title: control-continuous_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-26h_harvest-rep1

status: Public on Oct 05 2013

type: RNA

city: Ft. Detrick

first: John

middle: A.

last: Lewis

state: MD

address: 568 Doughten Drive

department: Biomarkers Program

country: USA

institute: U.S. Army Center for Environmental Health Research

description: gene expression data from L4 larvae

hyb_protocol: Biotin labeled cRNA was fragmented and hybridized to Affymetrix C. elegans whole genome GeneChips as recommended by Affymetrix.

scan_protocol: Hybridized  Affymetrix C. elegans whole genome GeneChips were then scanned as recommended by Affymetrix.

data_processing: Probe set expression levels were calculated using RMA processing of raw data within Partek Genomics Suite (Partek, Inc.).

label: Biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole organism

label_protocol: cDNA was synthesized using SuperScript Choice kit and a T24T7 primer following the manufacturer's protocol. Biotin labeled cRNA was synthesized using the Enzo BioArray High Yield Kit following the manufacturer's protocol.

growth_protocol: C. elegans cultures were grown in CeHR medium at 22.5 °C in T-75 tissue culture flasks with shaking at 70 rpm.

extract_protocol: Flash frozen worms were pulverized under liquid nitrogen in a Spex 6750 Freezer Mill. RNA was extracted from pulverized worms with Trizol followed by an additional purification step using RNeasy Midi columns. PolyA RNA was then isolated using OligoTex. All steps were performed following manufacturers recommendations.

treatment_protocol: Cultures of 250,000 synchronized L1 worms were grown in 30 mL CeHR medium. A separate T-75 culture flask was set up for each condition. After ~41 h, when 50% of the worms had passed the L3/L4 molt,  the exposures were initiated. Four flasks of worms were harvested prior to beginning the exposure as the 0 h controls. Equal volumes of water or dichlorvos stock (diluted for 0.6 µM or 15 µM final concentration as appropriate) were added to the remaining flasks, which were then returned to the incubator. The flasks were treated according to one of three protocols. In the first protocol, the set of flasks was incubated without interruption for the duration of the experiment (continuous) with flasks being harvested at 2, 8, 14, 20, and 26 h. The other two sets were incubated for 2 or 8 h, at which time the worms were centrifuged out of the exposure medium, washed 3 times with a modified CeHR medium (Washout Buffer), resuspended in fresh CeHR medium without dichlorvos, and returned to the incubator. Flasks were harvested at 6 h intervals following the washout through 26 h. Untreated controls (or shams) and low and high concentrations flasks were prepared for each harvest time of each of the three protocols.

tag: developmental stage

value: L4 larvae

tag: exposure concentration

value: 15 µM DDVP (high)

tag: exposure protocol duration

value: 8 hr

tag: harvest time


title: high_DDVP-continuous_expose-14h_harvest-rep1

description: gene expression data from L4 larvae

value: continuous


title: low_DDVP-continuous_expose-14h_harvest-rep1

description: gene expression data from L4 larvae

value: 0.6 µM DDVP (low)


title: control-2h_expose-26h_harvest-rep2

description: gene expression data from L4 larvae

value: 0 µM DDVP (control)

value: 2 hr


title: low_DDVP-continuous_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: control-8h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: control-2h_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-8h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-8h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: control-continuous_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: control-8h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: control-2h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: control-8h_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-2h_expose-20h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: hdaf2-100GLN-2

city: Neuherberg, Germany

first: Christian

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

country: Germany

institute: Helmholtz Zentrum München

description: This sample is of Fusrium fujikuroi delta-hdF2 mutant grown on 60 mM Gln (100%) medium. It is the first of second biological replicates for this condition in this experiment.

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi

source_name: Fusarium fujikuroi, delta-hdaf2, mycelium, growth medium: 60 mM Gln (100%)

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for three days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional three days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction

tag: strain

tag: genotype/variation


title: low_DDVP-2h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-2h_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: control-2h_expose-14h_harvest-rep1

description: gene expression data from L4 larvae


title: hdaf2-100GLN-1

description: This sample is of Fusrium fujikuroi delta-hdF2 mutant grown on 60 mM Gln (100%) medium. It is the first of two biological replicates for this condition in this experiment.


title: wt-100GLN-1

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the first of two biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, wild-type, mycelium, growth medium: 60 mM Gln (100%)

value: Wild-type


title: wt-100GLN-2

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the second of two biological replicates for this condition in this experiment.


title: hdaf2-10GLN-2

description: This sample is of Fusrium fujikuroi delta-hdF2 mutant grown on 6 mM Gln (10%) medium. It is the first of second biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, delta-hdaf2, mycelium, growth medium: 6 mM Gln (10%)


title: low_DDVP-2h_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: hdaf2-10GLN-1

description: This sample is of Fusrium fujikuroi delta-hdF2 mutant grown on 6 mM Gln (10%) medium. It is the first of two biological replicates for this condition in this experiment.


title: wt-10GLN-2

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the second of two biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, wild-type, mycelium, growth medium: 6 mM Gln (10%)


title: control-2h_expose-8h_harvest-rep1

description: gene expression data from L4 larvae


title: high_DDVP-continuous_expose-2h_harvest-rep1

description: gene expression data from L4 larvae


title: low_DDVP-continuous_expose-2h_harvest-rep1

description: gene expression data from L4 larvae


title: wt-10GLN-1

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the first of two biological replicates for this condition in this experiment.


title: control-continuous_expose-2h_harvest-rep1

description: gene expression data from L4 larvae


title: KT1218 - STA

status: Public on Oct 04 2013

city: Stanford

first: Purvesh

last: Khatri

state: CA

address: 279 Campus Dr., Beckman B235A

department: Medicine

institute: Stanford University

hyb_protocol: cDNA fragments were hybridized onto Affymetrix GeneChip Human Genome U133 plus 2.0 arrays (Affymetrix, Santa Clara, CA) followingthe manufacturer's protocol.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing:
Microarrays were normalized using RMA package in bioconductor.
The 101 samples in this series were normalized using Bioconductor version 2.8 (or 2.9).

label: biotin

organism: Homo sapiens

source_name: renal allograft biopsy_stable patient

label_protocol: RNA was amplified to cDNA and biotin labeled using the Ovation Biotin System (NuGEN Technologies, San Carlos, CA).

extract_protocol: For each kidney allograft biopsy, a separate core was stored in RNAlater (Ambion, Austin, TX) and stored at -20C until RNA extraction. Total RNA was extracted from each biopsy using TRIzol reagent. RNA integrity was checked with an RNA 6000 Nano LabChip Kit (Agilent Technologies, Waldbronn, Germany) on a 2100 Bioanalyizer (Agilent Technologies).

tag: patient group

value: stable patient (STA)

tag: tissue

value: renal allograft biopsy


title: KT877 - STA


title: KT543 - AR

source_name: renal allograft biopsy_patient with acute rejection

value: patient with acute rejection (AR)


title: KT955 - STA


title: KT575 - STA


title: KT979 - AR


title: KT922 - STA


title: KT1202 - STA


title: KT1114 - AR


title: KT736 - STA


title: KT657 - STA


title: low_DDVP-2h_expose-26h_harvest-rep1

description: gene expression data from L4 larvae


title: KT730 - STA


title: KT885 - AR


title: KT710 - STA


title: KT630 - STA


title: KT566 - STA


title: KT663 - STA


title: KT704 - STA


title: KT878 - STA


title: KT567 - STA


title: KT723 - STA


title: KT626 - STA


title: KT481 - STA


title: KT703 - STA


title: KT607 - STA


title: KT1009 - AR


title: KT966 - AR


title: KT659 - AR


title: KT619 - STA


title: KT773 - STA


title: KT917 - STA


title: KT628 - AR


title: KT529 - STA


title: KT867 - AR


title: KT809 - STA


title: KT554 - AR


title: KT592 - AR


title: KT965 - STA


title: KT863 - AR


title: KT552 - STA


title: KT871 - AR


title: KT954 - AR


title: KT948 - AR


title: KT689 - AR


title: KT758 - STA


title: KT688 - AR


title: KT1029 - AR


title: KT1030 - AR


title: KT1141 - AR


title: KT728 - AR


title: KT1012 - AR


title: KT769 - STA


title: KT713 - AR


title: KT696 - STA


title: KT1099 - AR


title: KT833 - STA


title: KT682 - AR


title: KT1003 - AR


title: KT1070 - AR


title: KT951 - AR


title: KT698 - STA


title: KT962 - AR


title: KT1089 - AR


title: KT649 - AR


title: KT618 - STA


title: KT775 - AR


title: KT1100 - AR


title: KT925 - STA


title: KT827 - AR


title: KT1063 - AR


title: KT669 - STA


title: KT610 - AR


title: KT1092 - AR


title: KT1045 - AR


title: KT1090 - AR


title: KT417 - STA


title: KT1016 - AR


title: KT548 - STA


title: KT1043 - AR


title: KT239 - STA


title: KT1041 - STA


title: KT755 - STA


title: KT591 - STA


title: KT1086 - AR


title: KT387 - STA


title: KT559 - AR


title: KT921 - STA


title: KT614 - STA


title: KT602 - STA


title: KT540 - STA


title: KT627 - STA


title: KT342 - STA


title: KT675 - STA


title: KT588 - STA


title: KT412 - STA


title: KT781 - STA


title: KT612 - STA


title: KT785 - STA


title: KT664 - STA


title: KT655 - STA


title: Pieter_113

city: Utrecht

first: Pieter

last: van Lierop

address: Lundlaan 6

department: Pediatrics

country: Netherlands

institute: UMC Utrecht

description:
113
Gene epxression from control

hyb_protocol: cRNA was hybridized on the GeneChip human genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA (45°C for 16-18 hours). Staining, washing and scanning procedures were carried out according to the manufacturer's protcocol (Affymetrix). All GeneChips were visually inspected for irregularities. The R package AffyQC-report was used for quality control and indicated high quality and overall comparability of all samples.

scan_protocol: Standard Affymetrix protocol

data_processing: raw intensity values of all samples were normalized by background correction and quantile normalization using the version 6.4 Robust Multichip Analysis (Partek).

source_name: age-matched control

label_protocol: Biotinylated antisense cRNA was prepared from 5 µg of total RNA using the one-cycle labeling (Affymetrix, Santa Clara, CA).

extract_protocol: Total cellular RNA was extracted using the PAXgeneTM blood RNA kit (Qiagen) according to the manufacturer’s protocol. RNA levels, quality and purity were assessed with the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Venous blood (2ml) was collected in PAXgene tubes (PreAnalytiX) and stored at –20°C until RNA extraction.

