title: C.D2 +Fe  infected  vs. C.D2 +Fe

city: Porto

first: Maria

middle: Salome

last: Gomes

address: Rua do Campo Alegre 823

department: IBMC/ICBAS

country: Portugal

institute: Universidad do Porto

description: pool of five mice each dye swap

hyb_protocol: The microarrays were immersed at 42°C in 6xSSC/0,5%SDS/1%BSA for 40 min and subsequently washed extensively with ddH2O at room temperature. Prior to hybridization, the spotted PCR products were denatured by immersing the slides at 95°C in ddH2O for 2 min. Excess of liquid was removed from the slides by centrifuging them briefly at 715xg in a microtiter plate centrifuge (Z320, Hermle, Wehingen, Germany). Prior to hybridization, the purified Cy3 and Cy5 labeled cDNAs were mixed, 5 µg poly(dA) and 1 µg human Cot1 DNA (both Gibco Invitrogen Corp., Carlsbad, Ca, USA) were added and subsequently evaporated in a vacuum Concentrator 5301 (Eppendorf, Hamburg, Germany) at 60°C. The resulting pellet was dissolved in 12 µl hybridization buffer (50% formamide / 6xSSC / 0,5%SDS / 5x Denhardt) and denatured by incubating at 95°C for 2 min. The probe was then transferred onto the array under a 24x24 mm coverslip and incubated in a humid chamber (GeneMachines, San Carlos, CA, USA) containing 2xSSC drops for providing humidity. Hybridization was performed for 12h to 16h in a 42°C waterbath (GFL, Burgwedel, Germany). After hybridization the microarrays were washed in 0,1xSSC / 0,1%SDS for 10 min and twice with 0,1xSSC for 5 min (on an orbital shaker), followed by a brief immersion of the slides in ddH2O. Finally, the washed slides were dried by centrifuging them briefly at 715xg in a microtiter plate centrifuge (Z320, Hermle, Wehingen, Germany). All washing steps were performed at room temperature.

scan_protocol: All microarrays were scanned on a GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA). For each microarray individual laser power and photomultiplier settings were used, allowing all signals to remain in the linear range of the scanner. Separate scan images for Cy3 and Cy5 were produced

data_processing: Intensity values for each spot were calculated by subtraction of the local background surrounding the spot. All spots were used for the calculation of a linear regression line. The regression line’s parameters (offset and slope) were used for normalization. The data evaluation performed using custom bioinformatic toll called Iron Chip Evealuation package (ICEP). “ICEP” is a software package designed specifically for “iron chip” data analyzing. This package is able to use all advantages of the Iron Chip microarray design.The values in the Sample data tables have been processed in a dyeswap aware fashion so the ratio presented for the first direction hybridization has the ratio cy3/cy5 whereas the 2nd direction hyb is the cy5/cy3 ratio accounting for the dyeswap.

source_name: C.D2 +Fe infected

label_protocol: Fluorescent cDNA probes were synthesized from 5 µg total RNA using a linear mRNA amplification protocol, exactly as described in (http://cmgm.stanford.edu/pbrown/protocols/ampprotocol_3.html). 3µg of the T7 RNA polymerase amplified antisense RNA was subsequently subjected to a direct labeling reaction by incorporation of Cy3 fluorescent dyes using random primers

growth_protocol:
The BALB/c (NRAMP1-S) and C.D2 (NRAMP1-R) congenic mouse strains were bred and housed at the Instituto de Biologia Molecular e Celular (IBMC) animal facility. The animals were kept inside individually ventilated cages, bearing high efficiency particulate air (HEPA) filters and were fed sterilized food and water ad libitum. For the experimental treatments, 8-12 weeks old females were used. All animal experiments were carried out in compliance with the animal ethics guidelines of the institute, and the national and European regulations for the care and handling of laboratory animals
Mycobacterium avium strain 2447, forming smooth transparent (SmT) colonies, was isolated from an AIDS patient and was a gift from Dr. F. Portaels (Institute of Tropical Medicine, Antwerp, Belgium). Mycobacteria were grown to mid-log phase in Middlebrook 7H9 medium (Difco, Sparks, MD) containing 0.05% Tween 80 (Sigma, St. Louis, MO) at 37ºC. Bacteria were harvested by centrifugation, suspended in a small volume of saline containing 0.05% Tween 80, briefly sonicated to disrupt bacterial clumps, diluted and stored in aliquots at -70ºC until use

extract_protocol: Total RNA was extracted from snap frozen liver samples using the Qiagen (Hilden, Gerrmany) Rneasy Midi Kit according to the manufactur's specifications.

treatment_protocol:
Mice were infected intravenously, through a lateral tail vein, with 106 CFU of M. avium. Control animals received the same volume of saline. At the time points of interest, mice were sacrificed and blood and tissues were harvested for the different analysis. For bacterial quantification, the livers and spleens were aseptically collected and homogenized in a 0.05% Tween 80 solution in distilled water. Serial dilutions were plated into Middlebrook 7H10 agar medium and the plates were incubated at 37 ºC for 1 week, when the colonies were counted
To induce iron overload, mice were injected intraperitoneally with 10 mg of iron, as iron-dextran (Sigma). Control mice received an equivalent amount of dextran (Sigma) by the same route. Animals were infected two weeks after the iron-dextran treatment.   Iron overload was confirmed by quantifying liver and spleen non-heme iron by the bathophenanthroline method as previously described (Rodrigues et al., 2006)

value: Liver

tag: gender

value: female

tag: strain

source_name: C.D2 +Fe


title: CGH: Soy late maturity FN mutant R45C30p24adm vs. Reference

status: Public on Aug 02 2011

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

country: USA

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

scan_protocol: Slides were scanned on the GenePix4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer instructions (NimbleGen CGH User Guide Ver 5.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

molecule: genomic DNA

organism: Glycine max

source_name: FN mutant R45C30p24adm

label_protocol: 1ug of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 5.1.

extract_protocol: Qiagen DNeasy

tag: tissue

value: Leaf sample

tag: genotype

value: fast neutron mutant

tag: phenotype

value: Mutant shows late maturity.  Mutant was known as "LM03" in Bolon et al. (Plant Physiol. 156:240-253)

tag: cultivar

value: M92-220 background

source_name: FN pooled reference

value: Leaf samples

value: 30 pooled soybean fast neutron mutants


title: co-culture fed by 40µmol TCE_rep2

status: Public on Aug 01 2011

type: RNA

city: Urbana

first: Yujie

last: Men

address: 205 N Mathews Ave

institute: University of Illinois at Urbana-Champaign

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using the MAS5 algorithm and R statistical program . Each microarray was normalized by global scaling the signal intensities to a value of 2500.

label: biotin

molecule: total RNA

organism:
Nitratidesulfovibrio vulgaris str. Hildenborough
Dehalococcoides mccartyi 195

source_name: 195/DVH co-culture fed by low TCE concentration grown on 3rd day

label_protocol: One µg of cDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: 15 replicates of 100mL culture were grown to early exponential phase when 90% of the given amount of trichloroethene was dechlorinated. For strain 195 on 7th day, for co-culture fed by 78µmol TCE on 5th day, for co-culture fed by 40µmol TCE on 3rd day, and for tri-culture fed by 40µmol TCE on 3rd day.  500mL cells were collected by filtration as one biological replicate. Three biological replicates were prepared.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit (Qiagen,Valencia, CA) according to the manufacturer’s instructions. cDNA was synthesized according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

tag: bacteria

value: co-culture

tag: agent

value: TCE

tag: tce concentration

tag: time

value: 3rd day


title: C.D2 +Fe  vs. C.D2 +Fe  infected

description: pool of five mice each

organism: Mus musculus

tag: age


title: co-culture fed by 40µmol TCE_rep3

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: 14178312 - LUC repet2 vs V2TS-7 repet2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Determine the level of expression in transgenic plants expressing geminiviral gene silencing suppressors.

hyb_protocol: V2TS-7 repet2 Cy5 / LUC repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: V2TS-7 repet2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=MS+Kanamycine  hygrometry=not controlled  Temperature=22ºC  Light=16h light-8h darkness

extract_protocol: V2TS-7 repet2:16ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: original entry

value: arabidopsis thaliana (columbia)  mutant (v2 overexpressing line) -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: Columbia

value: V2 overexpressing line

value: whole plant

source_name: LUC repet2

extract_protocol: LUC repet2:26ug. (Qiagen_RNeasy.pdf)

value: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: wild type


title: CGH: Soy late maturity FN mutant R64C05p31adm vs. Reference

source_name: FN mutant R64C05p31adm

value: Mutant shows late maturity.  Mutant was known as "LM04" in Bolon et al. (Plant Physiol. 156:240-253)


title: BALB/c +Fe vs. BALB/c  +Fe infected

description: pool of five mice each

source_name: BALB/c +Fe

value: Liver

value: female

value: BALB/c

source_name: BALB/c  +Fe infected


title: C.D2 infected vs. C.D2

description: pool of five mice each dye swap

source_name: C.D3 infected


title: BALB/c infected +Fe vs. BALB/c +Fe

description: pool of five mice each dye swap

source_name: BALB/c +Fe infected

source_name: BALB/c  +Fe


title: CGH: Soy low seed oil, high seed raffinose, high seed sucrose FN mutant R60C52p28a04 vs. Reference

source_name: FN mutant R60C52p28a04

value: Leaf sample

value: fast neutron mutant

value: Mutant shows low seed oil, high seed raffinose, high seed sucrose.  Mutant was known as "PO04" in Bolon et al. (Plant Physiol. 156:240-253)


title: co-culture fed by 78µmol TCE_rep3

source_name: 195/DVH co-culture fed by high TCE concentration grown on 5th day

value: 5th day


title: co-culture fed by 40µmol TCE_rep1

value: co-culture


title: C.D2 vs. C.D2 infected

description: pool of five mice each

source_name: C.D2 infected


title: BALB/c infected vs. BALB/c

description: pool of five mice each dye swap

source_name: BALB/c infected

source_name: BALB/c


title: co-culture fed by 78µmol TCE_rep2

value: TCE


title: co-culture fed by 78µmol TCE_rep1


title: CGH: Soy late maturity FN mutant R32C17p18bdm vs. Reference

source_name: FN mutant R32C17p18bdm

value: Mutant shows late maturity.  Mutant was known as "LM01" in Bolon et al. (Plant Physiol. 156:240-253)

value: M92-220 background

value: Leaf samples

value: 30 pooled soybean fast neutron mutants


title: 980307T

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

hyb_protocol: RNA samples were hybridized to Agilent Human miRNA Microarrays (V2) representing 723 human and 76 human viral miRNAs.

scan_protocol: scanned with the Agilent DNA Microarray Scanner (Model G2565BA) miRNA expression values were normalized against background signals using Feature Extraction Software (Agilent).

data_processing: The miRNA data was also subjected to a log 10 transformation followed by median centering across probes, prior to actual analysis.

organism: Homo sapiens

label_protocol: standard Agilent protocol

extract_protocol: Total RNA was extracted from primary tissues and cell lines using the miRVana miRNA Isolation Kit (Ambion, Inc, Austin,TX,USA) according to manufacturer’s instructions.

