title: CC56

description:
human brain tissue
4437568006_C


title: CC107

status: Public on Jun 30 2013

type: genomic

city: Changsha

first: Chao

last: Chen

state: Hunan

address: 110 Xiangya Road

department: State Key Lab of Medical Genetics

country: China

institute: Central South University

description:
human brain tissue
4437568005_I

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software
Matrix signal intensities value definition: Unmethylated and methylated signal intensities [linked as supplementary file on Series record]

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cerebellum

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Stanley human brain samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: cerebellum

tag: batch

tag: age

tag: pmi

tag: disease state

value: Dep.


title: CC63

description:
human brain tissue
4437568004_K

value: Schiz.


title: CC67

description:
human brain tissue
4437568005_H

value: Unaffected control


title: CC52

description:
human brain tissue
4437568005_B

value: BP


title: CC68_rep

description:
human brain tissue
4437568006_A


title: CC63_rep

description:
human brain tissue
4437568005_A


title: CC62

description:
human brain tissue
4437568005_C


title: CC54

description:
human brain tissue
4437568005_J


title: CC51

description:
human brain tissue
4437568005_E


title: CC130

description:
human brain tissue
4437568004_I


title: CC99

description:
human brain tissue
4437568004_L


title: CC138

description:
human brain tissue
4437568004_H


title: CC50

description:
human brain tissue
4437568004_G


title: CC70

description:
human brain tissue
4437568005_D


title: CC66

description:
human brain tissue
4437568005_G


title: CC36_rep

description:
human brain tissue
4408100016_L


title: CC408

description:
human brain tissue
4437568004_J


title: CC1_rep

description:
human brain tissue
4437568004_A


title: CC49

description:
human brain tissue
4437568004_E


title: CC61

description:
human brain tissue
4437568004_F


title: CC55

description:
human brain tissue
4437568004_B


title: CC32

description:
human brain tissue
4437568004_C


title: CC19

description:
human brain tissue
4437568004_D


title: CC74

description:
human brain tissue
4437568006_B


title: CC117

description:
human brain tissue
4408100016_E


title: CC37

description:
human brain tissue
4408100016_K


title: CC77

description:
human brain tissue
4408100016_J


title: CC106

description:
human brain tissue
4408100016_I


title: CC406

description:
human brain tissue
4408100016_G


title: CC27

description:
human brain tissue
4408100016_B


title: CC407

description:
human brain tissue
4408100016_H


title: CC140_rep

description:
human brain tissue
4408100016_A


title: CC98

description:
human brain tissue
4408100009_F


title: CC132

description:
human brain tissue
4408100009_I


title: CC113

description:
human brain tissue
4408100009_E


title: CC131

description:
human brain tissue
4408100016_C


title: CC126

description:
human brain tissue
4408100009_J


title: CC405

description:
human brain tissue
4408100016_D


title: CC139

description:
human brain tissue
4408100009_K


title: CC114

description:
human brain tissue
4408100009_D


title: CC112

description:
human brain tissue
4408100009_B


title: CC140

description:
human brain tissue
4408100009_L


title: CC115

description:
human brain tissue
4408100009_G


title: CC42

description:
human brain tissue
4207113145_G


title: CC123

description:
human brain tissue
4408100009_H


title: CC17

description:
human brain tissue
4408100016_F


title: CC43

description:
human brain tissue
4207113145_H


title: CC45_rep

description:
human brain tissue
4207113145_K


title: CC41

description:
human brain tissue
4207113145_F


title: CC404

description:
human brain tissue
4408100009_A


title: CC101

description:
human brain tissue
4408100009_C


title: CC47

description:
human brain tissue
4207113145_L


title: CC46

description:
human brain tissue
4207113145_J


title: CC48

description:
human brain tissue
4207113145_I


title: CC38

description:
human brain tissue
4207113145_E


title: CC30

description:
human brain tissue
4207113131_G


title: CC31

description:
human brain tissue
4207113145_A


title: CC12_rep

description:
human brain tissue
4207113131_A


title: CC44

description:
human brain tissue
4207113131_J


title: CC39

description:
human brain tissue
4207113131_H


title: CC45

description:
human brain tissue
4207113131_L


title: CC403

description:
human brain tissue
4207113131_F


title: CC40

description:
human brain tissue
4207113145_D


title: CC33

description:
human brain tissue
4207113131_B


title: CC35

description:
human brain tissue
4207113145_C


title: CC20

description:
human brain tissue
4207113131_C


title: CC16

description:
human brain tissue
4207113130_E


title: CC14

description:
human brain tissue
4207113130_C


title: CC28

description:
human brain tissue
4207113131_K


title: CC34

description:
human brain tissue
4207113131_D


title: CC12

description:
human brain tissue
4207113130_A


title: CC18

description:
human brain tissue
4207113130_G


title: CC26

description:
human brain tissue
4207113130_F


title: CC21

description:
human brain tissue
4207113130_B


title: CC23_rep

description:
human brain tissue
4207113130_L


title: CC24

description:
human brain tissue
4207113130_D


title: CC402

description:
human brain tissue
4207113130_J


title: CC11

description:
human brain tissue
4207113130_K


title: CC29

description:
human brain tissue
4207113130_H


title: CC15

description:
human brain tissue
4207113130_I


title: CC23

description:
human brain tissue
4207113125_L


title: CC401

description:
human brain tissue
4207113125_H


title: CC2

description:
human brain tissue
4207113125_I


title: CC400

description:
human brain tissue
4207113125_G


title: CC1

description:
human brain tissue
4207113125_A


title: CC8

description:
human brain tissue
4207113125_E


title: CC3

description:
human brain tissue
4207113125_K


title: CC13

description:
human brain tissue
4207113125_J


title: CC7

description:
human brain tissue
4207113125_C


title: CC5

description:
human brain tissue
4207113125_B


title: CuCPF29_3May07

status: Public on May 21 2013

type: RNA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

description: olfactory rosettes

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Bioconductor, GCRMA normalization log2

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: olfactory rosettes

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Zebrafish Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CEEH Genomics Core Laboratory followed by the manufacturer’s protocols using the GeneChip platform by Affymetrix.

tag: treatment

value: CPF= 0 , Cu= 0

value: olfactory rosettes, olfactory bulbs, and telencephalons


title: CuCPF24_4May07

description: olfactory rosettes


title: CuCPF25_21June07

description: olfactory rosettes


title: CuCPF28_21June07

description: olfactory rosettes


title: CuCPF27_3May07

description: olfactory rosettes


title: CC10

description:
human brain tissue
4207113125_D


title: CuCPF30_4May07

description: olfactory rosettes


title: CuCPF21_3May07

description: olfactory rosettes


title: CuCPF20_4May07

description: olfactory rosettes


title: CuCPF22_21June07

description: olfactory rosettes


title: CuCPF18_4May07

description: olfactory rosettes


title: CuCPF23_3May07

description: olfactory rosettes


title: CuCPF26_4May07

description: olfactory rosettes


title: CuCPF17_21June07

description: olfactory rosettes


title: CuCPF16_4May07

description: olfactory rosettes


title: CC9

description:
human brain tissue
4207113125_F


title: CuCPF19_3May07

description: olfactory rosettes


title: CC22

description:
human brain tissue
4207113131_E


title: CuCPF07_3May07

description: olfactory rosettes


title: CuCPF13_21June07

description: olfactory rosettes


title: CuCPF10_4May07

description: olfactory rosettes


title: CuCPF12_4May07

description: olfactory rosettes


title: CuCPF11_3May07

description: olfactory rosettes


title: CuCPF15_3May07

description: olfactory rosettes


title: CuCPF09_3May07

description: olfactory rosettes


title: CuCPF08_4May07

description: olfactory rosettes


title: CuCPF03_3May07

description: olfactory rosettes


title: CuCPF02_4May07

description: olfactory rosettes


title: CuCPF14_4May07

description: olfactory rosettes


title: CuCPF06_4May07

description: olfactory rosettes


title: CuCPF04_4May07

description: olfactory rosettes


title: CuCPF01_3May07

description: olfactory rosettes


title: CuCPF05_3May07

description: olfactory rosettes


title: CC25

description:
human brain tissue
4207113131_I


title: CC36

description:
human brain tissue
4207113145_B


title: GBS_L99192

status: Public on Apr 23 2013

description: fetal lung tissue

data_processing: Bioconductor software, RMA normalization log2 (Bioconductor version 2.8 and the affy package).

organism: Macaca nemestrina

source_name: fetal lung tissue

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Rhesus Macaque Genome Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CHDD Genomics Core Laboratory followed by the manufacturer's protocols using the GeneChip platform by Affymetrix.  Briefly, these methods include the synthesis of first- and second-strand cDNAs, the purification of double-stranded cDNA, the synthesis of cRNA by in vitro transcription (IVT), the recovery and quantitation of biotin-labeled cRNA, the fragmentation of this cRNA and subsequent hybridization to the microarray slide, the post-hybridization washings, and the detection of the hybridized cRNAs using a streptavidin-coupled fluorescent dye.

value: fetal lung

value: choriodecidual inoculation of Group B Streptococcus


title: SalineControl_M99183

description: fetal lung tissue

value: choriodecidual inoculation of saline


title: FS001-ref vs. FS001-709503

status: Public on Mar 01 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr, hybset spec. dye corr

organism: Canis lupus familiaris

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections)

tag: strain or line

value: Pool of 2 healthy individuals

value: Liver

value: healthy

value: extrahepatic portosystemic shunts

tag: disease

value: EH

tag: recovery (recovered = 1, non-recovered = 0)