tag: tissue/cell type

value: peripheral blood leucocytes (PBL)


title: KT624 - STA


title: Pieter_114

description:
114
Gene epxression from control


title: Pieter_111

description:
111
Gene epxression from control


title: Pieter_112

description:
112
Gene epxression from control


title: Pieter_106

description:
106
Gene epxression from control


title: Pieter_110

description:
110
Gene epxression from control


title: Pieter_104

description:
104
Gene epxression from control


title: Pieter_102

description:
102
Gene epxression from IBD patient


title: Pieter_54

description:
54
Gene epxression from IBD patient

source_name: pediatric IBD patients in clinical remission


title: Pieter_107

description:
107
Gene epxression from control


title: Pieter_105

description:
105
Gene epxression from control


title: Pieter_108

description:
108
Gene epxression from control


title: Pieter_53

description:
53
Gene epxression from IBD patient


title: Pieter_45

description:
45
Gene epxression from control


title: Pieter_52

description:
52
Gene epxression from IBD patient


title: Pieter_48-2

description:
48-2
Gene epxression from IBD patient


title: Pieter_47-2

description:
47-2
Gene epxression from IBD patient


title: Pieter_101

description:
101
Gene epxression from IBD patient


title: Pieter_40

description:
40
Gene epxression from IBD patient


title: Pieter_43

description:
43
Gene epxression from IBD patient


title: Pieter_50

description:
50
Gene epxression from IBD patient


title: Pieter_39

description:
39
Gene epxression from IBD patient


title: Pieter_44-2

description:
44-2
Gene epxression from IBD patient


title: Pieter_41

description:
41
Gene epxression from IBD patient


title: Pieter_38

description:
38
Gene epxression from IBD patient


title: Pieter_51

description:
51
Gene epxression from IBD patient


title: Pieter_36

description:
36
Gene epxression from IBD patient


title: Pieter_42

description:
42
Gene epxression from IBD patient


title: Pieter_34

description:
34
Gene epxression from IBD patient


title: Pieter_33

description:
33
Gene epxression from IBD patient


title: Pieter_37

description:
37
Gene epxression from IBD patient


title: Pieter_35

description:
35
Gene epxression from IBD patient


title: Pieter_31

description:
31
Gene epxression from IBD patient


title: Pieter_28

description:
28
Gene epxression from IBD patient


title: Pieter_30

description:
30
Gene epxression from IBD patient


title: Pieter_25

description:
25
Gene epxression from IBD patient


title: Pieter_21

description:
21
Gene epxression from IBD patient


title: Pieter_29

description:
29
Gene epxression from IBD patient


title: Pieter_22

description:
22
Gene epxression from IBD patient


title: Pieter_32

description:
32
Gene epxression from IBD patient


title: Pieter_26

description:
26
Gene epxression from IBD patient


title: Pieter_24

description:
24
Gene epxression from IBD patient


title: Pieter_27

description:
27
Gene epxression from IBD patient


title: Pieter_10-2

description:
10-2
Gene epxression from IBD patient


title: Pieter_02

description:
2
Gene epxression from IBD patient


title: Pieter_19-2

description:
19-2
Gene epxression from IBD patient


title: Pieter_14-2

description:
14-2
Gene epxression from IBD patient


title: Pieter_08

description:
8
Gene epxression from IBD patient


title: 09008 CML M-BC

city: Portland

first: Daniel

last: Bottomly

address: 3181 Sam Jackson Park Rd.

institute: OHSU

hyb_protocol: Amplified and labeled cDNA target samples were each hybridized to a Human Exon 1.0 ST array.

scan_protocol: Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software.

data_processing:
Data were processed using the oligo and pd.huex.1.0.st.v2 packages in R/Bioconductor and were summarized at the transcript level using the RMA method for only the core probesets.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na27.hg18.probeset.csv

source_name: CML M-BC

label_protocol: Samples were amplified and labeled using the Ambion WT Expression/Affymetrix WT Terminal Labeling protocol.

extract_protocol: Mononuclear cells from blood or bone marrow of patients with hematologic malignancies were isolated using a Ficoll gradient. Cell pellets were snap-frozen in liquid nitrogen and  cryopreserved at -80 C for subsequent batch extraction of RNA.  RNA was extracted using Qiagen RNeasy kits according to the manufacturer instructions, including performance of the optional on-column DNase treatment step.

value: PB

tag: gender

value: unknown

tag: ethnicity

tag: hyb. date


title: Pieter_11

description:
11
Gene epxression from IBD patient


title: Pieter_13-2

description:
13-2
Gene epxression from IBD patient


title: Pieter_05

description:
5
Gene epxression from IBD patient


title: 08167 PMF

source_name: PMF


title: Pieter_17-2

description:
17-2
Gene epxression from IBD patient


title: Pieter_06

description:
6
Gene epxression from IBD patient


title: 08062 MPN

source_name: MPN


title: Pieter_03

description:
3
Gene epxression from IBD patient


title: 08409 CNL

source_name: CNL


title: Pieter_20

description:
20
Gene epxression from IBD patient


title: Pieter_18-2

description:
18-2
Gene epxression from IBD patient


title: Pieter_4-2

description:
4-2
Gene epxression from IBD patient


title: Pieter_01

description:
1
Gene epxression from IBD patient


title: 08423 CNL


title: 09180 CMML

source_name: CMML

value: F

value: Non Hispanic/White


title: 09020 CMML

value: BM

value: M

value: Non-Hispanic/White


title: 09293 MPN


title: 08166 MPN, familial

source_name: MPN, familial


title: 08294 ET

source_name: ET


title: 07345 CML M-BC


title: 08109 CMML


title: 08319 PMF


title: 08235 MPN (ET)

source_name: MPN (ET)


title: 08432 JMML

source_name: JMML


title: 08216 CMML


title: 07324 CMML

value: Hispanic/Multiracial


title: 09404 AML, Pediatric

source_name: AML, Pediatric

value: Unknown/Unknown


title: 09015 AML, Pediatric


title: 09179 AML, Pediatric


title: 08053 AML, Pediatric


title: 07172 CMML


title: 07079 CMML


title: 09445 T-ALL

source_name: T-ALL


title: 09473 AML, Pediatric


title: 09107 AML, Pediatric

value: Hispanic/White


title: 08102 AML, Adult

source_name: AML, Adult

value: Leukapheresis


title: Me086

city: Memphis

first: Ansley

last: Stanfill

state: TN

address: 920 Madison Ave

institute: University of Tennessee Health Sciences Center

description: Me 86-1_Adipose-tissue_16September2009.CEL

hyb_protocol: GeneChip  hybridization oven (640) 17 hrs o/n at 45 degrees and 60 rpm

scan_protocol: 3000 7G and the Core Software used was GCOS v1.4

data_processing: Data were processed using GeneSpring software. RMA was applied for normalization.

source_name: adipose tissue, baseline

label_protocol: WT Sense Target labeling and controls kit

extract_protocol: Trizol (Invitrogen) and Rneasy Lipid kit (Qiagen)

tag: 6 month weight change

value: Male

tag: race

value: Caucasian

tag: pretransplant diabetes

value: Yes

tag: post transplant diabetes

tag: pre transplant hypertension


title: 10136 AML, Adult


title: Me085

description: Me 085-1-Adipose-tissue_20October2009.CEL

value: Female

value: No


title: 08024 AML, Adult


title: Me088

description: Me 088-1-Adipose-tissue_20October2009.CEL


title: Me089

description: Me 89-1_Adipose-tissue_16September2009.CEL


title: 09190 ALL (B), Pediatric

source_name: ALL (B), Pediatric


title: 09302 AML, pediatric

source_name: AML, pediatric

value: Non Hispanic/Asian


title: 10198 AML, Pediatric

value: PB


title: 09145 AML, Adult


title: Me080

description: Me80-6_Adipose-tissue_16September2009.CEL


title: 07335 AML, Adult

value: unknown


title: 08118 ALL (B), Pediatric

value: F


title: 08027 AML, Adult


title: Me075

description: Me 075-1-Adipose-tissue_20October2009.CEL

value: African American


title: Me087

description: Me 087-1-Adipose-tissue_20October2009.CEL


title: 07008 AML, Adult


title: Me071

description: Me 071-1-Adipose-tissue_20October2009.CEL


title: 09199 ALL (B), Pediatric

value: BM


title: Me084

description: Me 084-1-Adipose-tissue_20October2009.CEL


title: Me081

description: Me 081-1-Adipose-tissue_20October2009.CEL


title: 08419 ALL (B), Pediatric


title: T119 ALL (B), Pediatric


title: 09076 ALL (B), Pediatric


title: Me065

description: Me 65-6_Adipose-tissue_16September2009.CEL


title: Me062

description: Me 062-1-Adipose-tissue_20October2009.CEL


title: Me059

description: Me 059-1-Adipose-tissue_16October2009.CEL


title: 09177 ALL (B), Pediatric

value: M


title: Me039

description: Me 039-1-Adipose-tissue_16October2009.CEL


title: Me049

description: Me 049-1-Adipose-tissue_16October2009.CEL


title: Me064

description: Me 064-6-Adipose-tissue_20October2009.CEL


title: 09562 ALL (B), Pediatric

value: Non-Hispanic/White


title: Me046

description: Me 46-6_Adipose-tissue_16September2009.CEL


title: 09788 ALL (B), Pediatric


title: 08178 T-ALL


title: 09624 ALL (B), Pediatric


title: 09182 ALL (B), Pediatric

value: Non Hispanic/Pacific Islander


title: Me016

description: Me 016-1-Adipose-tissue_16October2009.CEL


title: Me028

description: Me 028-1-Adipose-tissue_16October2009.CEL


title: Me023

description: Me 023-1-Adipose-tissue_16October2009.CEL


title: Me061

description: Me 061-1-Adipose-tissue_20October2009.CEL


title: Me033

description: Me 033-1-Adipose-tissue_16October2009.CEL


title: Me034

description: Me 034-1-Adipose-tissue_16October2009.CEL


title: 09646 ALL (B), Pediatric


title: Me026

description: Me 026-1-Adipose-tissue_16October2009.CEL


title: 09206 ALL (B), Pediatric


title: Me011

description: Me 011-2-Adipose-tissue_16October2009.CEL


title: Me009

description: Me 09-2-Adipose-tissue_16October2009.CEL


title: 08431 ALL (B), Pediatric


title: Tumor 406

status: Public on Oct 03 2013

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Genome Studio V2011.2. The methylation score of each CpG is represented as an average beta value (AVG_Beta).

label: Cy3, Cy5

molecule: genomic DNA

source_name: lung, adenocarcinoma

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Total DNA was isolated by standard procedures.