value: gastric Tumor tissue


title: BALB/c vs. BALB/c infected

description: pool of five mice each


title: CGH: Soy late maturity FN mutant R36C59p19ddm vs. Reference

source_name: FN mutant R36C59p19ddm

value: Mutant shows latematurity.  Mutant was known as "LM02" in Bolon et al. (Plant Physiol. 156:240-253)


title: CGH: Soy early maturity FN mutant R11C04DSCW08YB#1 vs. Reference

source_name: FN mutant R11C04DSCW08YB#1

value: Mutant shows early maturity.  Mutant was known as "EM02" in Bolon et al. (Plant Physiol. 156:240-253)

source_name: FN pooled reference


title: strain 195_rep2

organism: Dehalococcoides mccartyi 195

source_name: strain 195, high TCE concentration, grown on 7th day

value: pure culture

value: 7th day


title: strain 195_rep1


title: strain 195_rep3


title: 980305T


title: 980305N

value: gastric normal tissue


title: 980211T


title: 980307N


title: 980255T


title: 980252N


title: Control sample #47

city: London

first: Matthew

last: Burton

address: Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered, transformed (vst) and normalised using quantile normalisation with the lumi package in R. The data were filtered before transformation and normalisation. The filter selected probes with at least one sample successfully detected (detection p-value <0.01 for at least one sample).

label: biotine

source_name: conjunctival surface swab

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

extract_protocol: Total RNA was extracted from conjunctival swabs that had been stored in RNAlater, using the Rneasy MICRO kit (Qiagen) with DNAse treatment - as per manufacturers instructions.

tag: disease state

value: Control


title: Trachomatious conjunctival scarring sample #552

value: Trachomatious conjunctival scarring without inflammation


title: 980184T


title: CGH: Soy early maturity FN mutant R23C06DSCW08YB#1vs. Reference

source_name: FN mutant R23C06DSCW08YB#1

value: Leaf sample

value: fast neutron mutant

value: Mutant shows early maturity.  Mutant was known as "EM03" in Bolon et al. (Plant Physiol. 156:240-253)


title: 980184N


title: Trachomatious conjunctival scarring with inflamation sample #70


title: Trachomatious conjunctival scarring sample #609


title: 980211N


title: CGH: Soy early maturity FN mutant R09C04DSCW08YB#1 vs. Reference

source_name: FN mutant R09C04DSCW08YB#1

value: Mutant shows early maturity.  Mutant was known as "EM01" in Bolon et al. (Plant Physiol. 156:240-253)


title: Trachomatious conjunctival scarring sample #487


title: 980252T


title: 980161T


title: Trachomatious conjunctival scarring sample #468


title: 980255N


title: Trachomatious conjunctival scarring sample #614


title: 980148T


title: 980148N


title: Trachomatious conjunctival scarring with inflamation sample #440


title: Control sample #27


title: Trachomatious conjunctival scarring with inflamation sample #272


title: 14178316 - LUC repet3 vs V2TS-7 repet3

hyb_protocol: V2TS-7 repet3 Cy5 / LUC repet3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: V2TS-7 repet3

extract_protocol: V2TS-7 repet3:12ug. (Qiagen_RNeasy.pdf)

value: arabidopsis thaliana (columbia)  mutant (v2 overexpressing line) -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: Columbia

value: V2 overexpressing line

value: whole plant

source_name: LUC repet3

extract_protocol: LUC repet3:21ug. (Qiagen_RNeasy.pdf)

value: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001):boyes:1.10,1.12

value: wild type


title: Trachomatious conjunctival scarring sample #23


title: Trachomatious conjunctival scarring sample #99


title: 980097T

value: gastric Tumor tissue


title: 980056N


title: 980048N


title: 980048T


title: 980035T


title: Trachomatious conjunctival scarring sample #505


title: 980095T


title: 980035N


title: 980028T


title: Trachomatious conjunctival scarring sample #486


title: Trachomatious conjunctival scarring sample #2


title: Trachomatious conjunctival scarring with inflamation sample #180


title: Trachomatious conjunctival scarring with inflamation sample #100


title: Trachomatious conjunctival scarring with inflamation sample #176


title: 980028N


title: 980021T


title: Trachomatious conjunctival scarring sample #624


title: 980021N


title: Control sample #29 C-29


title: 980011T


title: Control sample #36


title: 980025N


title: Trachomatious conjunctival scarring with inflamation sample #195


title: Control sample #40


title: Trachomatious conjunctival scarring with inflamation sample #238


title: Trachomatious conjunctival scarring sample #656


title: Trachomatious conjunctival scarring with inflamation sample #41


title: Control sample #31


title: 970024N


title: 980002N


title: 9614-1474N


title: 970001N


title: 8762-2942N


title: 8350-7354N


title: 980011N


title: 8350-7354T


title: 8297-3565T


title: Control sample #39


title: Control sample #22 C-22


title: 980002T


title: Trachomatious conjunctival scarring with inflamation sample #406


title: Control sample #42


title: Trachomatious conjunctival scarring with inflamation sample #384


title: Trachomatious conjunctival scarring with inflamation sample #76


title: Trachomatious conjunctival scarring sample #783


title: 8762-2942T


title: Control sample #43


title: 7726-3387T


title: 7662-9543T


title: 7726-3387N


title: 7555-4796T


title: 6525-6293T


title: 5768-9477T


title: Trachomatious conjunctival scarring with inflamation sample #191


title: 6166-9256T


title: Control sample #24


title: 4937-5233T


title: Control sample #32


title: Trachomatious conjunctival scarring sample #86


title: Control sample #37


title: Control sample #34


title: 4714-9013T


title: Trachomatious conjunctival scarring sample #456


title: 4714-9013N


title: 4937-5233N


title: 3887-7042N


title: 3726-2942T


title: 3726-2942N


title: Trachomatous trichiasis with inflammation sample #30

value: Trichiasis with inflammation


title: Trachomatous trichiasis with inflammation sample #23


title: Trachomatous trichiasis with inflammation sample #6


title: Trachomatous trichiasis with inflammation sample #9


title: Trachomatous trichiasis with inflammation sample #29


title: Trachomatous trichiasis with inflammation sample #7


title: 4365-8255N


title: Trachomatous trichiasis with inflammation sample #20


title: 3123-1321T


title: 2026-3644T


title: Trachomatous trichiasis with inflammation sample #5


title: Trachomatous trichiasis with inflammation sample #8


title: 3166-1621N


title: 3123-1321N


title: Trachomatous trichiasis with inflammation sample #10


title: 2108-0055T


title: Trachomatous trichiasis sample #31

value: Trichiasis without inflammation


title: Trachomatous trichiasis sample #26


title: Trachomatous trichiasis with inflammation sample #11


title: Trachomatous trichiasis with inflammation sample #4


title: Trachomatous trichiasis with inflammation sample #2


title: 2108-0055N


title: Trachomatous trichiasis sample #22


title: 20020999T


title: 20021007T


title: 20020846T


title: Trachomatous trichiasis sample #27


title: 20020999N


title: Trachomatous trichiasis sample #16


title: 20020720N


title: 20020455N


title: Trachomatous trichiasis sample #25


title: 20020720T


title: Trachomatous trichiasis sample #17


title: Trachomatous trichiasis sample #19


title: Trachomatous trichiasis sample #18


title: 20020448T


title: Trachomatous trichiasis sample #14


title: Trachomatous trichiasis sample #13


title: 20020448N


title: 20020195N


title: Trachomatous trichiasis sample #15


title: Trachomatous trichiasis sample #1


title: 20020032T


title: Control sample #8


title: 20020032N


title: 20020011T


title: 20010229T


title: Trachomatous trichiasis sample #12


title: 20010229N


title: 20020011N


title: Control sample #7


title: 0943-2729N


title: Control sample #4


title: Control sample #3


title: 2026-3644N


title: ASK_TTA-TTA [SIQ3]

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

country: Norway

institute: Norwegian University of Life Sciences

hyb_protocol: Custom printed Agilent oligonucleotide microarrays in the 4x44 format were hybridized with Cy3 labled cRNA according to the manufacturerÕs protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.7.1.1) according to Agilents GE1_107_Sep09 protocol)

data_processing: txt files produced by Feature Extraction were analyzed using the statistical software R with Bioconductor package limma. Signal intensities  (background corrected: gProcessed Signal) of duplicated spots were averaged and Control spots removed. Signal Intensities were quantile-normalized and log2 transformed.

organism: Salmo salar

source_name: ASK (Atlantic salmon kideney) cell culture (ATCC: CRL-2747)

label_protocol: The synthesis of cRNA was performed using the Quick Amp Labeling Kit, One color (Agilent p/n 5190-0442), according to manufacturerÕs protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

extract_protocol: RNA was extracted using QUIAzol followed by RNeasy column cleanup (Qiagen) according to the manufacturers protocols.

tag: cell line

value: ASK (Atlantic salmon kideney) cell culture (ATCC:CRL-2747)

tag: pretreatment

value: TTA

tag: treatment


title: ASK_TTA-ctr [SIQ3]

value: Control


title: Control sample #29


title: Control sample #25


title: Control sample #21


title: Control sample #17


title: Control sample #15


title: Control sample #22


title: 0521-8170T


title: ASK_TTA-TTAIC [SIQ3]

value: TTA+polyIC


title: ASK_ctr-ctr [SIQ3]


title: Control sample #1


title: ASK_ctr-IC [SIQ3]

value: polyIC


title: ASK_ctr-TTA [SIQ3]


title: Control sample #23


title: ASK_TTA-IC [SIQ3]


title: ASK_ctr-TTAIC [SIQ3]


title: 0521-8170N

value: gastric normal tissue


title: Control sample #12


title: E3CTR6

description: TODO

hyb_protocol: Custom printed Agilent oligonucleotide microarrays in the 4x44 format were hybridized with Cy3 labled cRNA according to the manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.7.1.1 according to Agilents GE1_107_Sep09 protocoll)

data_processing: txt files produced by Feature Extraction were analyzed using the statistical software R with Bioconductor package limma. Signal intensities  (background corrected: gProcessed Signal) of duplicated spots were averaged and Control spots removed. Signal Intensities were quantilenormalized and log2 transformed.

source_name: Heart ventricle

label_protocol: The synthesis of cRNA was performed using the Quick Amp Labeling Kit, One color (Agilent p/n 5190-0442), according to manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 5.7)

extract_protocol: Tissue samples were stored at -80. Total RNA was extracted by sample homogenization in QUIAzol followed by RNeasy column cleanup (Qiagen) according to the manufacturers protocols.

value: Heart ventricle

tag: diet

tag: sampling time point


title: E3CTR5

description: TODO


title: E3CTR4

description: TODO


title: E3CTR3

description: TODO


title: Control sample #19


title: Naïve.6

city: Seattle

first: Cameron

last: Turtle

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: Donor 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader.