title: SalineControl_5109

description: fetal lung tissue


title: GBS_A03159

description: fetal lung tissue


title: FS001-ref vs. FS001-801146

value: intrahepatic portosystemic shunts

value: IH


title: SalineControl_5081

description: fetal lung tissue


title: FS001-ref vs. FS001-708480


title: FS001-ref vs. FS001-802905


title: SalineControl_M05267

description: fetal lung tissue


title: GBS_K94129

description: fetal lung tissue


title: GBS_M02217

description: fetal lung tissue


title: GBS_5096

description: fetal lung tissue


title: SalineControl_4105

description: fetal lung tissue


title: FS001-ref vs. FS001-805947


title: FS001-ref vs. FS001-708039


title: FS001-ref vs. FS001-801372


title: FS001-ref vs. FS001-801884


title: FS001-ref vs. FS001-708588


title: FS001-ref vs. FS001-701886


title: FS001-ref vs. FS001-607366


title: FS001-ref vs. FS001-704794


title: FS001-ref vs. FS001-606771


title: FS001-ref vs. FS001-605365


title: FS001-ref vs. FS001-604154


title: FS001-ref vs. FS001-801993


title: FS001-ref vs. FS001-605851


title: FS001-ref vs. FS001-603731


title: FS001-ref vs. FS001-602940


title: FS001-ref vs. FS001-600773


title: FS001-ref vs. FS001-600132


title: FS001-ref vs. FS001-507284


title: FS001-ref vs. FS001-601808


title: FS001-ref vs. FS001-602680


title: FS001-ref vs. FS001-502439


title: FS001-ref vs. FS001-510646


title: FS001-ref vs. FS001-402604


title: FS001-ref vs. FS001-505127


title: FS001-ref vs. FS001-503131


title: FS001-ref vs. FS001-504897


title: FS001-ref vs. FS001-410021


title: FS001-ref vs. FS001-301714


title: FS001-ref vs. FS001-305063


title: FS001-ref vs. FS001-600716


title: FS001-ref vs. FS001-411685


title: FS001-ref vs. FS001-225613


title: FS001-ref vs. FS001-312931


title: FS001-ref vs. FS001-227889


title: FS001-ref vs. FS001-303088


title: FS001-ref vs. FS001-311674


title: FS001-ref vs. FS001-314221


title: FS001-ref vs. FS001-505433


title: FS001-ref vs. FS001-509325


title: FS001-ref vs. FS001-412553


title: FS001-ref vs. FS001-412070


title: FS001-ref vs. FS001-302176


title: FS001-805947 vs. FS001-ref


title: FS001-802905 vs. FS001-ref


title: FS001-801884 vs. FS001-ref


title: FS001-708039 vs. FS001-ref


title: FS001-708588 vs. FS001-ref


title: FS001-801146 vs. FS001-ref


title: FS001-801372 vs. FS001-ref


title: FS001-701886 vs. FS001-ref


title: FS001-801993 vs. FS001-ref


title: FS001-603731 vs. FS001-ref


title: FS001-606771 vs. FS001-ref


title: FS001-605365 vs. FS001-ref


title: FS001-600773 vs. FS001-ref


title: FS001-600132 vs. FS001-ref


title: FS001-505433 vs. FS001-ref


title: FS001-708480 vs. FS001-ref


title: FS001-709503 vs. FS001-ref


title: FS001-509325 vs. FS001-ref


title: FS001-607366 vs. FS001-ref


title: FS001-604154 vs. FS001-ref


title: FS001-605851 vs. FS001-ref


title: FS001-704794 vs. FS001-ref


title: FS001-602680 vs. FS001-ref


title: FS001-602940 vs. FS001-ref


title: FS001-504897 vs. FS001-ref


title: FS001-601808 vs. FS001-ref


title: FS001-510646 vs. FS001-ref


title: FS001-507284 vs. FS001-ref


title: FS001-600716 vs. FS001-ref


title: FS001-503131 vs. FS001-ref


title: FS001-505127 vs. FS001-ref


title: FS001-412553 vs. FS001-ref


title: FS001-411685 vs. FS001-ref


title: FS001-410021 vs. FS001-ref


title: FS001-311674 vs. FS001-ref


title: FS001-402604 vs. FS001-ref


title: FS001-305063 vs. FS001-ref


title: FS001-302176 vs. FS001-ref


title: FS001-227889 vs. FS001-ref


title: FS001-412070 vs. FS001-ref


title: FS001-502439 vs. FS001-ref


title: FS001-303088 vs. FS001-ref


title: FS001-301714 vs. FS001-ref


title: FS001-225613 vs. FS001-ref


title: MGMT.MAM.168.967

status: Public on Jan 10 2013

description: Mouse brains.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: R/Bioconductor affy package, RMA normalization log2

organism: Mus musculus

source_name: Mouse brains

label_protocol: For microarray hybridization, RNA was processed for hybridization to GeneChip? Mouse Genome 430 2.0 Array through a core facility in the Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer?s instructions.

extract_protocol: Total RNA purification was performed as described (PMID: 19380167). Briefly, tissues were dissolved by low-power sonication in a solution consisting of 4 M guanidinium thiocyanate and 0.1 M 2-mercaptoethanol. After sonication, sodium acetate (pH 4), phenol (pH 4), and a 24:1 mix of chloroform and isoamylic acid were added on ice; after vigorous vortexing, aqueous solution containing total RNA was separated by high-speed centrifugation at 4 ?C for 20 min. RNA was precipitated by adding an equal volume of isopropanol, and it was stored at -20 ?C overnight and then, pelleted by centrifugation for 20 min at maximum speed at 4 ?C, rinsed with 70% ethanol, and resuspended in an appropriate volume of nuclease-free water.

tag: genotype/variation

value: Mgmt-/-

tag: agent

value: Methylazoxymethanol

tag: time point

tag: gender

value: male

tag: strain

value: Eleven-week-old

value: brain


title: MGMT.MAM.48.961

description: Mouse brains.


title: FS001-314221 vs. FS001-ref


title: MGMT.MAM.6.949

description: Mouse brains.


title: MGMT.MAM.6.953

description: Mouse brains.


title: FS001-312931 vs. FS001-ref


title: MGMT.MAM.168.969

description: Mouse brains.


title: MGMT.MAM.6.951

description: Mouse brains.


title: MGMT.MAM.48.963

description: Mouse brains.


title: MGMT.VEH.168.923

description: Mouse brains.

value: vehicle


title: MGMT.MAM.24.959

description: Mouse brains.


title: MGMT.MAM.24.955

description: Mouse brains.


title: MGMT.MAM.168.971

description: Mouse brains.


title: MGMT.VEH.168.919

description: Mouse brains.


title: MGMT.MAM.48.965

description: Mouse brains.


title: MGMT.VEH.168.921

description: Mouse brains.


title: MGMT.MAM.24.957

description: Mouse brains.


title: MGMT.VEH.48.917

description: Mouse brains.


title: MGMT.VEH.48.913

description: Mouse brains.


title: MGMT.VEH.24.907

description: Mouse brains.


title: MGMT.VEH.24.909

description: Mouse brains.


title: MGMT.VEH.24.911

description: Mouse brains.


title: MGMT.VEH.6.901

description: Mouse brains.


title: MGMT.VEH.6.905

description: Mouse brains.


title: WT.MAM.168.743

description: Mouse brains.

value: wild-type


title: WT.MAM.168.745

description: Mouse brains.


title: WT.MAM.48.737

description: Mouse brains.


title: WT.MAM.168.747

description: Mouse brains.


title: WT.MAM.24.731

description: Mouse brains.


title: WT.VEH.24.711

description: Mouse brains.


title: WT.MAM.24.733

description: Mouse brains.


title: WT.MAM.48.739

description: Mouse brains.


title: WT.VEH.48.713

description: Mouse brains.


title: WT.MAM.6.727

description: Mouse brains.


title: WT.VEH.24.707

description: Mouse brains.


title: WT.VEH.168.723

description: Mouse brains.


title: WT.MAM.6.725

description: Mouse brains.


title: WT.VEH.48.717

description: Mouse brains.


title: WT.MAM.48.741

description: Mouse brains.


title: WT.MAM.24.735

description: Mouse brains.


title: WT.VEH.168.719

description: Mouse brains.


title: WT.VEH.48.715

description: Mouse brains.


title: WT.MAM.6.729

description: Mouse brains.


title: WT.VEH.6.703

description: Mouse brains.


title: WT.VEH.6.705

description: Mouse brains.


title: WT.VEH.168.721

description: Mouse brains.


title: WT.VEH.24.709

description: Mouse brains.


title: MGMT.VEH.48.915

description: Mouse brains.


title: MGMT.VEH.6.903

description: Mouse brains.


title: WT.VEH.6.701

description: Mouse brains.


title: MGMT.MAM.48.341

description: Mouse brains.


title: MGMT.MAM.6.327

description: Mouse brains.


title: MGMT.MAM.168.347

description: Mouse brains.


title: MGMT.MAM.6.325

description: Mouse brains.


title: MGMT.MAM.168.345

description: Mouse brains.


title: MGMT.MAM.48.339

description: Mouse brains.


title: MGMT.MAM.24.335

description: Mouse brains.


title: MGMT.MAM.24.331

description: Mouse brains.


title: MGMT.MAM.48.337

description: Mouse brains.


title: MGMT.MAM.24.333

description: Mouse brains.


title: MGMT.MAM.6.329

description: Mouse brains.


title: MGMT.MAM.168.343

description: Mouse brains.


title: MGMT.VEH.168.319

description: Mouse brains.


title: MGMT.VEH.168.323

description: Mouse brains.


title: MGMT.VEH.24.307

description: Mouse brains.


title: MGMT.VEH.24.309

description: Mouse brains.


title: MGMT.VEH.48.315

description: Mouse brains.


title: MGMT.VEH.6.301

description: Mouse brains.


title: MGMT.VEH.24.311

description: Mouse brains.


title: MGMT.VEH.6.303

description: Mouse brains.


title: MGMT.VEH.48.317

description: Mouse brains.


title: WT.MAM.48.139

description: Mouse brains.


title: MGMT.VEH.6.305

description: Mouse brains.


title: WT.MAM.168.145

description: Mouse brains.


title: MGMT.VEH.168.321

description: Mouse brains.


title: WT.MAM.48.141

description: Mouse brains.


title: MGMT.VEH.48.313

description: Mouse brains.


title: WT.MAM.48.137

description: Mouse brains.


title: WT.MAM.24.135

description: Mouse brains.


title: WT.MAM.168.143

description: Mouse brains.


title: WT.MAM.24.133

description: Mouse brains.


title: WT.VEH.168.123

description: Mouse brains.


title: WT.MAM.6.129

description: Mouse brains.


title: WT.MAM.6.127

description: Mouse brains.


title: WT.MAM.24.131

description: Mouse brains.


title: WT.MAM.6.125

description: Mouse brains.


title: WT.VEH.24.109

description: Mouse brains.


title: WT.VEH.24.107

description: Mouse brains.


title: WT.VEH.48.115

description: Mouse brains.


title: WT.VEH.24.111

description: Mouse brains.


title: WT.VEH.168.119

description: Mouse brains.


title: WT.VEH.48.113

description: Mouse brains.


title: WT.VEH.6.103

description: Mouse brains.


title: WT.VEH.6.105

description: Mouse brains.


title: WT.VEH.168.121

description: Mouse brains.


title: Domoic Acid 1wk set 3b

status: Public on Jan 03 2013

description: zebrafish whole brain

hyb_protocol: The RNA samples were labeled and prepared for hybridization onto a Zebrafish (V3) Gene Expression Microarray (Agilent Technologies, Inc. Santa Clara, CA) using the manufacturer’s established protocols. Hybridization and washing of these arrays was accomplished using HS 400 Pro hybridization and wash stations (Tecan Sysems, Inc., San Jose, CA).

