title: ID6 B cell CD20 1

description:
1718911527_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: Control.Cy3_Msi1.Cy5_2

status: Public on Jul 26 2011

type: RNA

city: san antonio

first: raquel

last: abreu

state: TX

address: 8403 Floyd Curl Drive

country: USA

institute: CCRI

description: Biological Replicate 1, duplicate dye swap 1

hyb_protocol: Samples were hybridized using Agilent's Gene Expression Hybridization Kit.

scan_protocol: Scanned with Agilent G2565BA Scanner, 10 µm resolution.

data_processing: TIFF images were quantified using Agilent Feature Extraction Software 8.5.

molecule: total RNA

organism: Homo sapiens

source_name: Daoy medulloblastoma cells

label_protocol: cRNA synthesis was carried out using Agilent's Low RNA Linear Amplification Kit Plus, two-color.

growth_protocol: Grown at 37°C in 5% CO2

extract_protocol: Phenol/chloroform extraction and isopropanol precipitation.

treatment_protocol: The cell lysate and antibody coated sepharose beads were incubated at room temperature while tumbling end over end. Following incubation, the beads were spun down and washed 4 times with ice cold NT2 buffer. Subsequently, the material was digested with proteinase K, extracted with phenol/chloroform, and precipitated with isopropanol.

tag: transient transfection with

value: RIP with Prebleed Antibody

tag: treatment time

value: 48 hours

value: RIP with Msi1 Antibody


title: ID6 LCL 2

city: Oxford

first: Josine

last: Min

address: Roosevelt Drive

country: United Kingdom

institute: The Wellcome Trust Centre for Human Genetics

description:
1718911544_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

hyb_protocol: Arrays were hybridised with labelled cRNA material and scanned according to manufacturer’s instructions.

scan_protocol: Manufacturer’s instructions

data_processing: The resultant data was parsed with the software package BeadStudio to produce raw intensity values for all probes. Signal was checked for quality using hybridisation and labelling controls internal to each array and subtracted for background within the statistical scripting environment, R v2.4.1. Signal was transformed and normalised using the variance stabilization algorithm as implemented in the vsn2 Bioconductor package.

label: biotin

source_name: LCL

label_protocol: Manufacturer’s instructions

extract_protocol: For the isolation of CD19 and CD20 B-cells, 40ml whole blood from EDTA tubes was collected and PBMCs were isolated by using a Ficoll-Paque™ gradient (Amersham). CD19 and CD20 B-cells were prepared by positive selection from the PBMCs by incubation with magnetic anti-CD19 or CD20 mAb-coated microbeads (MACS, Miltenyi Biotec). For the isolation of PBMCs from whole blood, BD Vacutainer® CPT Mononuclear Cell Preparation Tubes (Becton and Dickinson) were used. Total RNA was isolated from 5 ml of whole blood samples with the PAXGene Blood RNA system (Qiagen) and samples were left at room temperature for 24 hours before processing according to manufacturer’s instructions.Only two people at a time were sampled on any one day for logistical reasons. After blood draw standard protocols were followed for cell isolation, transformation or RNA extraction. With the exception of the PAXgene samples all RNA was isolated using TRI™ reagent (SIGMA) and resuspended in RNase free water.

treatment_protocol: For each individual, five different post venipuncture methods were performed. B Lymphocytes from 10ml of blood were isolated by tubes with sodium citrate. LCLs were generated by EBV-mediated transformation and cells were grown for eight weeks.

tag: method

value: EBV transformed LCL

tag: individual (indiv.id)

tag: visit

tag: ChIP

tag: yield

tag: rin

tag: tissue

value: LCL

tag: cell type

value: Lymphoblastoid cell line LCL


title: ID6 LCL 1

description:
1718911544_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: T2 toxin treated stationary phase, rep3

type: mixed

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

hyb_protocol: Slides were blocked with DCE according to the protocol at PMID 11266573. For hybridisation and washing protocols, see  http://www.ifr.ac.uk/safety/Microarrays/protocols.html

scan_protocol: Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using block median normalization.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium, T2 toxin treated, stationary phase

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Stationary phase cultures were obtained by aerated, overnight culture at 37 °C in 5 mL LB in 50 mL flasks. To obtain highly invasive late logarithmic cultures, 2 µL of a stationary phase culture was inoculated in 5 mL LB and grown for 5 hours at 37 °C without aeration.

extract_protocol: Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

treatment_protocol: T2 toxin-treated cultures contain 0.5 µg/mL of T2 toxin.

tag: strain

tag: growth phase

value: stationary

tag: treatment

value: T2 toxin

molecule: genomic DNA

source_name: S. typhimurium genomic DNA

tag: sample type

value: reference


title: Control.Cy3_Msi1.Cy5_1

description: Biological Replicate 1, dye swap 1


title: ID1 B cell CD19 1

description:
1718911544_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: B cell-CD19


title: A105Hplacenta_rep1

city: New York

first: Le

last: Jiang

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

hyb_protocol: The microarray slides were cleaned and placed in prehybridization buffer (5XSSC, 0.1%SDS and 1%BSA) for 1 hr at 45°C. The probe mixture was combined with 40 µl 2X hybridization buffer (50% Formamide, 10XSSC and 0.2% SDS) and then applied to the microarray slides in a hybridization chamber (Corning, Corning, NY) before incubating in a dark, 45°C water bath for approximately 42 hr.

scan_protocol: Scanned on an GenePix 4000B scanner. Scanned images were examined thoroughly and analyzed by GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA)

data_processing: Median normalization was carried out for each microarray slide, and background-subtracted data were imported into GeneSpring 7.3.1 (Agilent Technologies, Palo Alto, CA). LOESS normalization was applied to all microarray data.

organism: Bos taurus

source_name: in vitro placenta 90 days

label_protocol: Ten µg of total RNA was mixed with 2 µl random hexamers (3 µg/µl, Invitrogen, Carlsbad, CA), heated at 70°C for 5 min, snap-cooled on ice, and added to the following reaction mix: 6 µl 5X first strand buffer (Invitrogen), 3 µl 0.1 M DTT, 0.6 µl 25 mM dNTP (except for dTTP: 15 mM), 0.12 µl 50 mM aminoallyl-dUTP, 2 µl SuperScript III reverse transcriptase (200 U/µl, Invitrogen) and 0.5 µl RNase inhibitor (20 U/µl, Ambion, Austin, TX). The 30 µl reaction was then incubated at 25 °C for 10 min, followed by further incubation at 46 °C overnight.

extract_protocol: Total RNA from dissected tissues was extracted using the RNeasy mini/midi kit according to manufacture's instructions (Qiagen, Valencia, CA)

value: placenta

tag: in vitro or in vivo

value: in vitro

tag: gestation day

value: 90 days

source_name: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney

tag: reference


title: 624Hplacenta_rep2

source_name: in vivo placenta 90 days

value: in vivo

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: T2 toxin treated stationary phase, rep2


title: 624Hplacenta_rep1


title: 5400placenta_rep2


title: ID1 Whole Blood 1

description:
1718911584_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: WholeBlood

value: PAXgene

value: Whole Blood


title: ID1 LCL 1

description:
1718911544_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID1 Whole Blood 2

description:
1718911584_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID1 B cell CD20 2

description:
1718911584_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: B cell-CD20


title: ID1 PBMC 2

description:
1718911584_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: PBMC

value: PBMC


title: ID1 LCL 2

description:
1718911544_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID1 PBMC 1

description:
1718911584_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: 5400placenta_rep1


title: ID5 B cell CD20 2

description:
1718911531_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: T2 toxin treated stationary phase, rep1


title: T2 toxin treated log phase, rep3

source_name: S. Typhimurium, T2 toxin treated, log phase

value: log


title: F814placenta_rep2


title: F814placenta_rep1


title: T2 toxin treated log phase, rep2


title: ID5 B cell CD19 1

description:
1718911531_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: A151placenta_rep1


title: A151placenta_rep2


title: Y38liver_rep2

source_name: in vitro liver 180 days

value: liver

value: 180 days


title: ∆scsA stationary phase, rep1

source_name: S. Typhimurium, ∆scsA, stationary phase

treatment_protocol: None.