data_processing:
The resulting TIFF images were processed using GenomeStudio Gene Expression Module (GEM) software. Data quality was assessed using the Control Summary feature in GenomeStudio GEM. For a given analysis set, a GenomeStudio Probe-level Final Report was generated by combining the Sample Probe Profile and Control Probe Profile tables. The Final Report comprising the full dataset was initially processed using the Bioconductor package lumi by employing a background correction estimate and quantile normalization.  A small adjustment (i.e. 20 counts) was made to the entire dataset to make all intensity signals non-negative and these values were log2-transformed. The dataset was initially filtered using the ‘shorth’ function of the Bioconductor package genefilter, resulting in retention of 31,084 of 48,802 original probes. Each pairwise comparison was further filtered by discarding probes whose signal intensity was less than a defined signal “noise floor” across all arrays in the data subset. This was achieved by calculating the median of the ‘negative control’ probe signals for each array, averaging these values, and setting the noise floor as 3 times this average.
Differential gene expression was determined using the Bioconductor package limma, and a false discovery rate (FDR) method applied to correct for multiple testing. Significant differential gene expression was defined by a log2 ratio > 0.585 (± 1.5-fold) and FDR (adjusted p value) < 0.05.

label: Biotin

source_name: Naïve

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

growth_protocol: T cell subsets were freshly isolated from healthy adults.

extract_protocol: RNeasy Plus Minikit (Qiagen)

treatment_protocol: Effluxing CD161hi and non-effluxing CD161lo CD8+ TCM and TEM subsets were purified using magnetic bead separation and cell sorting to achieve >98% purity. CD8+ T cells were positively selected using CD8 Microbeads (Miltenyi Biotec, Germany), loaded with Rh123 (Sigma, St. Louis, MO) and cultured for 30 min to allow Rh123 efflux, then labeled with fluorochrome-conjugated antibodies to CD4, CD16, TCRγδ, Vα24, CD8, CD95, CD62L and CD161. CD161hi and CD161lo TCM and TEM subsets were sort-purified on a FACS ARIA equipped with 405 nm, 488 nm and 633 nm lasers (BD Biosciences). CD161hi TCM and TEM subsets were identified as CD62L+/Rh123lo/CD161hi and CD62L-/Rh123lo/CD161hi events, respectively, in the CD4-/CD16-/TcRγδ-/Vα24-/CD8+/CD95+ population.  CD161lo TCM and TEM subsets were identified as CD62L+/Rh123hi/CD161int/neg and CD62L-/Rh123hi/CD161int/neg events, respectively, in the CD4-/CD16-/TcRγδ-/Vα24-/CD8+/CD95+ population. Naive CD8+ T cells were identified as CD4-/CD16-/TcRγδ-/Vα24-/CD8+/CD95-/CD62Lhi events.

tag: donor

value: Healthy adult

tag: cell type

value: Peripheral blood T cells

tag: t cell subset

value: Naïve


title: Naïve.4

description: Donor 4


title: Naïve.5

description: Donor 5


title: E3CTR2

description: TODO

tag: tissue


title: E3CTR1

description: TODO


title: Naïve.3

description: Donor 3


title: Naïve.2

description: Donor 2


title: E3TTA6

description: TODO


title: E3TTA4

description: TODO


title: E3TTA3

description: TODO


title: E3TTA5

description: TODO


title: Naïve.1

description: Donor 1


title: E3TTA1

description: TODO

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.5.1.1) according to Agilents GE1_105_Dec08 protocoll)


title: Emlo.4

description: Donor 4

source_name: CD161lo effector memory

value: CD161lo effector memory


title: Emlo.6

description: Donor 6


title: Emlo.1

description: Donor 1


title: Emlo.3

description: Donor 3


title: Emlo.5

description: Donor 5


title: E3TTA2

description: TODO


title: ko6

city: Atlanta

first: Julia

last: Bugrysheva

state: GA

address: 1510 Clifton Rd Rm 3076

department: Department of Microbiology

institute: Emory Univeristy

description: Biological replicate 3 of 3, stk mutant JRS2516

hyb_protocol: Probes containing 50pmol Cy3 in the test cDNA (sample form the wild type or the mutants) and 50pmol Cy5 in the reference cDNA (pooled samples for the wild type and mutant from the same bilological replicates) were mixed and resuspended in 50ul hybridization buffer (Ambion) and hybridized to array slides overnight at 42C. Slides were washed and dried before scanning.

scan_protocol: Arrays were scanned on a GenePix 4000A scanner (Axon insruments). Images were quantified  using GenePix Pro 3.0 software.

data_processing: The intensity for each spot in each array was adjusted so the sum of Cy3 equals to the sum of Cy5 for this array, then the ratio Cy3/Cy5 that represents test/reference was calculated for each spot.  These ratios were averaged for every gene. Only the genes represented in the strain MGAS5005 were selected for further analysis. The average Cy3/Cy5 values for each gene were divided by the sum of Cy3/Cy5 values for all the genes on this array to normalize the expression values between arrays.  Normalized data were then log2 transformed and statistical analysis was performed using Significance Analysis of Microarray software.

organism: Streptococcus pyogenes

source_name: stk mutant

label_protocol: Labeled cDNA probes were generated from 10ug total RNA using the FairPlayIII Microarray Labeling Kit (Agilent Technologies) and Cy3 and Cy5 mono-reactive dyes (GE Healthcare Biosciences) as recommended by the manufacturers.

growth_protocol: Cells were collected from triplicate mid-exponential phase cultures of strains MGAS2221 and JRS2516 grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY) at 37C.

extract_protocol: RNA was purified using CsCl2 (McIver and Scott 1997), and contaminated DNA was removed with the Turbo DNA-free kit (Ambion).

tag: strain

tag: genotype/variation

value: stk mutant

source_name: pooled RNA for the wild type and stk mutant

value: MGAS2221 and JRS2516


title: Emlo.2

description: Donor 2


title: ko4

description: Biological replicate 2 of 3, stk mutant JRS2516


title: E2CTR6

description: TODO


title: ko5


title: Emhi.6

description: Donor 6

source_name: CD161hi effector memory

value: CD161hi effector memory


title: Emhi.5

description: Donor 5


title: Emhi.3

description: Donor 3


title: pH 5.8 16h rep. D / pH 5.8 31h rep. D

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

department: R&D

country: Finland

institute: Valio Ltd

hyb_protocol: The labeled cDNA samples were hybridized to microarrays following Agilent’s procedure titled “Two-Color Microarray-Based Gene Expression Analysis.” For each microarray, 825 ng of cyanine 3-labeled cDNA and 825 ng of cyanine 5-labeled cDNA were mixed with 11 µl of 10X GE Blocking Agent and 2.2 µl of 25X Fragmentation Buffer. Volume of this fragmentation mix was brought to 55 µl with nuclease-free water and mix was incubated at 60°C for exactly 30 minutes. After incubation, fragmentation reaction was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer, mixed gently and centrifuged for one minute at RT at 15800 × g. 100 µl of hybridization sample was loaded onto an array and hybridized at 65°C for 17 hours at 10 rpm with Agilent hybridization oven. Microarrays were washed twice with GE Wash Buffer 1 for one minute at RT and once with prewarmed (37°C) GE Wash Buffer 2 for one minute.

scan_protocol: Immediately after washing, microarrays were scanned at 5 µm resolution with a GenePix 4200 AL scanner (Axon Instruments) and stored as TIFF images. The fluorescence intensities were quantified and addressed to genomic ORFs with GenePix Pro 6.0 software (Axon Instruments / Molecular Devices Corp.). Microarray image analysis and feature detection were performed using GenePix Pro 6.0 software with default parameters, and results were further improved manually.

data_processing: Analyses were performed with the Bioconductor package for statistical analysis using the R programming language (Gentleman et al. 2004). The data were preprocessed with limma (Smyth and Speed 2003). The foreground and background median intensity estimates were corrected for the background using the normexp-function (offset set to 50) (Ritchie et al. 2007), normalized within arrays using loess (100 iterations, suspicious spots and probe sequences matching multiple hits or borders of the coding regions were down weight to zero, and intergenic probe sequences were down weight to 0.1) (Smyth and Speed 2003) and normalized between arrays using quantile normalization (Yang and Thorne 2003). Gene expression ratios were obtained by taking the average over the log2-transformed expression ratios of features describing the same gene and matching a single genetic coding locus. Expression ratios between conditions were calculated using linear models implemented in limma (Smyth 2004). Gene expression ratios were calculated for 2798 genes out of the total 2944 genes predicted to be encoded by the genome (95% coverage).

organism: Lacticaseibacillus rhamnosus GG

source_name: Total RNA at pH 5.8 time point 31h replicate D

label_protocol: Five micrograms of RNA were reverse transcribed to cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s protocol except that 6 µg of random primers (Invitrogen, 48190-011) were used instead of anchored oligo(dT)20 primers and random hexamers. The cDNA was fluorescently labeled using Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences) and purified with a column included in the SuperScript Indirect cDNA Labeling System kit.

growth_protocol: Bacterial cells were grown in whey medium in bioreactor at 37 °C. pH was maintained constant either at 5.8 or 4.8.

extract_protocol: One to four milliliters of bacterial culture were mixed with 2–8 mL of RNAprotect Bacteria reagent (Qiagen) and handled according to the manufacturer’s instructions. The cell pellets were stored at –70°C for subsequent RNA extraction. Cells were lysed with 10 mg/mL lysozyme (Amresco), 3 mg/mL proteinase K (Sigma-Aldrich), and 100 U of mutanolysin (Sigma-Aldrich) at 37°C for 30 minutes. The suspension was supplemented with 1 mL of preheated (65°C) TRIzol reagent (Invitrogen) and vortexed for 3 minutes. After incubation at RT for 5 minutes, the cell lysate was homogenized in a MagNA Lyser instrument (Roche) with <106 µm glass beads (Sigma-Aldrich) for four 30 s cycles at 6000 rpm. Between each cycle, the cells were chilled on ice for 1 minute. Cell debris was removed by centrifugation (12000 × g at 4°C for 15 min), and the lysate was extracted with 200 µl of chloroform by vortexing for 15 s. After incubation at RT for 3 min, the phases were separated by centrifugation (12000 × g at 4°C for 15 min). The aqueous phase was mixed with 500 µl of 80% ethanol for total RNA purification with an RNeasy Mini Kit (Qiagen). During RNA purification, DNA was removed using RNase-Free DNase (Qiagen) as described in the manual.

