title: dkfz_ETMR_15-0001

value: ETMR

value: cerebellar


title: dkfz_EPN_15-0014

status: Public on Feb 25 2016

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

description: Gene expression data from a brain tumor sample

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: brain tumor

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: affymetrix id

tag: institutional tumor diagnosis

value: EPN

tag: molecular subgroup

tag: gender

value: F

tag: age (years)

tag: tumor location

value: supratentorial (NOS)


title: dkfz_ETMR_15-0011

value: M


title: High Density Rice Array (HDRAG6.4) NSFTV37

type: genomic

city: Ithaca

first: Susan

middle: R.

last: McCouch

state: NY

address: 162 Emerson Hall

department: Plant Breeding & Genetics

country: USA

institute: Cornell University

description: High Density Rice Array assays 700,000 SNPs

hyb_protocol: The probe was generated using the BioPrime DNA labeling kit (Invitrogen, Cat. No: 18094-011) and hybridization conditions were based on the Affymetrix SNP 6.0 protocol as performed by Expression Analysis in N.C.. A preliminary enzyme digestion was not performed and human Cot-1 DNA was not included due to the small size of the rice genome and the fact that it has a much smaller proportion of repetitive DNA compared to human or other mammals for which the assay was originally optimized.

scan_protocol: Scanning and image acquisition was performed according to standard protocols for whole genome genotyping of Affymetrix chips by Expression Analysis in N.C.

data_processing:
Affymetrix Power Tools (APT) software (Affymetrix, Inc.) was used to extract individual probe intensities from Affymetrix .CEL files for each sample and the raw probe intensities were converted to log scale and output to a file which could be loaded by the genotype calling program ALCHEMY (Wright et al., 2010).  Genotype calling was then performed by ALCHEMY v1.07 as described in Wright et al. (2010) and in McCouch et al. (2015).
The file "matrix.csv" contains the Genotype Call (SNP call): AA, AB, BB  NoCall; 'Signal' = Call quality

molecule: genomic DNA

organism: Oryza sativa

source_name: young leaves of 6 weeks old plants grown in Ithaca U.S.A

label_protocol: A total of 50 ng of high-quality rice genomic DNA was used as template for labeled-probe generation. Probe labeling followed the manufacturer’s recommendation for the Affymetrix SNP assay kit and was performed at Expression Analysis in N.C..

growth_protocol: Rice plants for the Rice Diversity Panel 1 (RDP1) were grown in the Guterman greenhouse in Ithaca, NY using standard greenhouse management practices and pest control; genomic DNA was extracted from young leaves of 6 week old plants. Rice plants for the RDP2 were grown in the field during the wet season at IRRI, Philippines using standard crop management practices for irrigation and pest control; genomic DNA was extracted from young leaves of 6-8 week old plants.

extract_protocol: Rice genomic DNA was extracted from young green leaf tissue following the Qiagen plant DNeasy protocol.

tag: tissue

value: leaf


title: dkfz_EPN_15-0010


title: High Density Rice Array (HDRAG6.4) NSFTV45


title: dkfz_EPN_15-0001

value: frontal lobe


title: High Density Rice Array (HDRAG6.4) NSFTV36


title: dkfz_ETMR_15-0003

value: hemispheric (NOS)


title: dkfz_ETMR_15-0007

value: brainstem


title: High Density Rice Array (HDRAG6.4) NSFTV35


title: High Density Rice Array (HDRAG6.4) NSFTV34


title: dkfz_EPN_15-0002

value: parietal lobe


title: High Density Rice Array (HDRAG6.4) NSFTV32


title: dkfz_EPN_15-0006


title: dkfz_HGG_15-0016

value: GBM

value: corpus callosum/parietal lobe


title: dkfz_GBM_15-0008

value: temporal/parietal/occipital lobe


title: High Density Rice Array (HDRAG6.4) NSFTV33


title: dkfz_EPN_15-0016

value: parietal/temporal/occipital lobe


title: dkfz_ATRT_15-0012

value: AT/RT


title: High Density Rice Array (HDRAG6.4) NSFTV29


title: dkfz_HGG_15-0055


title: dkfz_MB_15-0047

value: MB


title: dkfz_ATRT_15-0008

value: frontal lobe, right


title: dkfz_EPN_15-0032


title: dkfz_ATRT_15-0007


title: dkfz_CNS-PNET_15-0293

value: CNS-PNET

value: parietal/temporal lobe, right


title: High Density Rice Array (HDRAG6.4) NSFTV27


title: High Density Rice Array (HDRAG6.4) NSFTV28


title: High Density Rice Array (HDRAG6.4) NSFTV26


title: High Density Rice Array (HDRAG6.4) NSFTV23


title: High Density Rice Array (HDRAG6.4) NSFTV30


title: High Density Rice Array (HDRAG6.4) NSFTV21


title: dkfz_CNS-PNET_15-0095

value: temporal/parietal lobe


title: dkfz_EPN_15-0037

value: EPN


title: dkfz_HGG_15-0030

value: F

value: fourth ventricle/brainstem


title: High Density Rice Array (HDRAG6.4) NSFTV20

value: leaf


title: High Density Rice Array (HDRAG6.4) NSFTV19


title: High Density Rice Array (HDRAG6.4) NSFTV25


title: dkfz_CNS-PNET_15-0185

value: PINEAL

value: M

value: hypothalamic, leptomeningeal spread


title: dkfz_GBM_15-0013

value: GBM


title: dkfz_ATRT_15-0009

value: fourth ventricle/vermis


title: dkfz_EPN_15-0019

value: cerebellar


title: dkfz_CNS-PNET_15-0228

value: frontal lobe


title: dkfz_HGG_15-0029

value: spinal (T5-7)


title: High Density Rice Array (HDRAG6.4) NSFTV16


title: High Density Rice Array (HDRAG6.4) NSFTV13


title: High Density Rice Array (HDRAG6.4) NSFTV22


title: High Density Rice Array (HDRAG6.4) NSFTV15


title: High Density Rice Array (HDRAG6.4) NSFTV11


title: dkfz_ATRT_15-0005

value: AT/RT

value: brainstem/cerebellopontine angle


title: dkfz_CNS-PNET_15-0262

value: CNS-PNET

value: supra-/intrasellar


title: High Density Rice Array (HDRAG6.4) NSFTV9


title: dkfz_CNS-PNET_15-0176

value: lateral ventricle


title: High Density Rice Array (HDRAG6.4) NSFTV10


title: dkfz_CNS-PNET_15-0217

value: ETMR

value: parietal/occipital lobe


title: High Density Rice Array (HDRAG6.4) NSFTV18


title: High Density Rice Array (HDRAG6.4) NSFTV17


title: dkfz_CNS-PNET_15-0224

value: temporal/parietal lobe


title: High Density Rice Array (HDRAG6.4) NSFTV8

value: leaf


title: dkfz_CNS-PNET_15-0184

value: parietal lobe


title: dkfz_CNS-PNET_15-0166

value: F


title: dkfz_CNS-PNET_15-0171

value: M


title: dkfz_CNS-PNET_15-0274


title: dkfz_CNS-PNET_15-0302

value: frontal lobe, right


title: High Density Rice Array (HDRAG6.4) NSFTV7


title: High Density Rice Array (HDRAG6.4) NSFTV5


title: High Density Rice Array (HDRAG6.4) NSFTV6


title: dkfz_CNS-PNET_15-0075


title: High Density Rice Array (HDRAG6.4) NSFTV3


title: High Density Rice Array (HDRAG6.4) NSFTV4


title: dkfz_CNS-PNET_15-0042

value: spinal (L3-S2)


title: High Density Rice Array (HDRAG6.4) NSFTV1


title: High Density Rice Array (HDRAG6.4) NSFTV2


title: dkfz_CNS-PNET_15-0319

value: temporal/parietal lobe, right


title: dkfz_CNS-PNET_15-0280

value: occipital lobe


title: dkfz_CNS-PNET_15-0057

value: parietal lobe, left


title: dkfz_CNS-PNET_15-0158

value: peduncular


title: HDM non-sensitized subject #NA24 HDM stimulated

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: NA24 H.CEL

hyb_protocol: The samples were hybridized to Human Gene ST1.0 microarrays according to standard Affymetrix protocols. This was performed by at the Ramaciotti Centre for Genomics, The University of New South Wales.

scan_protocol: The samples were scanned on an Affymetrix scanner at the Ramaciotti Centre for Genomics, The University of New South Wales.

data_processing:
The microarray data was preprocessed in R employing the RMA algorithm and a custom chip description file (primeviewhsentrezg, version 19). ComBat was used to adjust the data for batch effects.
RMA normalized expression values on the log2 scale, adjusted for batch effects with comBat.

label: Biotin

source_name: HDM nonallergic_HDM stimulated

label_protocol: Standardized kits from Affymetrix were used to label the samples at the Ramaciotti Centre for Genomics, The University of New South Wales.

growth_protocol: PBMC cultured in AIM-V medium for 24 hours

extract_protocol: Total RNA was extracted using TRIzol followed by RNeasy.

treatment_protocol:
PBMC were cultured in medium in the presence or absence of HDM (10 ug/ml).
After 24 hours, immunomagnetic separation was performed to purify CD4 T cells.

tag: subject id

tag: subject status

value: HDM non-sensitized subject

tag: phenotype

value: HDM nonallergic

tag: cell type

value: CD4 T cells isolated from PBMC

tag: culture condition

value: HDM stimulated


title: dkfz_CNS-PNET_15-0107

value: CNS-PNET

value: frontal lobe, left


title: HDM non-sensitized subject #NA23 HDM stimulated

description: NA23 H.CEL


title: dkfz_ETMR_15-0008

value: ETMR

value: thalamic/lateral ventricle


title: HDM non-sensitized subject #NA24  medium control

description: NA24 C.CEL

source_name: HDM nonallergic_Medium control

value: Medium control


title: dkfz_CNS-PNET_15-0050

value: F

value: frontal lobe


title: dkfz_CNS-PNET_15-0205

value: AT/RT

value: M

value: frontal/parietal lobe, left


title: HDM non-sensitized subject #NA22  medium control

description: NA22 C.CEL


title: HDM non-sensitized subject #NA22 HDM stimulated

description: NA22 H.CEL


title: dkfz_CNS-PNET_15-0305

value: intraventricular


title: HDM non-sensitized subject #NA21  medium control

description: NA21 C.CEL


title: HDM non-sensitized subject #NA21 HDM stimulated

description: NA21 H.CEL


title: dkfz_CNS-PNET_15-0045

value: unclassifiable

value: parietal lobe, left


title: dkfz_HGG_15-0035

value: GBM

value: thalamic


title: dkfz_CNS-PNET_15-0223


title: HDM non-sensitized subject #NA23  medium control

description: NA23 C.CEL

value: HDM non-sensitized subject

value: HDM nonallergic

value: CD4 T cells isolated from PBMC


title: dkfz_CNS-PNET_15-0256

value: CNS-PNET

value: EWS

value: spinal (L5)


