title: Q0105_p_12_M_57

description:
patient
array: HumanHT-12 V4.0

source_name: patient

value: patient

value: M

value: no

value: non


title: Heart_PCI_rep.2

status: Public on Sep 01 2015

type: RNA

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

country: Germany

institute: JUH

description: in vivo

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Direct Hybridization Assay protocol from Illumina.

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data were obtained using GenomeStudio (v 1.9.0)  and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via lumi package within Bioconductor and R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: heart muscle tissue, 6h sepsis (PCI)

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

growth_protocol: Animal experiments were carried out after approval of the local ethics committee.

extract_protocol: RNA was isolated from heart muscle tissue using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.

treatment_protocol: Referring to a recently published rodent model (Gonnert et al., J Surg Res. 2011), male 20 to 30 weeks old C57BL/6 Jackson mice were subjected to peritoneal contamination and infection (PCI). The animals received an intraperitoneal injection of 5 µl/g BW of a standardised human faeces suspension (4,25 ∙ 107 CFU/g BW; predicted to be lethal). Untreated mice were used as controls.

tag: strain

tag: gender

value: male

tag: tissue

value: heart muscle


title: MRC5 kras

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

organism: Homo sapiens

source_name: MRC5 cell

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

tag: transfection

value: overexpressed KRASG12V


title: NCI-H716 control

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental Molecular Medicine

country: Netherlands

institute: Academic Medical Center

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Data were RMA normalized

source_name: colorectal cancer cell line with methylated miR-200 loci

label_protocol: Not provided

extract_protocol: For single- and double-transduced cells, RNA was extracted 7 days after transduction using the NucleoSpin miRNA kit (Macherey-Nagel) and Microarrays of miR-200 overexpressing cell lines were performed using the GeneTitanTM MC system from Affymetrix according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany, on Affymetrix u133 plus 2.0 arrays.

treatment_protocol: Four CCS3 cell lines with high miR-200 promoter methylation (HUTU-80, MDST8, NCI-H716, and SW620) were transduced with lentiviral supernatant and sorted on GFP-positive cells after 48 hours. 24 hours after sorting a fraction of the miR-200ba429 transduced cells was transduced with miR-200c141 lentivirus.

tag: cell line

tag: cell type

value: colorectal cancer


title: Day1_Primed with LM-ΔActA, replicate 1

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

country: USA

institute: NHGRI-NIH

description: Day1_Primed with LM-ΔActA, replicate 1

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Gene 2.0 ST GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

label: Biotin

source_name: spleen

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

growth_protocol: BALB/cByJ and CByB6F1 mice were purchased from Jackson Laboratories.(Bar Harbor, ME)

extract_protocol: Total RNAs from liver tissues (including small and long RNAs) was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: Total body g irradiation was performed using a Gammacell 40 Cs-137 irradiator (MDS Nordion, Mississauga, ON) with a dose rate of 65 cGy/min.  Unirradiated animals were confined in an identical acrylic irradiation chamber for the same amount of time as irradiated animals. Mice were immunized with live of attenuated Listeria monocytogenes LM-ΔActA and 4 weeks later were exposed to a sublethal dose of 600 cGy of γ radiation.  Following irradiation, mice were vaccinated with LM-ΔActA at one time.

value: BALB/cByJ and CByB6F1

tag: protocol

value: Day1_Primed with LM-ΔActA


title: MDST8 + miR200ba429 + miR200c141


title: Q0100_c_13_M_55

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
control, brother of q_0099
array: HumanHT-12 V4.0

hyb_protocol: not provided

scan_protocol: Slides were scanned using Illumina BeadStation, and the signal was extracted by using Illumina BeadStudio software.

data_processing:
Raw data were analyzed by using Bioconductor packages in the R statistical environment.  Quality assessment was performed by examining the interarray Pearson correlation and clustering based on the top variant genes was assessed. Contrast analysis of differential expression was performed by using the LIMMA package.  After linear model fitting, a Bayesian estimate of differential expression was calculated.
This study included the use of two different arrays: Illumina HumanHT-12 V3.0 and HumanHT-12 V4.0. The raw and processed data (quantile normalized, log2 transformed data) for each array and the shared probes between the arrays that were analyzed in this study are available on the series level. The final processed data used in the analysis is available in the file "normalized_ageOut.csv" where age was regressed out.