value: lung

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: nsclc type

value: adenocarcinoma

tag: heatmap

value: yes

tag: curep code

tag: Stage

value: III

tag: smoker

tag: age

value: male

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 397

tag: tissue

value: I

tag: gender


title: Tumor 399

source_name: lung, squamous cell carcinoma

value: squamous cell carcinoma

tag: recurrence

tag: time_rec (years)

value: no


title: Tumor 407

value: II


title: Tumor 404


title: Tumor 388

value: female


title: Tumor 385


title: Tumor 400


title: Tumor 372


title: Tumor 403


title: Tumor 408


title: Tumor 382


title: Tumor 370


title: Tumor 384


title: Tumor 401

tag: 6th tnm stage

value: IB

tag: 7th tnm stage

value: unknown

tag: tumor size (cm)


title: Tumor 398


title: Tumor 383


title: Tumor 395


title: Tumor 396


title: Tumor 386


title: Tumor 381


title: Tumor 387


title: Tumor 376


title: Tumor 402


title: Tumor 375


title: Tumor 380


title: Tumor 379


title: Tumor 409


title: Tumor 371


title: Tumor 394


title: Tumor 377


title: Tumor 392


title: Tumor 378


title: Tumor 474


title: Tumor 391


title: Tumor 459


title: Tumor 485


title: Tumor 454


title: Tumor 467


title: Tumor 442


title: Tumor 456


title: Tumor 427


title: Tumor 450


title: Tumor 419


title: Tumor 453


title: Tumor 479


title: Tumor 444


title: Tumor 422


title: Tumor 484


title: Tumor 412


title: Tumor 465


title: Tumor 426


title: Tumor 480


title: Tumor 451


title: Tumor 425


title: Tumor 430


title: Tumor 436


title: Tumor 432


title: Tumor 478


title: Tumor 488


title: Tumor 471


title: Tumor 443


title: Tumor 473


title: Tumor 446


title: Tumor 429


title: Tumor 428


title: Tumor 482


title: Tumor 462


title: Tumor 410


title: Tumor 413


title: Tumor 461


title: Tumor 448


title: Tumor 466


title: Tumor 414


title: Tumor 464


title: Tumor 476


title: Tumor 460


title: Tumor 469


title: Tumor 458


title: Tumor 424


title: Tumor 421


title: Tumor 487


title: Tumor 418


title: Tumor 420


title: Tumor 438


title: Tumor 439


title: Tumor 486


title: Tumor 489


title: Tumor 411


title: Tumor 481


title: Tumor 445


title: Tumor 433


title: Tumor 417


title: Tumor 472


title: Tumor 457


title: Tumor 435


title: Tumor 447


title: Tumor 463


title: Tumor 434


title: Tumor 483


title: Tumor 437


title: Tumor 475


title: Tumor 468


title: Tumor 431


title: Tumor 415


title: Tumor 477


title: Tumor 490


title: Tumor 441


title: Tumor 452


title: Tumor 440


title: Tumor 470


title: Tumor 455


title: Tumor 423


title: Tumor 363


title: Tumor 449


title: Tumor 357


title: Tumor 244


title: Tumor 362


title: Tumor 261


title: Tumor 416


title: Tumor 237


title: Tumor 328


title: Tumor 259


title: Tumor 254


title: Tumor 350


title: Tumor 238

value: IIA


title: Tumor 342


title: Tumor 354


title: Tumor 345


title: Tumor 336

value: IA


title: Tumor 333


title: Tumor 242


title: Tumor 247


title: Tumor 361


title: Tumor 252


title: Tumor 346


title: Tumor 364


title: Tumor 338


title: Tumor 352


title: Tumor 327


title: Tumor 329


title: Tumor 258


title: Tumor 245


title: Tumor 367


title: Tumor 358


title: Tumor 264


title: Tumor 331


title: Tumor 211

value: IV


title: Tumor 368


title: Tumor 349


title: Tumor 340


title: Tumor 348


title: Tumor 248


title: Tumor 239


title: Tumor 236


title: Tumor 369


title: Tumor 337


title: Tumor 360


title: Tumor 405


title: Tumor 365


title: Tumor 339


title: Tumor 359


title: Tumor 309


title: Tumor 353


title: Tumor 260


title: Tumor 330


title: Tumor 341


title: Tumor 355


title: Tumor 269


title: Tumor 291


title: Tumor 275


title: Tumor 304


title: Tumor 301


title: Tumor 318


title: Tumor 274


title: Tumor 214


title: Tumor 253


title: Tumor 209


title: Tumor 255


title: Tumor 203


title: Tumor 201


title: Tumor 303


title: Tumor 205


title: Tumor 202


title: Tumor 220


title: Tumor 326


title: Tumor 267


title: Tumor 232


title: Tumor 287


title: Tumor 325


title: Tumor 268


title: Tumor 307


title: Tumor 313


title: Tumor 226


title: Tumor 219


title: Tumor 217


title: Tumor 194


title: Tumor 233


title: Tumor 286


title: Tumor 195


title: Tumor 284


title: Tumor 317


title: Tumor 292


title: Tumor 213


title: Tumor 316


title: Tumor 294


title: Tumor 283


title: Tumor 302


title: Tumor 192


title: Tumor 198


title: Tumor 277


title: Tumor 295


title: Tumor 212


title: Tumor 312


title: Tumor 321


title: Tumor 206


title: Tumor 305


title: Tumor 218


title: Tumor 200


title: Tumor 273


title: Tumor 285


title: Tumor 281


title: Tumor 308


title: Tumor 293


title: Tumor 297


title: Tumor 197


title: Tumor 221


title: Tumor 322


title: Tumor 282


title: Tumor 323


title: Tumor 324


title: Tumor 314


title: Tumor 225


title: Tumor 199


title: Tumor 306


title: Tumor 315


title: Tumor 196


title: Tumor 272


title: Tumor 296


title: Tumor 179


title: Tumor 173


title: Tumor 204


title: Tumor 30


title: Tumor 181


title: Tumor 18


title: Tumor 19


title: Tumor 168


title: Tumor 216


title: Tumor 280


title: Tumor 27


title: Tumor 17


title: Tumor 170


title: Tumor 183


title: Tumor 178


title: Tumor 171


title: Tumor 23


title: Tumor 278


title: Tumor 22


title: Tumor 20


title: Tumor 21


title: Tumor 172


title: Tumor 24


title: Tumor 25


title: Tumor 167


title: Tumor 271


title: Tumor 311


title: Tumor 266


title: Tumor 184


title: Tumor 176


title: Tumor 310


title: Tumor 28


title: Tumor 298


title: Tumor 265


title: Tumor 185


title: Tumor 175


title: Tumor 164


title: Tumor 279


title: Tumor 299


title: Tumor 166


title: Tumor 29


title: Tumor 319


title: Tumor 180


title: Tumor 160


title: Tumor 174


title: Tumor 300


title: Tumor 169


title: Tumor 270


title: Tumor 163


title: Tumor 290


title: Tumor 110


title: Tumor 165


title: Tumor 289


title: Tumor 182


title: Tumor 177


title: Tumor 161


title: Tumor 141


title: Tumor 138


title: Tumor 94


title: Tumor 37


title: Tumor 134


title: Tumor 132


title: Tumor 97


title: Tumor 35


title: Tumor 143


title: Tumor 158


title: Tumor 95


title: Tumor 112


title: Tumor 121


title: Tumor 85


title: Tumor 126


title: Tumor 90


title: Tumor 288


title: Tumor 139


title: Tumor 82


title: Tumor 81


title: Tumor 128


title: Tumor 80


title: Tumor 320


title: Tumor 151


title: Tumor 26


title: Tumor 159


title: Tumor 88


title: Tumor 137


title: Tumor 133


title: Tumor 109


title: Tumor 156


title: Tumor 101


title: Tumor 131


title: Tumor 91


title: Tumor 118


title: Tumor 113


title: Tumor 107


title: Tumor 111


title: Tumor 103


title: Tumor 117


title: Tumor 92


title: Tumor 34


title: Tumor 33


title: Tumor 153


title: Tumor 106


title: Tumor 142


title: Tumor 104


title: Tumor 154


title: Tumor 149


title: Tumor 129


title: Tumor 102


title: Tumor 83


title: Tumor 140


title: Tumor 36


title: Tumor 84


title: Tumor 150


title: Tumor 89


title: Tumor 146


title: Tumor 100


title: Tumor 123


title: Tumor 115


title: Tumor 155


title: Tumor 96


title: Tumor 98


title: Tumor 147


title: Tumor 86


title: Tumor 122


title: Tumor 144


title: Tumor 145


title: Tumor 130


title: Tumor 79


title: Tumor 127


title: Tumor 152


title: Tumor 119


title: Tumor 31


title: Tumor 136


title: Tumor 108


title: Tumor 114


title: Tumor 135


title: Tumor 157


title: 24h Mannitol control , ARPE-58

city: Malmo

first: Poya

last: Tababat-Khani

address: CRC, Jan Waldenstroms gata 35

department: Department of Clinical Sciences, Malmo

country: Sweden

institute: Lund University

hyb_protocol: Hybridization to the arrays was performed at the SCIBLU Genomics Centre at Lund University.

scan_protocol: Scanning was performed at the SCIBLU Genomics Centre at Lund University.

data_processing: Basic chip and experimental quality analyses were performed using Expression Console Software v1.1.2 (Affymetrix). Probe summarization and data normalization were performed with Robust Multi-array Analysis using Expression Console Software.

source_name: ARPE-19, control, mannitol, 24h

label_protocol: Labeling was performed at the SCIBLU Genomics Centre at Lund University.

growth_protocol: ARPE-19 cells were cultured in DMEM (Invitrogen Ltd, Paisley, UK) containing 100 mg/dL D-Glucose, Sodium Pyruvate, without L-Glutamine and Phenol Red, supplemented with GlutaMAX-I (L-Alanyl-L-Glutamine; Invitrogen) at a concentration of 4 mM, 10% FBS, Streptomycin 100 µg/ml and Penicillin 100 U/ml (Invitrogen). The cells were incubated in a humidified environment containing 5% CO2 at 37 °C. The medium was changed every third day and a final density of approximately 3 x 10^6 cells per cell culture flask was reached within seven days. The cultured RPE cells were washed once with PBS (pH 7.4 ± 0.05, Invitrogen) and treated with 0.05% trypsin-EDTA (Invitrogen). The detached cells were plated at a density of 3 x 10^4 cells in 500 µl of medium on glass cover slips (12 mm in diameter) and placed in cell culture wells (16 mm in diameter). The cell culture reached a final density of approximately 1 x 10^5 cells per cover slip, within 7 days, before laser treatment was performed.

extract_protocol: RNA extraction was performed using Nucleospin RNA XS (Machery-Nagel, Düren, Germany) at 2h, 6h and 24h after photocoagulation.