tag: genotype

value: ∆scsA


title: ∆scsA stationary phase, rep3

value: stationary


title: Y38liver_rep1


title: ∆scsA stationary phase, rep2


title: Control.Cy5_Msi1.Cy3_1

description: Biological Replicate 1, dye swap 2

tag: transient transfection with

value: RIP with Msi1 Antibody

tag: treatment time

value: 48 hours

value: RIP with Prebleed Antibody


title: T2 toxin treated log phase, rep1

value: T2 toxin

value: reference


title: ID4 B cell CD20 1

description:
1718911593_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: method

tag: individual (indiv.id)


title: ID5 LCL 1

description:
1718911531_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: EBV transformed LCL

tag: visit

tag: ChIP

value: LCL

value: Lymphoblastoid cell line LCL


title: ID4 Whole Blood 2

description:
1718911593_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: PAXgene

tag: yield

tag: rin


title: ID4 B cell CD20 2

description:
1718911593_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: tissue

tag: cell type


title: 45liver_rep2

value: in vitro

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: ID5 LCL 2

description:
1718911531_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID4 LCL 1

description:
1718911593_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID6 Whole Blood 1

description:
1718911594_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: Whole Blood


title: ID4 Whole Blood 1

description:
1718911593_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID6 Whole Blood 2

description:
1718911594_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID4 LCL 2

description:
1718911593_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID5 Whole Blood 2

description:
1718911594_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID5 B cell CD20 1

description:
1718911531_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: B cell-CD20


title: Wild type stationary phase, rep3

source_name: S. Typhimurium, wild type, stationary phase

tag: strain

tag: growth phase

value: wild type


title: Wild type stationary phase, rep2

tag: sample type


title: ID5 B cell CD19 2

description:
1718911531_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: B cell-CD19


title: ID5 Whole Blood 1

description:
1718911594_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: Chd3/4

type: genomic

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: custom array design 532663

hyb_protocol: Hybridization was performed by Nimblegen

scan_protocol: Arrays were scanned by Nimblegen

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Rattus norvegicus

source_name: Chd3/4 ChIP DNA from P15 rat sciatic nerve

label_protocol: ChIP DNA was amplified by whole genome amplification (Sigma), and then sent to Nimblegen for labeling with Cy3 or Cy5 per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: ChIP assays were performed on pooled P15 rat sciatic nerve samples.  6-10 pairs of sciatic nerve tissue was cross linked 1% formaldehyde in PBS for 20min as described (Jang et al., J. Neurochemistry, 2006; Jang and Svaren, JBC 2009).

value: P15 Sciatic Nerve

value: Sprague-Dawley

tag: antibody

value: Chd3/4, Santa Cruz, sc-11378

value: WGA-amplified ChIP DNA

source_name: Input ChIP DNA from P15 rat sciatic nerve


title: ∆scsA log phase, rep3

source_name: S. Typhimurium, ∆scsA, log phase

value: log

value: ∆scsA


title: Wild type stationary phase, rep1

value: stationary

value: reference


title: ∆scsA log phase, rep1


title: Wild type log phase, rep3

source_name: S. Typhimurium, wild type, log phase


title: ∆scsA log phase, rep2


title: 373liver_rep2

value: liver

tag: in vitro or in vivo

tag: gestation day

value: 180 days


title: ID5 PBMC 1

description:
1718911594_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: PBMC


title: 45liver_rep1

value: in vitro

tag: reference


title: ID2 B cell CD20 2

description:
1718911597_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: 711liver_rep2

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: Wild type log phase, rep2

tag: genotype


title: ID2 LCL 2

description:
1718911597_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: EBV transformed LCL

value: LCL

value: Lymphoblastoid cell line LCL


title: B-Gal - cells from healing skin of TCF mouse

city: Toronto

first: Saeid

last: Amini-Nik

state: ON

address: 101 College St

country: Canada

institute: Hospital For Sick Children

description: Gene expression data from B-Gal - cells in healing skin

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Partek Software

organism: Mus musculus

source_name: Healing wound cells which are B-Gal-

label_protocol: standard Affymetrix protocol

extract_protocol: RNA extraction kit from Qiagen

tag: source  tissue

value: skin scar tissue

value: TCF reporter mouse

tag: time

value: one week post wounding

value: B-Gal - cells from healing skin


title: 3234liver_rep2


title: B-Gal + cells from healing skin TCF mouse

description: Gene expression data from B-Gal + cells in healing skin

source_name: Healing wound cells which are B-Gal+

value: B-Gal + cells from healing skin


title: ID2 B cell CD19 2

description:
1718911597_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: method

tag: individual (indiv.id)

value: B cell-CD19


title: 373liver_rep1


title: ID5 PBMC 2

description:
1718911594_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: visit

tag: ChIP


title: ID2 LCL 1

description:
1718911597_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: LCL

tag: yield

tag: rin


title: Elongin A+/+ (EloA+/+), +RA

city: Nankoku

first: Takashi

last: yasukawa

state: Kochi

address: Kohasu, Oko-cho

department: Functional Genomics

country: Japan

institute: Kochi Medical School

description: Gene expression of RA-treated EBs derived from Elongin A+/+ ES cells

hyb_protocol: Microarray hybridization and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto-gridding, and image analysis were performed according to Applied Biosystems protocols using the 1700 Chemiluminescent Microarray Analyzer software (Version 1.0.3).

data_processing: Signal intensities across microarrays were quantile normalized.

label: DIG-UTP

source_name: Elongin A+/+ EBs, 2 μM RA

label_protocol: RNA (1 μg) was transcribed to DIG-labeled cRNA using an Applied Biosystems Chemiluminescent NanoAmpTM RT-IVT Labeling Kit (Applied Biosystems) according to the manufacturer’s instructions.

growth_protocol: DMEM/F12 (1:1) containing 15% FBS and N2

extract_protocol: Total RNA was isolated from EBs using a RNeasy mini kit (Qiagen) according to the manufacturer’s instructions, and the quality was determined using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: EBs were treated 2 μM retinoic acid for 4 days.

value: embryoid bodies derived from Elongin A+/+ ES cells


title: ID2 B cell CD20 1

description:
1718911597_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: tissue

tag: cell type

value: B cell-CD20


title: 3234liver_rep1


title: Elongin A-/- (EloA-/-), +RA

description: Gene expression of RA-treated EBs derived from Elongin A-/- ES cells

source_name: Elongin A-/- EBs, 2 μM RA

value: embryoid bodies derived from Elongin A-/- ES cells


title: ID3 B cell CD20 2

description:
1718911595_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: 51231liver_rep2

source_name: in vivo liver 180 days

value: liver

value: in vivo

source_name: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: Wild type log phase, rep1

tag: strain

tag: growth phase

value: log

value: wild type

source_name: S. typhimurium genomic DNA

value: reference


title: Cortisol treated stationary phase, rep3

scan_protocol: Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols.

source_name: S. Typhimurium, cortisol treated, stationary phase

treatment_protocol: Cortisol-treated cultures contain 1 µM of cortisol.

value: stationary

tag: treatment

value: cortisol

source_name: S. Typhimurium genomic DNA

tag: sample type


title: Cortisol treated stationary phase, rep2


title: 51231liver_rep1

tag: in vitro or in vivo

tag: gestation day

value: 180 days

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: Cortisol treated stationary phase, rep1


title: Untreated stationary phase, rep3

source_name: S. Typhimurium, untreated, stationary phase


title: Hepatocyte transgenic

city: Bonn

first: Peter

last: Kuckenberg

address: Sigmund Freud Str. 25

department: Institut of Pathology

country: Germany

institute: University Medical School Bonn

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Arrays were scanned in a GeneChip scanner 3000 (Affymetrix)

data_processing: Normalization and statistical data analyses were performed by an RMA algorithm performed with GeneSpring GX 10 software (Agilent)

source_name: transgenic mouse

label_protocol: RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For the Affymetrix array, 300ng of total RNA were used. Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: total RNA was extracted from cells with RNAeasy kit including DNAse digestion (Qiagen, Hilden, Germany)

treatment_protocol: Transgenic and control mice were treated with doxycycline (1mg/d i.p.) three times (0, 24 and 48h) and liver samples were collected after 52h. In addition, primary hepatocytes isolated from transgenic and control animals were cultured with doxycycline for 3 days (1µg/ml).

value: primary hepatocyte cultures

tag: background strain


title: ID3 B cell CD20 1

description:
1718911595_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID3 LCL 2

description:
1718911595_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: EBV transformed LCL

value: LCL

value: Lymphoblastoid cell line LCL


title: ID3 LCL 1

description:
1718911595_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: 9944 control animal

source_name: control mouse

value: primary liver tissue


title: A15liver_rep1

tag: reference


title: 9940 control animal


title: A15liver_rep2


title: Untreated stationary phase, rep2


title: Hepatocyte control


title: 711liver_rep1

source_name: in vitro liver 180 days

value: in vitro


title: ID3 B cell CD19 1

description:
1718911543_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

value: B cell-CD19


title: 6396liver_rep2


title: Untreated stationary phase, rep1


title: 4409liver_rep2


title: 9947 control animal


title: ID3 B cell CD19 2

description:
1718911543_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID2 PBMC 2

description:
1718911595_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: PBMC

value: PBMC


title: Cortisol treated log phase, rep3

source_name: S. Typhimurium, cortisol treated, log phase


title: 9943 control animal


title: 9949 transgenic animal


title: ID3 Whole Blood 2

description:
1718911543_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: WholeBlood

value: PAXgene

value: Whole Blood


title: 4409liver_rep1

value: liver

value: in vivo


title: ID3 Whole Blood 1

description:
1718911543_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: 9946 transgenic animal


title: 9933 transgenic animal


title: 322Hliver_rep1

source_name: in vitro liver 90 days

value: 90 days


title: 6396liver_rep1


title: Cortisol treated log phase, rep2

value: log

value: reference


title: Untreated log phase, rep3

source_name: S. Typhimurium, untreated, log phase


title: ID3 PBMC 1

description:
1718911543_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID3 PBMC 2

description:
1718911543_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: Untreated log phase, rep2


title: 4709liver_rep2


title: Cortisol treated log phase, rep1

value: cortisol


title: 322Hliver_rep2

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: Men1flf, Rbp2flf, RIP-Cre pancreatic islet repeat 1

city: Binney St

first: Andrew

last: Cherniack

state: MA

institute: Broad Institute

description: Pancreatic islets from 2 months old  mice with both the Men1 and the Rbp2 Gene knocked out

hyb_protocol: Fragmented and labeled  DNA target was hybridizated to Gene 1.0 ST arrays using the GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: The probe array was scanned using an Affymetrix® GeneChip® Scanner 3000.