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner (Agilent Technologies, Inc. Santa Clara, CA) through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: R/Bioconductor package Agi4x44PreProcess VSN normalization log2

label: Cy3 fluorescent label

source_name: Zebrafish whole brain

label_protocol: For microarray hybridization, RNA was processed for hybridization to Agilent Zebrafish Gene Expression Microarray (V2) through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

growth_protocol: Wild-type zebrafish (Danio rerio, AB strain) were obtained from Oregon State University, Sinnhuber Aquatic Research Laboratory (Corvallis, OR) and maintained at the Northwest Fisheries Science Center (NWFSC) in a ZebTec stand alone recirculating zebrafish rack system (Techniplast, Exton, PA). Fish were maintained at 26_C, kept on a 12h-12h light-dark cycle, and fed daily with commercially available fish feed.

extract_protocol: All fish were euthanized by decapitation followed by rapid removal of the brain for RNA extraction. During brain removal surgeries, the skullcap was opened, and the brain removed, rinsed in ice cold PBS, weighed, and immediately frozen in liquid nitrogen. The length of brain removal surgeries, from euthanasia to freezing in liquid nitrogen, averaged 1.6 ± 0.5 min (mean ± SD, n = 43). The entire brain was removed after cutting the brain stem and at the optic nerves as close to the eyes as possible. Total RNA was isolated from zebrafish brains using the miRNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the vendor’s defined method, and stored at -70_C.  The quantity (ng/uL) of RNA was determined measuring the OD260 with a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and the RNA purity was assessed measuring OD260/280 and OD260/230 ratios.  RNA integrity (quality) was characterized using the Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Only total RNA samples with appropriate size distribution, quantity, and A260/A280 as well as A260/A230 ratios of 1.8 – 2.1 were used for microarray-based analysis.

value: Domoic Acid

tag: time

tag: dose

value: 0.03 ug DA/g fish per week

value: whole brain


title: Domoic Acid 1wk recovery set 3

description: zebrafish whole brain

value: Domoic Acid + recovery

value: 36 wk treatment + 1wk recovery

value: 0.03 ug DA/g fish per week for the first 6 weeks then 0.02 ug DA/g fish once every two weeks


title: Control 36wks set 3

description: zebrafish whole brain

value: Control (PBS)


title: Domoic Acid 18wks set 3

description: zebrafish whole brain


title: Domoic Acid 12wks set 3

description: zebrafish whole brain


title: Control 12wks set 3

description: zebrafish whole brain


title: Control 5wk recovery set 3

description: zebrafish whole brain

value: Control (PBS) + recovery

value: 36 wk treatment + 5wk recovery


title: Control 24wks set 3

description: zebrafish whole brain


title: Domoic Acid 48hrs set 3b

description: zebrafish whole brain


title: Control 48hrs set 3b

description: zebrafish whole brain


title: Control 6wks set 3

description: zebrafish whole brain


title: Domoic Acid 6wks set 3a

description: zebrafish whole brain


title: Domoic Acid 24wks set 3

description: zebrafish whole brain


title: Control 1wk set 3b

description: zebrafish whole brain


title: Control 1wk recovery set 3

description: zebrafish whole brain


title: Domoic Acid 36wks set 3

description: zebrafish whole brain


title: Domoic Acid 5wk recovery set 3

description: zebrafish whole brain


title: Domoic Acid 1wk set 3a

description: zebrafish whole brain


title: Domoic Acid 48hrs set 3

description: zebrafish whole brain


title: Domoic Acid 24hrs set 3

description: zebrafish whole brain


title: WT.VEH.6.101

description: Mouse brains.


title: Control 6hrs set 3

description: zebrafish whole brain


title: Control 18wks set 3

description: zebrafish whole brain


title: Control 24hrs set 3

description: zebrafish whole brain


title: Control 48hrs set 3a

description: zebrafish whole brain


title: Control 1wk set 3a

description: zebrafish whole brain


title: Control 2wks set 3

description: zebrafish whole brain


title: Control 1wk recovery set 2

description: zebrafish whole brain


title: Domoic Acid 2wks set 3

description: zebrafish whole brain


title: Domoic Acid 6hrs set 3

description: zebrafish whole brain


title: Domoic Acid 1wk recovery set 2

description: zebrafish whole brain


title: Control 5wk recovery set 2

description: zebrafish whole brain


title: Domoic Acid 24wks set 2

description: zebrafish whole brain


title: Domoic Acid 12wks set 2

description: zebrafish whole brain


title: Control 12wks set 2

description: zebrafish whole brain


title: Domoic Acid 5wk recovery set 2

description: zebrafish whole brain


title: Domoic Acid 18wks set 2

description: zebrafish whole brain


title: Control 24wks set 2

description: zebrafish whole brain


title: Domoic Acid 36wks set 2

description: zebrafish whole brain


title: Control 18wks set 2

description: zebrafish whole brain


title: Control 6wks set 2

description: zebrafish whole brain


title: Control 2wks set 2

description: zebrafish whole brain


title: Domoic Acid 6wks set 2

description: zebrafish whole brain


title: Control 24hrs set 2

description: zebrafish whole brain


title: Control 36wks set 1

description: zebrafish whole brain


title: Domoic Acid 6hrs set 2

description: zebrafish whole brain


title: Domoic Acid 24hrs set 2

description: zebrafish whole brain


title: Domoic Acid 2wks set 2

description: zebrafish whole brain


title: Control 6hrs set 2

description: zebrafish whole brain


title: Control 36wks set 2

description: zebrafish whole brain


title: Control 1wk recovery set 1

description: zebrafish whole brain


title: Control 5wk recovery set 1

description: zebrafish whole brain


title: Control 18wks set 1

description: zebrafish whole brain


title: Domoic Acid 1wk recovery set 1

description: zebrafish whole brain


title: Domoic Acid 36wks set 1

description: zebrafish whole brain


title: Domoic Acid 24wks set 1

description: zebrafish whole brain


title: Domoic Acid 12wks set 1

description: zebrafish whole brain


title: Control 2wks set 1

description: zebrafish whole brain


title: Domoic Acid 18wks set 1

description: zebrafish whole brain


title: Control 24wks set 1

description: zebrafish whole brain


title: Control 12wks set 1

description: zebrafish whole brain


title: Domoic Acid 5wk recovery set 1

description: zebrafish whole brain


title: Control 1wk set 1

description: zebrafish whole brain


title: Domoic Acid 6wks set 1

description: zebrafish whole brain


title: Control 48hrs set 1

description: zebrafish whole brain


title: Domoic Acid 2wks set 1

description: zebrafish whole brain


title: Control 6wks set 1

description: zebrafish whole brain


title: Domoic Acid 1wk set 1

description: zebrafish whole brain


title: Domoic Acid 48hrs set 1

description: zebrafish whole brain


title: Control 24hrs set 1

description: zebrafish whole brain


title: Domoic Acid 24hrs set 1

description: zebrafish whole brain


title: Domoic Acid 6hrs set 1

description: zebrafish whole brain


title: Control 6hrs set 1

description: zebrafish whole brain


title: DS10 Ad5 IL1R

status: Public on Oct 03 2012

description: macrophages

data_processing: Bioconductor software, RMA normalization log2

source_name: macrophage

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from myeloid dendritic cells with TriZol reagent (Invitrogen) according to a standard protocol.  RNA integrity of individual samples was confirmed with an Agilent 2100 Bioanalyzer.   CD11c+ cells were purified to 97% purify from lung mononuclear cells by two consecutive rounds of magnetic cell separation using CD11c-antibody-labled magnetic beads and LS columns for positive cell selection as per manufacturer’s protocol (Miltenyi Biotech). The purity of CD11c+ cells was verified by flow cytometry prior to pooling CD11c+ cells from three mice for total RNA isolation. Two pools of CD11c+ cells from three mice each were prepared for WT and Il1a-/- experimental groups.

tag: cell type

value: CD11c+ lung mononuclear cells

value: HAdv5 hexon

tag: genetic background

tag: genotype

value: Il1r1 null


title: DS6 Ad5 WT

description: macrophages

value: wild type


title: DS18 PBS IL1R

description: macrophages

value: PBS control


title: DS14 TEA IL1R

description: macrophages

value: HAdv5 T424A hexon


title: DS13 TEA IL1R

description: macrophages


title: DS11 Ad5 IL1R

description: macrophages


title: DS15 TEA IL1R

description: macrophages


title: DS17 PBS IL1R

description: macrophages


title: DS9 TEA WT

description: macrophages


title: DS5 Ad5 WT

description: macrophages


title: DS7 TEA WT

description: macrophages


title: DS2 PBS WT

description: macrophages


title: DS1 PBS WT

description: macrophages


title: DS3 PBS WT

description: macrophages


title: DS12 Ad5 IL1R

description: macrophages


title: DS8 TEA WT

description: macrophages


title: DS4 Ad5 WT

description: macrophages


title: PBE_human

status: Public on Aug 19 2012

description: cultured human erythroblasts from human embryonic stem cells

data_processing: Affymetrix Expression Console v1.1 RMA normalization log2

source_name: mobilized peripheral blood-CD34+ cells-derived erythroid RNA

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer’s instructions.

extract_protocol: RNA was isolated by extraction with a commercially available kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: Erythroid cells were generated by culturing mobilized peripheral blood-CD34+ cells in an erythroid induction medium for 14 days. Total RNA was extracted.

tag: tissue source

value: mobilized peripheral blood

value: cultured human erythroblasts


title: ESE_human

source_name: ESC-derived erythroid RNA

treatment_protocol: Erythroid cells were generated by culturing dissociated day-7 embryoid bodies in an erythroid induction medium for 14 days. Total RNA was extracted.

tag: cell source

value: human embryonic stem cells


title: C3W4_hum

description: Mus musculus cells with some Homo sapiens chromosomes

treatment_protocol: human chromosome 11-containing MEL cells were generated via fusing hESC-derived erythroblasts with MEL cells. Each hybrid lines were cultured for up to 68 weeks.

tag: hybrid cell line

value: ES-E-hybrid line 3

value: cultured human erythroblasts x murine erythroleukemia heterospecific hybrids

tag: cell culture age

value: week 4

tag: gamma to beta globin switching phase

value: pre-switching phase

tag: globin expression status

value: stable gamma globin expression


title: C3W53_hum

value: week 53

value: post-switching phase

value: stable beta globin expression.


title: C22W27_hum

value: ES-E-hybrid line 22

value: week 27

tag: switching phase

value: undergoing gamma to beta globin switching


title: C10W27_hum

value: ES-E-hybrid line 10

value: undergoing gamma to beta globin switching.


title: C3W53_mus


title: C10W53_hum


title: C10W4_hum


title: C3W27_hum


title: C22W8_mus

value: week 8


title: DS16 PBS IL1R

description: macrophages

value: CD11c+ lung mononuclear cells

tag: treatment

value: PBS control

value: Il1r1 null


title: C3W27_mus

value: ES-E-hybrid line 3


title: C3W4_mus

value: cultured human erythroblasts x murine erythroleukemia heterospecific hybrids


title: C10W53_mus


title: C22W53_mus


title: C10W27_mus


title: C22W53_hum


title: Cranio245.21July2009

status: Public on Mar 04 2012

description:
Cranio245.21July2009.CEL
osteoblasts derived from human skull

data_processing: Affymetrix Expression Console software, RMA normalization log2

source_name: Human osteoblast cell lines

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer?s instructions.

growth_protocol: Patient osteoblast cell lines were grouped into batches of five. Batches were grouped by age, each containing the following: one control sample, one coronal case, one metopic case, and two cases of sagittal craniosynostosis to reduce bias introduced by culture condition variability.  Osteoblast cell lines stored in liquid nitrogen in freezing media consisting of 90% fetal bovine serum and 10% DMSO were thawed prior to culture.  All 249 osteoblast lines were grown in T25 flasks containing Waymouth?s Media (Sigma W1625 lot 097K8303) supplemented with 2X antibiotic (100X Pen/Strep/Fungizone, Hyclone SV30079.01, Lot JUA33955) and 10% FBS (Hyclone SH30070.03, Lot ATK33398).  Upon reaching 75% confluence, cells were trypsinized using 0.05% Trypsin (Hyclone SH30236.02, Lot J090511), counted and passaged at a cell density of 175,000 cells per 25cm2.  All cells were cultured at 37 degrees C, 5% CO2, and 99% humidity.