title: dkfz_CNS-PNET_15-0270


title: dkfz_ETMR_15-0002

value: ETMR

value: brainstem


title: HDM non-sensitized subject #NA20 HDM stimulated

description: NA20 H.CEL

value: HDM stimulated


title: HDM non-sensitized subject #NA19 HDM stimulated

description: NA19 H.CEL


title: dkfz_CNS-PNET_15-0190

value: AT/RT


title: HDM non-sensitized subject #NA20  medium control

description: NA20 C.CEL

value: Medium control


title: HDM non-sensitized subject #NA18 HDM stimulated

description: NA18 H.CEL


title: dkfz_CNS-PNET_15-0285

value: F

value: frontal/parietal lobe


title: dkfz_CNS-PNET_15-0147

value: frontal lobe, right


title: HDM non-sensitized subject #NA17 HDM stimulated

description: NA17 H.CEL


title: HDM non-sensitized subject #NA19  medium control

description: NA19 C.CEL


title: HDM non-sensitized subject #NA16  medium control

description: NA16 C.CEL


title: High Density Rice Array (HDRAG6.4) NSFTV31

value: leaf


title: HDM non-sensitized subject #NA15  medium control

description: NA15 C.CEL


title: HDM non-sensitized subject #NA16 HDM stimulated

description: NA16 H.CEL


title: HDM non-sensitized subject #NA15 HDM stimulated

description: NA15 H.CEL


title: HDM non-sensitized subject #NA17  medium control

description: NA17 C.CEL


title: HDM non-sensitized subject #NA18  medium control

description: NA18 C.CEL


title: HDM non-sensitized subject #NA14 HDM stimulated

description: NA14 H.CEL


title: HDM non-sensitized subject #NA13 HDM stimulated

description: NA13 H.CEL


title: HDM non-sensitized subject #NA12 HDM stimulated

description: NA12 H.CEL


title: HDM non-sensitized subject #NA13  medium control

description: NA13 C.CEL


title: HDM non-sensitized subject #NA14  medium control

description: NA14 C.CEL


title: HDM non-sensitized subject #NA12  medium control

description: NA12 C.CEL


title: HDM non-sensitized subject #NA10  medium control

description: NA10 C.CEL


title: dkfz_ATRT_15-0011

value: M

value: intraventricular


title: HDM non-sensitized subject #NA11  medium control

description: NA11 C.CEL

value: HDM non-sensitized subject


title: High Density Rice Array (HDRAG6.4) NSFTV24


title: HDM non-sensitized subject #NA10 HDM stimulated

description: NA10 H.CEL

value: HDM nonallergic


title: HDM non-sensitized subject #NA09  medium control

description: NA09 C.CEL

value: CD4 T cells isolated from PBMC


title: HDM non-sensitized subject #NA08 HDM stimulated

description: NA08 H.CEL


title: HDM non-sensitized subject #NA09 HDM stimulated

description: NA09 H.CEL


title: HDM non-sensitized subject #NA11 HDM stimulated

description: NA11 H.CEL


title: dkfz_CNS-PNET_15-0160

value: CNS-PNET

value: unclassifiable

value: parietal/occipital lobe


title: HDM non-sensitized subject #NA07  medium control

description: NA07 C.CEL


title: HDM non-sensitized subject #NA08  medium control

description: NA08 C.CEL


title: dkfz_CNS-PNET_15-0063

value: optic chiasm


title: dkfz_CNS-PNET_15-0226

value: frontal lobe


title: dkfz_ETMR_15-0006

value: ETMR

value: cerebellar/brainstem


title: HDM non-sensitized subject #NA06 HDM stimulated

description: NA06 H.CEL

value: HDM stimulated


title: HDM non-sensitized subject #NA06  medium control

description: NA06 C.CEL

value: Medium control


title: dkfz_CNS-PNET_15-0244

value: parietal/parasaggital


title: dkfz_CNS-PNET_15-0031

value: F

value: temporal lobe


title: dkfz_CNS-PNET_15-0066


title: dkfz_CNS-PNET_15-0074


title: dkfz_CNS-PNET_15-0295

value: M


title: dkfz_CNS-PNET_15-0026


title: dkfz_CNS-PNET_15-0197


title: HDM non-sensitized subject #NA05 HDM stimulated

description: NA05 H.CEL


title: dkfz_CNS-PNET_15-0119

value: AT/RT


title: HDM non-sensitized subject #NA07 HDM stimulated

description: NA07 H.CEL

value: HDM non-sensitized subject


title: dkfz_CNS-PNET_15-0146


title: HDM non-sensitized subject #NA05  medium control

description: NA05 C.CEL

value: HDM nonallergic


title: dkfz_CNS-PNET_15-0082

value: frontal/parietal lobe, right


title: HDM non-sensitized subject #NA04 HDM stimulated

description: NA04 H.CEL

value: CD4 T cells isolated from PBMC


title: dkfz_HGG_15-0032

value: GBM

value: pons


title: dkfz_CNS-PNET_15-0091

value: CNS-PNET


title: dkfz_CNS-PNET_15-0139

value: parietal/occipital lobe


title: HDM non-sensitized subject #NA04  medium control

description: NA04 C.CEL


title: dkfz_ETMR_15-0004

value: ETMR


title: dkfz_ETMR_15-0005


title: HDM non-sensitized subject #NA02  medium control

description: NA02 C.CEL


title: HDM non-sensitized subject #NA02 HDM stimulated

description: NA02 H.CEL


title: dkfz_CNS-PNET_15-0173


title: dkfz_HGG_15-0018


title: dkfz_CNS-PNET_15-0071


title: dkfz_CNS-PNET_15-0168


title: HDM non-sensitized subject #NA03 HDM stimulated

description: NA03 H.CEL


title: HDM non-sensitized subject #NA03  medium control

description: NA03 C.CEL


title: dkfz_CNS-PNET_15-0018


title: dkfz_HGG_15-0034

value: thalamic


title: HDM non-sensitized subject #NA01  medium control

description: NA01 C.CEL


title: HDM non-sensitized subject #NA01 HDM stimulated

description: NA01 H.CEL

value: HDM stimulated


title: dkfz_CNS-PNET_15-0035


title: HDM sensitized atopic subject without asthma #AN32 HDM stimulated

description: AN32 H.CEL

source_name: HDM allergic_HDM stimulated

value: HDM allergic


title: dkfz_ATRT_15-0006


title: dkfz_ATRT_15-0003

value: cerebellopontine angle


title: dkfz_ETMR_15-0009

value: F

value: parietal lobe


title: dkfz_ATRT_15-0002

value: M

value: posterior fossa


title: dkfz_CNS-PNET_15-0297


title: dkfz_EPN_15-0018

value: EPN

value: cerebellar


title: HDM sensitized atopic subject without asthma #AN32  medium control

description: AN32 C.CEL

source_name: HDM allergic_Medium control

value: Medium control


title: dkfz_HGG_15-0015

value: temporal lobe


title: HDM sensitized atopic subject without asthma #AN31 HDM stimulated

description: AN31 H.CEL

value: CD4 T cells isolated from PBMC


title: dkfz_HGG_15-0027

value: GBM


title: dkfz_HGG_15-0051


title: HDM sensitized atopic subject without asthma #AN31  medium control

description: AN31 C.CEL


title: dkfz_HGG_15-0020


title: dkfz_HGG_15-0026


title: HDM sensitized atopic subject without asthma #AN28 HDM stimulated

description: AN28 H.CEL


title: HDM sensitized atopic subject without asthma #AN30  medium control

description: AN30 C.CEL


title: dkfz_HGG_15-0021


title: dkfz_HGG_15-0028


title: HDM sensitized atopic subject without asthma #AN30 HDM stimulated

description: AN30 H.CEL


title: HDM sensitized atopic subject without asthma #AN28  medium control

description: AN28 C.CEL


title: HDM sensitized atopic subject without asthma #AN29  medium control

description: AN29 C.CEL


title: HDM sensitized atopic subject without asthma #AN29 HDM stimulated

description: AN29 H.CEL


title: dkfz_HGG_15-0022


title: HDM sensitized atopic subject without asthma #AN27  medium control

description: AN27 C.CEL


title: HDM sensitized atopic subject without asthma #AN26 HDM stimulated

description: AN26 H.CEL


title: dkfz_HGG_15-0023

value: frontal lobe


title: dkfz_HGG_15-0036


title: HDM sensitized atopic subject without asthma #AN27 HDM stimulated

description: AN27 H.CEL


title: HDM sensitized atopic subject without asthma #AN26  medium control

description: AN26 C.CEL


title: dkfz_HGG_15-0017


title: HDM sensitized atopic subject without asthma #AN25  medium control

description: AN25 C.CEL


title: HDM sensitized atopic subject without asthma #AN25 HDM stimulated

description: AN25 H.CEL


title: dkfz_HGG_15-0031


title: dkfz_HGG_15-0013

value: temporal lobe, right


title: HDM sensitized atopic subject without asthma #AN24 HDM stimulated

description: AN24 H.CEL


title: dkfz_HGG_15-0038


title: dkfz_HGG_15-0033

value: intraventricular, left


title: HDM sensitized atopic subject without asthma #AN23 HDM stimulated

description: AN23 H.CEL


title: HDM sensitized atopic subject without asthma #AN23  medium control

description: AN23 C.CEL


title: dkfz_HGG_15-0019


title: HDM sensitized atopic subject without asthma #AN24  medium control

description: AN24 C.CEL


title: dkfz_HGG_15-0037

value: thalamic, left


title: dkfz_HGG_15-0014

value: hemispheric, left


title: HDM sensitized atopic subject without asthma #AN21  medium control

description: AN21 C.CEL

value: HDM allergic


title: HDM sensitized atopic subject without asthma #AN21 HDM stimulated

description: AN21 H.CEL

value: HDM stimulated


title: dkfz_HGG_15-0008

value: frontal lobe, right


title: dkfz_HGG_15-0001

value: F


title: dkfz_HGG_15-0011

value: M

value: parietal/temporal lobe, left


title: HDM sensitized atopic subject without asthma #AN20 HDM stimulated

description: AN20 H.CEL


title: HDM sensitized atopic subject without asthma #AN19 HDM stimulated

description: AN19 H.CEL


title: dkfz_HGG_15-0005

value: temporal lobe, left


title: dkfz_HGG_15-0025


title: HDM sensitized atopic subject without asthma #AN19  medium control

description: AN19 C.CEL


title: control vs choline deficient

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

organism: Mus musculus

source_name: control fed

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: The mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of liver tissue were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Male CD-1mice (5 weeks) were fed either a choline-deficient diet (F2CDD, Oriental Yeast) or F2CDD plus 0.2% choline bitartrate for 3 weeks.

tag: strain

tag: Sex

value: male

source_name: choline-deficient fed


title: HDM sensitized atopic subject without asthma #AN20  medium control

description: AN20 C.CEL

value: Medium control


title: HDM sensitized atopic subject without asthma #AN17  medium control

description: AN17 C.CEL


title: HDM sensitized atopic subject without asthma #AN16 HDM stimulated

description: AN16 H.CEL


title: subject_20 [exon-level]

city: Irvine

first: Marquis

last: Vawter

state: CA

address: 837 Health Science Rd

department: Psychiatry

institute: University of California, Irvine

hyb_protocol: The fragmented and labeled DNA was combined with the Hybridization Control Kit (Affymetrix) to make the cocktail to be loaded onto the array. The cocktail was heated for 5 minutes at 99°C and cooled for 5 minutes at 45°C, then centrifuged 1 minute. A volume of 200 ul was loaded onto the array and the arrays were placed in a 45°C hybridization oven, at 60 rpm, to incubate for 17 hours.  The GeneChip Hybridization, Wash and Stain Kit (Affymetrix) was used with the Fluidics Station 450_0001 protocol.

scan_protocol: Scanning was performed using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Cel files were imported into Partek Genomics software using RMA, without background correction. The average of probe intensity was used to calculate probeset intensity. Downstream analysis included both exon level, and gene level using Partek Genomics software. A model that used diagnosis by probeset interaction was run on each transcript, and significant interactions were noted that passed bonferroni correction.
HuEx-1_0-st-v2.r2-SNPs-Excluded.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: anterioir cingulate cortex