data_processing: Data were processed with dChip.  Cel files were quantile normalized using MM2010052537.CEL as a base line.  Signal values were calculated with the average modelling method using the 5th percentile of regions for background subtraction.

source_name: pancreatic islets

label_protocol: Fragmented single-stranded DNA was labeled by TdT using the GeneChip® WT Terminal Labeling Kit.

growth_protocol: All mice were maintained at the research animal facility of the Dana-Farber Cancer Institute.

extract_protocol: Pancreatic islets were isolated from mice . Total RNA was harvested using RNeasy mini kit with on-column DNase digestion (Qiagen).

treatment_protocol: Mice were not treated.

tag: genotype/variation

value: Men1flf, Rbp2flf , RIP-Cre


title: ID4 B cell CD19 2

description:
1718911565_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: method


title: Untreated log phase, rep1


title: Men1flf, Rbp2flf, RIP-Cre pancreatic islet repeat 3


title: ID4 B cell CD19 1

description:
1718911565_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: individual (indiv.id)


title: ID4 PBMC 2

description:
1718911565_D
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: visit


title: ID4 PBMC 1

description:
1718911565_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: ChIP


title: Y52liver_rep1


title: Men1flf, Rbp2flf, RIP-Cre pancreatic islet repeat 4


title: ID2 Whole Blood 2

description:
1718911565_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: yield


title: Rbp2flf, RIP-Cre pancreatic islet repeat 3

description: Pancreatic islets from 2 months old  mice with the Rbp2 Gene knocked out

value: Rbp2flf, RIP-Cre


title: Y52liver_rep2


title: A105Hliver_rep1


title: Rbp2flf, RIP-Cre pancreatic islet repeat 2


title: 4709liver_rep1


title: Men1flf, Rbp2flf, RIP-Cre pancreatic islet repeat 2


title: Rbp2flf, RIP-Cre pancreatic islet repeat 4


title: 4429liver_rep2


title: ID2 Whole Blood 1

description:
1718911565_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: rin


title: Rbp2flf, RIP-Cre pancreatic islet repeat 1


title: A105Hliver_rep2

tag: tissue


title: 9941 transgenic animal

description: RMA expression value derived from Expression Console software; core-exon analysis


title: PD patient-derived iPS cell with SNCA A53T mutation corrected replicate 1

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data from Human induced pluripotent stem cell with A53T mutation corrected

hyb_protocol: Samples were prepared for hybridization using 15 µg biotinylated cRNA in a 1X hybridization cocktail according the Affymetrix hybridization conditions. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 7G and images were extracted and analyzed using Affymetrix GCOS software .

data_processing: Human Affymetrix HG-U133 array data were processed by Affy R package using RMA algorithm. Probe sets were remapped to ensembl genes using custom CDFs from University of Michigan BrainArray site (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp).

label_protocol: 375 ug total RNA was used to prepare biotinylated cRNA according to the manufacturer’s protocol (Affymetrix GeneChip 3’ Express Kit). Briefly, this method involves SuperScript II-directed reverse transcription using a T7-Oligo(dT) Promoter Primer to create first strand cDNA. RNase H-mediated second strand cDNA synthesis is followed by T7 RNA Polymerase directed in vitro transcription, which incorporates a biotinylated nucleotide analogs during cRNA amplification.

growth_protocol: hESCs and hiPSCs were maintained on mitomycin C inactivated mouse embryonic fibroblast (MEF) feeder layers in hESC medium [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (FBS) (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: RNA was isolated from hESCs and iPSCs, which were mechanically separated from feeder cells, using the RNeasy Mini Kit (Qiagen).

tag: cell type

value: induced pluripotent stem cells

value: SNCA wt


title: 4429liver_rep1


title: PD patient-derived iPS cell with SNCA A53T mutation corrected replicate 2

source_name: Human induced pluripotent stem cell with A53T mutation corrected


title: PD patien- derived iPS cell carrying SNCA A53T mutation replicate 1

description: Gene expression data from Human induced pluripotent stem cell carrying A53T mutation

value: SNCA A53T mutation


title: WIBR3 SNCA A53T mutation introduced replicate 2

description: Gene expression data from Human Embryonic Stem Cell Line WIBR3 with A53T mutation introduced

value: embryonic stem cells


title: Men1flf, RIP-Cre pancreatic islet repeat 1

description: Pancreatic islets from 2 months old  mice with the Men1 Gene knocked out

value: Men1flf, RIP-Cre


title: 624Hliver_rep1

source_name: in vivo liver 90 days


title: RIP-Cre pancreatic islet repeat 3

description: Pancreatic islets from 2 months old RIP-Cre mice

value: RIP-Cre


title: Men1flf, RIP-Cre pancreatic islet repeat 2


title: 5400liver_rep1


title: PD patient-derived iPS cell carrying SNCA A53T mutation replicate 2

source_name: Human induced pluripotent stem cell carrying A53T mutation


title: 624Hliver_rep2

source_name: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: F814liver_rep2


title: BGO1 SNCA A53T mutation introduced replicate 1

description: Gene expression data from Human Embryonic Stem Cell Line BGO1 with A53T mutation introduced


title: RIP-Cre pancreatic islet repeat 2


title: RIP-Cre pancreatic islet repeat 1


title: 5400liver_rep2


title: Nab2

description: custom array design 081105

source_name: Nab2 ChIP DNA from P15 rat sciatic nerve

value: P15 Sciatic Nerve

tag: strain

value: Sprague-Dawley

tag: antibody

value: Nab2, Santa Cruz, sc-22815

value: WGA-amplified ChIP DNA

source_name: Input ChIP DNA from P15 rat sciatic nerve


title: Mta2

description: custom array design 081105

source_name: Mta2 ChIP DNA from P15 rat sciatic nerve

value: Mta2, Santa Cruz, sc-9447


title: WIBR3-P39 replicate 1

description: Gene expression data from Human Embryonic Stem Cell Line WIBR3

source_name: Human Embryonic Stem Cell Line WIBR3


title: wild type pancreatic islet repeat 2

description: Pancreatic islets from 2 month old wt mice

value: wt


title: WIBR3 SNCA A53T mutation introduced replicate 1

source_name: Human Embryonic Stem Cell Line WIBR3 with A53T mutation introduced


title: WIBR3-P39 replicate 2


title: BGO1 SNCA A53T mutation introduced replicate 2

source_name: Human Embryonic Stem Cell Line BGO1 with A53T mutation introduced


title: Men1flf, RIP-Cre pancreatic islet repeat 3


title: wild type pancreatic islet repeat 3


title: A151liver_rep2

value: liver

value: in vivo

value: 90 days


title: F814liver_rep1

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: BGO1 replicate 2

description: Gene expression data from Human Embryonic Stem Cell Line BGO1

source_name: Human Embryonic Stem Cell Line BGO1


title: A151liver_rep1


title: BGO1 replicate 1


title: wild type pancreatic islet repeat 1

description: gene expression from 2 month old wild type mice


title: Sflexneri

status: Public on Jul 25 2011

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description: S. flexneri prototype

hyb_protocol: Microarrays are allowed to warm to room temperature for 30 minutes. The OligoB2 mixture (Affymetrix, P/N 900301) is heated to 65ºC for 5 minutes then mixed with the labeled and verified gDNA from above, DMSO and hybridization buffer included in the Affymetrix Hybridization, Wash and Stain kit (Affymetrix, P/N 900720). This solution is further denatured at 94ºC for 5 minutes. During this incubation the microarrays are equilibrated with prehybridization buffer and placed in the Affymetrix hybridization oven at 45ºC for 10 minutes rotating at 60 rpm. The labeled DNA is then hybridized to the microarray for 16 hours at 45ºC rotating at 60 rpm.

scan_protocol: Microarrays are washed and stained according to manufacturer’s specifications using two stain cycles and the prokaryotic washing protocol

data_processing: Initial data analysis was performed with the Gene Chip Operating System (GCOS) suite of tools provided by Affymetrix. Additional analysis utilized the Affymetrix power tools (APT) software (http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx). The data analysis parameters have been established empirically using known reference genomes included on the array. Within the APT, the MAS5 algorithm (Hubbell et al., 2002; Liu et al., 2002) was utilized with the perfect match and mismatch calculations and a Tau of 0.150 to detect which probes were present or absent (command= apt-probeset-summarize -a pm-mm,mas5-detect.calls=1.pairs=1.Tau=0.150 -d FDA_ECSGa520423F.cdf -o mas5_Analysis.dir --cel-files cel_file_list.txt).