extract_protocol: Following the plating of 175,000 cells per 25cm2, each osteoblast cell line was once again grown to 75% confluence, photographed for quality control purposes, washed twice with 1X PBS, and trypsinized.  An equal volume of media containing FBS was added after trypsin exposure, and cells were centrifuged twice at 200 x g for 10 minutes at 4degrees C in nuclease free 15ml conical tubes (Corning 430791).  In between the centrifugation steps, cells were washed once with 1X PBS.  Cell pellets were then kept on ice until RNA extraction. For RNA extraction, Roche High Pure miRNA Isolation Kit was used in accordance with the manufacturer's protocol (Roche 050080576001). RNA was stored immediately in -80 degrees C and submitted for microarray processing on dry ice.

tag: age months

value: M

tag: type

value: Control

tag: cell lines

value: osteoblast

tag: tissue

value: skull


title: Cranio239.15April2010

description:
Cranio239.15April2010.CEL
osteoblasts derived from human skull

tag: gender


title: Cranio244.24Sept09

description:
Cranio244.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio234.14April2010

description:
Cranio234.14April2010.CEL
osteoblasts derived from human skull

value: F


title: Cranio238.14April2010

description:
Cranio238.14April2010.CEL
osteoblasts derived from human skull


title: C10W4_mus

value: week 4

value: pre-switching phase

value: stable gamma globin expression


title: Cranio240.19April2010

description:
Cranio240.19April2010.CEL
osteoblasts derived from human skull


title: Cranio246.04Dec09

description:
Cranio246.04Dec09.CEL
osteoblasts derived from human skull


title: C22W27_mus

value: ES-E-hybrid line 22

value: week 27

value: undergoing gamma to beta globin switching


title: Cranio242.13April2010

description:
Cranio242.13April2010.CEL
osteoblasts derived from human skull

value: Sagittal Synostosis


title: Cranio247.13April2010

description:
Cranio247.13April2010.CEL
osteoblasts derived from human skull


title: Cranio236.04Dec09

description:
Cranio236.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio243.21July2009

description:
Cranio243.21July2009.CEL
osteoblasts derived from human skull


title: Cranio237.15April2010

description:
Cranio237.15April2010.CEL
osteoblasts derived from human skull


title: Cranio231.15April2010

description:
Cranio231.15April2010.CEL
osteoblasts derived from human skull


title: Cranio233.19April2010

description:
Cranio233.19April2010.CEL
osteoblasts derived from human skull


title: Cranio248.13April2010

description:
Cranio248.13April2010.CEL
osteoblasts derived from human skull


title: Cranio232.10Oct09

description:
Cranio232.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio235.14April2010

description:
Cranio235.14April2010.CEL
osteoblasts derived from human skull


title: Cranio249.19April2010

description:
Cranio249.19April2010.CEL
osteoblasts derived from human skull


title: Cranio229.15April2010

description:
Cranio229.15April2010.CEL
osteoblasts derived from human skull


title: Cranio241.19April2010

description:
Cranio241.19April2010.CEL
osteoblasts derived from human skull


title: Cranio230.04Dec09

description:
Cranio230.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio219.13April2010

description:
Cranio219.13April2010.CEL
osteoblasts derived from human skull


title: Cranio224.10Oct09

description:
Cranio224.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio223.13April2010

description:
Cranio223.13April2010.CEL
osteoblasts derived from human skull


title: Cranio220.14April2010

description:
Cranio220.14April2010.CEL
osteoblasts derived from human skull


title: Cranio226.24Sept09

description:
Cranio226.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio218.15April2010

description:
Cranio218.15April2010.CEL
osteoblasts derived from human skull


title: Cranio222.04Dec09

description:
Cranio222.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio221.24Sept09

description:
Cranio221.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio215.13April2010

description:
Cranio215.13April2010.CEL
osteoblasts derived from human skull


title: Cranio210.19April2010

description:
Cranio210.19April2010.CEL
osteoblasts derived from human skull


title: Cranio227.04Dec09

description:
Cranio227.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio228.15April2010

description:
Cranio228.15April2010.CEL
osteoblasts derived from human skull


title: Cranio207.24Sept09

description:
Cranio207.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio214.14April2010

description:
Cranio214.14April2010.CEL
osteoblasts derived from human skull


title: Cranio216.13April2010

description:
Cranio216.13April2010.CEL
osteoblasts derived from human skull


title: Cranio225.19April2010

description:
Cranio225.19April2010.CEL
osteoblasts derived from human skull


title: Cranio217.14April2010

description:
Cranio217.14April2010.CEL
osteoblasts derived from human skull


title: Cranio205.15April2010

description:
Cranio205.15April2010.CEL
osteoblasts derived from human skull

value: Coronal Synostosis R


title: Cranio206.15April2010

description:
Cranio206.15April2010.CEL
osteoblasts derived from human skull


title: Cranio212.15April2010

description:
Cranio212.15April2010.CEL
osteoblasts derived from human skull


title: Cranio213.04Dec09

description:
Cranio213.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio209.04Dec09

description:
Cranio209.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio204.19April2010

description:
Cranio204.19April2010.CEL
osteoblasts derived from human skull

value: Metopic Synostosis


title: Cranio202.14April2010

description:
Cranio202.14April2010.CEL
osteoblasts derived from human skull


title: Cranio211.14April2010

description:
Cranio211.14April2010.CEL
osteoblasts derived from human skull


title: C22W8_hum

description: Mus musculus cells with some Homo sapiens chromosomes

value: week 8


title: Cranio208.10Oct09

description:
Cranio208.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio201.19April2010

description:
Cranio201.19April2010.CEL
osteoblasts derived from human skull


title: Cranio203.13April2010

description:
Cranio203.13April2010.CEL
osteoblasts derived from human skull

value: Coronal Synostosis L


title: Cranio198.04Dec09

description:
Cranio198.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio193.04Dec09

description:
Cranio193.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio199.15April2010

description:
Cranio199.15April2010.CEL
osteoblasts derived from human skull


title: Cranio181.04Dec09

description:
Cranio181.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio194.15April2010

description:
Cranio194.15April2010.CEL
osteoblasts derived from human skull


title: Cranio183.14April2010

description:
Cranio183.14April2010.CEL
osteoblasts derived from human skull


title: Cranio188.14April2010

description:
Cranio188.14April2010.CEL
osteoblasts derived from human skull


title: Cranio186.14April2010

description:
Cranio186.14April2010.CEL
osteoblasts derived from human skull


title: Cranio195.10Oct09

description:
Cranio195.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio200.10Oct09

description:
Cranio200.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio185.13April2010

description:
Cranio185.13April2010.CEL
osteoblasts derived from human skull


title: Cranio197.14April2010

description:
Cranio197.14April2010.CEL
osteoblasts derived from human skull


title: Cranio174.24Sept09

description:
Cranio174.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio192.19April2010

description:
Cranio192.19April2010.CEL
osteoblasts derived from human skull


title: Cranio189.15April2010

description:
Cranio189.15April2010.CEL
osteoblasts derived from human skull


title: Cranio175.21July2009

description:
Cranio175.21July2009.CEL
osteoblasts derived from human skull


title: Cranio184.13April2010

description:
Cranio184.13April2010.CEL
osteoblasts derived from human skull


title: Cranio190.14April2010

description:
Cranio190.14April2010.CEL
osteoblasts derived from human skull


title: Cranio187.19April2010

description:
Cranio187.19April2010.CEL
osteoblasts derived from human skull


title: Cranio196.14April2010

description:
Cranio196.14April2010.CEL
osteoblasts derived from human skull


title: Cranio180.04Dec09

description:
Cranio180.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio176.24Sept09

description:
Cranio176.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio177.04Dec09

description:
Cranio177.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio191.15April2010

description:
Cranio191.15April2010.CEL
osteoblasts derived from human skull


title: Cranio179.14April2010

description:
Cranio179.14April2010.CEL
osteoblasts derived from human skull


title: Cranio182.13April2010

description:
Cranio182.13April2010.CEL
osteoblasts derived from human skull


title: Cranio172.10Oct09

description:
Cranio172.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio171.13April2010

description:
Cranio171.13April2010.CEL
osteoblasts derived from human skull


title: Cranio173.14April2010

description:
Cranio173.14April2010.CEL
osteoblasts derived from human skull


title: Cranio168.24Sept09

description:
Cranio168.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio169.10Oct09

description:
Cranio169.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio163.10Oct09

description:
Cranio163.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio167.13April2010

description:
Cranio167.13April2010.CEL
osteoblasts derived from human skull


title: Cranio170.10Oct09

description:
Cranio170.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio166.24Sept09

description:
Cranio166.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio158.21July2009

description:
Cranio158.21July2009.CEL
osteoblasts derived from human skull


title: Cranio164.10Oct09

description:
Cranio164.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio165.10Oct09

description:
Cranio165.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio152.13April2010

description:
Cranio152.13April2010.CEL
osteoblasts derived from human skull


title: Cranio162.15April2010

description:
Cranio162.15April2010.CEL
osteoblasts derived from human skull


title: Cranio153.15April2010

description:
Cranio153.15April2010.CEL
osteoblasts derived from human skull


title: Cranio159.24Sept09

description:
Cranio159.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio157.24Sept09

description:
Cranio157.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio155.21July2009

description:
Cranio155.21July2009.CEL
osteoblasts derived from human skull


title: Cranio160.24Sept09

description:
Cranio160.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio178.10Oct09

description:
Cranio178.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio150.04Dec09

description:
Cranio150.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio154.14April2010

description:
Cranio154.14April2010.CEL
osteoblasts derived from human skull


title: Cranio149.10Oct09

description:
Cranio149.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio148.10Oct09

description:
Cranio148.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio145.04Dec09

description:
Cranio145.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio144.21July2009

description:
Cranio144.21July2009.CEL
osteoblasts derived from human skull


title: Cranio156.24Sept09

description:
Cranio156.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio142.04Dec09

description:
Cranio142.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio161.24Sept09

description:
Cranio161.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio151.13April2010

description:
Cranio151.13April2010.CEL
osteoblasts derived from human skull


title: Cranio143.14April2010

description:
Cranio143.14April2010.CEL
osteoblasts derived from human skull


title: Cranio146.15April2010

description:
Cranio146.15April2010.CEL
osteoblasts derived from human skull


title: Cranio147.21July2009

description:
Cranio147.21July2009.CEL
osteoblasts derived from human skull


title: Cranio139.14April2010

description:
Cranio139.14April2010.CEL
osteoblasts derived from human skull


title: Cranio135.19April2010

description:
Cranio135.19April2010.CEL
osteoblasts derived from human skull


title: Cranio140.13April2010

description:
Cranio140.13April2010.CEL
osteoblasts derived from human skull


title: Cranio136.21July2009

description:
Cranio136.21July2009.CEL
osteoblasts derived from human skull


title: Cranio131.14April2010

description:
Cranio131.14April2010.CEL
osteoblasts derived from human skull


title: Cranio137.15April2010

description:
Cranio137.15April2010.CEL
osteoblasts derived from human skull


title: Cranio141.10Oct09

description:
Cranio141.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio124.14April2010