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

extract_protocol: All RNA samples were prepared using Trizol (Invitrogen) and treated with the RiboMinus Transcriptome Isolation Kit (Invitrogen). cDNA was prepared using the WT cDNA Synthesis and Amplification Kit (Affymetrix).

tag: diagnosis

value: bipolar disorder

value: Female


title: EAT_western diet_0.05% quercetin_rep7

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from epididymal adipose tissue after 18 week feeding of western diet containing 0.05% quercetin

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: epididymal adipose tissue, fed western diet with 0.05% quercetin for 18 weeks

label_protocol: The fragmented biotin-labeled aRNA was synthesized from the total RNA of each mouse using the GeneChip® 3′ IVT Express Kit (Affymetrix Japan KK, Tokyo, Japan).

growth_protocol: Five-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed at 24 ± 1°C, 55 ± 5% humidity, and 12 h light/dark photocycles (dark period from 8:00 to 20:00), with free access to water and a standard nonpurified diet for 1 week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were divided into three groups, housed in groups of three per cage, and fed one of the following diets: AIN93G (control); a high-fat, high-cholesterol, and high-sucrose Western-style diet [39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose] (Oriental Yeast Co., Tokyo, Japan); or the same Western diet supplemented with 0.05% quercetin for 18 weeks.

value: epididymal adipose tissue


title: EAT_western diet_0.05% quercetin_rep9


title: subject_19 [exon-level]

value: control

value: Male


title: subject_18 [exon-level]


title: HDM sensitized atopic subject without asthma #AN15  medium control

description: AN15 C.CEL

value: CD4 T cells isolated from PBMC


title: HDM sensitized atopic subject without asthma #AN15 HDM stimulated

description: AN15 H.CEL


title: EAT_western diet_0.05% quercetin_rep5


title: subject_12 [exon-level]


title: subject_10 [exon-level]


title: EAT_western diet_0.05% quercetin_rep6


title: HDM sensitized atopic subject without asthma #AN14 HDM stimulated

description: AN14 H.CEL


title: subject_17 [exon-level]


title: subject_8 [exon-level]


title: subject_14 [exon-level]


title: subject_9 [exon-level]


title: HDM sensitized atopic subject without asthma #AN14  medium control

description: AN14 C.CEL


title: EAT_western diet_0.05% quercetin_rep8


title: EAT_western diet_0.05% quercetin_rep3


title: subject_11 [exon-level]


title: dkfz_GBM_15-0012

value: GBM

value: hemispheric (NOS)


title: HDM sensitized atopic subject without asthma #AN11 HDM stimulated

description: AN11 H.CEL

value: HDM allergic


title: subject_4 [exon-level]


title: HDM sensitized atopic subject without asthma #AN16  medium control

description: AN16 C.CEL


title: HDM sensitized atopic subject without asthma #AN17 HDM stimulated

description: AN17 H.CEL

value: HDM stimulated


title: subject_6 [exon-level]


title: HDM sensitized atopic subject without asthma #AN11  medium control

description: AN11 C.CEL


title: HDM sensitized atopic subject without asthma #AN10 HDM stimulated

description: AN10 H.CEL


title: HDM sensitized atopic subject without asthma #AN10  medium control

description: AN10 C.CEL


title: subject_2 [exon-level]


title: HDM sensitized atopic subject without asthma #AN08 HDM stimulated

description: AN08 H.CEL


title: EAT_Western diet_rep6

description: Gene expression data from epididymal adipose tiessue after 18 week feeding of Western diet

source_name: epididymal adipose tissue, fed western diet for 18 weeks


title: EAT_Western diet_rep8


title: EAT_western diet_0.05% quercetin_rep1


title: EAT_western diet_0.05% quercetin_rep2


title: EAT_Western diet_rep9


title: EAT_Western diet_rep4


title: HDM sensitized atopic subject without asthma #AN08  medium control

description: AN08 C.CEL


title: EAT_Western diet_rep7


title: HDM sensitized atopic subject without asthma #AN07 HDM stimulated

description: AN07 H.CEL


title: HDM sensitized atopic subject without asthma #AN07  medium control

description: AN07 C.CEL


title: dkfz_EPN_15-0015

value: EPN

value: supratentorial (NOS)


title: EAT_Western diet_rep5


title: EAT_Western diet_rep2


title: dkfz_HGG_15-0012

value: M


title: subject_15 [exon-level]


title: dkfz_EPN_15-0004


title: subject_1 [exon-level]


title: dkfz_EPN_15-0009

value: F


title: subject_3 [exon-level]


title: EAT_western diet_0.05% quercetin_rep4


title: subject_16 [exon-level]


title: EAT_Western diet_rep1


title: EAT_Western diet_rep3


title: EAT_control diet_rep9

description: Gene expression data from epididymal adipose tiessue after 18 week feeding of control AIN93G diet

source_name: epididymal adipose tissue, fed control AIN93G diet for 18 weeks


title: HDM sensitized atopic subject without asthma #AN05 HDM stimulated

description: AN05 H.CEL


title: recuperated 4

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

hyb_protocol: The cDNA were fragmented and hybridized onto Rat Genome 230 2.0 Arrays at 45 degree Celcius for 16 h. Followed by wash and stain in Affymetrix Fluidics Station 450

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were normalized by RMA using Affymetrix Expression Console software

organism: Rattus norvegicus

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 4

label_protocol: The RNA was amplified using NuGen Ovation WTA Pico Kit and then fragmented and were biotin-labelled using GeneChip IVT labeling kit (Affymetrix)

extract_protocol: 14um frozen hypothalamic sections were fixed in 95% ethanol and stained with 1% cresyl violet, followed by dehydration in graded ethanol concentrations (50%, 75% and 100%).  Laser capture microdissection (LCM) was performed using a Zeiss PALM microlaser system to collect the arcuate nucleus and RNA was extracted using RNAqueous Micro RNA extraction kit (Ambion) in accordance with the manufacturer’s protocol.

treatment_protocol: On postnatal day 3, two experimental groups of offspring were established: controls (offspring of control dams) and recuperated (offspring of dams fed a low-protein diet (8% protein, w/v), but nursed by control dams. The animals were fed with standard chow until 3 months of age where the brains were collected for transcriptomic profiling

value: Wistar

value: hypothalamic arcuate nucleus


title: recuperated 6

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 6

value: male


title: HDM sensitized atopic subject without asthma #AN05  medium control

description: AN05 C.CEL

value: Medium control


title: HDM sensitized atopic subject without asthma #AN04 HDM stimulated

description: AN04 H.CEL


title: HDM sensitized atopic subject without asthma #AN02  medium control

description: AN02 C.CEL


title: subject_13 [exon-level]

value: bipolar disorder

value: Female


title: dkfz_EPN_15-0008


title: recuperated 5

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 5


title: HDM sensitized atopic subject without asthma #AN02 HDM stimulated

description: AN02 H.CEL


title: dkfz_EPN_15-0007


title: dkfz_EPN_15-0003


title: subject_5 [exon-level]


title: HDM sensitized atopic subject without asthma #AN04  medium control

description: AN04 C.CEL


title: dkfz_EPN_15-0027

value: parietal lobe


title: EAT_control diet_rep8

value: epididymal adipose tissue


title: dkfz_EPN_15-0005


title: EAT_control diet_rep7


title: EAT_control diet_rep5


title: EAT_control diet_rep3


title: EAT_control diet_rep4


title: EAT_control diet_rep6


title: recuperated 3

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 3


title: HDM sensitized atopic subject without asthma #AN01 HDM stimulated

description: AN01 H.CEL

value: CD4 T cells isolated from PBMC


title: subject_7 [exon-level]

value: control

value: Male


title: HDM sensitized atopic subject without asthma #AN01  medium control

description: AN01 C.CEL

value: HDM allergic


title: recuperated 1

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 1


title: HDM sensitized atopic subject with asthma #AA30  medium control

description: AA30 C.CEL

source_name: HDM allergic with asthma_Medium control

value: HDM allergic with asthma


title: HDM sensitized atopic subject with asthma #AA29 HDM stimulated

description: AA29 H.CEL

source_name: HDM allergic with asthma_HDM stimulated

value: HDM stimulated


title: recuperated 2

source_name: RNA extracted from the hypothalamic arcuate nucleus from recuperated animal 2


title: control 6

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 6


title: control 5

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 5


title: HDM sensitized atopic subject with asthma #AA30 HDM stimulated

description: AA30 H.CEL


title: EAT_control diet_rep2


title: HDM sensitized atopic subject with asthma #AA29  medium control

description: AA29 C.CEL


title: EAT_control diet_rep1


title: control 4

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 4


title: HDM sensitized atopic subject with asthma #AA31  medium control

description: AA31 C.CEL


title: control 3

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 3


title: control 2

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 2


title: HDM sensitized atopic subject with asthma #AA27 HDM stimulated

description: AA27 H.CEL


title: HDM sensitized atopic subject without asthma #AN06 HDM stimulated

description: AN06 H.CEL

source_name: HDM allergic_HDM stimulated


title: control 1

source_name: RNA extracted from the hypothalamic arcuate nucleus from control animal 1


title: HDM sensitized atopic subject with asthma #AA31 HDM stimulated

description: AA31 H.CEL


title: CD19+ B cells  CD24intCD38int  rep 5

city: Creteil

first: Caroline

last: Pilon

address: 51 avenue du Mal de Lattre de Tassigny

country: France

institute: INSERM U955 Eq21, Hopital Henri Mondor

description: CD19+CD24intCD38int sorted cells

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17h, 65°C) to an Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray using Agilent's recommended hybridization chamber and oven.

scan_protocol: After two washes (1/ with the Agilent Gene Expression Wash Buffer 1 for 1min at RT and 2/ with preheated Agilent Gene Expression Wash Buffer 2 at 37°C for 1min,), fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral blood CD19+CD24intCD38int cells

label_protocol: 250ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: RNA from fifteen human cell samples were lysed using SuperAmp Lysis Buffer (Miltenyi Biotec) according to the instructions of the SuperAmp Preparation Kit. SuperAmp RNA amplification was performed according to Miltenyi's Biotec's undisclosed procedure (base on a global PCR protocol using mRNA-derived cDNA.  RNA and cDNA were quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Peripheral blood mononuclear cells from freshly drawn whole blood were separed using gradient density centrifugation. CD20+ b cells were isolated using magnetic beads separation. CD19+ b cells were sorted by flow cytometry based on 2 markers CD24 and CD38: CD19+CD24hiCD38hi (test), CD19+CD24+CD38- (control 1) and CD19+CD24intCD38int (control 2)

value: Blood

tag: cells

value: B cells

tag: sorted cell


title: nTREG-Lymphatic Filariasis negative-rep4

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 4340_SM_1_Human_44_235-37-Treg-N-T-M_01_9312

hyb_protocol: All cDNAs were hybridized to the commercial Affymetrix human U133 plus 2.0 GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with EC 1.2 and scaled to 1250 [program-name = Expression Console, program-id = 1.2.0.20 ]

source_name: nTREG-Lymphatic Filariasis negative

label_protocol: Fragmented ds cDNAs were then end-labeled with biotin using terminal transferase (Nugen Inc.)