treatment_protocol: Before photocoagulation, a black paper was placed beneath the glass cover slip to facilitate absorption of the laser energy, as ARPE-19 cells in culture lack pigment. The black paper was soaked in medium 2 h prior to photocoagulation. Just before photocoagulation, the paper was placed in an empty well and the glass cover slip was moved onto the pigment source. Photocoagulation of the confluent RPE cells was accomplished with a frequency-doubled Nd:YAG laser (Visulas 532, Carl Zeiss, Oberkochen, Germany). Laser power and spot size were 300 mW and 200 µm, respectively. Duration time was 0.1 s regardless of the setting. Each 12 mm cover slip was subjected to 50 evenly distributed laser shots. Fresh complete medium was added after photocoagulation and the cells were returned to the CO2 incubator.

tag: cell line

tag: cell type

value: retinal pigment epithelial cells

tag: treatment 1

value: control

tag: treatment 2

value: mannitol

tag: time


title: Tumor 87

value: lung

tag: disease state

value: non-small cell lung cancer (NSCLC)

tag: nsclc type

value: adenocarcinoma

tag: heatmap

tag: curep code

tag: Stage


title: 24h Mannitol control , ARPE-37


title: 24h Mannitol control , ARPE-39


title: Tumor 120

tag: tissue

value: yes

value: III

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 125

value: I

tag: gender


title: 24h Mannitol control, ARPE-60


title: Tumor 124

value: male

tag: recurrence

value: no

tag: time_rec (years)

tag: 6th tnm stage

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 105

value: female


title: Tumor 75


title: Tumor 99

value: IB


title: 24h 22mM glucose control, ARPE-68

source_name: ARPE-19, control, 22mM glucose, 24h

tag: cell line

tag: cell type

tag: treatment 1

tag: treatment 2

value: 22mM glucose

tag: time


title: 24h 22mM glucose control, ARPE-67


title: Tumor 57

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage

value: IIA


title: Tumor 56

tag: tissue

tag: smoker

tag: age

tag: tnm

value: IA

tag: adjuvant chemotherapy


title: 24h 22mM glucose control, ARPE-32


title: 24h 22mM glucose laser treated, ARPE-26

source_name: ARPE-19, laser treated, 22mM glucose, 24h

value: laser treated


title: 24h 22mM glucose control, ARPE-33

value: retinal pigment epithelial cells


title: 24h 22mM glucose laser treated, ARPE-25


title: Tumor 71

tag: gender


title: Tumor 74


title: Tumor 70


title: Tumor 59

tag: recurrence

tag: time_rec (years)


title: 24h 22mM glucose laser treated, ARPE-57

tag: cell line

tag: cell type


title: Tumor 68

tag: 6th tnm stage

tag: 7th tnm stage

tag: tumor size (cm)


title: 24h 22mM glucose laser treated, ARPE-24

tag: treatment 1

tag: treatment 2

tag: time


title: Tumor 58

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage


title: Tumor 69

tag: tissue

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 63

tag: gender


title: Tumor 76

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage


title: Tumor 65

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 93


title: Tumor 78


title: Tumor 66


title: 24h 5mM glucose control, ARPE-9

source_name: ARPE-19, control, 5mM glucose, 24h

tag: cell line

tag: cell type

tag: treatment 1

value: control

tag: treatment 2

value: 5mM glucose

tag: time


title: 24h 5mM glucose laser treated, ARPE-54

source_name: ARPE-19, laser treated, 5mM glucose, 24h


title: 24h 5mM glucose laser treated, ARPE-55


title: 24h 5mM glucose laser treated, ARPE-8


title: 24h 5mM glucose control, ARPE-10


title: Tumor 62

value: lung

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage


title: 24h 5mM glucose control, ARPE-28


title: 24h 5mM glucose control, ARPE-29


title: Tumor 61

tag: tissue

value: non-small cell lung cancer (NSCLC)

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 148

value: adenocarcinoma

tag: gender


title: 24h 5mM glucose laser treated, ARPE-7


title: Tumor 72

value: yes

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 73


title: 6h 22mM glucose control, ARPE-127

source_name: ARPE-19, control, 22mM glucose, 6h

tag: cell line

tag: cell type

tag: treatment 1

tag: treatment 2

tag: time


title: 6h 22mM glucose control, ARPE-128


title: 6h 22mM glucose control, ARPE-126


title: 6h 22mM glucose laser treated, ARPE-52

source_name: ARPE-19, laser treated, 22mM glucose, 6h


title: 6h 22mM glucose laser treated, ARPE-51


title: Tumor 32

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage

value: II


title: Tumor 67

tag: tissue

value: I

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 55

tag: gender

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage

tag: 7th tnm stage


title: Tumor 77

tag: tumor size (cm)


title: 6h 22mM glucose laser treated, ARPE-22

tag: cell line

tag: cell type

tag: treatment 1

tag: treatment 2

tag: time


title: 6h 22mM glucose control, ARPE-125


title: 2h 22mM glucose control, ARPE-88

source_name: ARPE-19, control, 22mM glucose, 2h


title: 2h 22mM glucose control, ARPE-86


title: Tumor 64

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage

value: male


title: 2h 22mM glucose control, ARPE-84


title: Tumor 38

tag: tissue

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 41

tag: gender


title: 2h 22mM glucose control, ARPE-83


title: Tumor 39

value: no


title: Tumor 40

value: female


title: 2h 22mM glucose laser treated, ARPE-97

source_name: ARPE-19, laser treated, 22mM glucose, 2h


title: Tumor 53

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage

value: IB

tag: 7th tnm stage

tag: tumor size (cm)


title: 2h 22mM glucose laser treated, ARPE-96

tag: cell line

tag: cell type

tag: treatment 1

tag: treatment 2

value: 22mM glucose

tag: time


title: Tumor 44

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage


title: 2h 22mM glucose laser treated, ARPE-99


title: 6h 22mM glucose laser treated, ARPE-53


title: 6h 5mM glucose control, ARPE-135

source_name: ARPE-19, control, 5mM glucose, 6h


title: Tumor 47

tag: tissue

tag: smoker

tag: age

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 42

tag: gender


title: 2h 22mM glucose laser treated, ARPE-95


title: Tumor 45


title: Tumor 51

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 49


title: 6h 5mM glucose control, ARPE-132

tag: cell line

tag: cell type

tag: treatment 1

tag: treatment 2

tag: time


title: Tumor 54

tag: disease state

tag: nsclc type

tag: heatmap

tag: curep code

tag: Stage

value: IIB


title: Tumor 50

tag: tissue

tag: smoker

tag: age

tag: tnm

value: IA

tag: adjuvant chemotherapy


title: 6h 5mM glucose laser treated, ARPE-50

source_name: ARPE-19, laser treated, 5mM glucose, 6h

value: laser treated


title: Tumor 52

tag: gender


title: 6h 5mM glucose laser treated, ARPE-49

value: retinal pigment epithelial cells


title: 6h 5mM glucose laser treated, ARPE-48


title: Tumor 43


title: Tumor 189

value: squamous cell carcinoma


title: 6h 5mM glucose control, ARPE-133

value: control

value: 5mM glucose


title: Tumor 60

value: lung

value: non-small cell lung cancer (NSCLC)

value: III


title: 2h 5mM glucose control, ARPE-82

source_name: ARPE-19, control, 5mM glucose, 2h


title: MeCP2_KO_rep1

description: Sample name: R

hyb_protocol: Fluorescent aRNA targets were prepared using Agilent Quick Amp Labeling Kit. Microarray hybridization was performed at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers. Washing was performed in an ozone-free environment

scan_protocol: The slides were scanned using the Agilent DNA microarray scanner (part number G2505B)

data_processing: Data was extracted using Agilent Feature Extraction Software (version 10.5.1.1). The resulting .txt files were imported into the Agilent GeneSpring GX software (version 11.0). Normalization was performed using the Agilent FE one-color scenario (mainly median normalization). Genes marked present or marginal in all samples (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold-change screening. Unsupervised hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.0).

organism: Mus musculus

source_name: Whole Brain, MeCP2 KO, rep1

label_protocol: 1ug RNA is used for labeling with Cy3

extract_protocol: RNA was extracted using Trizol protocol (Life technologies) until getting the aqueous phase and then purified with Rneasy column kit (Qiagen). Following elution, DNAse treatment has been preformed with the Turbo DNAse kit (Ambion). Quantification and quality check were performed with Nanodrop and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.

tag: strain

value: 60 days

tag: genotype/variation

value: MeCP2 KO

value: whole brain


title: Wild_type_rep2

description: Sample name: S1

source_name: Whole Brain, wild-type, rep2

value: male

value: wild-type


title: in vitro induced myocytes (donor 2)

hyb_protocol: The resulting cRNA target was randomly fragmented using UDG (Uracil DNA Glycosylase) and APE1 (apurinic/apyrimidic endonuclease 1), labelled with the terminal transferase (WT Terminal Labelling kit, Affymetrix) and hybridized on the Human Gene 1.1 ST 16-array (Affymetrix, Santa Clara, CA)

scan_protocol: The hybridization reactions were processed and scanned according to the standard GeneTitanTM (Affymetrix, Santa Clara, CA) protocols.

data_processing: All arrays were globally scaled to a target-intensity value of 100 and then the scaling factor, background, noise, and percentage present were calculated according to the Command Console (AGCC 2.0) and Expression Console (EE 1.1) softwares (Affymetrix, Santa Clara, CA). All resulting datasets were filtered using the absolute call metric (present or absent) using Microsoft Access (Microsoft Corporation, Redmond, WA). The resulting values represent the transcript abundance (absolute value) following Affymetrix statistical’s procedure. Three biological replicates were done for each ASC sample and in vitro differentiated cells were analysed in duplicate.

source_name: Progenitor Myocytes

label_protocol: Biotinylated target RNA was prepared from 200 ng of total RNA using the Affymetrix protocol. Briefly, double-stranded cDNA was prepared from the RNA template using the Ambion WT Expression kit following manufacturer’s instructions.