description:
Cranio124.14April2010.CEL
osteoblasts derived from human skull


title: Cranio126.10Oct09

description:
Cranio126.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio129.13April2010

description:
Cranio129.13April2010.CEL
osteoblasts derived from human skull


title: Cranio132.24Sept09

description:
Cranio132.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio133.21July2009

description:
Cranio133.21July2009.CEL
osteoblasts derived from human skull


title: Cranio128.14April2010

description:
Cranio128.14April2010.CEL
osteoblasts derived from human skull


title: Cranio119.13April2010

description:
Cranio119.13April2010.CEL
osteoblasts derived from human skull


title: Cranio120.04Dec09

description:
Cranio120.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio114.04Dec09

description:
Cranio114.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio117.19April2010

description:
Cranio117.19April2010.CEL
osteoblasts derived from human skull


title: Cranio113.13April2010

description:
Cranio113.13April2010.CEL
osteoblasts derived from human skull


title: Cranio115.21July2009

description:
Cranio115.21July2009.CEL
osteoblasts derived from human skull


title: Cranio121.13April2010

description:
Cranio121.13April2010.CEL
osteoblasts derived from human skull


title: Cranio118.04Dec09

description:
Cranio118.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio125.04Dec09

description:
Cranio125.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio130.24Sept09

description:
Cranio130.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio138.14April2010

description:
Cranio138.14April2010.CEL
osteoblasts derived from human skull


title: Cranio116.04Dec09

description:
Cranio116.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio123.13April2010

description:
Cranio123.13April2010.CEL
osteoblasts derived from human skull


title: Cranio122.04Dec09

description:
Cranio122.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio134.19April2010

description:
Cranio134.19April2010.CEL
osteoblasts derived from human skull


title: Cranio127.10Oct09

description:
Cranio127.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio112.10Oct09

description:
Cranio112.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio111.19April2010

description:
Cranio111.19April2010.CEL
osteoblasts derived from human skull


title: Cranio109.14April2010

description:
Cranio109.14April2010.CEL
osteoblasts derived from human skull


title: Cranio108.13April2010

description:
Cranio108.13April2010.CEL
osteoblasts derived from human skull


title: Cranio104.10Oct09

description:
Cranio104.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio103.10Oct09

description:
Cranio103.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio105.04Dec09

description:
Cranio105.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio102.24Sept09

description:
Cranio102.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio092.14April2010

description:
Cranio092.14April2010.CEL
osteoblasts derived from human skull


title: Cranio098.14April2010

description:
Cranio098.14April2010.CEL
osteoblasts derived from human skull


title: Cranio106.10Oct09

description:
Cranio106.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio100.21July2009

description:
Cranio100.21July2009.CEL
osteoblasts derived from human skull


title: Cranio082.14April2010

description:
Cranio082.14April2010.CEL
osteoblasts derived from human skull


title: Cranio090.19April2010

description:
Cranio090.19April2010.CEL
osteoblasts derived from human skull


title: Cranio086.14April2010

description:
Cranio086.14April2010.CEL
osteoblasts derived from human skull


title: Cranio089.14April2010

description:
Cranio089.14April2010.CEL
osteoblasts derived from human skull


title: Cranio085.15April2010

description:
Cranio085.15April2010.CEL
osteoblasts derived from human skull


title: Cranio099.13April2010

description:
Cranio099.13April2010.CEL
osteoblasts derived from human skull


title: Cranio087.21July2009

description:
Cranio087.21July2009.CEL
osteoblasts derived from human skull


title: Cranio093.15April2010

description:
Cranio093.15April2010.CEL
osteoblasts derived from human skull


title: Cranio110.13April2010

description:
Cranio110.13April2010.CEL
osteoblasts derived from human skull


title: Cranio107.10Oct09

description:
Cranio107.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio083.15April2010

description:
Cranio083.15April2010.CEL
osteoblasts derived from human skull


title: Cranio088.13April2010

description:
Cranio088.13April2010.CEL
osteoblasts derived from human skull


title: Cranio096.24Sept09

description:
Cranio096.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio094.15April2010

description:
Cranio094.15April2010.CEL
osteoblasts derived from human skull


title: Cranio091.15April2010

description:
Cranio091.15April2010.CEL
osteoblasts derived from human skull


title: Cranio097.19April2010

description:
Cranio097.19April2010.CEL
osteoblasts derived from human skull


title: Cranio101.24Sept09

description:
Cranio101.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio084.13April2010

description:
Cranio084.13April2010.CEL
osteoblasts derived from human skull


title: Cranio095.10Oct09

description:
Cranio095.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio081.19April2010

description:
Cranio081.19April2010.CEL
osteoblasts derived from human skull


title: Cranio080.19April2010

description:
Cranio080.19April2010.CEL
osteoblasts derived from human skull


title: Cranio076.19April2010

description:
Cranio076.19April2010.CEL
osteoblasts derived from human skull


title: Cranio069.10Oct09

description:
Cranio069.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio077.24Sept09

description:
Cranio077.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio075.19April2010

description:
Cranio075.19April2010.CEL
osteoblasts derived from human skull


title: Cranio071.19April2010

description:
Cranio071.19April2010.CEL
osteoblasts derived from human skull


title: Cranio064.04Dec09

description:
Cranio064.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio070.10Oct09

description:
Cranio070.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio073.24Sept09

description:
Cranio073.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio065.14April2010

description:
Cranio065.14April2010.CEL
osteoblasts derived from human skull


title: Cranio074.13April2010

description:
Cranio074.13April2010.CEL
osteoblasts derived from human skull


title: Cranio063.24Sept09

description:
Cranio063.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio059.15April2010

description:
Cranio059.15April2010.CEL
osteoblasts derived from human skull


title: Cranio057.19April2010

description:
Cranio057.19April2010.CEL
osteoblasts derived from human skull


title: Cranio068.15April2010

description:
Cranio068.15April2010.CEL
osteoblasts derived from human skull


title: Cranio052.04Dec09

description:
Cranio052.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio072.19April2010

description:
Cranio072.19April2010.CEL
osteoblasts derived from human skull


title: Cranio078.04Dec09

description:
Cranio078.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio060.14April2010

description:
Cranio060.14April2010.CEL
osteoblasts derived from human skull


title: Cranio053.13April2010

description:
Cranio053.13April2010.CEL
osteoblasts derived from human skull


title: Cranio054.14April2010

description:
Cranio054.14April2010.CEL
osteoblasts derived from human skull


title: Cranio062.24Sept09

description:
Cranio062.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio079.13April2010

description:
Cranio079.13April2010.CEL
osteoblasts derived from human skull


title: Cranio056.13April2010

description:
Cranio056.13April2010.CEL
osteoblasts derived from human skull


title: Cranio061.04Dec09

description:
Cranio061.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio058.15April2010

description:
Cranio058.15April2010.CEL
osteoblasts derived from human skull


title: Cranio067.19April2010

description:
Cranio067.19April2010.CEL
osteoblasts derived from human skull


title: Cranio051.15April2010

description:
Cranio051.15April2010.CEL
osteoblasts derived from human skull


title: Cranio066.15April2010

description:
Cranio066.15April2010.CEL
osteoblasts derived from human skull


title: Cranio055.13April2010

description:
Cranio055.13April2010.CEL
osteoblasts derived from human skull


title: Cranio046.24Sept09

description:
Cranio046.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio047.13April2010

description:
Cranio047.13April2010.CEL
osteoblasts derived from human skull


title: Cranio048.13April2010

description:
Cranio048.13April2010.CEL
osteoblasts derived from human skull


title: Cranio049.21July2009

description:
Cranio049.21July2009.CEL
osteoblasts derived from human skull


title: Cranio042.21July2009

description:
Cranio042.21July2009.CEL
osteoblasts derived from human skull


title: Cranio044.10Oct09

description:
Cranio044.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio043.14April2010

description:
Cranio043.14April2010.CEL
osteoblasts derived from human skull


title: Cranio041.15April2010

description:
Cranio041.15April2010.CEL
osteoblasts derived from human skull


title: Cranio033.21July2009

description:
Cranio033.21July2009.CEL
osteoblasts derived from human skull


title: Cranio036.15April2010

description:
Cranio036.15April2010.CEL
osteoblasts derived from human skull


title: Cranio038.14April2010

description:
Cranio038.14April2010.CEL
osteoblasts derived from human skull


title: Cranio035.24Sept09

description:
Cranio035.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio031.15April2010

description:
Cranio031.15April2010.CEL
osteoblasts derived from human skull


title: Cranio028.14April2010

description:
Cranio028.14April2010.CEL
osteoblasts derived from human skull


title: Cranio050.13April2010

description:
Cranio050.13April2010.CEL
osteoblasts derived from human skull


title: Cranio045.24Sept09

description:
Cranio045.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio030.15April2010

description:
Cranio030.15April2010.CEL
osteoblasts derived from human skull


title: Cranio040.13April2010

description:
Cranio040.13April2010.CEL
osteoblasts derived from human skull


title: Cranio034.14April2010

description:
Cranio034.14April2010.CEL
osteoblasts derived from human skull


title: Cranio023.13April2010

description:
Cranio023.13April2010.CEL
osteoblasts derived from human skull


title: Cranio024.19April2010

description:
Cranio024.19April2010.CEL
osteoblasts derived from human skull


title: Cranio025.10Oct09

description:
Cranio025.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio039.13April2010

description:
Cranio039.13April2010.CEL
osteoblasts derived from human skull


title: Cranio022.19April2010

description:
Cranio022.19April2010.CEL
osteoblasts derived from human skull


title: Cranio026.04Dec09

description:
Cranio026.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio029.19April2010

description:
Cranio029.19April2010.CEL
osteoblasts derived from human skull


title: Cranio020.15April2010

description:
Cranio020.15April2010.CEL
osteoblasts derived from human skull


title: Cranio037.13April2010

description:
Cranio037.13April2010.CEL
osteoblasts derived from human skull


title: Cranio019.24Sept09

description:
Cranio019.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio017.13April2010

description:
Cranio017.13April2010.CEL
osteoblasts derived from human skull


title: Cranio021.13April2010

description:
Cranio021.13April2010.CEL
osteoblasts derived from human skull


title: Cranio018.19April2010

description:
Cranio018.19April2010.CEL
osteoblasts derived from human skull


title: Cranio032.14April2010

description:
Cranio032.14April2010.CEL
osteoblasts derived from human skull


title: Cranio027.19April2010

description:
Cranio027.19April2010.CEL
osteoblasts derived from human skull


title: Cranio014.10Oct09

description:
Cranio014.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio012.24Sept09

description:
Cranio012.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio015.24Sept09

description:
Cranio015.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio013.14April2010

description:
Cranio013.14April2010.CEL
osteoblasts derived from human skull


title: Cranio016.19April2010

description:
Cranio016.19April2010.CEL
osteoblasts derived from human skull


title: Cranio010.04Dec09

description:
Cranio010.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio011.04Dec09

description:
Cranio011.04Dec09.CEL
osteoblasts derived from human skull


title: Cranio009.10Oct09

description:
Cranio009.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio008.24Sept09

description:
Cranio008.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio004.14April2010

description:
Cranio004.14April2010.CEL
osteoblasts derived from human skull


title: Cranio003.15April2010

description:
Cranio003.15April2010.CEL
osteoblasts derived from human skull


title: Cranio005.24Sept09

description:
Cranio005.24Sept09.CEL
osteoblasts derived from human skull


title: Cranio006.15April2010

description:
Cranio006.15April2010.CEL
osteoblasts derived from human skull


title: Cranio007.10Oct09

description:
Cranio007.10Oct09.CEL
osteoblasts derived from human skull


title: Cranio002.14April2010

description:
Cranio002.14April2010.CEL
osteoblasts derived from human skull


title: Cranio001.15April2010

description:
Cranio001.15April2010.CEL
osteoblasts derived from human skull


title: Solitary fibrous tumor 2

status: Public on May 02 2011

city: Lund

first: Emely

last: Möller

address: Lund University Hospital

department: Clinical Genetics

country: Sweden

institute: Lund University

description: Global gene expression data

hyb_protocol: Biotinylated cDNA was hybridized to GeneChip Gene 1_0 st arrays. Arrays were washed and stained on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 (Affymetrix).

data_processing: Image analysis was perfomed using the GeneChip Operating Software (GCOS, Affymetrix). Background correction, normalization and probe summarization was done with the robust multichip average (RMA) algorithm implemented in the Expression Console software (Affymetrix).

source_name: soft tissue

label_protocol: cDNA was labelled with TdT using the WT Terminal Labeling kit (Affymetrix).