growth_protocol: Antigen presenting cells (APCs) and natural regulatory T cells (nTregs) were enriched using a Human Monocyte Enrichment Cocktail and the complete kit for Human CD4+CD127lowCD25+ Regulatory T cells (both from StemCell Technologies, Vancouver, Canada) following the manufacturer’s protocol

extract_protocol: RNA was extracted using AllPrep DNA/RNA® 96 kit (Qiagen) following the manufacturer’s recommendations

tag: subject group

value: filaria-uninfected (Fil-)

value: Natural regulatory T cells (nTregs)


title: CD19+ B cells  CD24intCD38int  rep 4

description: CD19+CD24intCD38int sorted cells


title: nTREG-Lymphatic Filariasis positive-rep1

description: 4362_SM_1_Human_66_99-15-Treg-P-B-F_01_2734

source_name: nTREG-Lymphatic Filariasis positive

value: filaria-infected (Fil+)


title: nTREG-Lymphatic Filariasis positive-rep2

description: 4363_SM_1_Human_67_123-19-Treg-P-B-M_01_3796


title: nTREG-Lymphatic Filariasis negative-rep2

description: 4320_SM_1_Human_24_87-13-Treg-N-B-M_01_9384


title: nTREG-Lymphatic Filariasis positive-rep3

description: 4387_SM_1_Human_91_223-35-Treg-P-T-M_01_9360


title: patient 6 post-relapse

type: SRA

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

library_source: transcriptomic

data_processing:
Data was analyzed using the Broad Picard Pipeline which includes demultiplexing and data aggregation.
Genome_build: Hg19. Raw data will be submitted to dbGaP.
Supplementary_files_format_and_content: Excel sheet containing RPKM values for each gene

molecule: polyA RNA

extract_protocol:
RNA was extracted from frozen tissue using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions, including the optional oncolumn DNase digest. All samples were quantified using Nanodrop and quality was evaluated using Agilent's Bioanalyzer 2100.
Total RNA was quantified using the Quant-iT™ RiboGreen® RNA Assay Kit (Invitrogen) and normalized to 4ng/ul. An aliquot of 200ng for each sample was transferred into library preparation which was an automated variant of the Illumina Tru Seq™ RNA Sample Preparation protocol (Revision A, 2010). This method uses oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly. The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or PerkinElmer JANUS Mini liquid handlers. Libraries were sequenced on an Illumina HiSeq 2500 instrument with paired-end reads of 76 base pairs.

treatment_protocol: Surgical biopsies were obtained prior to treatment with dabrafenib/trametinib and again  after the development of resistance. All tumor tissue was stored at -80°C until DNA  and RNA extraction was performed.

value: melanoma

tag: treatment

value: dabrafenib and tremetinib


title: nTREG-Lymphatic Filariasis negative-rep3

description: 4339_SM_1_Human_43_195-31-Treg-N-T-M_01_9314


title: patient 5 post-relapse


title: patient 3 post-relapse

value: dabrafenib


title: CD19+ B cells  CD24intCD38int  rep 3

description: CD19+CD24intCD38int sorted cells


title: HDM sensitized atopic subject with asthma #AA26  medium control

description: AA26 C.CEL

value: Medium control


title: HDM sensitized atopic subject with asthma #AA27  medium control

description: AA27 C.CEL


title: CD19+ B cells  CD24intCD38int  rep 1

description: CD19+CD24intCD38int sorted cells


title: HDM sensitized atopic subject with asthma #AA25  medium control

description: AA25 C.CEL


title: CD19+ B cells  CD24intCD38int  rep 2

description: CD19+CD24intCD38int sorted cells


title: CD19+ B cells  CD24+CD38-  rep 3

description: CD19+CD24+CD38- sorted cells

source_name: peripheral blood CD19+CD24+CD38- cells


title: CD19+ B cells  CD24+CD38-  rep 4

description: CD19+CD24+CD38- sorted cells


title: HDM sensitized atopic subject with asthma #AA24 HDM stimulated

description: AA24 H.CEL


title: patient 2 post-relapse


title: CD19+ B cells  CD24+CD38-  rep 2

description: CD19+CD24+CD38- sorted cells


title: patient 4 post-relapse


title: CD19+ B cells  CD24+CD38-  rep 5

description: CD19+CD24+CD38- sorted cells


title: HDM sensitized atopic subject with asthma #AA26 HDM stimulated

description: AA26 H.CEL


title: patient 1 post-relapse


title: nTREG-Lymphatic Filariasis negative-rep1

description: 4319_SM_1_Human_23_45-6-Treg-N-B-M_01_9385


title: HDM sensitized atopic subject with asthma #AA25 HDM stimulated

description: AA25 H.CEL


title: HDM sensitized atopic subject with asthma #AA23 HDM stimulated

description: AA23 H.CEL


title: patient 5 pre-treatment


title: HDM sensitized atopic subject with asthma #AA23  medium control

description: AA23 C.CEL


title: CD19+ B cells  CD24+CD38-  rep 1

description: CD19+CD24+CD38- sorted cells


title: patient 4 pre-treatment


title: HDM sensitized atopic subject without asthma #AN06  medium control

description: AN06 C.CEL

source_name: HDM allergic_Medium control


title: HDM sensitized atopic subject with asthma #AA24  medium control

description: AA24 C.CEL


title: CD19+ B cells  CD24hiCD38hi  rep 3

description: CD19+CD24hiCD38hi sorted cells

source_name: peripheral blood CD19+CD24hiCD38hi cells


title: HDM sensitized atopic subject with asthma #AA22 HDM stimulated

description: AA22 H.CEL


title: CD19+ B cells  CD24hiCD38hi  rep 4

description: CD19+CD24hiCD38hi sorted cells


title: patient 2 pre-treatment


title: CD19+ B cells  CD24hiCD38hi  rep 5

description: CD19+CD24hiCD38hi sorted cells


title: CD19+ B cells  CD24hiCD38hi  rep 2

description: CD19+CD24hiCD38hi sorted cells


title: HDM sensitized atopic subject with asthma #AA21 HDM stimulated

description: AA21 H.CEL


title: CD19+ B cells  CD24hiCD38hi  rep 1

description: CD19+CD24hiCD38hi sorted cells


title: HDM sensitized atopic subject with asthma #AA21  medium control

description: AA21 C.CEL


title: patient 3 pre-treatment


title: HDM sensitized atopic subject with asthma #AA20  medium control

description: AA20 C.CEL


title: HDM sensitized atopic subject with asthma #AA19 HDM stimulated

description: AA19 H.CEL


title: patient 1 pre-treatment


title: HDM sensitized atopic subject with asthma #AA22  medium control

description: AA22 C.CEL


title: HDM sensitized atopic subject with asthma #AA20 HDM stimulated

description: AA20 H.CEL


title: HDM sensitized atopic subject with asthma #AA19  medium control

description: AA19 C.CEL


title: HDM sensitized atopic subject with asthma #AA18 HDM stimulated

description: AA18 H.CEL


title: HDM sensitized atopic subject with asthma #AA18  medium control

description: AA18 C.CEL


title: Vandana_roots_WW_replicate 2

city: Los Banos

first: Manish

middle: L

last: Raorane

state: Laguna

address: UP college campus

department: Plant Breeding, Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

description: Gene expression in well water control roots of Vandana

hyb_protocol: 600ng of Cy 3-labeled, amplified cRNA with a specific activity of above 6 were used for subsequent hybridization following the steps of the One-color Microarray-Based Gene Expression Analysis protocol (Agilent). Hybridizations were carried out at 65C for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8X60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm double pass, Dye channel is set to Green and the green PMT is set to 100% ).

data_processing: The resultant microarray TIF images were processed to run batch extractions by choosing the appropriate grid using Agilent’s Feature Extraction Software version 11.0. The quantified feature text file was first analyzed for quality using the Agilent QC chart tool.

source_name: Vandana_roots_well water control

label_protocol: The Low Input Quick Amp Labeling kit for One-color Microarray-Based Gene Expression Analysis was used for labeling of RNA samples (50 ng) using cyanine 3 (Cy 3) fluorescent dye following the manufacturer’s instructions (Agilent). The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) according to the manufacturer’s protocol and the quantity was recorded using a NanoDrop spectrophotometer. Based on that data, the specific activity and yield of cRNA were calculated.

growth_protocol: Plants for the microarray analysis were grown during the 2013 wet season in soil-filled cylinders in a screenhouse. Seeds of Vandana, 481-B, IR64 and the OsNAM12.1 overexpression line (OsNAM Event 2) were sown in 5 biological replicates in a randomized complete block design for both the well watered and drought stress treatments.

extract_protocol: Total RNA was isolated from root tissues using the TRIzol reagent (Invitrogen) and RNAeasy columns (Qiagen). RNA concentration was measured using a NanoDrop UV-VIS spectrophotometer (Peqlab) and quality of RNA samples was evaluated using RNA Nano 6000 kit (Agilent) and Bioanalyzer (Agilent).

treatment_protocol: Soil in the well-watered treatment was maintained at field capacity for Vandana and 481-B and at 1.2x field capacity for IR64 and OsNAM Event 2, based on the adaptation of those genotypes. The drought stress treatment for all genotypes was a drydown from 75% of field capacity. Tissue samples from roots of five different plants of each genotype for each treatment were collected at 25 DAS. After collection, all samples were wrapped in aluminum foil and placed directly into liquid nitrogen before storing at − 80C.

tag: cultivar

value: Vandana

tag: stress

value: roots

tag: age

value: 25 days after sowing


title: HDM sensitized atopic subject with asthma #AA16 HDM stimulated

description: AA16 H.CEL

value: CD4 T cells isolated from PBMC


title: Vandana_roots_WW_replicate 3

value: control


title: Vandana_roots_WW_replicate 1


title: Vandana_roots_DD75%_replicate 3

description: Gene expression in drought stress roots of Vandana

source_name: Vandana_roots_drought stress

value: drought


title: DUSP4-T-3

city: Zhunan

first: Ching-Yu

last: Huang

state: Miao-Li

address: NO. 35, Keyan Rd.,

department: Immunology Research Center

country: Taiwan

institute: National Health Research Institutes

description: Gene expression data from MACS-sorted splenic T cell sample DUSP4 KO 3

hyb_protocol: 3.5 ug of labelling cDNA were hybridized for 16 hr at 45C on GeneChip (MoGene-2.0-st). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip scanner 3000 7G (Affymatrix), GeneChip® Command Console® Software.

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 5.5 ug fragmentation cDNA

growth_protocol: n/a; primary cells isolated via MACS methods without culture.

