gland, mid-day, rep 3

description: in vivo pineal gland


title: hypothalamus, mid-night, rep 2

description: in vivo hypothalamus

source_name: hypothalamus, mid-night

value: hypothalamus


title: liver, mid-day, rep 1

description: in vivo liver

source_name: liver, mid-day


title: hypothalamus, mid-day, rep 1

description: in vivo hypothalamus

source_name: hypothalamus, mid-day


title: pineal gland, mid-night, rep 3

description: in vivo pineal gland

value: pineal gland

value: mid-night


title: cortex, mid-night, rep 2

description: in vivo cortex

source_name: cortex, mid-night

value: cortex

value: Sprague-Dawley


title: pineal gland, mid-night, rep 1

description: in vivo pineal gland

value: 2-3 months


title: retina, mid-night, rep 2

description: in vivo retina

source_name: retina, mid-night

value: retina


title: cerebellum, mid-night, rep 2

description: in vivo cerebellum

source_name: cerebellum, mid-night

value: cerebellum


title: pineal gland, mid-night, rep 4

description: in vivo pineal gland


title: cortex, mid-day, rep 1

description: in vivo cortex

source_name: cortex, mid-day

value: mid-day


title: pineal gland, mid-day, rep 4

description: in vivo pineal gland


title: pineal gland, mid-day, rep 3

description: in vivo pineal gland


title: pineal gland, mid-night, rep 2

description: in vivo pineal gland


title: pineal gland, mid-day, rep 1

description: in vivo pineal gland


title: Control leaf (2)

status: Public on Jul 01 2008

city: Oxford

first: Alistair

middle: James

last: McCormick

address: South Parks Rd

department: Department of Plant Science

country: United Kingdom

institute: University of Oxford

hyb_protocol: All labelling, hybridizations of biotinylated cRNA to the GeneChip Sugarcane Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA) and data collection were performed by the Australian Genome Research Facility (AGRF, Melbourne, VIC, Australia).

scan_protocol: The scanner operating software, GCOS, converted the signal on each array into a DAT file, which was then used to generate CEL and CHP files for analysis (Casu et al., 2007).

data_processing: GeneSpring 7.3 (Agilent Technologies) was used for data analysis.

organism: Saccharum hybrid cultivar N19

source_name: Sugarcane (Saccharum spp. hybrids) leaf tissue

growth_protocol: Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006.  Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o.

extract_protocol:
Total RNA was extracted using the extraction protocol of Bugos et al. (1995).  Total RNA was checked for quality and integrity using a
Bioanalyser 2100 and the NanoChip protocol according to the manufacturer’s
directions (Agilent Technologies, Palo Alto, CA, USA). Labelled target used in
hybridisations was generated from 15 μg of total RNA using the One-Cycle
Eukaryotic Target Labeling Assay.

treatment_protocol: Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest.  The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base.  Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK).  At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany).  Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.

tag: Hybrid cultivar N19


title: Control leaf (4)

label_protocol: All labelling, hybridizations of biotinylated cRNA to the GeneChip Sugarcane Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA) and data collection were performed by the Australian Genome Research Facility (AGRF, Melbourne, VIC, Australia).

growth_protocol: Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006. Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o.

extract_protocol: Total RNA was extracted using the extraction protocol of Bugos et al. (1995). Total RNA was checked for quality and integrity using a Bioanalyser 2100 and the NanoChip protocol according to the manufacturer’s directions (Agilent Technologies, Palo Alto, CA, USA). Labelled target used in hybridisations was generated from 15 μg of total RNA using the One-Cycle Eukaryotic Target Labeling Assay.

treatment_protocol: Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest. The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base. Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK). At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany). Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.


title: retina, mid-day, rep 1

description: in vivo retina

source_name: retina, mid-day


title: Treated leaf (2)


title: pineal gland, mid-day, rep 2

description: in vivo pineal gland

source_name: pineal gland, mid-day


title: Treated leaf (4)


title: Control leaf (3)


title: Control leaf (1)


title: Treated leaf (1)


title: Sugarcane transcriptome - ch1: Drought_120h_Exp_2; ch2: control_120h_2 (L)

status: Public on May 20 2007

description: Plants under drought conditions (120h) x control plants, experiment 2

data_processing: Raw and background corrected data

organism: Saccharum hybrid cultivar SP90-1638

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 120h of exposure to drought conditions, experiment 2