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) and purified with Qiagen´s RNeasy kit according to the manufacturers´ instructions.

tag: sample type

value: tumor biopsy

value: Solitary fibrous tumor


title: Myxofibrosarcoma 1

description: Global gene expression data

value: Myxofibrosarcoma


title: Low-grade fibromyxoid sarcoma 12

description: Global gene expression data

value: Low-grade fibromyxoid sarcoma


title: Myxofibrosarcoma 5

description: Global gene expression data


title: Myxofibrosarcoma 6

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 10

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 16

description: Global gene expression data


title: Myxofibrosarcoma 2

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 13

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 17

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 6

description: Global gene expression data


title: Myxofibrosarcoma 3

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 6

description: Global gene expression data

value: Extraskeletal myxoid chondrosarcoma


title: Solitary fibrous tumor 4

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 14

description: Global gene expression data


title: Myxofibrosarcoma 4

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 7

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 15

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 9

description: Global gene expression data


title: Solitary fibrous tumor 3

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 1

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 3

description: Global gene expression data


title: Solitary fibrous tumor 5

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 11

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 4

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 5

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 2

description: Global gene expression data


title: Low-grade fibromyxoid sarcoma 8

description: Global gene expression data


title: Solitary fibrous tumor 1

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 5

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 4

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 3

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 2

description: Global gene expression data


title: Extraskeletal myxoid chondrosarcoma 1

description: Global gene expression data


title: Desmoid fibromatosis 5

description: Global gene expression data

value: Desmoid fibromatosis tumor


title: Desmoid fibromatosis 4

description: Global gene expression data


title: Desmoid fibromatosis 2

description: Global gene expression data


title: Desmoid fibromatosis 1

description: Global gene expression data


title: Desmoid fibromatosis 3

description: Global gene expression data


title: p97FE65NULL_3

status: Public on Dec 12 2010

description: Cerebral cortex tissue.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Center for Expression Arrays (http://ra.microslu.washington.edu/).

data_processing: Bioconductor GCRMA normalization log2

label_protocol: Conversion of double strand cDNA into cRNA was accomplished by in vitro transcription using the BioArray High Yield RNA Transcription Labeling kit (Enzo Diagnostics, Farmingdale, NY) according to the manufacturer’s instructions.

extract_protocol: RNA was converted into double strand cDNA with the SuperScript II double stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA) according to the GeneChipTM Expression Analysis Technical Manual (Chapter 1 section 2.1.15) (Affymetrix, Santa Clara, CA).

tag: Cerebral cortex tissues were dissected from five FE65 wild-type and p97FE65 null littermate pairs (6 months of age) for RNA purification and array analysis.


title: p97FE65NULL_1

description: Cerebral cortex tissue.


title: TAM-Co

status: Public on Dec 08 2010

description: primary mouse microglia

source_name: PBS Control

extract_protocol: RNA was isolated by extraction with a commercially available kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Twelve hours after incubation of polarized BT474 cells with PBS, BsDd, or PtDd, mRNA was analyzed using oligonucleotide microarrays.

tag: cell type

value: epithelial cancer cells (primary microglia)


title: FE65WT_4

description: Cerebral cortex tissue.


title: p97FE65NULL_4

description: Cerebral cortex tissue.


title: FE65WT_2

description: Cerebral cortex tissue.


title: FE65WT_1

description: Cerebral cortex tissue.


title: FE65WT_5

description: Cerebral cortex tissue.


title: p97FE65NULL_5

description: Cerebral cortex tissue.


title: TAM-Pt

description: primary mouse microglia

source_name: recombinant Ad3 PtDd


title: TAM-Bs

description: primary mouse microglia

source_name: recombinant Ad3 BsDd


title: FE65WT_3

description: Cerebral cortex tissue.


title: Desmoid fibromatosis 6

description: Global gene expression data


title: Subject10_EIB_positive_pre_exercise

status: Public on Nov 10 2010

description: The lower airway portion of the induced sputum.

source_name: Induced sputum from EIB positive person

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Affymetrix GeneChip Human Genome HG-U133A Arrays and hybridized according to manufacurer’s instructions.

extract_protocol: The lower airway portion of the induced sputum was selected using a transfer pipette and dispersed in dithiothreitol 0.1% (Calbiochem, La Jolla, CA) in a cool shaking water bath at 20oC for 15 min. A portion of the homogenized sputum was used to assess cell viability, cell count and cell differential. The dispersed induced sputum sample was centrifuged at 250 g for 10 min, the supernatant removed, and the cell pellet was immediately treated with caotropic lysis buffer. Total RNA was extracted using the RNeasy Mini protocol (Qiagen, Valencia, CA).

treatment_protocol: The University of Washington Institutional Review Board approved the study protocols, and written informed consent was obtained from all participants. Subjects 18-59 years of age were recruited who had a physician diagnosis of asthma for = 1 year, and used only an inhaled beta2-agonist for asthma treatment. In accordance with a priori definitions, asthmatics with a methacholine PC20 = 4 mg/ml were identified with = 20% fall in FEV1 following exercise challenge (EIB+ group) and asthmatic controls without EIB were identified with = 5% fall in FEV1 following exercise challenge (EIB- group). Potential participants were excluded if baseline FEV1 was = 65% predicted, history of smoking cigarettes within the prior year or = 7 pack-year smoking, treated for acute asthma within the prior month, hospitalized for asthma within the prior 3 months, or history of life threatening asthma. Participants were excluded if they had used an inhaled or oral corticosteroid, leukotriene modifier, long-acting antihistamine, cromone, or long-acting beta2-agonist in the 30 days prior to the study. Comparisons were also made to non-asthmatic subjects with negative methacholine (PC20 > 8 mg/ml) and dry air exercise challenge tests (< 20% fall in FEV1 following exercise). Epithelial brushings and endobronchial biopsies were obtained from subjects with asthma and EIB defined by a methacholine PC20 = 4 mg/mL and = 15% fall in FEV1 following exercise challenge. Some epithelial brushings from asthmatics were placed in primary culture and used at passage 1 or 2 for in vitro experiments as detailed in the supplemental material.

tag: Induced sputum was conducted with 3% hypertonic saline via an ultrasonic nebulizer (DeVilbiss, Somerset, PA, USA). At 2-min intervals, subjects were asked to clear saliva from their mouth and then expectorate sputum. Sputum was collected over 20 min and was pooled into a single sample container. The induced sputum was placed on ice immediately and processed within 15 min of collection.


title: Subject11_EIB_negative_pre_exercise

source_name: Induced sputum from EIB negative person


title: p97FE65NULL_2

description: Cerebral cortex tissue.


title: Subject11_EIB_negative_post_exercise


title: Subject10_EIB_positive_post_exercise


title: Subject9_EIB_positive_post_exercise


title: Subject9_EIB_positive_pre_exercise


title: Subject8_EIB_negative_post_exercise


title: Subject7_EIB_positive_post_exercise


title: Subject5_EIB_negative_pre_exercise


title: Subject6_EIB_negative_post_exercise


title: Subject5_EIB_negative_post_exercise


title: Subject3_EIB_positive_pre_exercise


title: Subject4_EIB_negative_post_exercise


title: Subject2_EIB_positive_pre_exercise


title: Subject1_EIB_positive_post_exercise


title: Subject8_EIB_negative_pre_exercise


title: Subject7_EIB_positive_pre_exercise


title: Subject6_EIB_negative_pre_exercise


title: Subject2_EIB_positive_post_exercise


title: Subject1_EIB_positive_pre_exercise


title: Subject4_EIB_negative_pre_exercise


title: CH3

status: Public on Oct 05 2010

description: primary mouse microglia

source_name: control normoxia

extract_protocol: RNA was isolated from cultured myocytes by extraction with a commercially available kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Primary mouse microglia from WT and TLR4 knockout WT and TLR4 knockout were exposed to hypoxic or hypoglycemic (ischemic) or normoxic or normoglycemic (control) conditions for 24 h in triplicate. All cells were then exposed to 24 h of normoxic or normoglycemic (reperfusion) conditions.

value: primary mouse microglia

tag: genotype

value: wild-type


title: TN3

description: primary mouse microglia

source_name: TLR4 knockout normoxia

value: TLR4 knockout


title: TH3

description: primary mouse microglia

source_name: TLR4 knockout hypoxia


title: TH2

description: primary mouse microglia


title: CH2

description: primary mouse microglia


title: CN2

description: primary mouse microglia


title: CH1

description: primary mouse microglia


title: CN3

description: primary mouse microglia


title: TN1

description: primary mouse microglia


title: 26A-1_mMncN2_482JH

status: Public on Oct 01 2010

description: Macrophages

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

data_processing: R/Bioconductor RMA normalization log2

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Arrays according to the manufacturer’s instructions.

growth_protocol: culture: Macrophages isolated by lavage from the peritoneum of C57BL/6 mice 5 days after i.p. injection of thioglycolate were plated on 35 mm dishes (Costar) in Dulbecco’s minimum essential medium (DMEM) supplemented with 2% lipoprotein-deficient bovine serum, LPDS, Sigma). After a 2 h incubation, macrophages were extensively washed to remove non-adherent cells, and then incubated for 48 h with 50 ug/mL of acetylated-LDL in 2% LPDS or 2% LPDS alone in a 5% CO2 atmosphere at 37oC. The medium was changed daily.

extract_protocol: RNA was extracted with the RNeasy micro kit (Qiagen, Valencia, CA).

treatment_protocol:
Macrophages were treated for 4 h with serum-free medium or serum-free medium supplemented with 50 ug/mL of HDL, washed twice with PBS, and then exposed for 4 h to serum-free medium or serum-free medium supplemented with 100 ng/mL of LPS.
reagents: LPS (Escherichia coli 055:B5), zymosan, and methyl-beta-cyclodextrin were purchased from Sigma. Poly I:C and R848 were purchased from InvivoGen. TLR4 agonistic antibody (UT12) was purchased from eBioscience.