source_name: control, brother of q_0099

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

extract_protocol: RNA was extracted from whole blood using the PAXgene extraction kit (Qiagen), then stored at -80C for subsequent analysis, as described below. RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

value: whole blood

tag: diagnosis

value: healthy control

tag: age

tag: Sex


title: NCI-H716 + miR200ba429


title: 3 days post-injured [exon-level]

city: Changzhou

first: Ding

last: Ya

state: Jiangsu

address: No. 185 Juqian street

department: Department of Orthopedics

country: China

institute: The Third Affiliated Hospital of Suzhou University

description: T10 spinal cord 3 day post-injured

hyb_protocol: GeneChip2 Hybridization, Wash, and Stain Kit (Affymetrix, Inc. US) was used for hybridization

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Affymetrix GCOS Software
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: wild-type, injured spinal cord

label_protocol: GeneChip2 WT Terminal Labeling Kit and Controls Kit (Affymetrix, Inc. US) was used for fragmentation and labeling of this single-stranded DNA

growth_protocol: not applicable

extract_protocol: All samples were snap frozen in liquid N2 and prepared using Trizol. RNA were purified using RNeasy Mini Kit (Qiagen, German), including a DNase digestion treatment. cDNA synthesis and amplification was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Inc. US)

treatment_protocol: not applicable

value: ICR

tag: genotype/variation

value: wild-type

value: 4 weeks

value: spinal cord injury

tag: time

value: 3 days post-injured


title: 1 day post-injured [exon-level]

description: T10 spinal cord 1 day post-injured

value: 1 day post-injured


title: HEK293 NC

source_name: HEK293 cell


title: MDST8 + miR200c141


title: 1 week post-injured [exon-level]

description: T10 spinal cord 1 week post-injured

value: 1 week post-injued


title: sham operation [exon-level]

description: T10 spinal cord

source_name: wild-type, normal spinal cord

value: sham operation

value: control


title: HEK293 kras


title: Q0099_c_15_F_55

description:
control, sister of q_0098
array: HumanHT-12 V4.0

source_name: control, sister of q_0098

value: F


title: Q0098_c_14_F_55

description:
control, sister of q_0099
array: HumanHT-12 V4.0

source_name: control, sister of q_0099


title: Q0097_c_24_M_14

description:
brother of q_0016
array: HumanHT-12 V4.0

source_name: brother of q_0016

value: M


title: Heart_CON_rep.4

description: in vivo

source_name: heart muscle tissue, untreated

value: male

value: heart muscle


title: Q0096_c_51_F_14

description:
mother of q_0016
array: HumanHT-12 V4.0

source_name: mother of q_0016


title: Heart_PCI_rep.1

description: in vivo


title: Q0094_p_9_M_54

description:
patient
array: HumanHT-12 V4.0

value: patient

tag: psychoticdisorder

value: no

tag: asd status

value: ASD


title: Q0093_p_19_M_53

description:
patient
array: HumanHT-12 V4.0

value: whole blood

value: non


title: Q0092_c_21_F_52

description:
control
array: HumanHT-12 V4.0

source_name: control

value: healthy control


title: MDST8 control

value: colorectal cancer


title: HUTU-80 + miR200c141 1:5


title: Q0091_c_19_F_51

description:
control
array: HumanHT-12 V4.0


title: Q0089_c_37_F_50

description:
mother of q_0088
array: HumanHT-12 V4.0

source_name: mother of q_0088


title: Heart_CON_rep.2

description: in vivo


title: Q0088_p_15_F_50

description:
patient
array: HumanHT-12 V4.0

value: yes


title: Heart_CON_rep.1

description: in vivo


title: HUTU-80 + miR200ba429


title: Q0087_c_57_M_49

description:
father of q_0085
array: HumanHT-12 V4.0

source_name: father of q_0085


title: MJR_PV+TMb1_001

city: Montreal

first: Martin

last: Richer

state: Quebec

address: 406 Duff Medical Building, 3775 University street

country: Canada

institute: McGill University

description: Memory P14_Pichinde Virus infection+anti-CD122_biological replicate 1