extract_protocol: For the expression microarray experiment in hASCs and in vitro differentiated cells, total RNA was prepared using TRIZOL® (Invitrogen, Carlsbad, CA) and further purified using RNeasy columns (Qiagen, GmbH) according to the manufacturer’s instructions. The integrity of RNA was monitored by both Byoanalyzer and spectrometric measurement

tag: cell type

value: Progenitor Myocytes


title: Tumor 46

source_name: lung, adenocarcinoma

value: adenocarcinoma

value: yes


title: Wild_type_rep1

description: Sample name: S

source_name: Whole Brain, wild-type, rep1


title: Tumor 48

value: II


title: Tumor 10

value: I

tag: recurrence

value: no

tag: time_rec (years)

tag: 6th tnm stage

value: IA

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 12

source_name: lung, squamous cell carcinoma

tag: disease state

tag: nsclc type

value: squamous cell carcinoma

tag: heatmap

value: unknown


title: Tumor 186

tag: tissue

value: lung

tag: curep code

tag: Stage


title: in vitro induced myocytes (donor 1)


title: 6h 5mM glucose control, ARPE-134

tag: cell line

value: retinal pigment epithelial cells

tag: treatment 1

value: control

tag: treatment 2

value: 5mM glucose

tag: time


title: 2h 5mM glucose control, ARPE-81


title: Tumor 190

value: non-small cell lung cancer (NSCLC)

tag: smoker

tag: age

tag: gender

tag: tnm

tag: adjuvant chemotherapy


title: Tumor 13

value: III


title: in vitro induced osteocytes (donor 1)

source_name: Progenitor Osteocytes

tag: cell type

value: Progenitor Osteocytes


title: 2h 5mM glucose control, ARPE-80


title: 6h 5mM glucose laser treated, ARPE-4

value: laser treated


title: in vitro induced osteocytes (donor 2)


title: Tumor 187

value: male


title: 2h 5mM glucose control, ARPE-79


title: Tumor 188


title: 2h 5mM glucose laser treated, ARPE-94

source_name: ARPE-19, laser treated, 5mM glucose, 2h


title: Tumor 9

value: adenocarcinoma


title: adipose- derived stem cells Donor 2

source_name: Adult stem cell

value: Adult stem cell


title: 2h 5mM glucose laser treated, ARPE-90


title: Tumor 8

value: yes

value: II


title: 2h 5mM glucose laser treated, ARPE-89


title: 2h 5mM glucose laser treated, ARPE-93


title: adipose- derived stem cells Donor 1


title: Mock transfection control

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

description: Mock Control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Beadstudio

source_name: HeLa cells

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

extract_protocol: Total RNA was extracted from the cell lysate using the mirVana kit (Ambion)

value: HeLa cervical cancer cell line

tag: treatment protocol

value: Mock transfection, with no RNA added


title: adipose- derived stem cells Donor 3


title: GAPDH siRNA

description: GAPDH siRNA

value: Transfection of GAPDH siRNA


title: MeCP2_KO_rep2

description: Sample name: R1

source_name: Whole Brain, MeCP2 KO, rep2

tag: strain

value: 60 days

tag: genotype/variation

value: MeCP2 KO

value: whole brain


title: Tumor 16

value: lung

tag: disease state

tag: nsclc type

tag: heatmap

value: female

value: unknown


title: Negative control siRNA

description: Negative Control

value: Transfection of negative control siRNA


title: Tumor 5

tag: tissue

value: non-small cell lung cancer (NSCLC)

value: squamous cell carcinoma

tag: curep code

tag: Stage

value: I

tag: recurrence

value: no

tag: time_rec (years)

tag: 6th tnm stage

value: IB

tag: 7th tnm stage

value: IIB

tag: tumor size (cm)


title: Tumor 6

value: yes

value: II

tag: smoker

tag: age

tag: gender

value: male

tag: tnm


title: brewery_A_run_8/brewery_B_run_1

status: Public on Oct 02 2013

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

description: Gene expression of cells from run 1 and run 8 from brewery D was analyzed.

hyb_protocol: The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s and Micromax TSA Kit recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

organism: Saccharomyces cerevisiae

source_name: yeast cells harvested by the end of fermentation from brewery cylindro-conical vessel

label_protocol: The indirect labeling by the tyramide-signal-amplification method (MicromaxTM TSATM labeling and detection Kit from Perkin Elmer life sciences, MPS 522) was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.

growth_protocol: Beer brewery process, industrial serial repitching

extract_protocol: The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied.

treatment_protocol: successive runs varied from 4 to 22

tag: strain

tag: run


title: brewery_A_run_4/brewery_B_run_1

description: Gene expression of cells from run 1 and run 4 from brewery C was analyzed.

value: HEBRU


title: brewery_A_run_5/brewery_B_run_1

description: Gene expression of cells from run 1 and run 5 from brewery B was analyzed.


title: Tumor 14

tag: disease state

value: adenocarcinoma

tag: adjuvant chemotherapy


title: Glu/Ethanol

description: Gene expression of stressed cells compared to stationary phase cells was analyzed.

hyb_protocol: The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s recommendations.

source_name: yeast cells harvested 24 h after exposure to high glucose concentrations

label_protocol: The indirect labeling by the tyramide-signal-amplification method was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.

growth_protocol: S. cerevisiae H155 was batch-cultured in 100 ml Erlenmeyer flasks at 30°C, 150 rpm in 50 ml Schatzmann medium (pH 5.4).

extract_protocol: The isolation of RNA was done by disruption of the cells under liquid nitrogen using mortar and pistil and then the Qiagen RNeasy Midi Kit with some modifications within the manufacturers´ protocol and the Qiagen RNase-Free DNase Set were applied. The RNA of the 3 parallels of each condition with S. cerevisiae H155 was pooled in an equimolar manner.

treatment_protocol: Comparison between unstressed and stressed cells

tag: stress

value: glucose 1 M

source_name: yeast cells harvested 24 h after exposure to ethanol

value: final volume of 7% (v/v) ethanol


title: brewery_A_run_1/brewery_B_run_4


title: brewery_A_run_22/brewery_B_run_1

description: Gene expression of cells from run 1 and run 22 from brewery A was analyzed.


title: Kstat/Kexp

source_name: yeast cells harvested during stationary phase

value: control:stationary phase

source_name: yeast cells harvested during exponential phase

value: exponential phase


title: brewery_A_run_1/brewery_B_run_22


title: Tumor 7

tag: tissue

value: lung

tag: nsclc type

tag: heatmap

value: female


title: Kexp/Glu


title: pH/Kstat

source_name: yeast cells harvested 24 h after applying low pH


title: SR4-19/SR4-20

description: Gene expression of cells from run 0 to run 20 from brewery A was analyzed. Run 2 was used as alignment control.

treatment_protocol: successive runs varied from 0 to 20, without 14


title: SR4-20/SR4-0


title: brewery_A_run_1/brewery_B_run_5


title: SR4-18/SR4-19


title: SR4-16/SR4-17


title: SR4-15/SR4-16


title: SR4-17/SR4-18


title: Ethanol/pH


title: SR4-9/SR4-10


title: SR4-13/SR4-15


title: SR4-12/SR4-13


title: SR4-11/SR4-12


title: SR4-10/SR4-11


title: SR4-7/SR4-8


title: SR4-8/SR4-9


title: brewery_A_run_1/brewery_B_run_8


title: Tumor 3

value: non-small cell lung cancer (NSCLC)

tag: curep code

tag: Stage


title: SR4-6/SR4-7


title: SR4-5/SR4-6


title: Tumor 15

value: squamous cell carcinoma

tag: recurrence

tag: time_rec (years)

tag: 6th tnm stage

value: IA


title: SR4-3/SR4-4


title: Tumor 2

value: I

tag: smoker

value: no

tag: 7th tnm stage

tag: tumor size (cm)


title: Tumor 1

value: III

tag: age

tag: gender

tag: tnm


title: SR4-2/SR4-3

tag: strain

tag: run


title: SR4-1/SR4-2


title: SR4-4/SR4-5


title: SR3-9/SR3-10

treatment_protocol: successive runs varied from 0 to 20, without run 14


title: SR3-6/SR3-7


title: SR3-8/SR3-9


title: SR3-5/SR3-6


title: SR3-7/SR3-8


title: SR3-3/SR3-4


title: SR3-11/SR3-12


title: SR3-12/SR3-13


title: SR3-10/SR3-11


title: SR3-4/SR3-5


title: SR3-18/SR3-19


title: SR3-19/SR3-20


title: SR3-16/SR3-17


title: SR3-20/SR3-0


title: SR4-0/SR4-1


title: SR3-17/SR3-18


title: SR3-15/SR3-16


title: SR3-2/SR3-3


title: SR3-13/SR3-15


title: 3_MCF7_6wks

city: Stockholm

first: Nicholas

last: Tobin

address: Cancer Center Karolinska

institute: Karolinska Institutet

description: Gene expression data from MCF7 breast cancer cell line grown in LTED culture for 6 weeks

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrixï GeneChipï Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChipï Expression Analysis Technical Manual)

data_processing: RMA

source_name: MCF7 cell line

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

extract_protocol: RNeasy mini (Qiagen) using the manufacturers protocols

tag: cell line

tag: treatment

value: estrogen deprivation

tag: time

value: 6 w


title: 5_BT474_ctrl

description: Gene expression data from BT474 breast cancer cell line, control

source_name: BT474 cell line

value: control

value: 0 d


title: 7_BT474_6wks

description: Gene expression data from BT474 breast cancer cell line grown in LTED culture for 6 weeks


title: 6_BT474_2days

description: Gene expression data from BT474 breast cancer cell line grown in LTED culture for 2 days

value: 2 d


title: 8_BT474_10mths

description: Gene expression data from BY474 breast cancer cell line grown in LTED culture for 10 months


title: 4_MCF7_10mths

description: Gene expression data from MCF7 breast cancer cell line grown in LTED culture for 10 months


title: 1_MCF7_ctrl

description: Gene expression data from MCF7 breast cancer cell line, control

scan_protocol: Affymetrixë GeneChipë Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChipë Expression Analysis Technical Manual)


title: 2_MCF7_2days

description: Gene expression data from MCF7 breast cancer cell line grown in LTED culture for 2 days


title: SR2-16/SR2-17

description: Gene expression of cells from run 0 to run 17 from brewery A was analyzed. Run 2 was used as alignment control.

treatment_protocol: successive runs varied from 0 to 17, without run 10

value: HEBRU


title: SR3-1/SR3-2


title: SR3-0/SR3-1


title: SR2-15/SR2-16


title: SR2-8/SR2-9


title: SR2-9/SR2-11


title: SR2-11/SR2-12


title: SR2-12/SR2-13


title: HEK293 cells transfected with V5-tag-HOXD13 vector,indepenent clone c that selected from mix clone

city: Taipei

first: Ping

last: Wu

address: NO.1 JEN AI ROAD SECTION 1 TAIPEI 100 TAIWAN R.O.C.

department: department of medicine

country: Taiwan

institute: Graduate Institute of Toxicology

description: Gene expression data of HEK293 cells transfected with V5-tag-HOXD13 vector and then selction by G418 for stable clone ,indepenent clone c that selected from mix clone

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed by JMP Genomics using GC-RMA as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37°C under a humidified atmosphere consisting of 20% O2 and 5% CO2.