value: Macrophages

tag: strain


title: TH1

description: primary mouse microglia


title: 38A-1_mMncL2_482JH_2

description: Macrophages


title: 43A-1_mMwtL3_482JH

description: Macrophages


title: TN2

description: primary mouse microglia


title: 42A-1_mMwtL2_482JH

description: Macrophages


title: 41A-1_mMwtL1_482JH

description: Macrophages


title: 44A-1_mMwtL4_482JH

description: Macrophages


title: 28A-1_mMncN4_482JH

description: Macrophages


title: 40A-1_mMncL4_482JH

description: Macrophages


title: 37A-1_mMncL1_482JH

description: Macrophages


title: 39A-1_mMncL3_482JH

description: Macrophages


title: CN1

description: primary mouse microglia


title: 25A-1_mMncN1_482JH

description: Macrophages


title: P0.5_wt_Pa_3

status: Public on Jul 27 2010

description: Mouse E14.5 neocortices and Postnatal day (P) 0.5 brains.

growth_protocol: Tbr1 mutant mice were maintained as heterozygotes on CD1 background. To generate Tbr1 homozygous null animals, heterozygous males were crossed with heterozygous females. The day of the vaginal plug was considered embryonic day (E) 0.5. Pregnant dams were deeply anesthetized with Avertin (3-3-tribromoethanol; Sigma) and killed by cervical dislocation, after which embryos were harvested. For immunological analysis or in situ hybridization, embryos were rapidly removed and perfused with 4% paraformaldehyde in 1×PBS (pH 7.4). Embryonic brains were postfixed by immersion in cold buffered (4°C) 4% paraformaldehyde for 4-16 h. Brains were cryoprotected in 30% sucrose in 0.1 M sodium phosphate (pH 7.0), frozen in optimum cutting temperature compound (Sakura Finetek), cryosectioned at 12 um, andmounted on Superfrost Plus slides (Thermo Fisher Scientific). Slides were stored at -80°C until needed. All experimental procedures were approved by the University of Washington and Seattle Children's Research Institute Institutional Animal Care and Use Committees.

extract_protocol: Total RNA purification was performed as described (PMID: 19380167). Briefly, tissues were dissolved by low-power sonication in a solution consisting of 4 M guanidinium thiocyanate and 0.1 M 2-mercaptoethanol. After sonication, sodium acetate (pH 4), phenol (pH 4), and a 24:1 mix of chloroform and isoamylic acid were added on ice; after vigorous vortexing, aqueous solution containing total RNA was separated by high-speed centrifugation at 4 °C for 20 min. RNA was precipitated by adding an equal volume of isopropanol, and it was stored at -20 °C overnight and then, pelleted by centrifugation for 20 min at maximum speed at 4 °C, rinsed with 70% ethanol, and resuspended in an appropriate volume of nuclease-free water.

tag: developmental stage

tag: genotype/variation

value: wild type

value: parietal brain


title: P0.5_wt_Oc_2

source_name: Mouse E14.5 neocortices and Postnatal day (P) 0.5 brains

value: occipital brain


title: P0.5_wt_Oc_4


title: P0.5_wt_Fr_2

value: frontal brain


title: P0.5_wt_Pa_4


title: P0.5_wt_Oc_3


title: P0.5_wt_Fr_1


title: P0.5_wt_Fr_3


title: P0.5_KO_Pa_4


title: P0.5_wt_Oc_1


title: P0.5_wt_Pa_2


title: P0.5_wt_Pa_1


title: P0.5_KO_Pa_2


title: P0.5_KO_Pa_3


title: P0.5_KO_Pa_1


title: P0.5_wt_Fr_4


title: 27A-1_mMncN3_482JH

description: Macrophages


title: P0.5_KO_Oc_3


title: Subject3_EIB_positive_post_exercise


title: E14.5_wt_3

value: neocortex


title: P0.5_KO_Fr_4


title: E14.5_wt_1


title: P0.5_KO_Oc_4


title: E14.5_KO_3


title: P0.5_KO_Oc_2


title: P0.5_KO_Fr_3


title: E14.5_wt_2


title: P0.5_KO_Fr_1


title: P0.5_KO_Fr_2


title: P0.5_KO_Oc_1


title: E14.5_KO_1


title: E14.5_KO_2


title: P.10.48.p.2.1002

status: Public on Jul 19 2010

description: primary hepatocytes

hyb_protocol: The standard hybridization protocol was used as recommended by GE Healthcare/Amersham Biosciences CodeLink UniSet Human 20K I Bioarray.

scan_protocol: GeneChips were scanned using the Axon 4000B scanner.

data_processing: CodeLink System Software - Analysis, version: 2.3.2. R/Bioconductor quantile normalized, no background subtraction, Imagene Signal.Mean, log2

source_name: primary human hepatocytes

label_protocol: For microarray hybridization, RNA was processed for hybridization to GE Healthcare/Amersham Biosciences Arrays according to the manufacturer's instructions.

growth_protocol:
Culture protocol: hepatocytes were cultured as described in Gross-Steinmeyer K, Stapleton PL, Tracy JH, Bammler TK, Strom SC, Buhler DR, Eaton DL. Modulation of aflatoxin B1-mediated genotoxicity in primary cultures of human hepatocytes by diindolylmethane, curcumin and xanthohumols.Toxicol Sci. 2009, 112:303-10.
Isolation protocol: primary hepatocytes were isolated as described in Strom, S. C., Pisarov, L. A., Dorko, K., Thompson, M. T., Schuetz, J. D., and Schuetz, E. G. (1996). Use of human hepatocytes to study P450 gene induction. Meth. Enzymol. 272, 388-401.

value: P

tag: dose (um)

tag: time (hr)

tag: batch

tag: liver

tag: reps

value: primary hepatocytes


title: S.50.48.p.2.1002

description: primary hepatocytes

tag: treatment

value: S


title: P.25.48.p.2.1002

description: primary hepatocytes


title: S.50.48.p.2.987

description: primary hepatocytes


title: P.10.48.p.2.985

description: primary hepatocytes


title: O.30.48.p.3.987

description: primary hepatocytes

value: O


title: O.30.48.p.3.985

description: primary hepatocytes


title: S.10.48.p.2.985

description: primary hepatocytes


title: S.10.48.p.2.987

description: primary hepatocytes


title: P.25.48.p.2.985

description: primary hepatocytes


title: S.50.48.p.2.985

description: primary hepatocytes


title: D.50.48.p.2.1002

description: primary hepatocytes

value: D


title: O.30.48.p.3.970

description: primary hepatocytes


title: P.25.48.p.2.970

description: primary hepatocytes


title: O.30.48.p.3.1002

description: primary hepatocytes


title: P.10.48.p.2.970

description: primary hepatocytes


title: D.10.48.p.2.1002

description: primary hepatocytes


title: c.0.0.p.2.1002

description: primary hepatocytes

value: c


title: c.0.0.p.2.985

description: primary hepatocytes


title: D.50.48.p.2.985

description: primary hepatocytes


title: D.10.48.p.2.985

description: primary hepatocytes


title: c.0.0.p.2.970

description: primary hepatocytes


title: S.10.48.p.2.1002

description: primary hepatocytes


title: c.0.48.p.1.1002

description: primary hepatocytes


title: c.0.48.p.1.970.1

description: primary hepatocytes


title: c.0.0.p.2.987

description: primary hepatocytes


title: c.0.48.p.1.987

description: primary hepatocytes


title: D.50.48.p.2.970

description: primary hepatocytes


title: c.0.48.p.1.985.1

description: primary hepatocytes


title: D.10.48.p.2.970

description: primary hepatocytes


title: c.0.48.p.1.970

description: primary hepatocytes


title: c.0.48.p.1.985

description: primary hepatocytes


title: SN_2hr_CON_P30

status: Public on Jul 07 2010

description: TAMH cells

extract_protocol: RNA was isolated from TAMH cells dosed with 2mM APAP, 2mM AMAP or control culture media for 2, 6 and 24-hour timepoints.  For each treatment, cells were grown to confluence in two 150cm2 tissue culture dishes and dosed.  At the end of each treatment, cells were harvested using a rubber scraper.  Cell pellets were collected by centrifugation, and washed using ice-cold DPBS.  Trizol reagent was added to the DPBS-washed pellet, vortexed and passed through a 22G needle multiple times to ensure complete cell lysis.  Chloroform was then added, and the mixture was spun in a microcentrifuge at 8200g.  The aqueous phase was isolated and dissolved in 70% ethanol.  The resulting mixture was loaded onto a Qiagen RNeasy column (Valencia, CA).  Purified total RNAs were eluted in sterile water according to the manufacturer’s protocol.

tag: cell line

value: TAMH

tag: media

value: TAMH cells were grown in serum-free Dulbecco’s modified Eagle’s medium/Ham’s F12 (1:1) media supplemented with 100nm dexamethasone, 10nM nicotinamide, 0.1% (v/v) gentamicin, and an ITS premix containing insulin (5mg/mL), transferrin (5mg/mL) and selenium (5ng/mL).

tag: passage

value: Cell passages between 25 and 35 were grown in a humidified incubator with 5% CO2 and 95% air at 37ºC.  During passages, cells were incubated for one minute with trypsin.  Cell detachment was monitored using a microscope.

tag: plating

value: Once detachment was complete, 5mL of 0.5mg/mL soybean trypsin inhibitor in Hank’s balanced salt solution was added before plating.


title: SN_6hr_APAP_P30

description: TAMH cells


title: SN_6hr_CON_P32

description: TAMH cells


title: SN_2hr_CON_P31

description: TAMH cells


title: SN_2hr_APAP_P30

description: TAMH cells


title: SN_2hr_AMAP_P31

description: TAMH cells


title: SN_6hr_APAP_P32

description: TAMH cells


title: SN_6hr_AMAP_P31

description: TAMH cells


title: SN_2hr_AMAP_P30

description: TAMH cells


title: SN_6hr_APAP_P31

description: TAMH cells


title: SN_2hr_APAP_P32

description: TAMH cells


title: SN_2hr_CON_P32

description: TAMH cells


title: SN_6hr_CON_P31

description: TAMH cells


title: SN_6hr_CON_P30

description: TAMH cells


title: SN_2hr_APAP_P31

description: TAMH cells


title: SN_2hr_AMAP_P32

description: TAMH cells


title: SN_6hr_AMAP_P30

description: TAMH cells


title: SN_6hr_AMAP_P32

description: TAMH cells


title: SN_24hr_CON_P32

description: TAMH cells


title: SN_24hr_CON_P30

description: TAMH cells


title: SN_24hr_APAP_P30

description: TAMH cells


title: SN_24hr_AMAP_P30

description: TAMH cells


title: SN_24hr_APAP_P31

description: TAMH cells


title: SN_24hr_APAP_P32

description: TAMH cells


title: SN_24hr_AMAP_P31

description: TAMH cells


title: SN_24hr_AMAP_P32

description: TAMH cells


title: HN_125

status: Public on Mar 31 2010

description: Airway epithelial cells

data_processing: R/Bioconductor GC-RMA normalization log2

source_name: Airway epithelial cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix GeneChip® Human HG-U133A Arrays according to the manufacturer’s instructions.