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse EXON 1.0 ST Arrays, and incubated at 45º C for 18 hr with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. The Mouse EXON 1.0 ST Array interrogates over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
Data were imported into Partek GS v. 6.12. The normalized log2 data was compared using an ANOVA model. Individual comparisons were done using a linear model function. Genes with a p-value of <0.01 and a fold-change >1.5 were analyzed further.
MoEx-1_0-st-v1.r2.pgf
oEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: P14 from Pichinde virus and anti-cd122 treated mice

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility. Briefly, 50 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. 3.3 ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation EXON Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Rneasy kit (Qiagen) according to manufacturer's instructions

treatment_protocol: CD8+ cells were enriched by Automacs followed by cell sorting

value: female

value: spleen

value: Memory P14 Tg CD8 T cells


title: 557229A10 - Fe0+pyo_shoots_2 vs Fe0_shoots_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Analyse de l’effet d’un traitement par la pyoverdine sur les gènes liés à l’homéostasie du fer et à l’induction des réactions de défense.

hyb_protocol: Fe0_shoots_2 Cy5 / Fe0+pyo_shoots_2 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: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

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: rosette - Hydroponic medium. Hygrometry: day:50 (average), night:70 (average) Temperature: day:20C, night: 18. Light: 160 µA.m-2.s-1, night: none.

treatment_protocol: Name:Fe_0µM - fe_0µm - fe_0µm,fe:quantity 0uM .

tag: ecotype

value: Columbia (Col-0)

value: 24 day

treatment_protocol: Name:Fe_0µM+pyo_25µM - fe_0µm+pyo_25µm - fe_0µm+pyo_25µm,fe_0µm+pyo_25µm:quantity 25uM .


title: 557229A12 - Fe0+pyo_shoots_3 vs Fe0_shoots_3

hyb_protocol: Fe0_shoots_3 Cy5 / Fe0+pyo_shoots_3 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.


title: MJR_PV+TMb1_002

description: Memory P14_Pichinde Virus infection+anti-CD122_biological replicate 2


title: HUTU-80 control


title: MJR_PV_003

description: Memory P14_Pichinde Virus infection_biological replicate 3

source_name: P14 from Pichinde virus infected mice


title: MJR_Saline_003

description: Memory P14_Saline_biological replicate 3

source_name: P14 from mock-infected mice


title: MJR_PV+TMb1_003

description: Memory P14_Pichinde Virus infection+anti-CD122_biological replicate 3


title: MJR_PV_001

description: Memory P14_Pichinde Virus infection_biological replicate 1


title: 557229A07 - Fe0_shoots_1 vs Fe0+pyo_shoots_1

hyb_protocol: Fe0+pyo_shoots_1 Cy5 / Fe0_shoots_1 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.


title: 557229A08 - Fe0+pyo_shoots_1 vs Fe0_shoots_1

hyb_protocol: Fe0_shoots_1 Cy5 / Fe0+pyo_shoots_1 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.


title: 557229A11 - Fe0_shoots_3 vs Fe0+pyo_shoots_3

hyb_protocol: Fe0+pyo_shoots_3 Cy5 / Fe0_shoots_3 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.


title: 557229A09 - Fe0_shoots_2 vs Fe0+pyo_shoots_2

hyb_protocol: Fe0+pyo_shoots_2 Cy5 / Fe0_shoots_2 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.


title: Q0086_c_55_F_49

description:
mother of q_0085
array: HumanHT-12 V4.0

source_name: mother of q_0085

value: F


title: HUTU-80 + miR200c141 1:3

source_name: colorectal cancer cell line with methylated miR-200 loci


title: MJR_Saline_002

description: Memory P14_Saline_biological replicate 2


title: MJR_PV_002

description: Memory P14_Pichinde Virus infection_biological replicate 2


title: 557229A06 - pyo_shoots_3 vs control_shoots_3

hyb_protocol: controle_shoots_3 Cy5 / pyo_shoots_3 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.

treatment_protocol: Name:Fe_25µM - fe_25µm - fe_25µm,fe:quantity 25uM .

treatment_protocol: Name:Fe_25µM+pyo_25µM - fe_25µm+pyo_25µm - fe_25µm+pyo_25µm,fe_25µm+pyo_25µm:quantity 25uM .


title: 557229A03 - control_shoots_2 vs pyo_shoots_2

hyb_protocol: pyo_shoots_2 Cy5 / controle_shoots_2 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.