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

treatment_protocol: n/a; primary cells isolated via MACS methods without treatment.

value: spleen

tag: genotype

value: dusp4 ko

value: 6-8 wk old


title: HDM sensitized atopic subject with asthma #AA16  medium control

description: AA16 C.CEL

source_name: HDM allergic with asthma_Medium control

value: HDM allergic with asthma


title: HDM sensitized atopic subject with asthma #AA15 HDM stimulated

description: AA15 H.CEL

source_name: HDM allergic with asthma_HDM stimulated

value: HDM stimulated


title: OsNAM Event 2_roots_WW_replicate 3

description: Gene expression in well water control roots of OsNAM Event 2

source_name: OsNAM Event 2_roots_well water control

value: OsNAM Event 2

tag: tissue


title: DUSP4-T-1

description: Gene expression data from MACS-sorted splenic T cell sample DUSP4 KO 1


title: OsNAM Event 2_roots_DD75%_replicate 3

description: Gene expression in drought stress roots of OsNAM Event 2

source_name: OsNAM Event 2_roots_drought stress


title: Vandana_roots_DD75%_replicate 2


title: OsNAM Event 2_roots_WW_replicate 1


title: DUSP4-T-2

description: Gene expression data from MACS-sorted splenic T cell sample DUSP4 KO 2


title: HDM sensitized atopic subject with asthma #AA12 HDM stimulated

description: AA12 H.CEL

tag: subject id


title: B6-T-3

description: Gene expression data from MACS-sorted splenic T cell sample WT 3

source_name: MACS-sorted splenic T cell sample WT 3

value: WT


title: HDM sensitized atopic subject with asthma #AA15  medium control

description: AA15 C.CEL

tag: subject status


title: OsNAM Event 2_roots_DD75%_replicate 2


title: Vandana_roots_DD75%_replicate 1


title: HDM sensitized atopic subject with asthma #AA12  medium control

description: AA12 C.CEL

tag: phenotype


title: OsNAM Event 2_roots_DD75%_replicate 1


title: HDM sensitized atopic subject with asthma #AA11 HDM stimulated

description: AA11 H.CEL

tag: cell type


title: HDM sensitized atopic subject with asthma #AA09 HDM stimulated

description: AA09 H.CEL

tag: culture condition


title: B6-T-1

description: Gene expression data from MACS-sorted splenic T cell sample WT 1

source_name: MACS-sorted splenic T cell sample WT 1


title: HDM sensitized atopic subject with asthma #AA08 HDM stimulated

description: AA08 H.CEL


title: HDM sensitized atopic subject with asthma #AA09  medium control

description: AA09 C.CEL


title: HDM sensitized atopic subject with asthma #AA11  medium control

description: AA11 C.CEL


title: HDM sensitized atopic subject with asthma #AA07 HDM stimulated

description: AA07 H.CEL


title: HDM sensitized atopic subject with asthma #AA08  medium control

description: AA08 C.CEL


title: 481-B_roots_WW_replicate 3

description: Gene expression in well water control roots of 481-B

source_name: 481-B_roots_well water control


title: 481-B_roots_DD75%_replicate 1

description: Gene expression in drought stress roots of 481-B

source_name: 481-B_roots_drought stress


title: 481-B_roots_DD75%_replicate 2


title: IR64_roots_WW_replicate 3

description: Gene expression in well water control roots of IR64

source_name: IR64_roots_well water control


title: 481-B_roots_WW_replicate 1


title: HDM sensitized atopic subject with asthma #AA03  medium control

description: AA03 C.CEL


title: HDM sensitized atopic subject with asthma #AA07  medium control

description: AA07 C.CEL


title: 481-B_roots_WW_replicate 2


title: HDM sensitized atopic subject with asthma #AA01 HDM stimulated

description: AA01 H.CEL


title: IR64_roots_WW_replicate 1


title: 481-B_roots_DD75%_replicate 3


title: HDM sensitized atopic subject with asthma #AA03 HDM stimulated

description: AA03 H.CEL


title: IR64_roots_DD75%_replicate 3

description: Gene expression in drought stress roots of IR64

source_name: IR64_roots_drought stress


title: IR64_roots_DD75%_replicate 1


title: IR64_roots_DD75%_replicate 2


title: Pooled LR-2

status: Public on Feb 24 2016

type: protein

city: Houston

first: Tsz-Kwong

last: Man

state: TX

address: 1102 Bates,

department: Pediatrics

institute: Baylor College of Medicine

hyb_protocol: Probe the array with diluted (1:500) human serum or plasma. 10 μl plasma was diluted into 5ml of Wash Buffer

scan_protocol: After washing with the Wash Buffer and one time rinsing with water, arrays were air-dried and scanned using ScanArray Express Microarray Scanner (PerkinElmer, Waltham, MA) at 635nm.

data_processing: The Background subtracted intensities of the whole array were normalized and log-transformed. The low intensity values were thresholded at 5. Ratios of intensities and p-values between groups were calculated by 2-sample t-test for detecting differentially abundant autoantibodies

label: AlexaFluor 647 dye labeled antibody

molecule: protein

source_name: Non-Metastatic osteosarcoma patients

label_protocol: Then the arrays were incubated with Alexa Fluor® 647 goat anti-human IgG (H+L) (1:2000) for 90 minutes.

growth_protocol: Not Applicable

treatment_protocol: Block the ProtoArray® Human Protein Microarray with Blocking Buffer.

value: Non-Metastatic osteosarcoma patients

value: pooled plasma

tag: molecule type

value: Autoantibody


title: Pooled LR-1

extract_protocol: Probe the array with diluted (1:500) human serum or plasma. 10 μl plasma was diluted into 5ml of Wash Buffer


title: HDM sensitized atopic subject with asthma #AA01  medium control

description: AA01 C.CEL

value: Medium control


title: IR64_roots_WW_replicate 2


title: Pooled HR-3

source_name: Metastatic osteosarcoma patients

value: Metastatic osteosarcoma patients


title: Pooled LR-3


title: Pooled HR-2


title: Pooled CTL-2

source_name: Healthy or noncancerous pediatric patients


title: Pooled HR-1


title: NRL_Liver_miRNA_PX_2w_1

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

description: Gene expression data from liver cells 2 weeks after exposed to PX

hyb_protocol: The cocktail was hybridized onto the custom designed Vharveyi520694 microarray (Affymetrix). Hybridization was carried out for 16 h at 49°C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were scanned using the GeneChip Scanner 3000. GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: CEL files were processed using the Bioconductor affy package.

source_name: Sub-lethal exposures of organophosphates, PX at 2w, biological rep1

label_protocol: Target preparation and hybridization to arrays: 600 ng of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures. The labeling reaction was carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol. Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX). The fragmentation from the reaction was carried out in a volume of 33 uL containing 1X fragmentation buffer (Ambion), labeled mRNA, and incubated at 70°C for 15 minutes. After incubation, the reaction was stopped by adding 1 uL of stop solution.

growth_protocol: The cells were cultured in 75 cm2 flasks using Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum.  Cells were grown in a 37°C incubator with 10% CO2 and 100% relative humidity until 80% confluent.

extract_protocol: Liver cells were harvested using 0.25% (w/v) Trypsin-0.53mM EDTA solution or cell detachment buffer (40 mM Tris HCl, pH 7.4, 140 mM NaCl, 1 mM EDTA) and the cells were span down at 2,000rpm, 10 minutes, the cell pellets were then resuspend in 1 mL of RNALater (Ambion, Austin, TX) and store at 4oC or -80oC until ready for RNA extraction.  Total RNA extraction was carried out using the mirVanaTM miRNA isolation kit (ThermoFisher Scientific) according to the manufacturer’s recommended protocol for total RNA extraction.  The quality and quantity of the RNA samples was determined by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), FlashGel® RNA cassettes (Lonza Inc., Walkersville, MD) and spectrophotometric readings using the NanoDrop ND2000 (Thermo Scientific).  The RNA samples were accepted for gene expression analysis if the A260/A280 ratios are between 1.9-2.1 and the ratio of intensities of the 28S and 18S rRNA are 1.5-2.5: 1.

treatment_protocol: Exposure to sub-lethal doses of three OPs: diisopropyl fluorophosphate (DFP), O,S-diethyl methylphosphonothioate (OSD), and paraoxon (PX) were carried out when cells reach 80% confluent level.  Dosing levels of these compounds was set at 20% of the IV LD50 in mouse for each, with a 4 hour exposure time.  The final OP concentrations were:  paraoxon at 5.4 uM, DFP at 49.6 uM, and OSD at 17 uM.

tag: cell line

value: ATCC® TIB-73

tag: tissue type

value: Embroyonic Liver


title: PBMC-derived macrophages, LPS 2

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

institute: TWINCORE

hyb_protocol: GeneChip® WT Terminal Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit P/N 702808 Rev. 6

scan_protocol: Affymetrix® GeneChip® Command Console® User Manual (P/N 702569).

data_processing: The data were preprocessed, normalised and analysed using the GCRMA and limma packages from R/Bioconductor software environment. The CDF was used according to GPL15034 and submitted the unique list of IDs and their expression values.

source_name: PBMC-derived Macrophages

label_protocol: The Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays Part Number 4425209 Rev. C 09/2009

growth_protocol: Primary monocytes were extracted from the blood samples of anonymous healthy male donors, donated by the luxembourgish Red Cross. The components of the blood (peripheral blood mononuclear cells - PBMCs -, plasma and erythrocytes) were separated by Ficoll density gradient separation. After a 10 minute centrifugation (1000 g at room temperature without break), the PBMCs layer was collected and the CD14+ monocytes were isolated by using the MACS® technology (magnetic separation) from Miltenyi Biotec (Bergisch Gladbach, Germany). Isolated CD14+ monocytes were plated at 4x106 cells per well in 6-well plates and differentiated for 11 days into macrophages using RPMI 1640 medium (VWR, Radnor, Pennsylvania) supplemented with 10% human serum, off the clot, type AB (A&E Scientific, PAA, Pasching, Austria, lot number: C02108-1021), 0.1mg/mL streptomycin, 100U/mL penicillin and 0.1mM L-glutamine (Invitrogen, Life Technologies, Carlsbad, California). During the differentiation, the medium was replaced with fresh medium on day 4 and day 7.

extract_protocol: Total RNA was extracted by using TRIZOL reagent (Sigma-Aldrich)

treatment_protocol: For the experiments, lipopolysaccharide (LPS, Sigma) was used at a final concentration of 10μg/mL.

value: PBMC-derived Macrophages


title: PBMC-derived macrophages, LPS 1


title: NRL_Liver_miRNA_PX_2w_2

source_name: Sub-lethal exposures of organophosphates, PX at 2w, biological rep2


title: PBMC-derived macrophages, Control 3


title: PBMC-derived macrophages, LPS 3


title: PBMC-derived macrophages, Control 2


title: NRL_Liver_miRNA_PX_2d_1

description: Gene expression data from liver cells 2 days after exposed to PX

source_name: Sub-lethal exposures of organophosphates, PX at 2d, biological rep1


title: NRL_Liver_miRNA_PX_2hr_1

description: Gene expression data from liver cells 2 hours after exposed to PX

source_name: Sub-lethal exposures of organophosphates, PX at 2h, biological rep1


title: NRL_Liver_miRNA_OSD_2w_2

description: Gene expression data from liver cells 2 weeks after exposed to OSD

source_name: Sub-lethal exposures of organophosphates, OSD at 2w, biological rep2


title: Pooled CTL-3

value: Healthy or noncancerous pediatric patients


title: NRL_Liver_miRNA_OSD_2d_1

description: Gene expression data from liver cells 2 days after exposed to OSD

source_name: Sub-lethal exposures of organophosphates, OSD at 2d, biological rep1


title: NRL_Liver_miRNA_PX_2d_2

source_name: Sub-lethal exposures of organophosphates, PX at 2d, biological rep2


title: NRL_Liver_miRNA_OSD_2d_2

source_name: Sub-lethal exposures of organophosphates, OSD at 2d, biological rep2


title: NRL_Liver_miRNA_OSD_2w_1

source_name: Sub-lethal exposures of organophosphates, OSD at 2w, biological rep1


title: PBMC-derived macrophages, Control 1


title: NRL_Liver_miRNA_OSD_2hr_1

description: Gene expression data from liver cells 2 hours after exposed to OSD

source_name: Sub-lethal exposures of organophosphates, OSD at 2h, biological rep1


title: NRL_Liver_miRNA_DFP_2w_2

description: Gene expression data from liver cells 2 weeks after exposed to DFP

source_name: Sub-lethal exposures of organophosphates, DFP at 2w, biological rep2


title: NRL_Liver_miRNA_OSD_2hr_2

source_name: Sub-lethal exposures of organophosphates, OSD at 2h, biological rep2


title: NRL_Liver_miRNA_DFP_2w_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2w, biological rep1


title: Pooled CTL-1


title: NRL_Liver_miRNA_DFP_2d_2

description: Gene expression data from liver cells 2 days after exposed to DFP

source_name: Sub-lethal exposures of organophosphates, DFP at 2d, biological rep2