organism: Shigella flexneri

source_name: Shigella flexneri, overnight growth

label_protocol: Approximately 7.5 mg of purified gDNA from above was digested with the DNAfree DNase kit (ABI, P/N AM1906) using timed samples to provide a sample with a size range of between 20 and 200 bp. DNAse was inactivated with the Inactivation Reagent provided with the kit. Sample ranges were determined by gel electrophoresis on a 4-20% gradient gel (Biorad, Cat #161-1235) with Low MW Ladder (Invitrogen Cat #10821-015). Digested DNA was labeled with biotin by the addition of biotin-11-ddATP (PerkinElmer, Cat # NEL548001EA), 2 µl terminal transferase enzyme (Promega, Cat # M1875) and appropriate buffers. The digests were incubated for 2 hours at 37ºC and the labeling was quenched with 0.5M EDTA. Verification of label incorporation was accomplished by mixing the biotin-labeled DNA with Immunopure NeutrAvidin (Pierce, Cat # 31000), incubation at room temperature for 5 minutes, electrophoresis on a 4-20% gradient gel (Biorad, Cat# 161-1105EDU) and visualization. A clear shift in size distribution from unlabeled to labeled DNA was verified prior to hybridization.

growth_protocol: Overnight growth in LB and genomic DNA isolation the following day

extract_protocol: Bacterial cultures were grown overnight from a population in 50 ml of Luria broth (LB) and genomic DNA was isolated according to standard methods (Ge & Taylor, 1992). Briefly, bacterial cells were concentrated by centrifugation, washed and suspended in isolation buffer (0.15 M Tris, 0.1 M EDTA, pH 8.0). Sodium dodecyl sulfate was added to 1% final concentration (vol/vol) and allowed to incubate for 1 hour at 55ºC or until the solution cleared. Two volumes of phenol:chloroform:isoamyl alcohol (25:24:1) were added and briefly mixed by vortexing. The resulting solution was separated by centrifugation at 12,000 x g for 15 minutes at 4ºC. The aqueous layer (top) was removed to a new tube and mixed with 2 volumes of chloroform. The mixture was separated by centrifugation at 12,000 x g for 15 minutes at 4ºC and the aqueous layer (top) was transferred to a clean tube. The aqueous layer was then extracted with at least 10 volumes of ice-cold ethanol. The precipitated DNA was spooled out of the mixture and suspended in TE (10 mM Tris/HCl, 1 mM EDTA, pH 8.0).

value: Shigella flexneri 2457T

value: S. flexneri prototype


title: Chd4

description: custom array design 081105

source_name: Chd4 ChIP DNA from P15 rat sciatic nerve

value: Chd4, Paul Wade, (Fujita et al., 2003)


title: PBS treatment rep3

city: Louisville

first: joseph

middle: calvin

last: kouokam

state: KY

address: 505 S. Hancock St.

department: Pharm  Tox

institute: U of L

description: Gene expression after 16 hr treatment with PBS

hyb_protocol: 1.65ug of each labeled cRNA sample were fragmented at 60 ºC for 30 min using an Agilent Gene Expression Hybridization kit (Agilent Technologies, Wilmington, De) followed by hybridization to a whole human genome Agilent  oligonucleotide slide containing four highdefinition 44K microarray (Agilent Technologies,Wilmington, De) at 65ºC for 17 hours.

scan_protocol: Sampled were scanned using an Agilent G2565BA microarray scanner system (Agilent Technologies, Wilmington, De).

data_processing:
one-color microarray images were extracted with the Feature Extraction software v 9.5.1 (Agilent Technologies, Wilmington, De) and the raw data imported into GeneSpring GX 10 software (Agilent Technologies, Wilmington, De) for  normalization and further analysis to yield a list of differentially expressed genes.
Benjammini and Hochberg was used and we considered only a fold change of at least 2.0 compared to the PBS treated samples to represent a meaningfully altered gene expression
The raw data files (.txt) were imported into GeneSpring (GX 11.1) and  normalized. The analysis was carried on using the 24097 genes filtered   by the flags in the raw data files where the entities were present or   marginal present in at least three out of the 30 samples.

source_name: Overnight treatment with 8 PBS  replicate 3

label_protocol: 200 ng RNA were used to generate cyanine 3 (Cy3) cRNA with the aid of Low RNA Input Linear Amplification kit, one-color (Agilent Technologies, Wilmington, De) according to the manufacturer’s instructions

growth_protocol: Cells were grown in keratinocyte serum-free medium (KSFM) supplemented with recombinant human epidermal growth factor (0.1 g/ml), bovine pituitary extract (50 μg/ml), calcium chloride (0.4 mM) and an antibiotic cocktail composed of penicillin and streptomycin at  final concentrations of 100 U/ml and 100 μg/ml

extract_protocol: The cells were lysed using a Qiagen Qiashredder, and total RNA was extracted using a Qiagen RNeasy Mini Kit following the manufacturer's instructions.

treatment_protocol: Cells were treated for 16 h with GRFT (0.1, 1 and 4 μM), control lectins  or the vehicle PBS at 37°C with 5% CO2

tag: treatment

value: PBS

tag: cell line

value: ecto-cervical cell line


title: Sboydii

description: S. boydii prototype

organism: Shigella boydii

source_name: Shigella boydii, overnight growth

value: Shigella boydii BS512

tag: sample type

value: S. boydii prototype


title: 53638

description: EIEC prototype

organism: Escherichia coli

source_name: Escherichia coli, overnight growth

value: Escherichia coli 53638

value: EIEC prototype


title: NB002

description: Neobaldder isolate

value: Escherichia coli NB002

value: Neobaldder isolate


title: Ssonnei

description: S. sonnei prototype

organism: Shigella sonnei

source_name: Shigella sonneii, overnight growth

value: Shigella sonneii 53G

value: S. sonnei prototype


title: CFT1

description: UPEC novel strain

value: Escherichia coli CFT1

value: UPEC novel strain


title: F38

description: UPEC novel strain

value: Escherichia coli F38


title: PBS treatment rep2

source_name: Overnight treatment with 8 PBS  replicate 2


title: PBS treatment rep1

source_name: Overnight treatment with 8 PBS  replicate 1


title: Sdys

description: S. dysernteriae prototype

organism: Shigella dysenteriae

source_name: Shigella dysentaeriae, overnight growth

value: Shigella dysentaeriae 1617

value: S. dysernteriae prototype


title: MGRFT 8μM treatment rep1

description: Gene expression after 16 hr treatment with 8 μM Lectin activity deficient mutant GRFT

source_name: Overnight treatment with 8 μM MGRFT  replicate 1

value: MGRFT 8μM


title: NB001

description: Neobaldder isolate

value: Escherichia coli NB001


title: MGRFT 8μM treatment rep3

source_name: Overnight treatment with 8 μM MGRFT  replicate 3


title: F11

description: UPEC prototype strain

value: Escherichia coli F11

value: UPEC prototype strain


title: MGRFT 1μM treatment rep3

description: Gene expression after 16 hr treatment with 1 μM Lectin activity deficient mutant GRFT

source_name: Overnight treatment with 1 μM MGRFT  replicate 3

value: MGRFT 1μM

value: ecto-cervical cell line


title: MGRFT 1μM treatment rep2

source_name: Overnight treatment with 1 μM MGRFT  replicate 2


title: GRFT 4μM treatment rep3

description: Gene expression after 16 hr treatment with 4 μM GRFT

source_name: Overnight treatment with 4 μM GRFT  replicate 3

value: GRFT 4μM


title: UTI536

description: UPEC prototype strain

value: Escherichia coli UTI536


title: F24

description: UPEC novel strain

value: Escherichia coli F24


title: MGRFT 8μM treatment rep2

source_name: Overnight treatment with 8 μM MGRFT  replicate 2


title: MGRFT 1μM treatment rep1

source_name: Overnight treatment with 1 μM MGRFT  replicate 1


title: GRFT 4μM treatment rep2

source_name: Overnight treatment with 4 μM GRFT  replicate 2


title: CFT073

description: UPEC prototype strain

value: Escherichia coli CFT073


title: GRFT 4μM treatment rep1

source_name: Overnight treatment with 4 μM GRFT  replicate 1


title: GRFT 0.1μM treatment rep2

description: Gene expression after 16 hr treatment with 0.1 μM GRFT

source_name: Overnight treatment with 0.1 μM GRFT  replicate 2

value: GRFT 0.1μM


title: Control normal prostate cell line RWPE.1

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

description: To export to gene expression data based on unique probe identifier, we use Sample Probe ID Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual.

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions.