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

treatment_protocol: HEK293 cells was transfected  with HA-tag HOXD9 or V5-tag HOXD13 vector, and futher compared the profile with corresponding tag control cells


title: SR2-14/SR2-15


title: SR2-7/SR2-8


title: SR2-6/SR2-7


title: HEK293 cells transfected with V5-tag-HOXD13 vector,mix clone

description: Gene expression data of HEK293 cells transfected with V5-tag-HOXD13 vector and then selction by G418 for stable clone ,mix clone


title: HEK293 cells transfected with V5-tag-HOXD13 vector,indepenent clone b that selected from mix clone

description: Gene expression data of HEK293 cells transfected with V5-tag-HOXD13 vector and then selction by G418 for stable clone ,indepenent clone b that selected from mix clone


title: HEK293 cells transfected with V5-tag-HOXD13 vector,indepenent clone a that selected from mix clone

description: Gene expression data of HEK293 cells transfected with V5-tag-HOXD13 vector and then selction by G418 for stable clone ,indepenent clone a that selected from mix clone


title: SR2-5/SR2-6


title: HEK293 cells transfected with V5-tag vector,biological rep3

description: Gene expression data of HEK293 cells transfected with V5-tag vector and then selction by G418 for stable clone ,biological rep3


title: SR2-4/SR2-5


title: SR2-3/SR2-4


title: HEK293 cells transfected with HA-tag-HOXD9 vector,mix clone

description: Gene expression data of HEK293 cells transfected with HA-tag-HOXD9 vector and then selction by G418 for stable clone ,mix clone


title: HEK293 cells transfected with HA-tag-HOXD9 vector,indepenent clone a that selected from mix clone

description: Gene expression data of HEK293 cells transfected with HA-tag-HOXD9 vector and then selction by G418 for stable clone ,indepenent clone a that selected from mix clone


title: SR2-2/SR2-3


title: HEK293 cells transfected with HA-tag-HOXD9 vector,indepenent clone b that selected from mix clone

description: Gene expression data of HEK293 cells transfected with HA-tag-HOXD9 vector and then selction by G418 for stable clone ,indepenent clone b that selected from mix clone


title: HEK293 cells transfected with HA-tag-HOXD9 vector,indepenent clone c that selected from mix clone

description: Gene expression data of HEK293 cells transfected with HA-tag-HOXD9 vector and then selction by G418 for stable clone ,indepenent clone c that selected from mix clone


title: HEK293 cells transfected with V5-tag vector,biological rep2

description: Gene expression data of HEK293 cells transfected with V5-tag vector and then selction by G418 for stable clone ,biological rep2


title: HEK293 cells transfected with V5-tag vector,biological rep1

description: Gene expression data of HEK293 cells transfected with V5-tag vector and then selction by G418 for stable clone ,biological rep1


title: SR2-13/SR2-14


title: SR2-1/SR2-2


title: SR2-0/SR2-1


title: SR1-18/SR1-1

description: Gene expression of cells from run 1 to run 18 from brewery A was analyzed. Run 2 was used as alignment control.

treatment_protocol: successive runs varied from 1 to 18


title: SR1-11/SR1-12


title: SR1-13/SR1-14


title: SR1-14/SR1-15


title: SR1-12/SR1-13


title: SR1-16/SR1-17


title: SR1-17/SR1-18


title: SR1-10/SR1-11


title: SR1-15/SR1-16


description: Gene expression data of HEK293 cells transfected with HA-tag vector and then selction by G418 for stable clone,biological rep3


title: MII stage oocyte, amphiregulin -/-, biological rep 3

city: San Francisco

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Hybridization was followed by GeneChip Expression Analysis Technical Manual 702232 Rev. 2

scan_protocol: GeneChips were scanned using the the Affymetrix GCS3000 microarray system

data_processing: Microarray data were normalized using the Robust Multi-array Average (RMA) method. RMA was performed using the affy library in Bioconductor and a custom chip definition file (CDF) representing the latest RefSeq probe mapping to the mouse genome (Mouse4302_Mm_REFSEQ, Version 16.0.0), downloaded from the Microarray Lab of the Molecular and Behavioral Neuroscience Institute, University of Michigan.

source_name: polysome bound transcripts from mouse MII-stage oocytes, Areg -/-

label_protocol: cDNA was fragment and labeled using NuGEN WT-Ovation FFPE System & Encore Biotin Module

extract_protocol: Polysome bound mRNAs were purified using Rneasy Plus Micro kit (Qiagen), and then reverse-transcribed and linearly amplified with WT-Ovation FFPE RNA Amplification System V2 (NuGEN).

treatment_protocol: Forty-eight hours (h) after PMSG injection, mice were stimulated with hCG for 0, or 14 h, and GV and MII stage oocytes were collected.

tag: tissue

value: oocyte

value: MII

tag: background

value: Areg -/-


title: SR1-8/SR1-9


title: SR1-7/SR1-8


title: SR1-9/SR1-10


description: Gene expression data of HEK293 cells transfected with HA-tag vector and then selction by G418 for stable clone,biological rep2


title: HepG2_control_4hr_rep1

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

institute: Academia Sinica

description: gene expression after 0.08% DMSO treatment for 4hr

data_processing: The data were normalised using quantile normalisation with illumina GenomeStudio software

source_name: HepG2 cell lines, 0.08% DMSO, 4 hr

growth_protocol: Human hepatocellular carcinoma HepG2 cell line cultured in Minimum Essential Medium Eagle supplemented with 10% fetal bovine serum (FBS), 2.2 g/L sodium bicarbonate, 0.1 mM Non-Essential Amino Acids, 1 mM sodium pyruvate, and 10 ml/L Penicillin-Streptomycin-Amphotericin solution (Biological Industries).  Cells were cultured at 37°C and 5% CO2.

extract_protocol: RNA was extracted with High pure RNA isolation kit (Roche) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: A 50 mM stock solution of Berberine chloride (Sigma-Aldrich) was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control. Comparing miRNA profiles of 40 M berberine-treated HepG2 human hepatoma cell line to those of control cells sampled after 2 and 4 hours treatment

value: HepG2 cell line


title: SR1-5/SR1-6


title: SR1-4/SR1-5


title: MII stage oocyte, amphiregulin -/-, biological rep 2

tag: Stage


title: GV stage oocyte, amphiregulin -/-, biological rep 2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: polysome bound transcripts from mouse GV-stage oocytes, Areg -/-

value: GV


title: MII stage oocyte, wild type, biological rep 3

source_name: polysome bound transcripts from mouse MII-stage oocytes, wild type

value: wild type


title: GV stage oocyte, amphiregulin -/-, biological rep 1


title: MII stage oocyte, amphiregulin -/-, biological rep 1


title: LNCaP_Cell line_untreated

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Prostate cancer_cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol:
xenografts: 2 x 2 x 2 mm3 tissue fragments were implanted subcutaneously at the flanks of in adult male Balb/c nude mice, along with a 12.5 mg sustained-release testosterone pellet. Animals in the AE -group were sacrificed when the tumors reached at a shortest diameter of 8 mm.
Cell lines: The cells were incubated in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin and 1% L-glutamine under a 5% CO2 atmosphere at 37°C.

extract_protocol: Xenografts were excised, immediately snap-frozen in liquid nitrogen, and stored at -80°C. Tissue lysates were prepared using the QIAshredder® kit from Qiagen. RNA was extracted from xenograft lysates and cell lines using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol:
Androgen Deprivation Therapy (ADT): In xenografts, castration  and removal of the testosterone pellet were performed at a shortest tumor diameter of 12 mm. The animals were sacrificed when the tumor diameter had regressed to 8 mm.
Hypoxia: Exponentially growing cells were plated and incubated for 2 days, following replacement of cell medium prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

tag: sample type

value: cell line

value: LNCaP

tag: cell type

value: human prostate carcinoma epithelial cells

tag: androgen sensitivity

value: Androgen sensitive

value: untreated


title: HEK293 cells transfected with HA-tag vector,biological rep1

description: Gene expression data of HEK293 cells transfected with HA-tag vector and then selction by G418 for stable clone ,biological rep1


title: HepG2_berberine_4hr_rep1

description: gene expression after berberine chloride treatment for 4 hr

source_name: HepG2 cell lines, berberine chloride , 4 hr


title: LNCaP_Cell line_hypoxia exposed

value: hypoxia exposed


title: GV stage oocyte, amphiregulin -/-, biological rep 3


title: SR1-3/SR1-4


title: SR1-6/SR1-7


title: SR1-2/SR1-3


title: MII stage oocyte, wild type, biological rep 2


title: SR1-1/SR1-2


title: 22RV1_Cell line_untreated


title: 22RV1_Cell line_hypoxia exposed


title: GV stage oocyte, wild type, biological rep 3

source_name: polysome bound transcripts from mouse GV-stage oocytes, wild type


title: MII stage oocyte, wild type, biological rep 1


title: GV stage oocyte, wild type, biological rep 2


title: Xenograft_androgen deprived

source_name: Prostate cancer_xenograft

value: xenograft

value: androgen deprived


title: GV stage oocyte, wild type, biological rep 1


title: Xenograft_androgen exposed

value: untreated (androgen exposed)


title: placental tissues from the PE and Control,replicate 3

status: Public on Oct 01 2013

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

hyb_protocol: Fluorescent dye-labelled cDNA was hybridised to an Agilent SurePrint G3 Human GE 8x60K Microarray.

scan_protocol: scanning were carried out on Agilent’s Microarray Platform according to Agilent’s standard protocols. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: global mean normalization, probes with an intensity <400 were filtered out for further analysis.

source_name: placental tissues from the PE,replicate 3

label_protocol: RNA was amplified and labelled according to a previous protocol. Briefly, total RNA was used to synthesize the double strand cDNA. RNA was amplified by in vitro transcription using Ambion’s MessageAmp™ II aRNA Amplification Kits (Life Technologies, Austin, TX, USA). Then, aRNA was reverse transcribed into cDNA and further labelled with Klenow enzyme. cDNA from placental tissue of PE was labelled with Cy5-dCTP and cDNA from control placental tissue was labelled with Cy3-dCTP.

growth_protocol: Placental samples were collected from women complicated by severe preeclampsia (n=5) and women with normal pregnancies (n=5) at Peking Union Medical College Hospital. Severe preeclampsia was defined as blood pressure ≥160/100mmHg, measured at least 6 h apart, in combination with proteinuria  ≥3g/24 hours or ≥2+ (dipstick), developing after 20 weeks of pregnancy. Women who had a history of cardiovascular, renal, and other hypertension-associated diseases were excluded, but family history of PE was not recorded.

extract_protocol: Total RNA was extracted from placental tissues with using Trizol reagent (Life technologies, Gaithersburg, MD). RNA quality was evaluated using formaldehyde agarose gel electrophoresis and was quantified via spectrophotometry (Nano drop, Wilmington, DE).