title: NRL_Liver_miRNA_PX_2hr_2

source_name: Sub-lethal exposures of organophosphates, PX at 2h, biological rep2


title: NRL_Liver_miRNA_DFP_2d_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2d, biological rep1


title: NRL_Liver_miRNA_DFP_2hr_2

description: Gene expression data from liver cells 2 hours after exposed to DFP

source_name: Sub-lethal exposures of organophosphates, DFP at 2h, biological rep2


title: patient 6 pre-treatment

value: melanoma


title: NRL_Liver_miRNA_DFP_2hr_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2h, biological rep1


title: NRL_Liver_miRNA_Control_2w_2

description: Gene expression data from liver cells without OP exposure, 2 weeksafter experimental exposure occurred

source_name: Sub-lethal exposures of organophosphates, control at 2w, biological rep2


title: NRL_Liver_miRNA_Control_2d_2

description: Gene expression data from liver cells without OP exposure, 2 days after experimental exposure occurred

source_name: Sub-lethal exposures of organophosphates, control at 2d, biological rep2


title: NRL_Liver_miRNA_Control_2hr_2

description: Gene expression data from liver cells without OP exposure, 2hours after experimental exposure occurred

source_name: Sub-lethal exposures of organophosphates, control at 2h, biological rep2


title: NRL_Liver_miRNA_Control_2d_1

source_name: Sub-lethal exposures of organophosphates, control at 2d, biological rep1


title: NRL_Liver_miRNA_Control_2hr_1

source_name: Sub-lethal exposures of organophosphates, control at 2h, biological rep1


title: NRL_Liver_miRNA_Control_2w_1

source_name: Sub-lethal exposures of organophosphates, control at 2w, biological rep1


title: 26_Dy15

city: Thousand Oaks

first: Mara

last: Campbell

address: 1 Amgen Center Drive

institute: Amgen

description: Loop design

hyb_protocol: Overnight hybridizations at 650C per manufacturer’s instructions

scan_protocol: All arrays were scanned on the Agilent Surescaner Scanner (Agilent p/n G2600D). Agilent Scan Control Software version 9.1.5.1 was used for array scanning. Array files were processed using Agilent Feature Extraction software 11.0.1.1.

data_processing: Extracted feature intensities for each channel on each array were processed separately by subtracting the lower 0.1th percentile from all intensities and then taking the log base 2. The transformed intensities were mapped using a non-linear function to a proprietary target density to ensure the distributions of the intensities were comparable between arrays and channels. Samples were processed in batches that roughly corresponded to samples from individual cohorts but with a small number of samples repeated between batches to allow estimation and removal of additive linear effects of batch and channel. Finally, replicates of any identical sequences on the array were averaged to produce values called gene intensities. Supplied data tables includes normalized log base 2 intensities.

label: Cy3, Cy5

source_name: systemic lupus erythematosus (SLE) patient

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color (Agilent Cat # 5188-5340) per manufacturer’s instructions.

extract_protocol: Total RNA was isolated from PAXgene whole blood tubes (BD Cat # 762165) using the PAXgene RNA Kit. (Qiagen Cat # 762164) on the Qiacube automated sample prep system

treatment_protocol: Blood from healthy volunteers (n=4) was collected into sodium heparin tubes, and then untreated or treated with 294 pM recombinant human IFN-γ for 0, 24, or 48 hours with incubation at 37oC, 5 % CO2. The blood was then added to PAXgene tubes and processed for RNA purification. Twenty six subjects with stable, mild to moderate SLE were administered placebo or a single dose of AMG 811 ranging from 2 mg to 180 mg SC or 60 mg IV. Whole blood PAXgene tube samples were collected from all cohorts at baseline, day-1 (pre-dose), and at days 15, 56, and end of study (EOS) after treatment Arrays were hybridized in a Loop design.

value: Whole Blood

tag: subject number

value: SLE patient 26

tag: treatment day

value: day 15

tag: dose


title: 25_Dy15

description: Loop design

value: SLE patient 25


title: 26_Dy56

description: Loop design

value: day 56


title: 23_EOS

description: Loop design

value: SLE patient 23

value: end of study


title: 26_Dy1

description: Loop design

value: day 1


title: 24_Dy15

description: Loop design

value: SLE patient 24


title: 25_Dy1

description: Loop design


title: 25_EOS

description: Loop design


title: 23_Dy15

description: Loop design


title: 26_EOS

description: Loop design


title: 23_Dy56

description: Loop design


title: 24_EOS

description: Loop design


title: 25_Dy56

description: Loop design


title: 24_Dy1

description: Loop design


title: 22_Dy56

description: Loop design

value: SLE patient 22


title: 22_Dy1

description: Loop design


title: 21_EOS

description: Loop design

value: SLE patient 21


title: 24_Dy56

description: Loop design


title: 22_Dy15

description: Loop design


title: 22_EOS

description: Loop design


title: 21_Dy1

description: Loop design


title: B6-T-2

description: Gene expression data from MACS-sorted splenic T cell sample WT 2

source_name: MACS-sorted splenic T cell sample WT 2

value: spleen

value: WT

value: 6-8 wk old


title: 21_Dy56

description: Loop design


title: 20_Dy1

description: Loop design

value: SLE patient 20


title: 20_EOS

description: Loop design


title: 19_EOS

description: Loop design

value: SLE patient 19


title: 23_Dy1

description: Loop design


title: 21_Dy15

description: Loop design


title: 17_EOS

description: Loop design

value: SLE patient 17


title: 16_Dy56

description: Loop design

value: Whole Blood

value: SLE patient 16


title: 19_Dy1

description: Loop design


title: 17_Dy56

description: Loop design


title: 20_Dy56

description: Loop design


title: 19_Dy56

description: Loop design


title: 15_Dy15

description: Loop design

value: SLE patient 15

value: day 15


title: 14_Dy15

description: Loop design

value: SLE patient 14


title: 16_Dy1

description: Loop design


title: 15_Dy56

description: Loop design

value: day 56


title: 18_EOS

description: Loop design

value: SLE patient 18

value: end of study


title: 18_Dy56

description: Loop design


title: 16_Dy15

description: Loop design


title: 14_Dy56

description: Loop design


title: 15_Dy1

description: Loop design

value: day 1


title: 19_Dy15

description: Loop design


title: 18_Dy1

description: Loop design


title: 16_EOS

description: Loop design


title: 15_EOS

description: Loop design


title: 17_Dy1

description: Loop design


title: 14_EOS

description: Loop design


title: 13_Dy1

description: Loop design

value: SLE patient 13


title: 20_Dy15

description: Loop design


title: 13_Dy15

description: Loop design


title: 12_EOS

description: Loop design

value: SLE patient 12


title: 13_Dy56

description: Loop design


title: 12_Dy15

description: Loop design


title: 11_EOS

description: Loop design

value: SLE patient 11


title: 12_Dy1

description: Loop design


title: 12_Dy56

description: Loop design


title: 11_Dy56

description: Loop design


title: 13_EOS

description: Loop design


title: 14_Dy1

description: Loop design


title: 10_EOS

description: Loop design

value: SLE patient 10


title: 9_EOS

description: Loop design

value: SLE patient 9


title: 10_Dy56

description: Loop design


title: 8_Dy56

description: Loop design

value: SLE patient 8


title: 8_EOS

description: Loop design


title: 9_Dy56

description: Loop design


title: 10_Dy15

description: Loop design


title: 9_Dy15

description: Loop design


title: 9_Dy1

description: Loop design


title: 8_Dy15

description: Loop design


title: 7_Dy1

description: Loop design

value: SLE patient 7


title: 11_Dy15

description: Loop design


title: 8_Dy1

description: Loop design


title: 10_Dy1

description: Loop design


title: 7_Dy56

description: Loop design


title: 6_Dy56

description: Loop design

value: SLE patient 6


title: 11_Dy1

description: Loop design

value: Whole Blood


title: 6_EOS

description: Loop design


title: 6_Dy15

description: Loop design


title: 6_Dy1

description: Loop design


title: 5_EOS

description: Loop design

value: SLE patient 5


title: 4_Dy15

description: Loop design

value: SLE patient 4


title: 5_Dy1

description: Loop design


title: 5_Dy56

description: Loop design


title: 4_Dy1

description: Loop design


title: 4_Dy56

description: Loop design


title: 4_EOS

description: Loop design


title: 3_EOS

description: Loop design

value: SLE patient 3


title: 5_Dy15

description: Loop design

value: day 15


title: 3_Dy56

description: Loop design

value: day 56


title: 3_Dy1

description: Loop design


title: 2_EOS

description: Loop design

value: SLE patient 2


title: 3_Dy15

description: Loop design


title: 2_Dy56

description: Loop design


title: 2_Dy1

description: Loop design


title: 1_Dy56

description: Loop design

value: SLE patient 1


title: 1_EOS

description: Loop design

value: end of study


title: 1_Dy1

description: Loop design

value: day 1


title: CD34+ 25mM Glu+Met_rep2

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

description: CD34-5B II_(HuGene-1_0-st-v1).CEL

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

source_name: CD34+ 25mM Glu+Met

label_protocol: 250 ng total RNA was used as input for amplification using Ambion WT expression sense kit (Life Technilogies, Grand Island, NY, USA), Poly A control was added as suggested by WT expression kit manual. cDNA amplification products were fragmented and labeled with biotin using Affymetrix GeneChip WT terminal labeling kit, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit, and then washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples were isolated from HUVEC using the RNeasy Mini Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed (RIN > 7.0) on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Human umbilical cord blood

value: primary CD34+ cells

tag: glucose concentration

value: 25 mM (high)

tag: metformin added

value: Yes

tag: sample group

value: Hi Glu + Met


title: CD34+ 25mM Glu_rep1

description: CD34-5A I _(HuGene-1_0-st-v1).CEL

source_name: CD34+ 25mM Glu

value: No

value: Hi Glu


title: CD34+ 16.5mM+Met+Hyp_rep1

description: CD34-4B I_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 16.5mM+Met+Hyp

value: 16.5 mM (high)

value: Hi Glu + Met + Hyp


title: CD34+ 25mM Glu+Met_rep1

description: CD34-5B I_(HuGene-1_0-st-v1).CEL


title: CD34+ 5.5mM+Hyp_rep1

description: CD34-2A I REPEATED_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 5.5mM+Hyp

value: 5.5 mM (normal)

value: Hyp


title: 2_Dy15

description: Loop design

value: Whole Blood

value: day 15


title: CD34+ 16.5mM+Met_rep2

description: CD34-3B II_(HuGene-1_0-st-v1).CEL


title: CD34+ 16.5mM+Met_rep1

description: CD34-3B I_(HuGene-1_0-st-v1).CEL


title: CD34+ 5.5mM+Hyp_rep2

description: CD34-2A II_(HuGene-1_0-st-v1).CEL


title: CD34+ 5.5mM+Met_rep1

description: CD34-1B I REPEATED-2_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 5.5mM+Met

value: Met


title: CD34+ 16.5mM Glu_rep2

description: CD34-3A II_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 16.5mM Glu


title: CD34+ 25mM Glu_rep2

description: CD34-5A II_(HuGene-1_0-st-v1).CEL


title: 1_Dy15

description: Loop design

value: SLE patient 1


title: CD34+ 16.5mM+Met+Hyp_rep2

description: CD34-4B II_(HuGene-1_0-st-v1).CEL


title: CD34+ 5.5mM+Met+Hyp_rep2

description: CD34-2B II_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 5.5mM+Met+Hyp

value: Met + Hyp


title: CD34+ 16.5mM Glu_rep1

description: CD34-3A I_(HuGene-1_0-st-v1).CEL


title: CD34+ 5.5mM+Met_rep2

description: CD34-1B II_(HuGene-1_0-st-v1).CEL


title: CD34+ 16.5mM+Hyp_rep2

description: CD34-4A II_(HuGene-1_0-st-v1).CEL

value: Hi Glu + Hyp


title: CD34+ 16.5mM+Hyp_rep1

description: CD34-4A I_(HuGene-1_0-st-v1).CEL

value: Human umbilical cord blood


title: CD34+ 5.5mM+Met+Hyp_rep1

description: CD34-2B I_(HuGene-1_0-st-v1).CEL

value: primary CD34+ cells


title: CD34+ 5.5mM Glu_rep1

description: CD34-1A I_(HuGene-1_0-st-v1).CEL

source_name: CD34+ 5.5mM Glu

value: Normal


title: CD34+ 5.5mM Glu_rep2


title: HOM MEF BASAL REP3

city: Belfast

first: Emma

last: Kerr

address: 97 Lisburn Rd

department: PGJCCR

institute: Queen's University Belfast

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data are generated using GenomeStudio. The subset are then filtered to remove any non expressed probes using the detection p-value from Illumina: if for a given probe all the detection p-value for the samples are above 0.01 it is removed (considered not expressed). Data are transformed using the Variance Stabilization Transformation (VST) from lumi which is close to log2 transformation but without bias at low and high intensity. Data is then normalised to remove technical variation between arraysusing quantile normalisation.