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin.

source_name: control normal prostate cell line

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.

extract_protocol: Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.

value: control normal prostate cell


title: GRFT 1μM treatment rep2

description: Gene expression after 16 hr treatment with 1 μM GRFT

source_name: Overnight treatment with 1 μM GRFT  replicate 2

value: GRFT 1μM


title: GRFT 1μM treatment rep3

source_name: Overnight treatment with 1 μM GRFT  replicate 3


title: Prostate cancer cell line LNCap.FGC

source_name: prostate cancer cell line

value: prostate cancer cell

value: LNCaP-FGC


title: Prostate cancer cell line PC3


title: GRFT 0.1μM treatment rep3

source_name: Overnight treatment with 0.1 μM GRFT  replicate 3


title: E24377A

description: ETEC prototype strain

source_name: Escherichia coli, overnight growth

value: Escherichia coli E24377A

value: ETEC prototype strain


title: Prostate cancer cell line DU145


title: GRFT 1μM treatment rep1

source_name: Overnight treatment with 1 μM GRFT  replicate 1


title: Control normal prostate cell line RWPE.1 [MET]

description: Control normal prostate cell RWPE.1

hyb_protocol: Fluorescence signals corresponding to C or T nucleotides were measured and the data were used to assign a quantitative measure of methylation level (β value).

data_processing: Each methylation data point represents the fluorescent signal from the methylated (M) and unmethylated (U) allele. Background intensity was computed from a set of negative controls and subtracted from each analytical data point. The ratio of the fluorescent signals from the two alleles was then computed. The β value is a quantitative measure of DNA methylation levels of specific CpGs and ranges from 0 for completely unmethylated to 1 for completely methylated. Data processing were performed on Illumina BeadStudio software. We normalized β value data using Quantile normalization between samples.

source_name: control normal prostate cell

label_protocol: Bisulfite conversion of genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research, Orange, CA) according to the Manufacturer's instructions.

extract_protocol: Genomic DNA for the Infinium methylation assay was extracted by standard methods using the Wizard Genomic DNA Purification System (Promega, Madison, WI).


title: K-12

description: Lab adapated isolate

value: Escherichia coli K-12

value: Lab adapated isolate


title: Prostate cancer cell line PC3 [MET]

description: Prostate cancer cell line PC3


title: HS

description: Human commensal

value: Escherichia coli HS

value: Human commensal


title: CV-N 4 μM treatment rep3

description: Gene expression after 16 hr treatment with 4 μM CV-N

source_name: Overnight treatment with 4 μM CV-N  replicate 3

value: CV-N 4 μM


title: CV-N 4 μM treatment rep1

source_name: Overnight treatment with 4 μM CV-N  replicate 1

value: ecto-cervical cell line


title: B7A

description: ETEC prototype strain

value: Escherichia coli B7A


title: GRFT 0.1μM treatment rep1

source_name: Overnight treatment with 0.1 μM GRFT  replicate 1


title: CV-N 0.5 μM treatment rep3

description: Gene expression after 16 hr treatment with 0.5 μM CV-N

source_name: Overnight treatment with 0.5 μM CV-N replicate 3

value: CV-N 0.5 μM


title: 17-2

description: EAEC prototype strain

value: Escherichia coli 17-2

value: EAEC prototype strain


title: CV-N 0.5 μM treatment rep2

source_name: Overnight treatment with 0.5 μM CV-N  replicate 2


title: JM221

description: EAEC prototype strain

value: Escherichia coli JM221


title: Slide 344245

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6 .  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of celR mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F635 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown to OD600 of 0.2 in CM17 medium

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Four replicate cultures.

value: Wild type

source_name: F532 Mean

value: celR mutant


title: Prostate cancer cell line DU145 [MET]

description: Prostate cancer cell line DU145

value: prostate cancer cell


title: Ec042

description: EAEC prototype strain

value: Escherichia coli Ec042


title: Prostate cancer cell line LNCap.FGC [MET]

description: Prostate cancer cell line LNCap.FGC

value: LNCaP-FGC


title: Slide 344244

description: Sample 1


title: CV-N 0.05 μM treatment rep2

description: Gene expression after 16 hr treatment with 0.05 μM CV-N

source_name: Overnight treatment with 0.05 μM CV-N  replicate 2

value: CV-N 0.05 μM


title: 101-1

description: EAEC prototype strain

value: Escherichia coli 101-1


title: CV-N 0.5 μM treatment rep1

source_name: Overnight treatment with 0.5 μM CV-N replicate 1


title: 55989

description: EAEC prototype strain

value: Escherichia coli 55989


title: BPA 50 mg/kg/time (High)

city: Noda

first: Masakazu

last: Umezawa

state: Chiba

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

description:
Sample 4 High
Scanned with High sensitivity settings

hyb_protocol: Labelled cDNA sample was hybridised using gapped cover glass. Slides placed in humidified chamber for 20 h at 51 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 0.2x SSC and 0.02x SSC, each at 42 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays were scanned using Perkin Elmar ScanArray Light scanner and ScanArray Express 3.0 software.

data_processing: Data analysis was carried out using ScanArray Express 3.0 and SilicoCyte (Cytogenomics Ltd.). The mean values from each channel were normalized using the LOWESS algorithm and log10 transformed. Normalised and log 10 transformed values were used to calculate the Cy3/Cy5 fluorescence ratios. Data was compiled from two repeated scanns (Low and High sensitivity settings) on each array with a dye-swap replicate, thus providing two technical repeats.

source_name: prenatally received corn oil

label_protocol: RNAs were pooled equally from each sample to 45 g for each group, purified using the RNeasy Micro Kit (Qiagen, Hilden, Germany) and reverse-transcribed to yield complementary DNA (cDNA) labeled with Cy3 or Cy5 fluorescent dye using the SuperScript Indirect cDNA Labeling Core Kit (Invitrogen, CA, USA) and the SuperScript Indirect cDNA Labeling System Purification Kit (Invitrogen). Cy3- and Cy5-labeled samples were purified using the CyScribe GFX Purification Kit (GE Healthcare Bio-Sciences, Little Chalfont, UK).

growth_protocol: Female ICR mice of the first day of pregnancy were purchased from Japan SLC Inc. (Shizuoka Japan) and housed under controlled temperature (23 ± 1 °C), humidity (55 ± 5%) and light (12 h light/12 h dark cycle with light on at 8:00 a.m.) with ad libitum access to chow and water.

extract_protocol: Testis tissue for gene expression analysis was homogenized in Isogen (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA was isolated according to the manufacturer’s protocol and suspended in RNase-free water.

treatment_protocol: BPA (0, 5, 50 mg/kg/time) or DEHP (0, 2, 20 mg/kg/time) was administered subcutaneously to pregnant mice on days 7 and 14 of pregnancy. BPA doses were based on the lowest observed adverse effect level (LOAEL) of chronic oral BPA intake (50 mg/kg/day) in rats (U.S. NTP 1982). 20 mg/kg of DEHP was above the no observed adverse effect level (NOAEL) of 7-day oral DEHP intake (14 mg/kg/day) (Lamb et al. 1987). Mice in the control group received only corn oil, on the same schedule as the treated groups.

value: ICR

value: testis

source_name: prenatally received BPA (50 mg/kg/time)


title: ConA 1 μM treatment rep3

description: Gene expression after 16 hr treatment with 1 μM ConA

source_name: Overnight treatment with 1 μM ConA Replicate 3

value: ConA 1 μM


title: ConA 1 μM treatment rep2

source_name: Overnight treatment with 1 μM ConA Replicate 2

value: ecto-cervical cell line


title: CV-N 0.05 μM treatment rep3

source_name: Overnight treatment with 0.05 μM CV-N replicate 3


title: hESC WIBR3

description: CNV array data for Human Embryonic Stem Cell Line WIBR3

hyb_protocol: All DNA samples were processed hybridized according to the publisher’s protocol using the Genome-Wide human SNP Nsp/Sty 6.0 protocol and SNP 6.0 arrays (Affymetrix).

scan_protocol: See manufacturer's protocol

data_processing: CEL files from Affymetrix SNP 6.0 arrays were processed using Affymetrix Genome Console. Samples were normalized agains 270 International HapMap samples as provided by Affymetrix. All the arrays passed the quality control requirements having contast QC (Quality Control) values and MAPD (Median absolute pairwise difference) values within required bounderies.

label: Biotin

source_name: Human Embryonic Stem Cell Line WIBR3

label_protocol: See manufacturer's protocol

extract_protocol: DNA was isolated from hESCs and iPSCs, which were mechanically separated from feeder cells, using the DNeasy Blood and tissue Kit (Qiagen).

value: embryonic stem cells

value: SNCA wt


title: E22

description: EPEC prototype strain

source_name: Escherichia coli, overnight growth

value: Escherichia coli E22

value: EPEC prototype strain


title: B171

description: EPEC prototype strain

value: Escherichia coli B171


title: E110019

description: EPEC prototype strain

value: Escherichia coli E110019


title: BPA 50 mg/kg/time (Low)

description:
Sample 4 Low
Scanned with Low sensitivity settings


title: CV-N 0.05 μM treatment rep1

source_name: Overnight treatment with 0.05 μM CV-N replicate 1


title: BGO1-SNCA-A53T/WT

description: CNV array data for Human Embryonic Stem Cell Line BGO1 with A53T mutation introduced

value: SNCA A53T mutation


title: BPA 5 mg/kg/time (Low)

description:
Sample 3 Low
Scanned with Low sensitivity settings

source_name: prenatally received BPA (5 mg/kg/time)


title: hESC BGO1

description: CNV array data for Human Embryonic Stem Cell Line BGO1

source_name: Human Embryonic Stem Cell Line BGO1


title: BPA 5 mg/kg/time (High)

description:
Sample 3 High
Scanned with High sensitivity settings


title: WIBR3-SNCA-A53T/WT-1C

description: CNV array data for Human Embryonic Stem Cell Line WIBR3 with A53T mutation introduced


title: DEHP 2 mg/kg/time (High)

description:
Sample 1 High
Scanned with High sensitivity settings

source_name: prenatally received DEHP (2 mg/kg/time)


title: 8624

description: EHEC prototype strain

value: Escherichia coli 8624

value: EHEC prototype strain


title: TX1999

description: EHEC novel strain

value: Escherichia coli TX1999

value: EHEC novel strain


title: Sakai

description: EHEC prototype strain

value: Escherichia coli Sakai


title: OK1114

description: EHEC novel strain

value: Escherichia coli OK1114


title: DEHP 2 mg/kg/time (Low)

description:
Sample 1 Low
Scanned with Low sensitivity settings

value: ICR


title: ConA 1 μM treatment rep1

source_name: Overnight treatment with 1 μM ConA Replicate 1


title: WIBR3-IPS-SNCA-A53T(1lox)-6

description: CNV array data for Human induced pluripotent stem cell carrying A53T mutation

value: induced pluripotent stem cells


title: 15R - pool (18.11) 2

status: Public on Jul 24 2011

city: Antwerp

first: Xuan Bich

last: Trinh

address: Oosterveldlaan 24

country: Belgium

institute: TCRU St. Augustinus GZA hospitals

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus Kit (Agilent) and following the manufacturer's instructions.