value: GG

tag: medium ph

source_name: Total RNA at pH 5.8 time point 16h replicate D


title: pH 5.8 12h rep. D / pH 4.8 12h rep. D

source_name: Total RNA at pH 5.8 time point 12h replicate D

source_name: Total RNA at pH 4.8 time point 12h replicate D


title: ko3


title: pH 5.8 20h rep. D / pH 5.8 31h rep. D

source_name: Total RNA at pH 5.8 time point 20h replicate D


title: pH 5.8 12h rep. A / pH 4.8 12h rep. A

source_name: Total RNA at pH 5.8 time point 12h replicate A

source_name: Total RNA at pH 4.8 time point 12h replicate A


title: pH 4.8 31h rep. A / pH 5.8 31h rep. A

source_name: Total RNA at pH 4.8 time point 31h replicate A

source_name: Total RNA at pH 5.8 time point 31h replicate A


title: pH 4.8 31h rep. D / pH 5.8 31h rep. D

source_name: Total RNA at pH 4.8 time point 31h replicate D


title: pH 5.8 12h rep. C / pH 4.8 12h rep. C

source_name: Total RNA at pH 4.8 time point 12h replicate C

source_name: Total RNA at pH 5.8 time point 12h replicate C


title: pH 5.8 31h rep. C / pH 4.8 31h rep. C

source_name: Total RNA at pH 5.8 time point 31h replicate C

source_name: Total RNA at pH 4.8 time point 31h replicate C


title: pH 5.8 16h rep. D / pH 5.8 20h rep. D


title: pH 5.8 12h rep. D / pH 5.8 31h rep. D


title: Emhi.4

description: Donor 4


title: ko2

description: Biological replicate 1 of 3, stk mutant JRS2516

source_name: stk mutant


title: Emhi.2

description: Donor 2


title: pH 5.8 12h rep. D / pH 5.8 20h rep. D


title: ko1

source_name: pooled RNA for the wild type and stk mutant


title: Trachomatous trichiasis sample #21

source_name: conjunctival surface swab


title: wt6

description: Biological replicate 3 of 3, wild type MGAS2221

source_name: wild type

value: wild type


title: Emhi.1

description: Donor 1

source_name: CD161hi effector memory


title: pH 5.8 12h rep. D / pH 5.8 16h rep. D

source_name: Total RNA at pH 5.8 time point 12h replicate D

source_name: Total RNA at pH 5.8 time point 16h replicate D


title: wt5


title: pH 5.8 20h rep. C / pH 5.8 31h rep. C

source_name: Total RNA at pH 5.8 time point 20h replicate C


title: pH 5.8 4h rep. D / pH 5.8 16h rep. D

source_name: Total RNA at pH 5.8 time point 4h replicate D


title: pH 5.8 4h rep. D / pH 5.8 12h rep. D


title: pH 5.8 16h rep. C / pH 5.8 31h rep. C

source_name: Total RNA at pH 5.8 time point 16h replicate C


title: pH 5.8 16h rep. C / pH 5.8 20h rep. C


title: pH 5.8 4h rep. D / pH 5.8 20h rep. D

source_name: Total RNA at pH 5.8 time point 20h replicate D


title: wt4

description: Biological replicate 2 of 3, wild type MGAS2221


title: pH 5.8 4h rep. C / pH 5.8 20h rep. C

source_name: Total RNA at pH 5.8 time point 4h replicate C


title: pH 5.8 4h rep. D / pH 5.8 31h rep. D

source_name: Total RNA at pH 5.8 time point 31h replicate D


title: pH 5.8 4h rep. C / pH 5.8 31h rep. C


title: pH 5.8 12h rep. C / pH 5.8 31h rep. C


title: Cmlo.6

description: Donor 6

source_name: CD161lo central memory

value: CD161lo central memory


title: wt2

description: Biological replicate 1 of 3, wild type MGAS2221


title: wt3


title: wt1


title: pH 5.8 12h rep. C / pH 5.8 20h rep. C

source_name: Total RNA at pH 5.8 time point 12h replicate C


title: pH 5.8 12h rep. C / pH 5.8 16h rep. C


title: pH 5.8 4h rep. C / pH 5.8 12h rep. C


title: Cmlo.5

description: Donor 5


title: pH 5.8 12h rep. A / pH 5.8 20h rep. A

source_name: Total RNA at pH 5.8 time point 20h replicate A

source_name: Total RNA at pH 5.8 time point 12h replicate A


title: pH 5.8 16h rep. A / pH 5.8 20h rep. A

source_name: Total RNA at pH 5.8 time point 16h replicate A


title: pH 5.8 20h rep. A / pH 5.8 31h rep. A

source_name: Total RNA at pH 5.8 time point 31h replicate A


title: Cmlo.4

description: Donor 4


title: pH 5.8 16h rep. A / pH 5.8 31h rep. A


title: pH 5.8 12h rep. A / pH 5.8 31h rep. A


title: pH 5.8 4h rep. C / pH 5.8 16h rep. C


title: Cmlo.3

description: Donor 3


title: Cmlo.2

description: Donor 2


title: pH 5.8 4h rep. A / pH 5.8 20h rep. A

source_name: Total RNA at pH 5.8 time point 4h replicate A


title: pH 5.8 4h rep. A / pH 5.8 31h rep. A


title: Cmlo.1

description: Donor 1


title: Cmhi.5

description: Donor 5

source_name: CD161hi central memory

value: CD161hi central memory


title: pH 5.8 4h rep. A / pH 5.8 12h rep. A


title: Cmhi.6

description: Donor 6


title: pH 5.8 4h rep. A / pH 5.8 16h rep. A


title: pH 5.8 12h rep. A / pH 5.8 16h rep. A


title: Cmhi.4

description: Donor 4


title: pH 4.8 12h rep. D / pH 4.8 31h rep. D

source_name: Total RNA at pH 4.8 time point 12h replicate D

source_name: Total RNA at pH 4.8 time point 31h replicate D


title: Cmhi.3

description: Donor 3


title: pH 4.8 20h rep. D / pH 4.8 31h rep. D

source_name: Total RNA at pH 4.8 time point 20h replicate D


title: pH 4.8 16h rep. D / pH 4.8 20h rep. D

source_name: Total RNA at pH 4.8 time point 16h replicate D


title: pH 4.8 16h rep. D / pH 4.8 31h rep. D


title: Cmhi.1

description: Donor 1


title: pH 4.8 12h rep. D / pH 4.8 20h rep. D


title: pH 4.8 4h rep. D / pH 4.8 20h rep. D

source_name: Total RNA at pH 4.8 time point 4h replicate D


title: 300 Min Treated Cy3 vs. Control Cy5 Rep. 2

city: Braunschweig

first: Michael

last: Reck

address: Inhoffenstr. 7

department: Microbial Communication

country: Germany

institute: Helmholtz Centre for Infection Research

description: 300 Min DyeSwap 2/2, Repl. 2

hyb_protocol: 760 ng of each Cy3- and Cy5 labelled RNA was fracmented and hybridised to the microarray at 65°C for 16 h using the Agilent Hybridisation Chamber and Agilent Hybridisation Kit according to the manufacturer`s instructions.

scan_protocol: the array was scanned using the Agilent DNA Microarray Scanner at 5 µm resolution and the raw data were extracted using Agilent Feature Extraction software (V9.5)

data_processing: The data were processed by Bioconductor packages written in R language (http://www.r-project.org). The linear models for microarray analysis (LIMMA) package was used for background correction, Loess normalisation of the two chanels of one array, quantile-normalisation between different arrays and identification of differentially expressed genes.

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans, untreated, 300 min

label_protocol: RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany)

growth_protocol: biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24 well polystyrene plates (Greiner, Germany), than the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml)

extract_protocol: total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)

treatment_protocol: biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment

value: untreated

value: biofilm

tag: genotype

value: wildtype

tag: time point

value: 300 min

source_name: Streptococcus mutans, treated, 300 min

value: treated


title: pH 4.8 4h rep. D / pH 4.8 31h rep. D

tag: time


title: 300 Min Treated Cy3 vs. Control Cy5 Rep. 3

description: 300 Min DyeSwap 2/2, Repl. 3


title: 300 Min Treated Cy5 vs. Control Cy3 Rep. 3

description: 300 Min DyeSwap 1/2, Repl. 3


title: pH 4.8 4h rep. D / pH 4.8 16h rep. D


title: wild_tumor_78k

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Affymetrix System Manual

scan_protocol: Refer to the Affymetrix System Manual

data_processing: Raw scan data were normalized with the use of RMA algorithm, based on Core exons' signal intensities using Expression Console software ver.1.1 (Affymetrix).

source_name: mouse hepatocellular carcinoma, DEN-treated, KLF6 +/+

label_protocol: Refer to the Affymetrix System Manual

extract_protocol: Using frozen non-tumor liver and hepatocellular carcinoma tissues, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: KLF6 +/- mice were previously generated by homologous recombination in which exon 2 was targeted using an 11-kb targeting construct, and replaced with neomycin/lacZ cassette. After selection with neomycin, the ES clones were injected into C57BL/6 mouse blastocysts and implanted into pseudo pregnant females; two lines of KLF6 +/- mice were generated from the resulting chimeric animals (Blood 107;1357, Oncogene 26;4428).  Whereas KLF6 -/- mice are embryonic lethal, KLF6 +/- animals had no demonstrable abnormalities in the absence of any stressor. Male KLF6 +/- mice were bred with wild type C57BL/6 to generate mixed litters of KLF6 +/- and KLF6 +/+ animals. Progeny were genotyped using PCR-amplified tail DNA, using primers as previously described (Oncogene 26;4428). Amplified fragments were separated on a 2.5% agarose gel, revealing bands of ~200 bp (wild type KLF6) and ~100 bp (Neo), as expected.  At 2 weeks of age, KLF6 +/+ and KLF6 +/- mice were injected intraperitoneally with either a single dose of diethyl nitrosamine (DEN), 5 µg/g body weight in 100 µl of saline, or vehicle alone. Vehicle and DEN-treated mice were maintained on standard chow, and then sacrificed 3, 6 or 9 months later.  At the time of sacrifice the animals were weighed, and blood and liver samples were harvested for analysis and tumor quantification.