source_name: MEF, KRASG12D/G12D GENOTYPE, BIOLOGICAL REPLICATE

label_protocol: Standard Illumina protocol

growth_protocol: Embryos collected at day E12.5 and cultured in DMEM supplemented with 10% FBS, 2 mM L-Glutamine for one passage before recombination of loxP sites with adenovirus-Cre (5 × 107 plaque-forming units/1 x 106 cells). Cells were recovered in DMEM/FBS/L-GLN for 2 passages before extraction.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 1x10^6 passage 3 MEFs were plated (10cm dish) and grown for 48hrs before extraction.

tag: strain

tag: developmental stage

value: embryo E12.5

value: KRASG12D/G12D; p53Fx/Fx

value: mouse embryonic fibroblasts


title: HOM MEF BASAL REP2

tag: genotype


title: HET MEF BASAL REP3

source_name: MEF, KRASG12D/WT GENOTYPE, BIOLOGICAL REPLICATE

value: KRASG12D/WT; p53Fx/Fx


title: HOM MEF BASAL REP1


title: HET MEF BASAL REP2


title: HET MEF BASAL REP1


title: NRL_Liver_PX_2w_1

data_processing:
CEL files were processed using the Bioconductor affy package.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Sub-lethal exposures of organophosphates, PX at 2w, biological rep1

value: ATCC® TIB-73

value: Embroyonic Liver


title: NRL_Liver_PX_2w_3

source_name: Sub-lethal exposures of organophosphates, PX at 2w, biological rep3


title: NRL_Liver_PX_2h_1

source_name: Sub-lethal exposures of organophosphates, PX at 2h, biological rep1


title: NRL_Liver_PX_2d_3

source_name: Sub-lethal exposures of organophosphates, PX at 2d, biological rep3


title: NRL_Liver_PX_T0_1

description: Gene expression data from liver cells exposed to PX at time 0

source_name: Sub-lethal exposures of organophosphates, PX at T0


title: NRL_Liver_PX_2d_2

source_name: Sub-lethal exposures of organophosphates, PX at 2d, biological rep2


title: NRL_Liver_OSD_2w_2

source_name: Sub-lethal exposures of organophosphates, OSD at 2w, biological rep2


title: NRL_Liver_OSD_2h_1

source_name: Sub-lethal exposures of organophosphates, OSD at 2h, biological rep1


title: NRL_Liver_PX_2w_2

source_name: Sub-lethal exposures of organophosphates, PX at 2w, biological rep2


title: NRL_Liver_DFP_2w_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2w, biological rep1


title: NRL_Liver_OSD_2d_2

source_name: Sub-lethal exposures of organophosphates, OSD at 2d, biological rep2


title: NRL_Liver_OSD_T0_1

description: Gene expression data from liver cells exposed to OSD at time 0

source_name: Sub-lethal exposures of organophosphates, OSD at T0


title: NRL_Liver_DFP_2w_3

source_name: Sub-lethal exposures of organophosphates, DFP at 2w, biological rep3


title: NRL_Liver_DFP_2w_2

source_name: Sub-lethal exposures of organophosphates, DFP at 2w, biological rep2


title: NRL_Liver_PX_2h_2

source_name: Sub-lethal exposures of organophosphates, PX at 2h, biological rep2


title: NRL_Liver_OSD_2h_2

source_name: Sub-lethal exposures of organophosphates, OSD at 2h, biological rep2


title: NRL_Liver_OSD_2d_1

source_name: Sub-lethal exposures of organophosphates, OSD at 2d, biological rep1


title: NRL_Liver_OSD_2d_3

source_name: Sub-lethal exposures of organophosphates, OSD at 2d, biological rep3


title: NRL_Liver_DFP_2d_3

source_name: Sub-lethal exposures of organophosphates, DFP at 2d, biological rep3


title: NRL_Liver_DFP_2d_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2d, biological rep1


title: NRL_Liver_DFP_T0_1

description: Gene expression data from liver cells exposed to DFP at time 0

source_name: Sub-lethal exposures of organophosphates, DFP at T0


title: NRL_Liver_OSD_2w_1

source_name: Sub-lethal exposures of organophosphates, OSD at 2w, biological rep1


title: NRL_Liver_DFP_2h_1

source_name: Sub-lethal exposures of organophosphates, DFP at 2h, biological rep1


title: NRL_Liver_OSD_2w_3

source_name: Sub-lethal exposures of organophosphates, OSD at 2w, biological rep3


title: NRL_Liver_DFP_2d_2

source_name: Sub-lethal exposures of organophosphates, DFP at 2d, biological rep2


title: NRL_Liver_PX_2d_1

description: Gene expression data from liver cells 2 days after exposed to PX

source_name: Sub-lethal exposures of organophosphates, PX at 2d, biological rep1


title: NRL_Liver_DFP-2h_2

source_name: Sub-lethal exposures of organophosphates, DFP at 2h, biological rep2


title: NRL_Liver_Control_2w_2

source_name: Sub-lethal exposures of organophosphates, control at 2w, biological rep2


title: NRL_Liver_Control_2d_3

source_name: Sub-lethal exposures of organophosphates, control at 2d, biological rep3


title: NRL_Liver_Control_2d_1

source_name: Sub-lethal exposures of organophosphates, control at 2d, biological rep1


title: NRL_Liver_Control_2h_1

source_name: Sub-lethal exposures of organophosphates, control at 2h, biological rep1


title: NRL_Liver_Control_2w_1

source_name: Sub-lethal exposures of organophosphates, control at 2w, biological rep1


title: NRL_Liver_Control_2h_2

source_name: Sub-lethal exposures of organophosphates, control at 2h, biological rep2


title: NRL_Liver_Control_2w_3

source_name: Sub-lethal exposures of organophosphates, control at 2w, biological rep3


title: NRL_Liver_Control_2d_2

source_name: Sub-lethal exposures of organophosphates, control at 2d, biological rep2


title: control cerebral meninges, biological rep5

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Gene expression data from control cerebral meninges

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix raw data was normalized using the PLIER algorithms (Affymetrix Technical Note. Guide to Probe Logarithmic Intensity Error Estimation. http://affymetrix.com/support/technical/technotesmain.affx). The data from the three comparison groups were from three batches of Affymetrix experiments, and were normalized separately.

source_name: control cerebral meninges

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix small sample amplification protocol from app. 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed using RNeasy® Mini Kit (Qiagen)

tag: tissue

value: cerebral meninges

tag: age

value: Newborn

value: control


title: 542865_A10_532

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: Total RNA recovered from fresh frozen tissue from untreated Cynomolgus monkey.

hyb_protocol: Hybridization was performed following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Scanning was performed on a NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA (see www.nimblegen.com).

data_processing: The raw data (.pair file) was subjected to background correction, quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.)

organism: Macaca fascicularis

source_name: spleen, female, Mauritius

label_protocol: Labeling was performed using 10 ng of total RNA as input following the standard operating protocol on a Biomek FXp workstation (Beckman Coulter Inc., Brea, CA, USA) with the NuGen Ovation Pico WTA System V2 (NuGEN Technologies, Inc., SanCarlos, CA, USA; see http://www.nugeninc.com). Cy3 labeling of cDNA was performed with the Roche NimbleGen One Color DNA Labeling Kit according to manufacturer's instructions (NimbleGen Systems Inc., Madison, WI USA; see www.nimblegen.com).

growth_protocol: Tissue samples were supplied by contract research organizations and taken from untreated animals of GLP drug-safety studies in accordance with current animal welfare standards. Tissues were stored at -80°C until RNA extraction.

extract_protocol: Tissues were homogenized in tubes prefilled with 1.4 mm ceramic beads and Qiagen's lysis reagent RLT using a FastPrep-24 instrument (MP Biomedicals, Solon, OH, USA). Total RNA from lysates was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Untreated

value: spleen

tag: gender

value: female

value: 4 years

tag: weight

value: ~4 kg

tag: origin

value: Mauritius

tag: monkey identifier


title: 543410_A02_532

source_name: spleen, male, Mauritius

value: male

value: ~5 kg


title: control cerebral meninges, biological rep7


title: control cerebral meninges, biological rep9


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebral meninges, biological rep3

description: Gene expression data from mutant (Pdgfc-/-; Pdgfra GFP/+) cerebral meninges

value: mutant (Pdgfc-/-; Pdgfra GFP/+)


title: 542865_A05_532


title: 543410_A10_532


title: control cerebral meninges, biological rep4


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebral meninges, biological rep2


title: 542865_A07_532


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebral meninges, biological rep4


title: control cerebral meninges, biological rep6


title: NRL_Liver_Control_T0_1

description: Gene expression data from liver cells without OP exposure

source_name: Sub-lethal exposures of organophosphates, control at T0

tag: cell line


title: control cerebral meninges, biological rep3


title: 543410_A03_532


title: control cerebral meninges, biological rep2


title: 543410_A12_532

source_name: spleen, female, Vietnam

value: 3 years

value: Vietnam


title: control cerebral meninges, biological rep1


title: 542865_A06_532

source_name: spleen, female, China / Mainland Southeast Asia

value: China / Mainland Southeast Asia


title: 543410_A07_532


title: control cerebral meninges, biological rep8


title: mutant (Pdgfc-/-; Pdgfra GFP/+) cerebral meninges, biological rep1


title: 542865_A01_532

source_name: spleen, male, Vietnam


title: 543410_A09_532


title: 542865_A04_532


title: 542865_A12_532


title: 543410_A01_532


title: 543410_A06_532


title: 7_Dy15

description: Loop design

source_name: systemic lupus erythematosus (SLE) patient

value: Whole Blood

value: SLE patient 7

tag: subject id

value: day 15


title: 542865_A03_532

source_name: spleen, female, Philippines

value: 5.5 years

value: Philippines


title: 542865_A11_532

source_name: spleen, male, Philippines


title: 542865_A08_532

value: ~6 kg


title: 543410_A11_532

value: spleen

value: 6.8 years


title: 543053_A09_532

source_name: lung, male, Mauritius

value: lung

value: 4 years


title: 544236_A12_532

source_name: lung, female, Mauritius

value: female

value: ~4 kg

value: Mauritius


title: 543053_A08_532

value: male

value: ~5 kg


title: 544236_A02_532


title: 543410_A08_532

value: 6.5 years


title: 544236_A03_532

source_name: lung, female, China / Mainland Southeast Asia

value: 3 years

value: China / Mainland Southeast Asia


title: 544236_A08_532

source_name: lung, female, Philippines

value: 6.6 years


title: 543053_A02_532

source_name: lung, male, Philippines


title: 552645_A10_532

source_name: lung, male, Vietnam

value: Vietnam


title: 543053_A05_532


title: 544236_A09_532


title: 543408_A05_532

source_name: liver, male, Mauritius

value: liver


title: 543053_A04_532


title: 543053_A10_532

value: Philippines


title: 544236_A04_532


title: 544236_A11_532


title: 552645_A09_532

source_name: lung, female, Vietnam


title: 543053_A01_532


title: 552645_A12_532


title: 552645_A06b_532


title: 543410_A04_532


title: 543053_A12_532


title: 543053_A11_532

value: 5.5 years


title: 544236_A10_532

value: ~6 kg


title: 543012_A12_532

source_name: liver, female, Mauritius


title: 543408_A09_532


title: 543408_A04_532


title: 543012_A04_532


title: 543012_A01_532


title: 543012_A07_532


title: 543408_A12_532


title: 543012_A10_532

source_name: liver, male, Vietnam


title: 544502-MAFA_MU_5-vs-MAFA_MU_ref

description: array CGH fluorescence intensity ratio of Cy3-labeled DNA fragments  from test samples (ch1) relative to Cy5-labeled DNA fragments from the reference (ch2)