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent)

data_processing: The data were then extracted from images by the Feature Extraction software 6.1 (Agilent). The raw data were processed in Bioconductor in R software packages. Data was normalized using the LOWESS normalization method. Filtering was done by selecting expressions below a threshold (log 2 of 100) that are present in at least 25% of the arrayed samples.

source_name: ovarian cancer sample 15R

label_protocol: fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using a fluorescent linear amplification kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (Perkin- Elmer, Boston, MA), following the user's manual.

extract_protocol: Total RNA was isolated from frozen primary ovarian tumor samples using the TRIzol reagent (Invitrogen, Burlington, ON, Canada) and finally dissolved in RNase-free H2O. Total RNA (5-10 μg) was treated with DNase using the RNase-free DNase kit and RNeasy spin columns (Qiagen, Mississauga, ON). Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2-0.5 μg/μl. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: drug response status

value: chemoresistant

value: pool of samples


title: 10S - pool (18.11) 1

source_name: ovarian cancer sample 10S

value: chemosensitive


title: 14R - pool (18.11) 1

source_name: ovarian cancer sample 14R


title: 9S - pool (18.11) 2

source_name: ovarian cancer sample 9S


title: 13R - pool (18.11) 2

source_name: ovarian cancer sample 13R


title: 10S - pool (18.11) 2


title: 12R - pool (16.11) 1

source_name: ovarian cancer sample 12R


title: EDL933

description: EHEC prototype strain

value: Escherichia coli O157:H7 str. EDL933


title: 12R - pool (16.11) 2


title: 11R - pool (16.11) 2

source_name: ovarian cancer sample 11R


title: 15R - pool (18.11) 1


title: 9S - pool (18.11) 1


title: 13R - pool (18.11) 1


title: 11R - pool (16.11) 1


title: DEHP 20 mg/kg/time (Low)

description:
Sample 2 Low
Scanned with Low sensitivity settings

source_name: prenatally received corn oil

value: testis

source_name: prenatally received DEHP (20 mg/kg/time)


title: 10R - pool (16.11) 2

source_name: ovarian cancer sample 10R


title: 10R - pool (16.11) 1


title: CV-N 4 μM treatment rep2

source_name: Overnight treatment with 4 μM CV-N replicate 2

value: CV-N 4 μM

value: ecto-cervical cell line


title: 7S - pool (16.11) 1

source_name: ovarian cancer sample 7S


title: 8S - pool (16.11) 1

source_name: ovarian cancer sample 8S


title: 7S - pool (16.11) 2


title: 9R - pool (15.11) 2

source_name: ovarian cancer sample 9R


title: 8S - pool (16.11) 2


title: 9R - pool (15.11) 1


title: 8R - pool (15.11) 2

source_name: ovarian cancer sample 8R


title: WIBR3-IPS-SNCA-A53T-Corr-1

description: CNV array data for Human induced pluripotent stem cell with A53T mutation corrected

value: SNCA wt


title: 8R - pool (15.11) 1


title: Slide 344246

description: Sample 3

source_name: F532 Mean

value: Wild type

source_name: F635 Mean

value: celR mutant


title: 6S - pool (15.11) 1

source_name: ovarian cancer sample 6S


title: 6R - pool (12.11) 1

source_name: ovarian cancer sample 6R


title: 5S - pool (15.11) 2

source_name: ovarian cancer sample 5S


title: 5S - pool (15.11) 1


title: 7R - pool (15.11) 1

source_name: ovarian cancer sample 7R


title: 7R - pool (15.11) 2


title: 5R - pool (12.11) 1

source_name: ovarian cancer sample 5R


title: 3S - pool (12.11) 2

source_name: ovarian cancer sample 3S


title: 4R - pool (12.11) 2

source_name: ovarian cancer sample 4R


title: 5R - pool (12.11) 2


title: 6S - pool (15.11) 2


title: 4R - pool (12.11) 1


title: 4S - pool (12.11) 1

source_name: ovarian cancer sample 4S


title: 1R - pool (11.11) 2

source_name: ovarian cancer sample 1R


title: 1R - pool (11.11) 1


title: 3R - pool (11.11) 1

source_name: ovarian cancer sample 3R


title: 2R - pool (11.11) 1

source_name: ovarian cancer sample 2R


title: 3R - pool (11.11) 2


title: 3S - pool (12.11) 1


title: 2S - pool (11.11) 1

source_name: ovarian cancer sample 2S


title: 2R - pool (11.11) 2


title: 6R - pool (12.11) 2


title: 1S - pool (11.11) 2

source_name: ovarian cancer sample 1S


title: 1S - pool (11.11) 1


title: 4S - pool (12.11) 2


title: C/EBPβ-UTR + 3T3RasV12, replicate 2

status: Public on Jul 23 2011

city: Frederick

middle: F

last: Johnson

address: Bldg 539, rm 122, 1050 Boyles St., NCI-Frederick

department: Center for Cancer Research

institute: NCI

hyb_protocol: Three replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000

data_processing: Following QC checks, microarray probe level data were normalized, background adjusted, and summarized with the RMA algorithm (Robust Multichip Analysis)

source_name: C/EBPβ-UTR + 3T3RasV12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.  RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled using Affymetrix One Cycle Target Labeling kit following manufacturer’s protocol

growth_protocol: NIH-3T3 cells were purchased from ATCC and passaged in DMEM supplemented with 10% FCS and pen/strep.

extract_protocol: Total RNA was extracted from 3T3 cells using Rneasy Kits (Qiagen) according to manufacturer's instructions

treatment_protocol: Cells were sequentially infected with retroviruses expressing H-RasV12 and C/EBPβ or C/EBPβ-UTR and selected using puromycin and hygromycin. After selection, cells were plated at equivalent densities and harvested 48-72 hours later.

value: infected with retroviruses expressing H-RasV12 and C/EBPβ-UTR


title: C/EBPβ-UTR + 3T3RasV12, replicate 3


title: floxed control, biological rep3

city: Erlangen

first: Christoph

last: Becker

address: Hartmannstrasse 14

institute: University of Erlangen-Nuremberg

description: Gene expression data from intestinal epithelial cells of floxed control mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneScan 3000 7G.

data_processing: Data were normalized using the Robust Multi-array Average (RMA) algorithm, and analyzed with the FlexArray Suite.

source_name: IEC from floxed control mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: not applicable

extract_protocol: Extraction of total RNA was performed using the Qiagen RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: not applicable

value: intestinal epithelial cells

tag: genotype

value: casp8 flox, villinCre negative


title: 14R - pool (18.11) 2

source_name: ovarian cancer sample 14R

tag: reference


title: caspase-8 deficient, biological rep3

description: Gene expression data from intestinal epithelial cells of conditional caspase-8 deficient mice

source_name: IEC from caspase-8 deficient mice

value: casp8 flox, villinCre positive


title: 3T3RasV12, replicate 3

tag: genotype/variation

value: infected with retroviruses expressing H-RasV14


title: caspase-8 deficient, biological rep1


title: C/EBPβ + 3T3RasV12, replicate 3

source_name: C/EBPβ + 3T3RasV12

value: infected with retroviruses expressing H-RasV12 and C/EBPβ


title: 3T3RasV12, replicate 1

value: infected with retroviruses expressing H-RasV12


title: 2S - pool (11.11) 2


title: caspase-8 deficient, biological rep2


title: floxed control, biological rep1


title: floxed control, biological rep2


title: C/EBPβ + 3T3RasV12, replicate 1


title: 3T3RasV12, replicate 2

value: infected with retroviruses expressing H-RasV13


title: C/EBPβ + 3T3RasV12, replicate 2


title: Control diet supplemented with resveratrol-enriched grape extract, male pig number 2216

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

hyb_protocol: Following fragmentation, 15 cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA), using CEL files obtained from GCOS software (Affymetrix).

organism: Sus scrofa

source_name: male pig, CT-GE-RES group

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 4 μg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Pigs' heparinised blood was processed within two hours after extraction and used to isolate PBMNCs. Isolation was carried out under sterile conditions to avoid the activation of monocytes. Blood was diluted 1:1 with RPMI 1640 cell culture medium and processed by density gradient centrifugation with Histopaque-1077 (Sigma Aldrich) according to the manufacturer instructions. After washing the cells (x2) with phosphate buffer solution (PBS), the PBMNCs were lysed using RLT Buffer (Qiagen) and stored at –80 C for RNA extraction.

extract_protocol: Total RNA was isolated using an RNeasy  Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80C.