tag: tissue type

value: hepatocellular carcinoma


title: wild_tumor_79k


title: pH 4.8 12h rep. D / pH 4.8 16h rep. D


title: pH 4.8 16h rep. C / pH 4.8 20h rep. C

source_name: Total RNA at pH 4.8 time point 16h replicate C

source_name: Total RNA at pH 4.8 time point 20h replicate C


title: wild_tumor_75k


title: Cmhi.2

description: Donor 2

value: Healthy adult


title: pH 4.8 12h rep. C / pH 4.8 20h rep. C

source_name: Total RNA at pH 4.8 time point 12h replicate C


title: pH 4.8 16h rep. C / pH 4.8 31h rep. C

source_name: Total RNA at pH 4.8 time point 31h replicate C


title: wild_tumor_41k


title: 300 Min Treated Cy5 vs. Control Cy3 Rep. 2

description: 300 Min DyeSwap 1/2, Repl. 2


title: 300 Min Treated Cy3 vs. Control Cy5 Rep. 1

description: 300 Min DyeSwap 2/2, Repl. 1


title: pH 4.8 12h rep. C / pH 4.8 31h rep. C


title: wild_liver_78n

source_name: mouse liver, DEN-treated, KLF6 +/+

value: liver


title: wild_liver_75n


title: 120 Min Treated Cy3 vs. Control Cy5 Rep. 1

description: 120 Min DyeSwap 2/2, Repl. 1

source_name: Streptococcus mutans, untreated, 120 min

value: 120 min

source_name: Streptococcus mutans, treated, 120 min


title: wild_liver_79n


title: wild_liver_41n


title: 120 Min Treated Cy3 vs. Control Cy5 Rep. 2

description: 120 Min DyeSwap 2/2, Repl. 2


title: pH 4.8 12h rep. C / pH 4.8 16h rep. C


title: pH 4.8 20h rep. C / pH 4.8 31h rep. C


title: 120 Min Treated Cy5 vs. Control Cy3 Rep. 2

description: 120 Min DyeSwap 1/2, Repl. 2


title: pH 4.8 4h rep. D / pH 4.8 12h rep. D


title: 300 Min Treated Cy5 vs. Control Cy3 Rep. 1

description: 300 Min DyeSwap 1/2, Repl. 1


title: hetero_tumor_58k

source_name: mouse hepatocellular carcinoma, DEN-treated, KLF6 +/-


title: 120 Min Treated Cy5 vs. Control Cy3 Rep. 1

description: 120 Min DyeSwap 1/2, Repl. 1


title: pH 4.8 4h rep. C / pH 4.8 12h rep. C

source_name: Total RNA at pH 4.8 time point 4h replicate C


title: pH 4.8 20h rep. A / pH 4.8 31h rep. A

source_name: Total RNA at pH 4.8 time point 20h replicate A

source_name: Total RNA at pH 4.8 time point 31h replicate A


title: 60 Min Treated Cy3 vs. Control Cy5 Rep. 3

description: 60 Min DyeSwap 2/2, Repl. 3

source_name: Streptococcus mutans, untreated, 60 min

value: 60 min

source_name: Streptococcus mutans, treated, 60 min


title: pH 4.8 16h rep. A / pH 4.8 31h rep. A

source_name: Total RNA at pH 4.8 time point 16h replicate A


title: pH 4.8 4h rep. C / pH 4.8 31h rep. C


title: pH 4.8 12h rep. A / pH 4.8 31h rep. A

source_name: Total RNA at pH 4.8 time point 12h replicate A


title: pH 4.8 12h rep. A / pH 4.8 16h rep. A


title: pH 4.8 4h rep. C / pH 4.8 20h rep. C


title: pH 4.8 4h rep. A / pH 4.8 20h rep. A

source_name: Total RNA at pH 4.8 time point 4h replicate A


title: pH 4.8 4h rep. A / pH 4.8 31h rep. A


title: pH 4.8 4h rep. C / pH 4.8 16h rep. C


title: pH 4.8 16h rep. A / pH 4.8 20h rep. A


title: pH 4.8 4h rep. A / pH 4.8 16h rep. A


title: pH 4.8 4h rep. A / pH 4.8 12h rep. A


title: pH 4.8 20h rep. A / pH 4.8 12h rep. A


title: hetero_tumor_43k


title: hetero_liver_58n

source_name: mouse liver, DEN-treated, KLF6 +/-


title: hetero_tumor_147k


title: 60 Min Treated Cy5 vs. Control Cy3 Rep. 3

description: 60 Min DyeSwap 1/2, Repl. 3


title: 60 Min Treated Cy3 vs. Control Cy5 Rep. 2

description: 60 Min DyeSwap 2/2, Repl. 2


title: 60 Min Treated Cy3 vs. Control Cy5 Rep. 1

description: 60 Min DyeSwap 2/2, Repl. 1


title: 60 Min Treated Cy5 vs. Control Cy3 Rep. 1

description: 60 Min DyeSwap 1/2, Repl. 1


title: hetero_liver_43n


title: hetero_tumor_148k


title: 60 Min Treated Cy5 vs. Control Cy3 Rep. 2

description: 60 Min DyeSwap 1/2, Repl. 2


title: 40 Min Treated Cy3 vs. Control Cy5 Rep. 1

description: 40 Min Dye Swap 2/2

source_name: Streptococcus mutans, untreated, 40 min

value: 40 min

source_name: Streptococcus mutans, treated, 40 min


title: hetero_liver_147n


title: Peripheral blood healthy control C038_Hind

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description: Hybridized to Mapping50K_Hind240

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files and CHP files (generated by Affymetrix GeneChip Command Console using the BRLMM algorithm) were processed by Affymetrix Genotyping Console 4.0. For this analysis, the protocol of un-paired samples was followed. Briefly, the parameters were set as follows: quantile normalization was performed at the perfect match (PM) probe level, followed by summarization of the signal intensity for each allele of each SNP. Genomic smoothing was set to 0.5 Mb and a five state Hidden Markov Model (HMM) was applied for smoothing and segmenting CN data. The different states were defined as follows: 0=homozygous deletion; 1=heterozygous deletion; 2=normal diploid; 3=single copy gain and 4=amplification. Each SNP was fitted to one of the possible CN states with a transition decay of 10 Mb and a threshold for SNP outlier of 1000 bp.
CHP files of 4 cell lines and 38 healty controls.

source_name: Peripheral blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was obtained from cell lines or peripheral blood with PureLink genomic DNA kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Peripheral blood healthy control

tag: subject id

tag: gender

value: female


title: 20 Min Treated Cy3 vs. Control Cy5 Rep. 3

description: 20 Min DyeSwap 2/2, Repl. 3

source_name: Streptococcus mutans, untreated, 20 min

value: 20 min

source_name: Streptococcus mutans, treated, 20 min


title: 40 Min Treated Cy5 vs. Control Cy3 Rep. 1

description: 40 Min Dye Swap 1/2


title: hetero_liver_148n


title: 20 Min Treated Cy5 vs. Control Cy3 Rep. 3

description: 20 Min DyeSwap 1/2, Repl. 3


title: 20 Min Treated Cy3 vs. Control Cy5 Rep. 1

description: 20 Min DyeSwap 2/2, Repl. 1


title: 20 Min Treated Cy3 vs. Control Cy5 Rep. 2

description: 20 Min DyeSwap 2/2, Repl. 2


title: 20 Min Treated Cy5 vs. Control Cy3 Rep. 2

description: 20 Min DyeSwap 1/2, Repl. 2


title: Peripheral blood healthy control C037_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C036_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C035_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C034_Hind

description: Hybridized to Mapping50K_Hind240


title: 20 Min Treated Cy5 vs. Control Cy3 Rep. 1

description: 20 Min DyeSwap 1/2, Repl. 1


title: 253142210044_TIGR4_CY5_3101_00_CY3.mev.refIsIB.out

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Query/Reference) from the normalized .mev file:
3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Streptococcus pneumoniae

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in blood agar plates in an anaerobic chamber, overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.

treatment_protocol: None.

organism: Streptococcus pneumoniae TIGR4


title: 253142210052_TIGR4_CY5_SK1128_CY3.mev.refIsIB.out

organism: Streptococcus infantis


title: 253142210053_TIGR4_CY5_272_98_CY3.mev.refIsIB.o


title: 253142210052_TIGR4_CY5_SK664_CY3.mev.refIsIB.out

organism: Streptococcus oralis


title: 253142210052_TIGR4_CY5_SK140_CY3.mev.refIsIB.out


title: 253142210052_TIGR4_CY5_SK1127_CY3.mev.refIsIB.out


title: 253142210053_TIGR4_CY5_1015_97_CY3.mev.refIsIB.out


title: 253142210051_TIGR4_CY5_SK1069_CY3.mev.refIsIB.out

organism: Streptococcus pseudopneumoniae


title: 253142210051_TIGR4_CY5_1754_96_CY3.mev.refIsIB.out

growth_protocol: cells were grown in blood agar plates in an anaerobic chamber, overnight at 37 degrees celcius


title: Peripheral blood healthy control C033_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C032_Hind

description: Hybridized to Mapping50K_Hind240


title: Treated Cy3 vs. Control Cy5 Rep. 4

description: Dye Swap 2/2, Rep. 4

hyb_protocol: 760 ng of each Cy3- and Cy5 labelled RNA was fracmented and hybridised to the microarray at 65°C for 16 h using the Agilent Hybridisation Chamber and Agilent Hybridisation Kit according to the manufacter`s instructions.

source_name: Streptococcus mutans, untreated

growth_protocol: Biofilms (initial OD600 = 0.01) were grown in THBS medium supplemented with (0.25 µg/ml) and without carolacton for 8 hours in 24 well polystyrene plates (Greiner, Germany).

source_name: Streptococcus mutans, treated


title: Treated Cy3 vs. Control Cy5 Rep. 3

description: Dye Swap 2/2, Rep. 3


title: Peripheral blood healthy control C031_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210048_TIGR4_CY5_6525_99_CY3.mev.refIsIB.out


title: 253142210051_TIGR4_CY5_SK1068_CY3.mev.refIsIB.out


title: 253142210051_TIGR4_CY5_A121_CY3.mev.refIsIB.out


title: 253142210048_TIGR4_CY5_7113_99_CY3.mev.refIsIB.out


title: Treated Cy3 vs. Control Cy5 Rep. 1

description: DyeSwap 2/2, Rep. 1


title: Treated Cy3 vs. Control Cy5 Rep. 2

description: DyeSwap 2/2, Rep. 2


title: 253142210050_tigr4_cy5_TIGR4_plate_replicate2_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C030_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210048_TIGR4_CY5_3028_06_CY3.mev.refIsIB.out


title: 253142210047_TIGR4_CY5_Path53_CY3.mev.refIsIB.out


title: 253142210048_TIGR4_CY5_3226_06_CY3.mev.refIsIB.out


title: Treated Cy5 vs. Control Cy3 Rep. 4

description: DyeSwap 1/2, Rep. 4


title: Peripheral blood healthy control C029_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C028_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210050_tigr4_cy5_TIGR4_column_replicate1_CY3.mev.refIsIB.out


title: Treated Cy5 vs. Control Cy3 Rep. 1

description: DyeSwap 1/2, Rep. 1


title: 253142210050_tigr4_cy5_TIGR4_plate_replicate1_CY3.mev.refIsIB.out


title: Treated Cy5 vs. Control Cy3 Rep. 2

description: DyeSwap 1/2, Rep. 2


title: Treated Cy5 vs. Control Cy3 Rep. 3

description: DyeSwap 1/2, Rep. 3


title: 253142210050_tigr4_cy5_TIGR4_column_replicate2_CY3.mev.refIsIB.out


title: 5135

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: The bacterial strain used throughout this study was L. plantarum IMDO 130201, an isolate obtained from a 10-day laboratory wheat sourdough fermentation performed through back-slopping (Van der Meulen et al., 2007). The strain was stored at –80°C in wheat sourdough simulation medium (W-SSM; Vrancken et al., 2008), supplemented with 25 % (vol/vol) glycerol as cryoprotectant. W-SSM was also used as the medium to perform simulated wheat sourdough fermentations.

hyb_protocol: Samples were hybridized for 16 h using a HS 4800 Pro automated hybridization station (Tecan Systems Inc., San Jose, CA), as described previously (Weckx et al., 2009), except that with the only difference that 130 µL hybridization mixture was used instead of 210 µL.

scan_protocol: Slides were scanned using the Agilent scanner (Agilent) and images were analysed using ArrayVision v7 (GE Healthcare).

data_processing: We apply a background correction, i.e. we subtract the local background for the local foreground intensities.  We compute the base 2 log-ratios (ratio of Cy5/Cy3). Per slide, a Loess correction per print tip on the average log-ratios was applied, to remove non-linear dye effects and print-tip effects per array. We average the log-ratios over the replicates (# = 3) on the array.