treatment_protocol: Placental biopsies were obtained immediately after delivery. Samples of approximately 0.2–0.5 cm3 were excised from central cotyledons close to the umbilical cord in order to reduce the possible bias due to regional differences in gene expression. After extensive washing in saline solution to remove excessive blood, the samples were stored in RNALater reagent.

tag: condition

value: Pre-eclampsia

value: placenta

source_name: placental tissues from Control,replicate 3

value: control


title: placental tissues from the PE and Control,replicate 5

source_name: placental tissues from the PE,replicate 5

source_name: placental tissues from Control,replicate 5


title: placental tissues from the PE and Control,replicate 4

source_name: placental tissues from the PE,replicate 4

source_name: placental tissues from Control,replicate 4


title: placental tissues from the PE and Control,replicate 1

source_name: placental tissues from the PE,replicate 1

source_name: placental tissues from Control,replicate 1


title: CMLbonemarrow_classic 15

city: Bari

first: Francesco

last: Albano

address: P.zza G. Cesare, 11

country: Italy

institute: University of Bari

description: SAMPLE 15

hyb_protocol: Labeled cRNAs were hybridized for 17 hours at 65°C and 10 RPM on the Agilent SurePrint G3 Human GE 8x60K Microarray slide (Agilent Technologies) using the Agilent’s Microarray Hybridization Oven.

scan_protocol: Slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies) according to the Agilent_G3_GX_1Color protocol.

data_processing: Scanned images were processed using the Agilent Feature Extraction software (v10.7.3.1), raw data were quantile normalized and differentially expressed genes were selected by unpaired t-test and Multiple Testing Correction of Benjamini-Hochberg, considering as statistically significant those presenting a p-value less than 0.05 and a fold-change equal or higher than 2.

source_name: CML_bone marrow_classic

label_protocol: Twenty-five nanograms of each sample were labeled using the Low Input Quick Amp Labeling kit (Agilent).

extract_protocol: Whole RNA was extracted by ultracentrifugation in caesium chloride density gradient. RNA quality was determined using the 2100 Bioanalyzer; only cellular samples of high quality characterized by RNA integrity numbers  ranging from 8 to 10 were selected.

treatment_protocol: Total white blood cells were isolated from CML BM samples by hypotonic red cell lysis, washed, transferred into a guanidinium isothiocyanate-containing buffer, and stored at -80°C.

value: male

tag: disease type

value: chronic myeloid leukemia (CML)

tag: translocation type

value: classic t(9;22) rearrangement

value: bone marrow

value: total white blood cells


title: CMLbonemarrow_classic 10

description: SAMPLE 10

value: female


title: placental tissues from the PE and Control,replicate 2

source_name: placental tissues from the PE,replicate 2

source_name: placental tissues from Control,replicate 2


title: CMLbonemarrow_classic 16

description: SAMPLE 16


title: CMLbonemarrow_classic 19

description: SAMPLE 19


title: CMLbonemarrow_classic 12

description: SAMPLE 12


title: CMLbonemarrow_classic 18

description: SAMPLE 18


title: CMLbonemarrow_classic 17

description: SAMPLE 17


title: CMLbonemarrow_classic 11

description: SAMPLE 11


title: CMLbonemarrow_classic 9

description: SAMPLE 9


title: CMLbonemarrow_classic 14

description: SAMPLE 14


title: CMLbonemarrow_classic 20

description: SAMPLE 20


title: SR2-17/SR2-0

description: Gene expression of cells from run 0 to run 17 from brewery A was analyzed. Run 2 was used as alignment control.

source_name: yeast cells harvested by the end of fermentation from brewery cylindro-conical vessel

value: HEBRU


title: CMLbonemarrow_variant 8

description: SAMPLE 8

source_name: CML_bone marrow_variant

value: variant t(9;22) rearrangement


title: CMLbonemarrow_classic 13

description: SAMPLE 13


title: CMLbonemarrow_variant 3

description: SAMPLE 3


title: CMLbonemarrow_variant 7

description: SAMPLE 7


title: CMLbonemarrow_variant 4

description: SAMPLE 4


title: One_human_hair_root_rep1_subject #B

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

country: Japan

institute: Japan Aerospace Exploration agency

description: Gene expression from a hair root of subject B

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 0.025 ml containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) each GE Wash Buffers were all supplied with 0.005% Triton X-102, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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: 1hair root, rep1, subject #B

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Approximately 2-3 mm of the hair root was used as sources for RNA extraction. The hair root was cut into about 15 fragments (each fragment is 0.1-0.2 mm) using micro surgical knife under stereoscopic microscope.  The collected fragments were immersed in 800 μl of ISOGEN reagent (Nippon Gene, Toyama, Japan) into tube.  These samples into tubes were stirring (15 second × 2 times) using Sonication device, Bioruptor UCD-250 (COSMO BIO, Tokyo, Japan).  Then, RNA was purified from the hair lysate with ISOGEN kit as described previously.  Briefly, these tubes were allowed the mixture to stand for 5 minutes at room temperature, after which 200 μl of chloroform was added.  The subsequent processed for RNA purification were performed according to manufacturer’s instructions.  After isolation, RNA pellet was washed with 70 % ethanol, air dried, and resuspended in 10 μl of RNA free water (Gibco-BRL, Gaithersburg, MD) and total RNA was quantified at 260 nm using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE).

value: 1 hair root

tag: subject

value: B


title: Five_human_hair_roots_rep3_subject #B

description: Gene expression from five hair roots of subject B

source_name: 5hair roots, rep3, subject #B

value: 5 hair root

tag: gender


title: Five_human_hair_roots_rep4_subject #A

description: Gene expression from five hair roots of subject A

source_name: 5hair roots, rep4, subject #A

value: A


title: Ten_human_hair_roots_rep1_subject #A

description: Gene expression from ten hair roots of subject A

source_name: 10hair roots, rep1, subject #A

value: 10 hair root


title: CMLbonemarrow_variant 1

description: SAMPLE 1


title: tumours of the 1st grade of malignancy replicate

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: Biological replicate 2 of 4

hyb_protocol: The hybridization was performed with canine-specific AMADID Release GE 4x44K microarrays (Agilent, USA) using Gene Expression Hybridization Kit (Agilent, USA) according to the manufacturer`s protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: tumours of the 1st grade

label_protocol: The Quick Amp Labeling Kit (Agilent, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA) for oligo microarrays used in gene expression profiling and other downstream analyses.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% (v/v) heat-inactivated fetal bovine serum (FBS), penicillin-streptomycin (50 iU mL–1), and fungizone (2.5 mg mL–1) (reagents obtained from Sigma Aldrich, USA), in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol.

treatment_protocol: Cancer cells were grown and sorted monocytes were then layered on the top of each cell line. CMTMR was used to stain the cancer cells population prior to addition of the sorted monocyte population. The co-culture was maintained for at least 72 hrs. After the 72 hrs of co-culture the cells were harvested by trypsynization and sorted using FACS Aria II (Becton Dickinson, USA) into two tubes: not-stained macrophages and stained cancer cells.

tag: disease state

value: less malignant

source_name: tumours of the 3rd grade

value: the most malignant


title: CMLbonemarrow_variant 6

description: SAMPLE 6


title: Five_human_hair_roots_rep1_subject #B

source_name: 5hair roots, rep1, subject #B


title: CMLbonemarrow_variant 2

description: SAMPLE 2


title: Five_human_hair_roots_rep2_subject #B

source_name: 5hair roots, rep2, subject #B


title: tumours of the 3rd grade og malignancy

description: Biological replicate 1 of 4


title: tumours of the 3rd grade of malignancy replicate

description: Biological replicate 2 of 4


title: tumours of the 1st grade of malignancy

description: Biological replicate 1 of 3


title: Five_human_hair_roots_rep3_subject #A

source_name: 5hair roots, rep3, subject #A


title: CMLbonemarrow_variant 5

description: SAMPLE 5


title: Five_human_hair_roots_rep2_subject #A

source_name: 5hair roots, rep2, subject #A


title: Five_human_hair_roots_rep1_subject #A

source_name: 5hair roots, rep1, subject #A


title: One_human_hair_root_rep3_subject #A

description: Gene expression from a hair root of subject A

source_name: 1hair root, rep3, subject #A


title: One_human_hair_root_rep4_subject #A

source_name: 1hair root, rep4, subject #A


title: 4wk neurons, WIBR3-Con1

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data from differentiating neurons

hyb_protocol: Hybridization to the affymetrix Primeview human expression array was performed per manufacturer's instructions

scan_protocol: Scanning of the affymetrix Primeview human expression array was performed per manufacturer's instructions

data_processing: Data were processed by MAS5 normalization in Bioconductor, then renormalized to external spike-ins according to Lovén J, Orlando DA, Sigova AA, Lin CY et al. Revisiting global gene expression analysis. Cell 2012 Oct 26;151(3):476-82. PMID: 23101621

source_name: 4-week differentiating neurons from WIBR3-Con1 line

label_protocol: 100ng of total RNA was used to prepared biotinylated aRNA using the 3' IVT Express kit (affymetrix)

growth_protocol: NPs were cultured in neural medium containing bFGF; 2- and 4-week neurons were cultured in differentiation medium without bFGF for the said period of time.

extract_protocol: Total RNA was extracted using Trizol protocol and purified using the Rneasy kit and eluted in 50ul nuclease-free water, a fixed amount of ERCC RNA spike-in was added.

treatment_protocol: Cells were collected, and five million cells were homogenized in 0.5ml Trizol reagent.

tag: genotype/variation

value: MECP2 wild-type

value: 4-week differentiating neurons


title: One_human_hair_root_rep1_subject #A

source_name: 1hair root, rep1, subject #A

value: male


title: 4wk neurons, WIBR3-Mut1

source_name: 4-week differentiating neurons from WIBR3-Mut1 line

value: MECP2 mutant


title: One_human_hair_root_rep2_subject #A

source_name: 1hair root, rep2, subject #A


title: 2wk neurons, WIBR3-Mut1

source_name: 2-week differentiating neurons from WIBR3-Mut1 line

value: 2-week differentiating neurons


title: 4wk neurons, WIBR1-Mut

source_name: 4-week differentiating neurons from WIBR1-Mut line


title: 2wk neurons, WIBR3-Con1

source_name: 2-week differentiating neurons from WIBR3-Con1 line


title: 4wk neurons, WIBR1-Con

source_name: 4-week differentiating neurons from WIBR1-Con line


title: 2wk neurons, WIBR1-Con

source_name: 2-week differentiating neurons from WIBR1-Con line


title: 2wk neurons, WIBR3-Mut2

source_name: 2-week differentiating neurons from WIBR3-Mut2 line


title: Manila clam sampled in Marghera [PM_05]