treatment_protocol: PBMNCs were isolated from the following groups: i) CT (animals fed a standard commercial pig chow for 4 months), n=4 arrays (2 females, 2 males); ii) AD (animals fed an atherogenic diet containing 5.5% beef tallow, 10% coconut oil and 1% cholic acid for 4 months), n=4 arrays (2 females, 2 males); iii) AD-GE (animals fed an atherogenic diet supplemented with grape extract 1 g GE/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); iv) AD-GE-RES (animals fed an atherogenic diet supplemented with resveratrol-enriched grape extract 1 g GE/70 Kg animal body weight equivalent to 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); v) AD-RES (animals fed an atherogenic diet supplemented with resveratrol, 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); vi) CT-GE-RES (animals fed a standard commercial pig chow supplemented with resveratrol-enriched grape extract 1 g GE/70 Kg animal body weight equivalent to 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males).

tag: gender

value: male

value: Peripheral blood mononuclear cells (PBMNCs)

tag: diet

value: Control diet supplemented with resveratrol-enriched grape extract (CT-GE-RES)


title: Control diet supplemented with resveratrol-enriched grape extract, male pig number 2179


title: DEHP 20 mg/kg/time (High)

description:
Sample 2 High
Scanned with High sensitivity settings

source_name: prenatally received corn oil

value: ICR

value: testis

source_name: prenatally received DEHP (20 mg/kg/time)


title: diploid control ESC biologcal rep3

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: gene expression profile of a male diploid ES cell line

hyb_protocol: sample processing, labelling and primary data analysis were performed by Imagenes, Berlin

scan_protocol: scanning were performed by Imagenes, Berlin

data_processing: data were normalized using the RMA algorithm.

source_name: diploid ES cell line

label_protocol: labelling were performed by Imagenes, Berlin

growth_protocol: mouse ES cells cultured in 2i medium

extract_protocol: RNA was extraced using the Quiagen Rneasy Kit

treatment_protocol: RNA was extracted at d2 after passaging

value: diploid ES cell


title: haploid ESC HAP2 p21

description: gene expression profile of a haploid ES cell line

source_name: haploid ES cell line

value: F1 CBAxB6

value: haploid ES cell


title: haploid ESC HAP1 p24


title: haploid ESC HTG1 p11

value: mixed transgenic


title: diploid control ESC biologcal rep1


title: diploid control ESC biologcal rep2


title: C/EBPβ-UTR + 3T3RasV12, replicate 1

value: infected with retroviruses expressing H-RasV12 and C/EBPβ-UTR


title: Control diet supplemented with resveratrol-enriched grape extract, female pig number 2186

source_name: female pig, CT-GE-RES group

value: female


title: Atherogenic diet supplemented with resveratrol, male pig number 2177

source_name: male pig, AD-RES group

value: Atherogenic diet supplemented with resveratrol (AD-RES)


title: Control diet supplemented with resveratrol-enriched grape extract, female pig number 2223


title: Atherogenic diet supplemented with resveratrol, female pig number 2222

source_name: female pig, AD-RES group


title: Atherogenic diet supplemented with resveratrol, male pig number 2176


title: Atherogenic diet supplemented with resveratrol-enriched grape extract, male pig number 2191

source_name: male pig, AD-GE-RES group

value: Atherogenic diet supplemented with resveratrol-enriched grape extract (AD-GE-RES)


title: Atherogenic diet supplemented with resveratrol-enriched grape extract, male pig number 2184


title: M3-S4(0.005):hcf-1(pk924) vs daf-16(RX5);hcf-1(pk924)(L4)

city: Ithaca

first: Gizem

last: Rizki

address: 526 Campus Road, 341 Biotech

institute: Cornell University

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.005%

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Scan Power : 100 PMT Volts : 668 Pixel Size : 5 Laser on time : 27643 Laser Power : 1.86 Scan Date : 2008-08-20 Scan Temperature : 29.87 Scan Time : 11:54:46 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 960, 2680

organism: Caenorhabditis elegans

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol:
Culture Methods : Synchronized by hatching in M9 at 16C and developed at 25C
Developmental Stage : L4

extract_protocol: Extraction method : Trizol/Qiagen Rneasy Kit

tag: strain name

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636


title: M3-S4(1):hcf-1(pk924) vs daf-16(RX5);hcf-1(pk924)(L4)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 967 Pixel Size : 5 Laser on time : 27764 Laser Power : 2.12 Scan Date : 2008-08-20 Scan Temperature : 34.63 Scan Time : 13:56:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1000, 2800


title: Atherogenic diet supplemented with resveratrol, female pig number 2228


title: M3-S3(0.1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (L4) DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA5 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 747 Pixel Size : 5 Laser on time : 27719 Laser Power : 2.01 Scan Date : 2008-08-20 Scan Temperature : 33.13 Scan Time : 13:10:49 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 18440


title: M3-S4(0.1):hcf-1(pk924) vs daf-16(RX5);hcf-1(pk924)(L4)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 751 Pixel Size : 5 Laser on time : 27701 Laser Power : 2.01 Scan Date : 2008-08-20 Scan Temperature : 32.52 Scan Time : 12:55:02 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1000, 2760


title: Atherogenic diet supplemented with resveratrol-enriched grape extract, female pig number 2208

source_name: female pig, AD-GE-RES group


title: Atherogenic diet supplemented with grape extract, male pig number 2193

source_name: male pig, AD-GE group

value: Atherogenic diet supplemented with grape extract (AD-GE)


title: M3-S3(1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (L4) DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA5 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 969 Pixel Size : 5 Laser on time : 27783 Laser Power : 2.14 Scan Date : 2008-08-20 Scan Temperature : 35.24 Scan Time : 14:14:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 18560


title: M3-S4(0.5):hcf-1(pk924) vs daf-16(RX5);hcf-1(pk924)(L4)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.5%

scan_protocol: Scan Power : 100 PMT Volts : 863 Pixel Size : 5 Laser on time : 27861 Laser Power : 2.20 Scan Date : 2008-08-20 Scan Temperature : 36.52 Scan Time : 15:37:33 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.5

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 2760


title: M3-S3(0.5):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (L4) DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA5 compared in this experiment. Scan settings=AutoPMT 0.5%

scan_protocol: Scan Power : 100 PMT Volts : 896 Pixel Size : 5 Laser on time : 27880 Laser Power : 2.20 Scan Date : 2008-08-20 Scan Temperature : 36.92 Scan Time : 15:56:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.5

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 18520


title: Atherogenic diet supplemented with resveratrol-enriched grape extract, female pig number 2202


title: M3-S3(0.005):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (L4) DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until mid-L4 stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA5 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 676 Pixel Size : 5 Laser on time : 27659 Laser Power : 1.88 Scan Date : 2008-08-20 Scan Temperature : 30.60 Scan Time : 12:11:50 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1000, 18440


title: Atherogenic diet supplemented with grape extract, female pig number 2207

source_name: female pig, AD-GE group


title: M3-S2(1):hcf-1(pk924) vs N2 (YA)

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy5 and N2-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 925 Pixel Size : 5 Laser on time : 27798 Laser Power : 2.13 Scan Date : 2008-08-20 Scan Temperature : 35.54 Scan Time : 14:29:25 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 34240

growth_protocol:
Culture Methods : Synchronized by hatching in M9 at 16C and developed at 25C
Developmental Stage : Young adult


title: M3-S2(0.5):hcf-1(pk924) vs N2 (YA)

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy5 and N2-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.5%

scan_protocol: Scan Power : 100 PMT Volts : 866 Pixel Size : 5 Laser on time : 27898 Laser Power : 2.20 Scan Date : 2008-08-20 Scan Temperature : 37.19 Scan Time : 16:16:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.5

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 34200


title: Atherogenic diet supplemented with grape extract, male pig number 2192


title: Galanthamine 72h

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

institute: Karlsruhe Institute of Technology

description: This file contains all technological and biological replicates (i.e. from the same and different biological source, repspectively) that were performed with this particular toxin at this particular concentration. The Dye-Swap Designe was utilised.

hyb_protocol: 1) Removal of unincorporated nucleotides over Microcon 30 spin columns (Millipore, Bedford, MA). 2) The concentrated probes were hybridized to the microarray in 1xDIG Easy-Hyb buffer (Hoffmann-La Roche, Basel, CH) overnight at 42 C. 3) Cover slips were removed from the slides by flushing with 4xSSC. 4) Slides were washed in pre-warmed wash buffer 1 (2xSSC, 0.1% SDS) for 5 minutes at 42 C. 5) Washing in buffer 2 (0.1xSSC, 0.1% SDS) for 10 minutes at room temperature. 6) Washing in 0.1xSSC four times for 1 min at room temperature. 7) The slides were briefly dipped into 0.01xSSC at room temperature. 8) Centrifugation for 7 min at 800 rpm in an Eppendorf 5810R centrifuge.

scan_protocol: 1) Scanned on an GenePix 4000B dual-laser scanner from Molecular Devices 2) Both channels (532 nm for Cy3 and 635 nm for Cy5) were scanned in parallel 3) Data was stored as 16-bit TIFF files 4) The channels for Cy3 and Cy5 were balanced in each scan for approximately the same intensity profile. 5) Each array was scanned three times (low, medium and high scan) with different signal amplification factors (voltage settings of the photomultiplier tubes), but with the same laser power. 6) Raw data was retrieved with GenePix Pro 6.0 software from Axon Instruments . 7) Data processing was performed 8) The absolute intensity values span the range from 0 to 65536. 9) The scans were performed with a resolution of 10 um.