hyb_protocol: Hybridization was performed with 34 ug of Cy3- and 34 ug of Cy5-labeled DNA for 72 h at 42°C following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

scan_protocol: Microarray drying and scanning was performed in an ozone-free NoZone workspace consisting of a NoZone enclosure and a NoZone ozone scrubber (AlphaMetrix Biotech GmbH, Rödemark, Germany). For scanning a NimbleGen MS200 Microarray Scanner was used at 2 μm pixel resolution following the standard operating protocol of NimbleGen Systems Inc., Madison, WI USA. See www.nimblegen.com.

data_processing:
array CGH probe intensities were subjected to LOESS spatial correction (Smyth GK, Speed TP (2003): Normalization of cDNA microarray data. Methods), background correction, and q-spline normalization (Workman et al. (2002): A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol) as implemented in the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI). In addition, the GC base pair content of each probe (120405_Cynomolgus5_CGH_UX1.gcstats) was used for the generation of waviness corrected, normalized array CGH probe intensity ratios as implemented in the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI). Copy number changes were identified with the segMNT v1.1 algorithm (Molla M (2007): Novel Uses for Machine Learning and Other Computational Methods for the Design and Interpretation of Genetic Microarrays. In PhD thesis University of Wisconsin-Madison Department of Computer Sciences) with a min. number of 5 probes per segment as implemented into the NimbleGen DEVA software, version 1.2 (Roche NimbleGen, Inc., Madison, WI).
normalized log2 (test=ch1/reference=ch2) ratio per probe for raw data file and log2 segmentation value for processed data file

label_protocol: 500 ng of DNA from one animal tissue at a time and 500 ng of reference DNA - pooled DNA from blood specimens of 25 male Cynomolgus monkeys - were used for labeling by an isothermal Klenow fill-in reaction with either Cy3 or Cy5 random nonamer primer using the Roche NimbleGen Dual color labeling kit according to manufacturer's instructions (Roche NimbleGen, Inc., Madison, WI). Labeling Hybridization Controls were spiked-in as quality controls for copy number variation detection (Roche NimbleGen, Inc., Madison, WI).

growth_protocol: Tissue and blood samples were supplied by contract research organizations and taken from untreated animals of GLP drug-safety studies in accordance with current animal welfare standards. Tissues were stored at -80°C until DNA extraction.

extract_protocol: Spleen tissues were homogenized in tubes prefilled with 1.4 mm ceramic beads and QiaGen’s lysis reagent ALT using a FastPrep-24 instrument (MP Biomedicals, Solon, OH, USA) and then incubated with Proteinase K at 55°C for 1 h followed by RNAse A treatment at 25°C for 2 min (Qiagen Inc., Valencia, CA). Blood specimens (0.2 ml) were incubated at 70°C for 10 min in QiaGen’s lysis reagent ALT with Proteinase K and RNAse A. Genomic DNA from lysates was extracted using the QIAamp Mini kit (Qiagen Inc., Valencia, CA, USA).  DNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: Ch1: DNA recovered from fresh frozen tissue from untreated Cynomolgus monkey

value: Male

value: ~ 5 kg

treatment_protocol: Ch2 reference DNA:  pooled DNA from blood specimens of 25 male Cynomolgus monkeys

value: 3-10 years

tag: weigth


title: 543111-MAFA_MU_6-vs-MAFA_MU_ref

value: 4 years


title: 543408_A03_532


title: 543012_A03_532

source_name: liver, female, Vietnam

value: female

value: ~4 kg


title: 543113-MAFA_MU_1-vs-MAFA_MU_ref

value: Mauritius


title: 543114-MAFA_MU_2-vs-MAFA_MU_ref


title: 543408_A08_532


title: 543012_A05_532

source_name: liver, male, Philippines

value: male


title: 544661-MAFA_MU_4-vs-MAFA_MU_ref

value: Female

value: ~ 4 kg


title: 545037-MAFA_MU_7-vs-MAFA_MU_ref


title: 543012_A11_532

source_name: liver, female, China / Mainland Southeast Asia

value: 3 years

value: China / Mainland Southeast Asia


title: 543012_A06_532


title: 543408_A07_532


title: Unstimulated Whole Blood 48hrs (3)

description: Loop design

source_name: healthy volunteer

value: Whole Blood

tag: subject number

value: Healthy volunteer 3

tag: treatment day


title: Unstimulated Whole Blood 48hrs (4)

description: Loop design

value: Healthy volunteer 4

tag: dose


title: 543408_A11_532

source_name: liver, female, Philippines

value: liver

value: 5.5 years

value: ~5 kg

value: Philippines


title: 543408_A06_532

value: ~6 kg


title: E0771/Shplac1

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

hyb_protocol: standard Affymetrix protocol

data_processing: The data were analyzed using Affy R package and RMA was chose as the normalization method.

source_name: Medullary breast adenocarcinoma cell line originally isolated as a spontaneous tumor from C57BL/6 mouse

label_protocol: Standard one-cycle Affymetrix protocol

growth_protocol: E0771 cells were mainained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was extracted from cell lines using using the QIAGEN Rneasy Mini Kit, and its quality confirmed using an Agilent 2100 Bioanalyzer and RNA 6000 LabChips. RNA from E0771 cells transduced with scrambled RNA (Ctl) or Plac1 shRNA (sh) was reverse transcribed and hybridized to an Affymetrix mouse 430A 2.0 GeneChip.

treatment_protocol: E0771 cells expressing high levels of Plac1 were transduced with a lentivirus expressing a Plac1 shRNA (E0771/shPlac1)


title: 543012_A09_532

value: 6.5 years


title: E0771/Scram


title: 543012_A08_532

value: female

value: 6.6 years


title: Unstimulated Whole Blood 24hrs (3)

description: Loop design


title: Unstimulated Whole Blood 4 (Time 0)

description: Loop design


title: Unstimulated Whole Blood 3 (Time 0)

description: Loop design


title: 546716-MAFA_MU_3-vs-MAFA_MU_ref

value: 4 years

value: Mauritius

value: Male

value: 3-10 years


title: 543291-MAFA_MU_8-vs-MAFA_MU_ref

value: Female

value: ~ 4 kg


title: Unstimulated Whole Blood 24hrs (4)

description: Loop design

value: Whole Blood


title: Unstimulated Whole Blood 48hrs (2)

description: Loop design

value: Healthy volunteer 2


title: 543012_A02_532

value: 6.8 years


title: 543289-MAFA_VN_1-vs-MAFA_MU_ref

value: ~ 5 kg

value: Vietnam


title: 543871-MAFA_VN_4-vs-MAFA_MU_ref

value: 3 years


title: Unstimulated Whole Blood 24hrs (2)

description: Loop design


title: 543870-MAFA_VN_3-vs-MAFA_MU_ref


title: Unstimulated Whole Blood 2 (Time 0)

description: Loop design


title: 543869-MAFA_VN_2-vs-MAFA_MU_ref


title: 545247_A09_532

source_name: kidney, male, Mauritius

value: kidney

value: male

value: ~5 kg


title: 545248_A09_532


title: 546775_A08_532


title: 543742-MAFA_MSA_3-vs-MAFA_MU_ref

value: China / Mainland Southeast Asia


title: 546768-MAFA_MSA_1-vs-MAFA_MU_ref


title: Unstimulated Whole Blood 48hrs (1)

description: Loop design

value: Healthy volunteer 1


title: Unstimulated Whole Blood 1 (Time 0)

description: Loop design


title: Whole Blood + IFN-g 48hrs (4)

description: Loop design

value: Healthy volunteer 4


title: 545248_A01_532

source_name: kidney, female, Mauritius

value: female

value: 4 years

value: ~4 kg

value: Mauritius


title: 543743-MAFA_PH_1-vs-MAFA_MU_ref

value: Male

value: Philippines

value: 3-10 years


title: 545247_A06_532


title: VdG56

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

institute: The University of Illinois at Chicago

description:
Replicate 1
idat file: 9256321010

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

source_name: VCaP, MDV3100-Resistant

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

growth_protocol: Cells grown in their respective growth media with 10% FBS and Pen/Strep.  Cells were treated either with DMSO vehicle (Parental Untreated); 10uM MDV3100/Enzalutamide for 48 hours (48hrs MDV3100), or for at least 6 months in 10uM MDV3100 (MDV3100-Resistant)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with vehicle (DMSO), or 10uM enzalutamide and RNA extracted directly from plate.

value: VCaP

value: Prostate Cancer Cell Line


title: 545247_A02_532


title: Whole Blood + IFN-g 24hrs (4)

description: Loop design

value: Whole Blood


title: VdG14

description:
Replicate 3
idat file: 9257302016


title: 545247_A12_532


title: 545248_A03_532

source_name: kidney, male, Vietnam

value: 3 years

value: Vietnam


title: Unstimulated Whole Blood 24hrs (1)

description: Loop design


title: VdG73

description:
Replicate 2
idat file: 9255013011


title: VdG24

description:
Replicate 3
idat file: 9257302016

source_name: VCaP, Parental Untreated


title: 547036-MAFA_MSA_2-vs-MAFA_MU_ref

value: Female

value: ~ 4 kg


title: 543148-MAFA_PH_5-vs-MAFA_MU_ref

value: 5.5 years

value: ~ 6 kg


title: VdG35

description:
Replicate 4
idat file: 9257302030


title: 543151-MAFA_PH_4-vs-MAFA_MU_ref

value: 6.5 years


title: 543167-MAFA_PH_6-vs-MAFA_MU_ref

value: ~ 5 kg


title: 545247_A07_532

value: kidney

value: male

value: 4 years

value: ~5 kg


title: VdG40

description:
Replicate 1
idat file: 9257302051


title: 546775_A04_532

value: female

value: ~4 kg

value: Mauritius


title: 543344-MAFA_PH_3-vs-MAFA_MU_ref

value: 6.6 years

value: Philippines

value: Male

value: 3-10 years


title: Whole Blood + IFN-g 48hrs (3)

description: Loop design

value: Whole Blood

value: Healthy volunteer 3


title: Whole Blood + IFN-g 4 (Time 0)

description: Loop design

value: Healthy volunteer 4