title: 557229A02 - pyo_shoots_1 vs control_shoots_1

hyb_protocol: controle_shoots_1 Cy5 / pyo_shoots_1 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.


title: Q0084_c_34_F_17

description:
mother of q_0021
array: HumanHT-12 V4.0

source_name: mother of q_0021


title: Q0083_c_51_F_48

description:
mother of q_0082
array: HumanHT-12 V4.0

source_name: mother of q_0082


title: Q0082_p_21_F_48

description:
patient
array: HumanHT-12 V4.0

source_name: patient


title: 557229A04 - pyo_shoots_2 vs control_shoots_2

hyb_protocol: controle_shoots_2 Cy5 / pyo_shoots_2 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.


title: Q0079_c_35_F_45

description:
mother of q_0078
array: HumanHT-12 V4.0

source_name: mother of q_0078


title: Q0085_p_24_F_49

description:
patient
array: HumanHT-12 V4.0


title: Q0078_p_12_F_45

description:
patient
array: HumanHT-12 V4.0


title: 3 weeks post-injured [gene-level]

description: T10 spinal cord 3 weeks post-injured

source_name: wild-type, injured spinal cord

value: ICR

value: wild-type

value: 4 weeks

value: spinal cord injury

value: 3 weeks post-injured


title: 557229A05 - control_shoots_3 vs pyo_shoots_3

hyb_protocol: pyo_shoots_3 Cy5 / controle_shoots_3 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.


title: 1 day post-injured [gene-level]

description: T10 spinal cord 1 day post-injured

value: 1 day post-injured


title: 557229A01 - control_shoots_1 vs pyo_shoots_1

hyb_protocol: pyo_shoots_1 Cy5 / controle_shoots_1 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.


title: 1 week post-injured [gene-level]

description: T10 spinal cord 1 week post-injured

value: 1 week post-injued


title: sham operation [gene-level]

description: T10 spinal cord

source_name: wild-type, normal spinal cord

value: sham operation

value: control


title: MJR_Saline_001

description: Memory P14_Saline_biological replicate 1


title: Q0075_c_52_F_8

description:
mother of q_0001
array: HumanHT-12 V4.0

source_name: mother of q_0001

value: whole blood

value: healthy control


title: Q0076_c_21_F_43

description:
control
array: HumanHT-12 V4.0


title: Q0077_c_14_M_44

description:
control
array: HumanHT-12 V4.0

value: M


title: Q0074_c_52_F_42

description:
grandmother of q_0072 and mother of q_0073
array: HumanHT-12 V4.0


title: 557182A12 - Fe0+pyo_roots_3 vs Fe0_roots_3

hyb_protocol: Fe0_roots_3 Cy5 / Fe0+pyo_roots_3 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.

growth_protocol: roots - Hydroponic medium. Hygrometry: day:50 (average), night:70 (average) Temperature: day:20C, night: 18. Light: 160 µA.m-2.s-1, night: none.


title: 3 days post-injured [gene-level]

description: T10 spinal cord 3 day post-injured

value: 3 days post-injured


title: 557182A09 - Fe0_roots_2 vs Fe0+pyo_roots_2

hyb_protocol: Fe0+pyo_roots_2 Cy5 / Fe0_roots_2 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.


title: Q0072_p_6_M_42

description:
patient
array: HumanHT-12 V4.0

hyb_protocol: not provided

value: patient

value: no

value: non


title: Q0056_p_22_M_37

description:
patient
array: HumanHT-12 V4.0

value: yes

value: ASD


title: 557182A08 - Fe0+pyo_roots_1 vs Fe0_roots_1

hyb_protocol: Fe0_roots_1 Cy5 / Fe0+pyo_roots_1 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.

value: Columbia (Col-0)


title: 557182A10 - Fe0+pyo_roots_2 vs Fe0_roots_2

hyb_protocol: Fe0_roots_2 Cy5 / Fe0+pyo_roots_2 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.


title: 557182A11 - Fe0_roots_3 vs Fe0+pyo_roots_3

hyb_protocol: Fe0+pyo_roots_3 Cy5 / Fe0_roots_3 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.