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

description: hepatopancreas RNA of Manila clam

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization  of gPRocessed signalusing R2.6.1 statistical software

label: Cyanine 3

organism: Ruditapes philippinarum

source_name: Hepatopancreas of Manila clam collected during January 2011 in the Venice lagoon (Marghera), Italy

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: sample location

value: Marghera


title: 4wk neurons, WIBR3-Con2

source_name: 4-week differentiating neurons from WIBR3-Con2 line


title: 4wk neurons, WIBR3-Mut2

source_name: 4-week differentiating neurons from WIBR3-Mut2 line


title: Hox10 knockdown embryos (Cy5) vs. control embryos (Cy3)

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

description:
M5C3
Dye-swap of C5M3.

hyb_protocol: A set of fluorescently labeled cRNA targets (750ng for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using the GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.

data_processing: The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default conditions of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the analysis.

organism: Ciona intestinalis

source_name: tail region of Hox10 MO-injected embryos

label_protocol: Cyanine-5 (Cy5) or cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Ciona intestinalis were obtained from the National BioResource Project in Japan.

extract_protocol: Total RNA was extracted from each of the tail regions by the acid guanidium thiocyanate-phenol-chloroform method.

treatment_protocol: Approximately 250 Hox10 morpholino(MO) (0.64mM)-injected embryos and control embryos at the tailbud stage (18 hours after fertilization) were cut between the tail and the trunk, and each of the tail regions was collected.

tag: age

value: 18 hrs post-fertilization

value: tail region

value: Hox10 morpholino injection

source_name: tail region of control embryos

value: intact


title: 2wk neurons, WIBR3-Con2

source_name: 2-week differentiating neurons from WIBR3-Con2 line


title: Control embryos (Cy5) vs. Hox10 knockdown embryos (Cy3)

description:
C5M3
Dye-swap of M5C3.

tag: treatment


title: NPs, WIBR3-Con1

description: Gene expression data from neural precursors

source_name: NPs from WIBR3-Con1 line

value: Neural precursors


title: LNCaP/shCCAR1/DHT(+), biological rep2

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

description:
Gene expression data from LNCaP cells
8_ShCC+

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays. 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: Image analysis was performed by Affymetrix GCOS Software, and data was normalized by RMA.

source_name: LNCaP prostate cancer cells

label_protocol: Total RNA was reverse-transcribed, and the double stranded cDNAs were used to generate biotin-labeled cRNA.

growth_protocol: LNCaP cells were grown in RPMI supplemented with 5% dextran/charcoal-stripped FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen)

treatment_protocol: LNCaP cells expressing shNS or shCCAR1 were treated with ethanol or 10 nM DHT for 24 hr.

tag: cell line

value: LNCaP

tag: shRNA

value: shRNA against CCAR1 (shCC)

tag: agent

value: DHT


title: NPs, WIBR3-Mut2

source_name: NPs from WIBR3-Mut2 line


title: NPs, WIBR3-Con2

source_name: NPs from WIBR3-Con2 line


title: 2wk neurons, WIBR1-Mut

source_name: 2-week differentiating neurons from WIBR1-Mut line


title: HepG2_Control-NP

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

description: mRNA isolated from HepG2 cell

hyb_protocol: The amplified RNA was fragmented using 4.8μL of 5X fragmentation buffer (GeneChip® WT Terminal labeling kit; Affymetrix;P/N 900671) and hybridized to the gene containing over 33,290 transcripts, as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix). After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.

data_processing: Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console1.1 . To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out.

label_protocol: About 300ng of total RNA from each sample was converted to cDNA, after amplification the double strands of cDNA was labelled with biotin-labeling (Ambion® WT Expression kit)

growth_protocol: Cells were maintained in culture flasks with MEM media at 37oC with 5% CO2

extract_protocol: Total RNA from control and SiO2 treated samples (100 mg/L for 24 h) were extracted by using RNA extraction kit (NucleoSpin, Macherey-Nagel)

value: hepatoma


title: HepG2_SiO2-NP

description: mRNA isolated from HepG2 cell

treatment_protocol: The cells were exposed to 100 mg/L (prepared in MEM media from stock) dose for 24h


title: NPs, WIBR1-Mut

source_name: NPs from WIBR1-Mut line


title: LNCaP/shCCAR1/DHT(+), biological rep1

description:
Gene expression data from LNCaP cells
7_ShCC+


title: NPs, WIBR1-Con

source_name: NPs from WIBR1-Con line


title: NPs, WIBR3-Mut1

source_name: NPs from WIBR3-Mut1 line


title: LNCaP/shCCAR1/DHT(-), biological rep2

description:
Gene expression data from LNCaP cells
6_ShCC-

value: control


title: Manila clam sampled in Marghera [PM_04]

description: hepatopancreas RNA of Manila clam


title: Manila clam sampled in Marghera [PM_02]

description: hepatopancreas RNA of Manila clam


title: Manila clam sampled in Marghera [PM_01]

description: hepatopancreas RNA of Manila clam


title: Manila clam sampled in Marghera [PM_03]

description: hepatopancreas RNA of Manila clam


title: LNCaP/shNS/DHT(+), biological rep2

description:
Gene expression data from LNCaP cells
4_ShN+

value: Non-specific shRNA (shNS)


title: Manila clam sampled in Colmata [CO_04]

description: hepatopancreas RNA of Manila clam

source_name: Hepatopancreas of Manila clam collected during January 2011 in the Venice lagoon (Colmata), Italy

value: Colmata


title: LNCaP/shCCAR1/DHT(-), biological rep1

description:
Gene expression data from LNCaP cells
5_ShCC-


title: Manila clam sampled in Colmata [CO_05]

description: hepatopancreas RNA of Manila clam


title: Manila clam sampled in Colmata [CO_02]

description: hepatopancreas RNA of Manila clam


title: LNCaP/shNS/DHT(-), biological rep2

description:
Gene expression data from LNCaP cells
2_ShN-


title: Manila clam sampled in Colmata [CO_03]

description: hepatopancreas RNA of Manila clam


title: Manila clam sampled in Chioggia [CH_05]

description: hepatopancreas RNA of Manila clam

source_name: Hepatopancreas of Manila clam collected during January 2011 in the Venice lagoon (Chioggia), Italy

value: Chioggia


title: VEC_117_male_21O2_VitDctrl

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

hyb_protocol: GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix GeneChip® Fluidics Station 450: protocol FS450_0007 for Cartridge Arrays.

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC_3_1_1).

data_processing:
Gene Expression Console v.1.1, Affymetrix (Expression Console EC_1_1_2) using Affymetrix default analysis settings for generation of CEL files.
Data Pre-Processing (Partek Software, v.6.5: RMA (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)); Biostatistical data analysis: R/Bioconductor.

source_name: Isolated and in vitro cultured placental cells, venous endothelial cells, male

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671).

growth_protocol: Prior to microarray analysis, 800,000 cells were seeded on 1% (v/v) gelatin-coated flasks (75 cm²) using Endothelial Basal Medium (EBM, Cambrex, Clonetics, USA) supplemented with the EGM-MV BulletKit (Clonetics). Endothelial cells were cultured for 48 h at 21% O2/5% CO2 environment at 37°C.

extract_protocol: RNA isolation with the Qiagen Mini kit according to the manufacturer.

treatment_protocol: No treatments.

tag: tissue

value: placenta

value: venous endothelial cells

value: male


title: Manila clam sampled in Chioggia [CH_03]

description: hepatopancreas RNA of Manila clam


title: LNCaP/shNS/DHT(+), biological rep1

description:
Gene expression data from LNCaP cells
3_ShN+


title: Manila clam sampled in Chioggia [CH_02]

description: hepatopancreas RNA of Manila clam


title: LNCaP/shNS/DHT(-), biological rep1

description:
Gene expression data from LNCaP cells
1_ShN-


title: Manila clam sampled in Chioggia [CH_04]

description: hepatopancreas RNA of Manila clam


title: VEC_92_male_21O2_VitDctrl


title: AEC_98_male_21O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, arterial endothelial cells, male

value: arterial endothelial cells


title: VEC_98_male_21O2_VitDctrl


title: AEC_92_male_21O2_VitDctrl


title: Manila clam sampled in Chioggia [CH_01]

description: hepatopancreas RNA of Manila clam


title: VEC_100_male_21O2_VitDctrl


title: Manila clam sampled in Colmata [CO_01]

description: hepatopancreas RNA of Manila clam


title: AEC_100_male_21O2_VitDctrl


title: VEC_84f_female_21O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, venous endothelial cells, female

value: female


title: clam exposed for 7 days to 1000 µg IBU/l  [1000_T4_04]

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%).

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software.

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples.

treatment_protocol: digestive gland of Manila clam exposed for 7 days to 1000 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

tag: time point

value: 7 days

value: 1000 µg IBU/l


title: clam exposed for 7 days to 1000 µg IBU/l  [1000_T4_05]

source_name: digestive gland of Manila clam exposed for 7 days to 1000 µg IBU/l


title: VEC_127_female_21O2_VitDctrl

tag: cell type


title: VEC_135_female_21O2_VitDctrl


title: VEC_105_female_21O2_VitDctrl


title: clam exposed for 7 days to 1000 µg IBU/l  [1000_T4_01]


title: clam exposed for 5 days to 1000 µg IBU/l  [1000_T3_02]

treatment_protocol: digestive gland of Manila clam exposed for 5 days to 1000 µg IBU/l Clams were maintained in glass aquaria (without sediment) containing aerated seawater (1 l per animal) in the same thermo-haline conditions that were used during 7 days of  acclimatization. Every day, seawater was changed and IBU and microalgae (I. galbana, at an initial concentration of about 150,000 cells/l) were added.

value: 5 days


title: clam exposed for 5 days to 1000 µg IBU/l  [1000_T3_06]

source_name: digestive gland of Manila clam exposed for 5 days to 1000 µg IBU/l


title: clam exposed for 5 days to 1000 µg IBU/l  [1000_T3_05]


title: clam exposed for 7 days to 1000 µg IBU/l  [1000_T4_03]


title: clam exposed for 7 days to 1000 µg IBU/l  [1000_T4_02]


title: AEC_84f_female_21O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, arterial endothelial cells, female


title: AEC_117_male_21O2_VitDctrl


title: clam exposed for 5 days to 1000 µg IBU/l  [1000_T3_03]


title: AEC_135_female_21O2_VitDctrl


title: clam exposed for 5 days to 1000 µg IBU/l  [1000_T3_01]


title: AEC_127_female_21O2_VitDctrl


title: SCT_91_female_20O2_VitDctrl

source_name: Isolated and in vitro cultured placental cells, syncytiotrophoblasts, female

value: syncytiotrophoblasts


title: SCT_93_female_20O2_VitDctrl


title: AEC_105_female_21O2_VitDctrl