organism: Lactiplantibacillus plantarum

source_name: 292 L plantarum G3 pH4.5

label_protocol: RNA was linearly amplified using Genisphere SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy5 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.

extract_protocol: To obtain total RNA from L. plantarum IMDO 130201, 5 mL of fermentation medium of a mid-exponential growth phase culture, was collected in 10 mL RNAprotect (Qiagen, Hilden, Germany), mixed, and kept at room temperature for minimum 5 min. Subsequently, the sample was centrifuged at 5,000 Í g for 15 min and the RNA was isolated from the resulting cell pellet by applying an enzymatic lysis using mutanolysin and lysozyme, after which the RNA was extracted from the resulting mixture by using an RNeasy minikit (Qiagen) following standard instructions and including mechanical disruption of the cells using glass beads, as described previously (Weckx et al., 2009).  As the RNA profiles, obtained after capillary electrophoresis using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) showed an unexpected peak at the lower size range, possibly due to the presence of small RNA molecules (e.g., tRNA), an additional RNA clean-up step was performed. To remove the small RNA molecules, the Microcon YM-50 (Millipore, Bedford, MA) was used according to the Manufacturer’s standard instructions. Sampling was performed in duplicate, resulting in two technical repeat samples for each pH value.

tag: bacterial strain

tag: flour type

value: wheat

tag: depositor

tag: sampling time

tag: ph

tag: repeat

source_name: 294 L plantarum G6 pH5

label_protocol: RNA was linearly amplified using Genisphere SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy3 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.


title: Peripheral blood healthy control C026_Hind

description: Hybridized to Mapping50K_Hind240

tag: cell type


title: Peripheral blood healthy control C025_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210013_TIGR4_CY5_212_95_CY3.mev.refIsIB.out


title: 253142210047_TIGR4_CY5_7318_06_CY3.mev.refIsIB.out


title: 253142210013_TIGR4_CY5_1464_00_CY3.mev.refIsIB.out


title: 5801

source_name: 349 L plantarum G7 5.5

source_name: 288 L plantarum G5 pH3.5


title: 253142210012_TIGR4_CY5_6006_99_CY3.mev.refIsIB.out


title: 253142210013_TIGR4_CY5_8886_06_CY3.mev.refIsIB.out


title: 253142210013_TIGR4_CY5_4935_00_CY3.mev.refIsIB.out


title: 253142210047_TIGR4_CY5_Path30_CY3.mev.refIsIB.out


title: 253142210046_TIGR4_CY5_8149_06_CY3.mev.refIsIB.out


title: 253142210012_TIGR4_CY5_6116_05_CY3.mev.refIsIB.out


title: 253142210012_TIGR4_CY5_3990_07_CY3.mev.refIsIB.out


title: 253142210012_TIGR4_CY5_7000_06_CY3.mev.refIsIB.out


title: 253142210046_TIGR4_CY5_8380_05_CY3.mev.refIsIB.out


title: 5800


title: Peripheral blood healthy control C022_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210011_TIGR4_CY5_7848_05_CY3.mev.refIsIB.out


title: 253142210047_TIGR4_CY5_3414_99_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C027_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C024_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C023_Hind

description: Hybridized to Mapping50K_Hind240


title: 5131

source_name: 293 L plantarum G6 pH5.0

source_name: 295 L plantarum G7 pH5.5


title: 253142210046_TIGR4_CY5_7252_05_CY3.mev.refIsIB.out


title: 253142210026_TIGR4_CY5_SK100_CY3.mev.refIsIB.out

growth_protocol: Cells were grown in blood agar plates in an anaerobic chamber, overnight at 37 degrees celcius.


title: Peripheral blood healthy control C019_Hind

description: Hybridized to Mapping50K_Hind240


title: 5134

source_name: 290 L plantarum G4 pH4.0


title: 253142210011_TIGR4_CY5_4070_00_CY3.mev.refIsIB.out


title: 253142210011_TIGR4_CY5_6004_05_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C020_Hind

description: Hybridized to Mapping50K_Hind240


title: 5128

source_name: 289 L plantarum G4 pH4.0


title: 5133


title: 253142210010_TIGR4_CY5_8187_05_CY3.mev.refIsIB.out


title: 253142210011_TIGR4_CY5_5421_05_CY3.mev.refIsIB.out


title: 253142210025_TIGR4_CY5_Verbist99_CY3.mev.refIsIB.out


title: 5130

source_name: 291 L plantarum G3 pH4.5


title: 5205


title: 253142210026_TIGR4_CY5_SK143_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C017_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210010_TIGR4_CY5_5359_07_CY3.mev.refIsIB.out


title: 253142210045_TIGR4_CY5_8457_05_CY3.mev.refIsIB.out


title: 253142210046_TIGR4_CY5_3370_06_CY3.mev.refIsIB.out


title: 253142210045_TIGR4_CY5_5873_06_CY3.mev.refIsIB.out


title: 253142210025_TIGR4_CY5_SK686_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C016_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210010_TIGR4_CY5_4314_99_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C018_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C015_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C014_Hind

description: Hybridized to Mapping50K_Hind240


title: 5129


title: Peripheral blood healthy control C013_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210024_TIGR4_CY5_7907_05_CY3.mev.refIsIB.out


title: 253142210043_TIGR4_CY5_7473_05_CY3.mev.refIsIB.out


title: 253142210045_TIGR4_CY5_3949_05_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C011_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C009_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210010_TIGR4_CY5_3423_00_CY3.mev.refIsIB.out


title: 253142210009_TIGR4_CY5_Split28_CY3.mev.refIsIB.out


title: 253142210009_TIGR4_CY5_DANK258_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C006_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C008_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C007_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210044_TIGR4_CY5_6670_05_CY3.mev.refIsIB.out


title: 253142210025_TIGR4_CY5_Nautes95000655_CY3.mev.refIsIB.out


title: 253142210025_TIGR4_CY5_SK685_CY3.mev.refIsIB


title: 253142210024_TIGR4_CY5_5317_99_CY3.mev.refIsIB.out


title: 253142210024_TIGR4_CY5_8312_05_CY3.mev.refIsIB.out


title: 253142210044_TIGR4_CY5_6313_99_CY3.mev.refIsIB.out


title: 253142210045_TIGR4_CY5_4050_00_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C010_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C012_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210043_TIGR4_CY5_4901_05_CY3.mev.refIsIB.out


title: 253142210043_TIGR4_CY5_5351_00_CY3.mev.refIsIB.out


title: 253142210044_TIGR4_CY5_6278_05_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C005_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210042_TIGR4_CY5_5653_05_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C004_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210023_TIGR4_CY5_SK680_CY3.mev.refIsIB.out


title: killifish hatchling_control_rep11

city: Pendleton

first: Lisa

middle: J

last: Bain

state: SC

address: P. O. Box 709

department: Biological Sciences

institute: Clemson University

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis Hybridization Protocol

scan_protocol: Agilent G2505B Scanner, Agilent Feature Extraction V 10.7.3.1, Agilent Feature Extraction Protocol GE1_107_Sep09

data_processing: The background subtracted intensity values from each scan was subjected to variance stabilized normalization (VSN)

organism: Fundulus heteroclitus

source_name: Killifish hatchling, control

label_protocol: Agilent Quick Amp labeling kit, One-Color Cy3

extract_protocol: Qiagen RNeasy Mini

treatment_protocol: Fertilized eggs were exposed to 0 or 25ppm arsenic in water until hatch

tag: developmental stage

value: <24hr post hatch


title: 253142210043_TIGR4_CY5_3088_07_CY3.mev.refIsIB.out

tag: strain


title: Peripheral blood healthy control C021_Hind

description: Hybridized to Mapping50K_Hind240


title: killifish hatchling_control_rep6


title: killifish hatchling_control_rep8


title: killifish hatchling_control_rep7


title: Peripheral blood healthy control C003_Hind

description: Hybridized to Mapping50K_Hind240


title: Peripheral blood healthy control C002_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210024_TIGR4_CY5_2584_08_Canada_19F_CY3.mev.refIsIB.out


title: 253142210023_TIGR4_CY5_7290_06_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C001_Hind

description: Hybridized to Mapping50K_Hind240


title: 253142210023_TIGR4_CY5_0926_01_CY3.mev.refIsIB.out


title: 253142210042_TIGR4_CY5_6519_05_CY3.mev.refIsIB.out


title: 253142210022_TIGR4_CY5_567_98_CY3.mev.refIsIB.out


title: Cervical cancer cell line SiHa_Hind

description: Hybridized to Mapping50K_Hind240

source_name: Cervical cancer cell line

value: Cervical cancer cell line

tag: cell line

value: SiHa


title: killifish hatchling_control_rep9


title: 253142210022_TIGR4_CY5_58173_CY3.mev.refIsIB.out


title: killifish hatchling_control_rep4


title: 253142210022_TIGR4_CY5_SK681_CY3.mev.refIsIB.out


title: Cervical cancer cell line HeLa_Hind

description: Hybridized to Mapping50K_Hind240

value: HeLa


title: 253142210021_TIGR4_Cy5_3608_06_CY3.mev.refIsIB.out


title: 253142210021_TIGR4_Cy5_2937_00_CY3.mev.refIsIB.out


title: 253142210023_TIGR4_CY5_1873_00_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C038_Xba

description: Hybridized to Mapping50K_Xba240

source_name: Peripheral blood


title: 253142210022_TIGR4_CY5_238_95_CY3.mev.refIsIB.out


title: Cervical cancer cell line CaSki_Hind

description: Hybridized to Mapping50K_Hind240

value: CaSki


title: 253142210021_TIGR4_Cy5_5864_06_CY3.mev.refIsIB.out


title: 253142210009_TIGR4_CY5_241_98_CY3.mev.refIsIB.out


title: killifish hatchling_control_rep3


title: Peripheral blood healthy control C037_Xba

description: Hybridized to Mapping50K_Xba240


title: killifish hatchling_control_rep2


title: killifish hatchling_control_rep5


title: killifish hatchling_25ppm arsenic_rep11

source_name: Killifish hatchling, 25ppm arsenic exposure


title: 253142210038_TIGR4_CY5_7303_05_CY3.mev.refIsIB.out


title: 253142210038_TIGR4_CY5_4213_07_CY3.mev.refIsIB.out


title: killifish hatchling_control_rep1


title: Cervical cancer cell line CaLo_Hind

description: Hybridized to Mapping50K_Hind240

value: CaLo


title: 253142210038_TIGR4_CY5_7721_99_CY3.mev.refIsIB.out


title: killifish hatchling_25ppm arsenic_rep10


title: 253142210037_TIGR4_CY5_5700_06_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C036_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210038_TIGR4_CY5_3021_07_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C035_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210036_TIGR4_CY5_Split11_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C034_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210037_TIGR4_CY5_3286_01_CY3.mev.refIsIB.out