data_processing: 1) Raw data are retrieved with GenePix 2) Quality control on spot level 3) Local background correction. 4) Averaging of the two spots for each gene. 5) Consensus signals are calculated from low, medium and high scan based on a Least Squares Algorithm. 6) Log transformation. 7) locally weighted regression smoother (LOESS). 8) Scaling to a common MAD. 9) t-test 10) adjustment of p-values for multiplicity 11) Quality control on array level.

organism: Danio rerio

source_name: mRNA from 200-800 zebrafish embryos that were exposed to Galanthamine 72h

label_protocol: Labeled cDNA was synthesized from 1-2 ug mRNA using the Amersham direct cDNA labeling kit (Amersham Europe, Freiburg, Germany).

growth_protocol: as described in Westerfield 1993

extract_protocol: 1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany). 2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).

treatment_protocol: Wildtype AB or ABO strain zebrafish embryos were used for this study. 5 somite stage embryos were treated with 1mM Galanthamine hydrobromide (Sigma G1660) in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX). The control embryos were transferred to the same batch of embryo medium used to prepare galanthamine solution. At this concentration GAL causes myopathology without causing morbidity (Behra et. al.). The embryos were observed daily and the few dead embryos discarded to prevent fungal growth. The number of dead embryos in control vs. treated group was similar.

value: AB*,AB2O2,AB2O2 Golden and AB2O2 Leo

value: whole body mRNA

source_name: mRNA from 200-800 zebrafish embryos that were not exposed to a toxic environment


title: Atherogenic diet, male pig number 2189

source_name: male pig, AD group

value: Atherogenic diet (AD)


title: Atherogenic diet supplemented with grape extract, female pig number 2199


title: Atherogenic diet, female pig number 2188

source_name: female pig, AD group


title: Control diet, male pig number 2225

source_name: male pig, Control group

value: male

value: Control diet (CT)


title: M3-S1(0.5):N2 vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and N2-Cy5 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 0.5%

scan_protocol: Scan Power : 100 PMT Volts : 845 Pixel Size : 5 Laser on time : 27920 Laser Power : 2.21 Scan Date : 2008-08-20 Scan Temperature : 37.37 Scan Time : 16:35:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.5

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1120, 49960


title: M3-S1(0.1):N2 vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and N2-Cy5 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 715 Pixel Size : 5 Laser on time : 27748 Laser Power : 2.11 Scan Date : 2008-08-20 Scan Temperature : 34.08 Scan Time : 13:40:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 49960


title: Control diet, female pig number 2174

source_name: female pig, Control group

value: Peripheral blood mononuclear cells (PBMNCs)


title: Atherogenic diet, female pig number 2185


title: Control diet, female pig number 2180


title: M3-S1(0.005):N2 vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and N2-Cy5 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 648 Pixel Size : 5 Laser on time : 27688 Laser Power : 1.89 Scan Date : 2008-08-20 Scan Temperature : 31.88 Scan Time : 12:40:41 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005


title: M2-S4(0.005):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 669 Pixel Size : 5 Laser on time : 26741 Laser Power : 1.84 Scan Date : 2008-08-08 Scan Temperature : 31.27 Scan Time : 12:25:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005


title: M2-S4(0.1):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 762 Pixel Size : 5 Laser on time : 26798 Laser Power : 2.03 Scan Date : 2008-08-08 Scan Temperature : 33.74 Scan Time : 13:22:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1


title: M3-S1(1):N2 vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and N2-Cy5 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 918 Pixel Size : 5 Laser on time : 27812 Laser Power : 2.14 Scan Date : 2008-08-20 Scan Temperature : 35.88 Scan Time : 14:44:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1120, 49920


title: Control diet, male pig number 2194

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.


title: brain_14d_273 ug/L diazepam_replicate 3

city: Muttenz

first: Daniela

middle: Maria

last: Oggier

address: Gründenstrasse 40

department: School of Lifesciences

country: Switzerland

institute: University of Applied Sciences Northwestern Switzerland

description: Gene expression after 14 d exposure to 273 ug/L diazepam

hyb_protocol: Cy-3-labeled cRNA samples (1.65 µg) were mixed with Agilent blocking solution, subsequently fragmented randomly to 100-200 bp at 65 °C with fragmentation buffer and resuspended in hybridization buffer as provided by the gene expression hybridization Kit (Agilent Technologies). Target cRNA samples (100 µL) were hybridized to the Agilent Zebrafish 4x44K Gene Expression Microarray for 17 h at 65 °C. The hybridized arrays were then washed using Agilent GE wash buffers 1 and 2 according to the manufacturer's instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Agilent p/n G2565BA) at 5 μm resolution with the green photomultiplier tube set to 100% and a scan area of 61 x 21.6 mm.

data_processing: Image generation and feature extraction was performed using the Agilent Feature Extraction (FE) software version 9.5.3. Quality control was additionally considered before performing the statistical analysis. These included array hybridization pattern inspection: absence of scratches, bubbles, areas of non-hybridization, proper grid alignment, spike performance in controls with a linear dynamic range of 5 orders of magnitude and the number of green-feature non-uniformity outliers which should be below 100 for all samples.

source_name: Male zebrafish, 14 d, 273 ug/L diazepam, replicate 3

label_protocol: Total RNA samples (600 ng) were reverse-transcribed into double-strand cDNA in the presence of RNA poly-A controls with the Agilent One-Color RNA Spike-In Kit. Cy3 labeling and hybridization were performed according to the manufacturer's manual. After reverse-transcription of RNA into double-stranded cDNA, double-strand cDNA was in vitro transcribed into cRNA in the presence of Cy3 labeled nucleotides using a Low RNA Input Linear Amp Kit +Cy dye (Agilent Technologies, Basel, Switzerland). The Cy3-labeled cRNA was purified using an RNeasy mini kit (Qiagen, Basel, Switzerland), and quality and quantity was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. Only cRNA samples with a total cRNA yield higher than 2 µg and a dye incorporation rate between 9 pmol/µg and 20 pmol/µg were used for hybridization.

extract_protocol: Total RNA was extracted from male zebrafish brains using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). Total RNA concentrations were measured spectrophotometrically using a NanoDrop ND-1000 UV-VIS Spectrophotometer at 260 nm. The integrity of each RNA sample was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Basel, Switzerland). Only samples containing a 260/280 nm ratio between 1.8-2.1, a 28S/18S ratio between 1.5-2 and an RNA integrity number (RIN) > 8 were processed further.

treatment_protocol: The experimental setup consisted of four replicates of water controls and two diazepam doses. Twenty male zebrafish per replicate were held in 20-L stainless steel tanks in well-aerated exposure water. Fish were exposed for 14 d to the nominal concentrations of 273 ng/L and 273 μg/L diazepam, respectively. The lower concentration (273 ng/L) was assumed to represent the worst case environmental concentration, and 273 μg/L refers to the NOEC in the early life stages test (12). During the experiment fish survival, appearance and behavior were determined.   A 48 h static-renewal procedure was used to minimize handling stress for the fish. Thereby after 24 h, food remains and feces were removed by siphoning 1/3 of the water and replacement by new exposure water containing the appropriate diazepam concentrations. After 48 h, the water renewal procedure was repeated, but this time by replacing total tank water (20 L). The quality of the exposure water was continuously monitored by the oxygen concentration determination (>70%), the pH value (6.7-7.2) and the temperature (27±1 °C).

value: brain

tag: developmental stage

tag: age

value: adult

value: 273 ug/L diazepam


title: M2-S4(1):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA4 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 935 Pixel Size : 5 Laser on time : 26855 Laser Power : 2.14 Scan Date : 2008-08-08 Scan Temperature : 35.70 Scan Time : 14:18:28 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1


title: M2-S3(1):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 935 Pixel Size : 5 Laser on time : 26868 Laser Power : 2.16 Scan Date : 2008-08-08 Scan Temperature : 36.18 Scan Time : 14:31:10 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1


title: brain_14d_273 ug/L diazepam_replicate 2

source_name: Male zebrafish, 14 d, 273 ug/L diazepam, replicate 2


title: brain_14d_273 ug/L diazepam_replicate 4

source_name: Male zebrafish, 14 d, 273 ug/L diazepam, replicate 4


title: M2-S3(0.005):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 662 Pixel Size : 5 Laser on time : 26759 Laser Power : 1.93 Scan Date : 2008-08-08 Scan Temperature : 32.06 Scan Time : 12:42:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 18440


title: M3-S2(0.005):hcf-1(pk924) vs N2 (YA)

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy5 and N2-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 663 Pixel Size : 5 Laser on time : 27674 Laser Power : 1.89 Scan Date : 2008-08-20 Scan Temperature : 31.21 Scan Time : 12:25:46 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005


title: M2-S3(0.1):hcf-1(pk924) vs. daf-16(RX5);hcf-1(pk924) (YA)

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy5 and d16;hcf1-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 757 Pixel Size : 5 Laser on time : 26812 Laser Power : 2.07 Scan Date : 2008-08-08 Scan Temperature : 34.20 Scan Time : 13:35:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 18480