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 120h, experiment 2


title: Sugarcane transcriptome - ch2: Drought_120h_Exp_1; ch1: control_120h_1 (R)

description: Plants under drought conditions (120h) x control plants, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 120h, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 120h of exposure to drought conditions, experiment 1


title: Sugarcane transcriptome - ch1: Drought_120h_Exp_2; ch2: control_120h_2 (R)


title: Sugarcane transcriptome - ch2: Drought_120h_Exp_1; ch1: control_120h_1 (L)


title: Sugarcane transcriptome - ch2: Drought_24h_Exp_1; ch1: control_24h_1 (R)

description: Plants under drought conditions (24h) x control plants, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 24h, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 24h of exposure to drought conditions, experiment 1


title: Sugarcane transcriptome - ch2: Endophytic interaction_HR_exp_2; ch1: control_2 (R)

description: Plants infected with Herbaspirillum spp. x control plants, experiment 2

organism: Saccharum hybrid cultivar SP70-1143

tag: Control sugarcane plantlets (variety SP 70-1143, pool of 5 individuals), experiment 2

tag: Sugarcane plantlets (variety SP 70-1143, pool of 5 individuals) infected with a mixture of Herbaspirillum seropedicae (HRC54 strain) and Herbaspirillum rubrisubalbicans (HCC103 strain), 1 day after inoculation, experiment 2


title: Treated leaf (3)


title: Sugarcane transcriptome - ch1: Drought_72h_Exp_2; ch2: control_72h_2 (R)

description: Plants under drought conditions (72h) x control plants, experiment 2

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 72h of exposure to drought conditions, experiment 2

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 72h, experiment 2


title: Sugarcane transcriptome - ch1: Endophytic interaction_HR_exp_1; ch2: control_1 (R)

description: Plants infected with Herbaspirillum spp. x control plants, experiment 1

tag: Sugarcane plantlets (variety SP 70-1143, pool of 5 individuals) infected with a mixture of Herbaspirillum seropedicae (HRC54 strain) and Herbaspirillum rubrisubalbicans (HCC103 strain), 1 day after inoculation, experiment 1

tag: Control sugarcane plantlets (variety SP 70-1143, pool of 5 individuals), experiment 1


title: Sugarcane transcriptome - ch2: Drought_72h_Exp_1; ch1: control_72h_1 (R)

description: Plants under drought conditions (72h) x control plants, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 72h, experiment 1

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 72h of exposure to drought conditions, experiment 1


title: Sugarcane transcriptome - ch2: Drought_72h_Exp_1; ch1: control_72h_1 (L)


title: Sugarcane transcriptome - ch1: Drought_72h_Exp_2; ch2: control_72h_2 (L)


title: Sugarcane transcriptome - ch2: Endophytic interaction_GD_exp_2; ch1: control_2 (R)

description: Plants infected with Gluconacetobacter diazotrophicus x control plants, experiment 2

tag: Sugarcane plantlets (variety SP 70-1143, pool of 5 individuals) infected with Gluconacetobacter diazotrophicus (PAL5 strain), 1 day after inoculation, experiment 2


title: Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2 (R)

description: Plants under drought conditions (24h) x control plants, experiment 2

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 individuals) collected after 24h of exposure to drought conditions, experiment 2

tag: Leaves of sugarcane, variety SP90-1638 (pool of 6 control plants) collected after 24h, experiment 2


title: Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2 (L)


title: Sugarcane transcriptome - ch2: Endophytic interaction_HR_exp_2; ch1: control_2 (L)


title: Sugarcane transcriptome - ch2: Endophytic interaction_GD_exp_2; ch1: control_2 (L)


title: Sugarcane transcriptome - ch2: Drought_24h_Exp_1; ch1: control_24h_1 (L)


title: Sugarcane transcriptome - ch1: Endophytic interaction_GD_exp_1; ch2: control_1 (R)

description: Plants infected with Gluconacetobacter diazotrophicus x control plants, experiment 1

tag: Sugarcane plantlets (variety SP 70-1143, pool of 5 individuals) infected with Gluconacetobacter diazotrophicus (PAL5 strain), 1 day after inoculation, experiment 1