title: 253142210037_TIGR4_CY5_3056_00_CY3.mev.refIsIB.out


title: 253142210037_TIGR4_CY5_9255_06_CY3.mev.refIsIB.out


title: killifish hatchling_25ppm arsenic_rep19


title: Peripheral blood healthy control C033_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210036_TIGR4_CY5_SK137_CY3.mev.refIsIB.out

organism: Streptococcus mitis


title: 253142210009_TIGR4_CY5_183_95_CY3.mev.refIsIB.out


title: 253142210021_TIGR4_Cy5_0711_00_CY3.mev.refIsIB.out


title: killifish hatchling_25ppm arsenic_rep5


title: killifish hatchling_25ppm arsenic_rep14


title: killifish hatchling_25ppm arsenic_rep6


title: killifish hatchling_25ppm arsenic_rep8


title: killifish hatchling_25ppm arsenic_rep7


title: 253142210035_TIGR4_CY5_VERBIST_120_CY3.mev.refIsIB.out


title: 253142210035_TIGR4_CY5_SK616_CY3.mev.refIsIB.out


title: 253142210036_TIGR4_CY5_Gro101_95_CY3.mev.refIsIB.out


title: 253142210020_TIGR4_CY5_7329_05_CY3.mev.refIsIB.out


title: 253142210035_TIGR4_CY5_HOLLAND_0138_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C032_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C031_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210020_TIGR4_CY5_2008008776_CY3.mev.refIsIB.out


title: 253142210036_TIGR4_CY5_Gro93_95_CY3.mev.refIsIB.out


title: 253142210020_TIGR4_CY5_4389_07_CY3.mev.refIsIB.out


title: killifish hatchling_25ppm arsenic_rep3


title: Peripheral blood healthy control C029_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C030_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C028_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210020_TIGR4_CY5_1018_00_CY3.mev.refIsIB.out


title: killifish hatchling_25ppm arsenic_rep1


title: 253142210034_TIGR4_CY5_SK1137_CY3.mev.refIsIB.out


title: 253142210035_TIGR4_CY5_1398_96_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C027_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C026_Xba

description: Hybridized to Mapping50K_Xba240


title: C20N_vs_TFN_ratios

first: Natalie

last: Fedorova

department: Infectious Disease

institute: JCVI

hyb_protocol: Hybridization was performed according to the JCVI’s protocols (http://www.pga.tigr.org/sop/M005_1a.pdf)

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using  GenePix Pro 3.0 software.   PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible.  Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities.  Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: LOWESS normalized, flip-dye analyzed, inslide replicate averaged log2 ratio (experimental/control)

organism: Arachis hypogaea

source_name: Peanut cultivar C20 not inoculated with Aspergillus flavus and A. paraciticus

label_protocol: Labeling was performed according to the JCVI’s protocols (http://www.pga.tigr.org/sop/M005_1a.pdf)

growth_protocol: Peanut immature kernel seeds harvested 90 days after planting

extract_protocol: Frozen kernels were ground in liquid nitrogen, and total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). The amount and quality of the total RNA was measured with a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

tag: cultivar

tag: tissue

value: immature kernel seed

tag: infection

source_name: Peanut cultivar TF not inoculated with Aspergillus flavus and A. paraciticus

value: TF


title: C20Y_vs_C20N_ratios

source_name: Peanut cultivar C20 inoculated with Aspergillus flavus and A. paraciticus spores 60 days after planting and harvested 30 days after inoculation

value: A. flavus and A. paraciticus

treatment_protocol: not inoculated with Aspergillus flavus and A. paraciticus


title: 253142210008_TIGR4_CY5_5720_06_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria


title: Peripheral blood healthy control C025_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210034_TIGR4_CY5_Holland1765_CY3.mev.refIsIB.out


title: C20Y_vs_TFY_ratios

source_name: Peanut cultivar TF inoculated with Aspergillus flavus and A. paraciticus spores 60 days after planting and harvested 30 days after inoculation


title: 253142210019_TIGR4_CY5_Verbist_186_CY3.mev.refIsIB.out


title: 253142210019_TIGR4_CY5_58095_CY3.mev.refIsIB.out


title: TFY_vs_TFN_ratios

treatment_protocol: inoculated with Aspergillus flavus and A. paraciticus spores 60 days after planting and harvested 30 days after inoculation


title: Peripheral blood healthy control C022_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210034_TIGR4_CY5_SK1125_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C023_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210008_TIGR4_CY5_5350_99_CY3.mev.refIsIB.out


title: 253142210019_TIGR4_CY5_TIGR4_CY3.mev.refIsIB.out


title: 253142210008_TIGR4_CY5_3703_06_CY3.mev.refIsIB.out


title: 253142210019_TIGR4_CY5_7720_99_CY3.mev.refIsIB.out


title: 253142210034_TIGR4_CY5_218_95_CY3.mev.refIsIB.out


title: 253142210018_TIGR4_CY5_Verbist_143_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C021_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C024_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210008_TIGR4_CY5_2346_99_CY3.mev.refIsIB.out


title: 253142210033_TIGR4_CY5_L27F_CY3.mev.refIsIB.out


title: 253142210033_TIGR4_CY5_8304_05_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C020_Xba

description: Hybridized to Mapping50K_Xba240


title: bASC#3

city: Richmond

first: Lynne

last: Elmore

state: VA

address: 1101 E. Marshall St

department: Pathology

institute: VCU

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method using RMAExpress (Version: 0.4 alpha 7).

source_name: breast-derived mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: MSCs were isolated from residual adipose tissues from reduction mammoplasties, lipoaspirates, and residual bone marrow specimens

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

treatment_protocol: Tissues were cut into 5 – 10mm cubes, washed with sterile PBS and then digested in 1% collagenase at 37°C. Collagenase was neutralized with 10% FBS and the stromal vascular fraction was pelleted by centrifugation for 10 minutes at 400xg at room temperature. Red blood cells from the cell pellet was lysed with 160mM NH4Cl. The resulting suspensions were serially filtered through 100μm and 40μm filters followed by centrifugation at 400xg for 10 minutes. The cells were cultured overnight in low glucose DMEM with 30% fetal bovine serum (FBS) and 2% penicillin/streptomycin to allow attachment to standard plastic tissue culture dishes.

value: breast-derived mesenchymal stem cells


title: Ab-ASC#8

source_name: abdomen-derived mesenchymal stem cells

value: abdomen-derived mesenchymal stem cells


title: BMMSC Control

source_name: bone marrow-derived mesenchymal stem cells


title: 253142210018_TIGR4_CY5_39366_CY3.mev.refIsIB.out


title: bASC#2


title: Peripheral blood healthy control C019_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210007_TIGR4_CY5_3230_06_CY3.mev.refIsIB.out


title: 253142210033_TIGR4_CY5_8036_06_CY3.mev.refIsIB.out


title: bASC#1


title: 253142210007_TIGR4_CY5_415_98_CY3.mev.refIsIB.out


title: 253142210007_TIGR4_CY5_4798_99_CY3.mev.refIsIB.out


title: 253142210007_TIGR4_CY5_111_95_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C018_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210032_TIGR4_CY5_SK674_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C017_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C016_Xba

description: Hybridized to Mapping50K_Xba240


title: BMMSC

description: LACZ

value: bone marrow-derived mesenchymal stem cells


title: 253142210033_TIGR4_CY5_7102_99_CY3.mev.refIsIB.out


title: 253142210032_TIGR4_CY5_SK555_CY3.mev.refIsIB.out


title: 253142210018_TIGR4_CY5_2050_00_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C015_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210032_TIGR4_CY5_SK608_CY3.mev.refIsIB.out


title: SE_TREATMENT

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Expression Console (Affymetrix) was used to generate the RMA file

organism: Canis lupus familiaris

source_name: Canine Spontaneous Sarcoma

label_protocol: Affymetrix standard protocol

growth_protocol: Spontaneous Tumors from Dogs

extract_protocol: RNAs were extracted with Qiagen RNA easy mini

treatment_protocol: Tissue used for gene expression analysis was placed immediately into RNAlater before RNA isolation

value: Sarcoma tumor

tag: treatment

value: hyperthermia


title: SE_BASE


title: 253142210006_TIGR4_CY5_3293_00_CY3.mev.refIsIB.out


title: 253142210018_TIGR4_CY5_1048_CY3.mev.refIsIB.out


title: DB_TREATMENT


title: 253142210006_TIGR4_CY5_3222_06_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C014_Xba

description: Hybridized to Mapping50K_Xba240

value: Peripheral blood healthy control

value: female


title: Peripheral blood healthy control C012_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210006_TIGR4_CY5_Holland_1771_CY3.mev.refIsIB.out


title: DB_BASE


title: AR_BASE


title: 253142210031_TIGR4_CY5_SK614_CY3.mev.refIsIB.out


title: 253142210031_TIGR4_CY5_SK607_CY3.mev.refIsIB.out


title: AR_TREATMENT


title: Peripheral blood healthy control C013_Xba

description: Hybridized to Mapping50K_Xba240


title: SP_TREATMENT


title: Peripheral blood healthy control C010_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C011_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210032_TIGR4_CY5_OSLO_67_95_CY3.mev.refIsIB.out


title: 253142210030_TIGR4_CY5_909_96_CY3.mev.refIsIB.out


title: 253142210017_TIGR4_CY5_Holland_1656_CY3.mev.refIsIB.out


title: 253142210031_TIGR4_CY5_Holland1674_CY3.mev.refIsIB.out


title: SP_BASE


title: 253142210031_TIGR4_CY5_SK596_CY3.mev.refIsIB.out


title: 253142210030_TIGR4_CY5_181_95_CY3.mev.refIsIB.out


title: SKES1_Sty1

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

country: Spain

institute: Centro de Investigación del Cáncer

description: Hybridized to 500K_Sty

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the the Gene Array reader (Affymetrix)

data_processing:
CEL files were processed to study copy number alterations using GTYPE 4.1 and CNAT 4.0 software (Affymetrix), smoothing = 0.1, using the Mapping 500K Sample Data Set (http://www.affymetrix.com/support/technical/sample_data/500k_data.affx) which includes CEL files from 48 samples (96 hybridizations, considering both Nsp and Sty arrays) belonging to the International Hap Map project, as healthy references.
Sample tables are the CNAT output, which includes the log2ratio and the results of the HMM segmentation algorithm.

source_name: SKES1 Ewing's Sarcoma cell line

growth_protocol: The SKES1 cell lines was cultured in McCoy's medium supplemented with 15% FBS

extract_protocol: DNA was extracted using QIAamp DNA Mini Kit (Qiagen) following manufacturer's instructions for extracting DNA from cell lines

treatment_protocol: no treatment was applied, the cell line was used in normal growing conditions.