extract_protocol: RTotal RNA was extracted from epithelial cells using the QIAGEN RNeasy kit (Vic, Australia).

treatment_protocol:
tissue: Epithelial cells were collected by bronchial brushing and cultured.
media: For culture, cells were washed once in RPMI-1640 media and the cell pellet resuspended in bronchial epithelial basal media (BEBM, Clonetics, CA) supplemented with bovine pituitary extract (50 mM), insulin (5 mM), hydrocortisone (0.5 mM), gentamicin (0.001%, v/v), amphotericin B (0.0005%, v/v), retinoic acid (0.1 µM), transferrin (10 mM), triiodothyronine (6.5 µM), epinephrine (6.5 µM) and human recombinant epidermal growth factor (EGF: 0.5 µM).
plating: The plate was incubated for 20 minutes (37C, 5% CO2) to allow the macrophages to adhere. The suspended epithelial cells were aspirated from the plate, and the macrophages removed using trypsin (0.25%) for subsequent analysis.
passage: The cells were seeded into a culture vessel (25 cm2 growth surface area) pre-coated with a mixture of fibronectin, collagen and bovine serum albumin, and maintained at 37C in a humidified incubator. Twenty-four hours post-isolation, unattached cells were collected. These cells were reseeded into the same culture vessel, with fresh media containing Ultroser G (2% v/v; BioSepra, CA), a serum substitute. The collection and reseeding of viable unattached cells was repeated at both 48 and 72 hours post isolation. Subsequent cultures were fed every second day and were usually passaged every 13–16 days.

value: epithelial cells


title: HN_97

description: Airway epithelial cells


title: HN_122

description: Airway epithelial cells


title: HN_127

description: Airway epithelial cells


title: AA_135

description: Airway epithelial cells


title: AA_124

description: Airway epithelial cells


title: AA_87

description: Airway epithelial cells


title: HN_109

description: Airway epithelial cells


title: AA_88

description: Airway epithelial cells


title: AA_128

description: Airway epithelial cells


title: HN_119

description: Airway epithelial cells


title: AA_126

description: Airway epithelial cells


title: AA_78

description: Airway epithelial cells


title: HN_64

description: Airway epithelial cells


title: WT_3_treated

status: Public on Jan 04 2010

description: cultured myocytes.

treatment_protocol: Transgenic mice overexpressing CHF1/Hey2 in the myocardium under the control of the mlc2v promoter and neonatal mouse cardiac myocyte culture was performed as previously described. To induce hypertrophy, neonatal myocytes in serum free medium were exposed to media with 20% fetal bovine serum for 24 hours.

tag: cultured myocytes


title: WT_4_treated

description: cultured myocytes.


title: AA_71

description: Airway epithelial cells

tag: cell type


title: TG_5_treated

description: cultured myocytes.


title: TG_7_treated

description: cultured myocytes.


title: WT_1

status: Public on Jan 20 2010

description: Samples were heart ventricle total RNA 1 week after aortic banding, from either wild type or CHF1/Hey2 transgenic mice overexpressing CHF1/Hey2 in the myocardium.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through a Core Facility at the Harvard Partners Center for Genetics and Genomics (Cambridge, MA),.

source_name: heart

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Arrays and hybridized according to manufacurer’s instructions.

extract_protocol: RNA was isolated from frozen heart tissue by homogenization with a Polytron homogenizer and then extraction with a commercially available kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: male mice, 8-12 weeks old, wild type and CHF1/Hey2 transgenic (myocardial specific, mlc2v promoter) on an FVB background, treated with ascending aortic banding for one week.

tag: Samples were heart ventricle total RNA isolated 1 week after ascending aortic banding, taken from 8-12 week old male wild type and CHF1/Hey2 transgenic mice


title: WT_7_treated

description: cultured myocytes.


title: WT_4


title: WT_6_treated

description: cultured myocytes.


title: WT_1_treated

description: cultured myocytes.


title: TG_1_treated

description: cultured myocytes.


title: AA_98

description: Airway epithelial cells


title: WT_5_treated

description: cultured myocytes.


title: TG_6_treated

description: cultured myocytes.


title: WT_5_no_treatment

description: cultured myocytes.


title: TG_4


title: WT_3


title: WT_2_treated

description: cultured myocytes.


title: TG_4_treated

description: cultured myocytes.


title: TG_3_treated

description: cultured myocytes.


title: TG_2_treated

description: cultured myocytes.


title: WT_2


title: TG_3


title: TG_1


title: WT_2_no_treatment

description: cultured myocytes.


title: WT_3_no_treatment

description: cultured myocytes.


title: WT_1_no_treatment

description: cultured myocytes.


title: TG_2


title: WT_4_no_treatment

description: cultured myocytes.


title: SN_24hr_CON_P31

description: TAMH cells


title: TG_5_no_treatment

description: cultured myocytes.


title: TG_2_no_treatment

description: cultured myocytes.


title: TG_6_no_treatment

description: cultured myocytes.


title: TG_4_no_treatment

description: cultured myocytes.


title: TG_3_no_treatment

description: cultured myocytes.


title: TG_1_no_treatment

description: cultured myocytes.


title: zebrafish brain6 low

status: Public on Jul 06 2009

description: Wild type zebrafish (Danio rerio, ABC strain) were obtained from the University of Oregon, Zebrafish International Resource Center (Eugene, OR, USA) and maintained at the Northwest Fisheries Science Center in a self-contained re-circulating aquaculture ZMOD system (Marine Biotech Inc.).  The facility is operated according to standard procedures for zebrafish husbandry and research (Westerfield 1995).  Fish were maintained at 26°C, kept on a 14:10 h light-dark cycle, and fed daily with purified ground salmon feed and brine shrimp. Fish were not fed on the morning of each exposure experiment.

source_name: brain

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Zebrafish Genome Arrays and hybridized according to manufacurer’s instructions.

extract_protocol: Total RNA was extracted from individual snap frozen zebrafish brains using a standard TRIzol procedure with the inclusion of 1 µl RNAse inhibitor/sample.

treatment_protocol: To quantify DA-induced neurobehavioral excitotoxicity in zebrafish, adult fish were exposed to DA via intracoelomic (IC) injection at several doses.  For injection, fish were netted individually, placed into Ziplock bags and injected through the bag at a point midway between the pectoral fins and the anus.  Contents (10 ml) were slowly injected into the IC cavity.  IC injections consisted of a vehicle control (phosphate buffered saline (PBS) only) or DA dissolved in PBS.  Eight exposure doses (0.21 ± 0.01, 0.25 ± 0.03, 0.32 ± 0.04, 0.47 ± 0.07, 0.82 ± 0.09, 1.2 ± 0.15, 1.6 ± 0.1, and 3.2 ± 0.5 µg DA/g body weight; n = 4 fish per treatment) were used.  After injection, four fish from each treatment were placed in 1-liter clear plastic tanks and observed for 6 h.  Behavioral toxicity was quantified by the presence or absence of circle or spiral swimming.  Time to the onset of excitotoxicity and the number of fish affected were recorded for each treatment.  Percentages of fish affected at each dose were used to generate a dose-response curve and an EC50 for behavioral toxicity using Graphpad Prism® software (San Diego, CA).  All DA exposure doses were confirmed by HPLC-UV analysis (see HPLC verification of DA exposure doses below). All animal studies were carried out under approved IACUC protocols at the University of Washington.


title: zebrafish brain7 high

tag: Wild type zebrafish (Danio rerio, ABC strain) were obtained from the University of Oregon, Zebrafish International Resource Center (Eugene, OR, USA) and maintained at the Northwest Fisheries Science Center in a self-contained re-circulating aquaculture ZMOD system (Marine Biotech Inc.).  The facility is operated according to standard procedures for zebrafish husbandry and research (Westerfield 1995).  Fish were maintained at 26°C, kept on a 14:10 h light-dark cycle, and fed daily with purified ground salmon feed and brine shrimp. Fish were not fed on the morning of each exposure experiment.


title: X3A.1_A28CR11_205PR RAT WAT

status: Public on Oct 23 2007

data_processing: GeneTraffic version 3.2-11 GCRMA normalization

organism: Rattus norvegicus

source_name: white adipose tissue

label_protocol: Total RNA (2 ug) was labeled and hybridized to the RAE230 2.0 arrays and hybridized according to manufacurer’s instructions.

extract_protocol: Total RNA was extracted from frozen tissue samples by homogenization in Trizol® (Life Technologies, Grand Island, NY) and chloroform extraction followed by purification on an RNeasy® Mini column (Qiagen, Valencia, CA).

treatment_protocol: Tissues (n=5-7 animals per group) were obtained from the NIH-NIA aging rodent tissue bank. According to supplier records, animals were housed in a specific pathogen free barrier facility under contract with BioReliance. AL animals were housed 3 per cage and CR animals were housed singly. CR (60% of AL) was initiated at 4 months of age with a switch from the NIH 31 to NIH fortified diet. F344 male rats were sacrificed at 4 months (4AL) or 28 months of age (28AL, 28CR). Animals with gross tumor pathologies were excluded from the study. All animals were euthanized by CO2 asphixiation and tissues were frozen in liquid nitrogen then stored at –80°C. Subcutaneous WAT was collected from the abdominal region. Recorded body weights differed dramatically between the 3 groups (4AL = 253±8 g, 28AL = 382±20 g, 28CR = 288±7 g) and heart weight as a fraction of body weight was not significantly different between the groups (data not shown). The apical ~1/3 of the heart was homogenized for the expression studies. Sections from the cut face were stained with haematoxylin and eosin to confirm expected aging-associated pathology changes.


title: X7A.1_A4AL20_205PR RAT WAT

description: According to supplier records, animals were housed in a specific pathogen free barrier facility under contract with BioReliance. AL animals were housed 3 per cage and CR animals were housed singly. CR (60% of AL) was initiated at 4 months of age with a switch from the NIH 31 to NIH fortified diet. F344 male rats were sacrificed at 4 months (4AL) or 28 months of age (28AL, 28CR). Animals with gross tumor pathologies were excluded from the study. All animals were euthanized by CO2 asphixiation and tissues were frozen in liquid nitrogen then stored at –80°C. Subcutaneous WAT was collected from the abdominal region. Recorded body weights differed dramatically between the 3 groups (4AL = 253±8 g, 28AL = 382±20 g, 28CR = 288±7 g) and heart weight as a fraction of body weight was not significantly different between the groups (data not shown). The apical ~1/3 of the heart was homogenized for the expression studies. Sections from the cut face were stained with haematoxylin and eosin to confirm expected aging-associated pathology changes.

tag: Tissues (n=5-7 animals per group) were obtained from the NIH-NIA aging rodent tissue bank.


title: X8A.1_A4AL23_205PR RAT WAT


title: X2A.1_A28CR10_205PR RAT WAT


title: X5A.1_A28AL8_205PR RAT WAT


title: X19A.1_A4AL21_205PR RAT WAT


title: zebrafish brain9 high


title: zebrafish brain8 high


title: X6A.1_A28AL10_205PR RAT WAT


title: zebrafish brain5 low


title: zebrafish brain1 control