tag: sample type

value: cell line

value: Ewing's Sarcoma


title: 253142210017_TIGR4_CY5_798_97_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C009_Xba

description: Hybridized to Mapping50K_Xba240

tag: subject id


title: 253142210029_TIGR4_CY5_L28F_CY3.mev.refIsIB.out


title: 253142210030_TIGR4_CY5_274_95_CY3.mev.refIsIB.out


title: 253142210029_TIGR4_CY5_39349_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C006_Xba

description: Hybridized to Mapping50K_Xba240

tag: gender


title: Peripheral blood healthy control C005_Xba

description: Hybridized to Mapping50K_Xba240


title: Peripheral blood healthy control C008_Xba

description: Hybridized to Mapping50K_Xba240


title: MI_TREATMENT


title: Peripheral blood healthy control C007_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210030_TIGR4_CY5_135_95_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C004_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210005_TIGR4_CY5_8505_06_CY3.mev.refIsIB.out


title: 253142210017_TIGR4_CY5_276_95_CY3.mev.refIsIB.out


title: 253142210006_TIGR4_CY5_288_95_CY3.mev.refIsIB.out


title: JP_BASE


title: ER_TREATMENT


title: 253142210017_TIGR4_CY5_173_97_CY3.mev.refIsIB.out


title: 253142210029_TIGR4_CY5_138_98_CY3.mev.refIsIB.out


title: 253142210005_TIGR4_CY5_7177_06_CY3.mev.refIsIB.out


title: 253142210029_TIGR4_CY5_156_95_CY3.mev.refIsIB.out


title: MI_BASE


title: JP_TREATMENT


title: Peripheral blood healthy control C003_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210005_TIGR4_CY5_7163_99_CY3.mev.refIsIB.out


title: 253142210016_TIGR4_CY5_7322_05_CY3.mev.refIsIB.out


title: ER_BASE


title: Peripheral blood healthy control C001_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210028_TIGR4_CY5_48242_CY3.mev.refIsIB.out


title: 253142210028_TIGR4_CY5_272_98_CY3.mev.refIsIB.out


title: 253142210028_TIGR4_CY5_282_98_CY3.mev.refIsIB.out


title: Peripheral blood healthy control C002_Xba

description: Hybridized to Mapping50K_Xba240


title: Cervical cancer cell line HeLa_Xba

description: Hybridized to Mapping50K_Xba240

value: Cervical cancer cell line


title: 253142210027_TIGR4_CY5_SK637_CY3.mev.refIsIB.out


title: SK_TREATMENT


title: CB_TREATMENT


title: CB_BASE


title: 253142210028_TIGR4_CY5_141_98_CY3.mev.refIsIB.out


title: 253142210016_TIGR4_CY5_6968_06_CY3.mev.refIsIB.out


title: SK_BASE


title: Cervical cancer cell line SiHa_Xba

description: Hybridized to Mapping50K_Xba240

value: SiHa


title: Cervical cancer cell line CaLo_Xba

description: Hybridized to Mapping50K_Xba240


title: GB_BASE


title: 253142210004_TIGR4_CY5_7202_06_CY3.mev.refIsIB.out


title: 253142210004_TIGR4_CY5_8008_06_CY3.mev.refIsIB.out


title: 253142210027_TIGR4_CY5_SK342_CY3.mev.refIsIB.out


title: HW_TREATMENT


title: GB_TREATMENT


title: Cervical cancer cell line CaSki_Xba

description: Hybridized to Mapping50K_Xba240


title: 253142210027_TIGR4_CY5_SK572_CY3.mev.refIsIB.out


title: 253142210005_TIGR4_CY5_3492_00_CY3.mev.refIsIB.out


title: 253142210027_TIGR4_CY5_SK575_CY3.mev.refIsIB.out


title: 253142210016_TIGR4_CY5_6378_99_CY3.mev.refIsIB.out


title: 253142210004_TIGR4_CY5_5028_03_CY3.mev.refIsIB


title: 253142210004_TIGR4_CY5_3143_06_CY3.mev.refIsIB.out


title: MS_TREATMENT


title: 253142210026_TIGR4_CY5_SK335_CY3.mev.refIsIB.out


title: 253142210042_TIGR4_CY5_5477_07_CY3.mev.refIsIB.out


title: 253142210065_TIGR4_CY5_SK1124_CY3.mev.refIsIB.out


title: MS_BASE


title: 253142210065_TIGR4_CY5_SK598_CY3.mev.refIsIB.out


title: 253142210064_TIGR4_CY5_A9880_CY3.mev.refIsIB.out


title: 253142210065_TIGR4_CY5_SK675_CY3.mev.refIsIB.out


title: HW_BASE


title: 253142210026_TIGR4_CY5_SK255_CY3.mev.refIsIB.out

organism: Streptococcus oralis SK255


title: SM_TREATMENT


title: BL_BASE


title: 253142210003_TIGR4_CY5_Path41_CY3.mev.refIsIB.out


title: 253142210003_TIGR4_CY5_7555_05_CY3.mev.refIsIB.out


title: 253142210065_TIGR4_CY5_SK609_CY3.mev.refIsIB.out


title: 253142210064_TIGR4_CY5_A9812_CY3.mev.refIsIB.out


title: GK_TREATMENT


title: DC_TREATMENT


title: 253142210015_TIGR4_CY5_8404_05_CY3.mev.refIsIB.out


title: GK_BASE


title: 253142210015_TIGR4_CY5_8148_06_CY3.mev.refIsIB.out


title: BL_TREATMENT


title: 253142210016_TIGR4_CY5_140_98_CY3.mev.refIsIB.out


title: 253142210003_TIGR4_CY5_5812_99_CY3.mev.refIsIB.out


title: 253142210042_TIGR4_CY5_4331_07_CY3.mev.refIsIB.out


title: 253142210015_TIGR4_CY5_5318_05_CY3.mev.refIsIB.out


title: DC_BASE


title: 253142210003_TIGR4_CY5_6288_05_CY3.mev.refIsIB.out


title: 253142210041_TIGR4_CY5_3337_06_CY3.mev.refIsIB.out


title: ND_TREATMENT


title: 253142210041_TIGR4_CY5_3071_00_CY3.mev.refIsIB.out


title: ND_BASE


title: SC_TREATMENT


title: 253142210041_TIGR4_CY5_1555_00_CY3.mev.refIsIB.out


title: 253142210014_TIGR4_CY5_48166_CY3.mev.refIsIB.out


title: 253142210064_TIGR4_CY5_68020_CY3.mev.refIsIB.out


title: BB_TREATMENT


title: 253142210040_TIGR4_CY5_6314_05_CY3.mev.refIsIB.out


title: 253142210015_TIGR4_CY5_3224_06_CY3.mev.refIsIB.out


title: 253142210064_TIGR4_CY5_1015_97_CY3.mev.refIsIB.out


title: Arabidopsis VND7XVE Experiment 2

city: Athens

first: Zheng-Hua

last: Ye

address: 2502 Miller Plant Sciences

department: Plant Biology

institute: University of Georgia

hyb_protocol: Standard Affymetrix GeneChip Technology.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: Expression values are calculated based on the difference of the PM signal and MM signal at each of the probe pairs using the Affymetrix GeneChip Operating System (GCOS). This software employs statistical algorithms to calculate qualitative and quantitative expression values for each transcript. It also generates a statistical p-value, which suggests the level of confidence in each of the qualitative measurements.

organism: Arabidopsis thaliana

source_name: Arabidopsis protoplasts

label_protocol: Affymetrix One-Cycle Eukaryotic Target Labeling kit.

extract_protocol: Total RNA was isolated using the QIAGEN Plant RNA isolation kit.

tag: genotype/variation

tag: treatment group

value: cycloheximide+estradiol


title: Arabidopsis VND7XVE Experiment 1


title: 253142210040_TIGR4_CY5_1042_00_CY3.mev.refIsIB.out


title: BB_BASE


title: 253142210040_TIGR4_CY5_3980_07_CY3.mev.refIsIB.out


title: 253142210041_TIGR4_CY5_3037_06_CY3.mev.refIsIB.out


title: Arabidopsis VND7XVE Control 2

value: cycloheximide


title: 253142210063_TIGR4_CY5_39371_CY3.mev.refIsIB.out


title: JB_BASE


title: Arabidopsis VND7XVE Control 1


title: 253142210040_TIGR4_CY5_3130_06_CY3.mev.refIsIB.out


title: 253142210063_TIGR4_CY5_L25F_CY3.mev.refIsIB.out


title: 253142210039_TIGR4_CY5_7369_05_CY3.mev.refIsIB.out


title: 253142210063_TIGR4_CY5_58084_CY3.mev.refIsIB.out


title: JB_TREATMENT


title: SC_BASE


title: 253142210002_TIGR4_CY5_Split3_CY3.mev.refIsIB.out


title: 253142210063_TIGR4_CY5_160_95_CY3.mev.refIsIB.out


title: MF_TREATMENT


title: 253142210062_TIGR4_CY5_SK691_CY3.mev.refIsIB.out


title: Arabidopsis SND1XVE Experiment 2


title: MF_BASE


title: Arabidopsis SND1XVE Control 1


title: Arabidopsis SND1XVE Experiment 1


title: Arabidopsis SND1XVE Control 2


title: 253142210014_TIGR4_CY5_34369_24F_CY3.mev.refIsIB.out


title: CPF (0.5mg/l) + DZN (1mg/l) vs. Control. Replicate 1

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

institute: King's College London

hyb_protocol: The cDNA samples were hybridized to the arrays using a modified version of the Genisphere Array 900 HS protocol.

scan_protocol: ScanArray Express HT (PerkinElmer Inc) Software: Easy Quant with Adaptive circle.

data_processing: Preprocessing and normalization was done in the R software (http://www.r-project.org/), version 2.10.1, using Limma package, version 3.2.3 (Smyth, 2005). Loess method (Smyth & Speed, 2003) was used for normalization within arrays and normalization between arrays was done using aquantile method (Yang,et al., 2003), both of them included in limma package. The expression data from all the treatments were normalized together with the expression data from identical treatments at 16C (GEO accession number GSE16719), to allow comparison between both dataset. Outliers from each experiment were identified and removed using a linear model. Expression values from each treatment were treated in separately linear models. The models fit expression values according to the treatment (CPF, DZN or Mixture) and remove values outside the 0.995 confidence interval, one spot at the time, recursively. No more than 6 values were allowed to be removed.

organism: Caenorhabditis elegans

source_name: Nematodes treated with 0.5mg/l of Chlorpyrifos and 1mg/l of Diazinon

label_protocol: cDNA was obtained form a minimum of 400 ng/µl of total RNA, using Array 900 HS kit (Genisphere, http://www.genisphere.com) and Superscript II (Invitrogen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and cleaned up with the RNeasy Micro kit (Qiagen, http://www1.qiagen.com/)

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 24° C until L3 was reached. At 72 hours of age, nematodes kept at 24° C were at the L3 stage. Chlorpyrifos (Cyren®/Nufos®, Cheminova A/S, Lemvig, Denmark) and Diazinon (Supelco, Bellefonte, Pennsylvania, USA) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/l of Chlorpyrifos and 1mg/l of Diazinon. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.

tag: Stage

value: L3/L4 nematodes (72h at 24°C)

source_name: Control nematodes


title: CPF (0.5mg/l) + DZN (1mg/l) vs. Control. Replicate 3


title: 253142210061_TIGR4_CY5_SK564_CY3.mev.refIsIB.out


title: 253142210062_TIGR4_CY5_Oslo49_65_CY3.mev.refIsIB.out


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