title: Q0005_p_13_F_10

description:
patient
array: HumanHT-12 V4.0

value: F


title: Q0041_p_7_F_28

description:
patient
array: HumanHT-12 V4.0


title: q047_c_39_F_30

description:
mother of q_0045
array: HumanHT-12 V4.0

source_name: mother of q_0045


title: q051_c_6_F_32

description:
control
array: HumanHT-12 V4.0


title: q060_c_13_F_39

description:
control
array: HumanHT-12 V4.0


title: Q0073_c_26_F_42

description:
mother of q_0072
array: HumanHT-12 V4.0

source_name: mother of q_0072


title: q052_c_17_F_33

description:
control
array: HumanHT-12 V4.0

source_name: control


title: q050_c_45_M_31

description:
father of q_0048
array: HumanHT-12 V4.0

source_name: father of q_0048


title: 557182A07 - Fe0_roots_1 vs Fe0+pyo_roots_1

hyb_protocol: Fe0+pyo_roots_1 Cy5 / Fe0_roots_1 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.


title: q059_p_7_F_38

description:
patient (adopted)
array: HumanHT-12 V4.0

source_name: patient (adopted)


title: q061_c_14_F_39

description:
control
array: HumanHT-12 V4.0


title: 557182A04 - pyo_roots_2 vs control_roots_2

hyb_protocol: controle_roots_2 Cy5 / pyo_roots_2 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.


title: 557182A03 - control_roots_2 vs pyo_roots_2

hyb_protocol: pyo_roots_2 Cy5 / controle_roots_2 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.


title: 557182A05 - control_roots_3 vs pyo_roots_3

hyb_protocol: pyo_roots_3 Cy5 / controle_roots_3 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.


title: q063_c_50_F_40

description:
mother of q_0062
array: HumanHT-12 V4.0

source_name: mother of q_0062


title: 557182A02 - pyo_roots_1 vs control_roots_1

hyb_protocol: controle_roots_1 Cy5 / pyo_roots_1 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.


title: q027_c_44_F_20

description:
mom of q_0026
array: HumanHT-12 V4.0

source_name: mom of q_0026


title: q048_p_8_F_31

description:
patient
array: HumanHT-12 V4.0


title: q055_p_30_M_36

description:
patient
array: HumanHT-12 V4.0


title: q045_p_10_M_30

description:
patient
array: HumanHT-12 V4.0


title: q046_c_46_M_30

description:
father of q_0045
array: HumanHT-12 V4.0

source_name: father of q_0045


title: Control VS AgNPs Replicate 5

city: Belvaux

first: Sebastien

last: Cambier

state: - select a state -

address: 41 rue du brill

department: ERIN

country: Luxembourg

institute: LIST - Luxembourg Institute of Science and Technology

description:
Biological replicate 1 of 5. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample15-2B

hyb_protocol: 825 ng of cRNA were used for hybridization after fragmentation with Blocking Agent , 25 X Fragmentation Buffer at 60°C for 30 min. 2x Gee Hybridization Buffer HI-RPM (55 µL) provided in the kit was added to each tube to stop the fragmentation reaction then 100 µL were used for hybridization. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using GenePixPro 6.0 software.

data_processing: GenePixPro 6.0 software was used for background subtraction and intensity adjustment.

organism: Danio rerio

source_name: Entire zebrafish larvae

label_protocol: 200 ng of total RNA were primed with 2 µl of 100 µM T7 promotor primer at 65°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of cDNA master mix (4.7 µL) containing cyanine 3-CTP or cyanine 5-CTP. Then was synthesized by adding Transcription master mix containing Cy3-CTP or Cy5-CTP during 2 h incubation at 40°C.

growth_protocol: Zebrafish eggs maintained in fresh autoclaved conditioned water. Embryos/larvae in respective petri dishes were incubated in 28°C from the day of fertilization (0 dpf) until 5 dpf. Viable embryos/larvae were registered on a daily basis and dead individuals were removed.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: On 5 dpf an equal number of larvae were transferred to each exposure tank (1 L), they were left alone to acclimate until the exposure start on 6 dpf, and one groups was exposed to silver nanoparticles (0.01 mg/L), one group to silver nitrate (0.01 mg/L) and one control group with conditioned water and methylene blue.

value: AB

value: wild type

value: 21 days

tag: condition

value: AgNPs

value: whole larvae

value: Control


title: Control VS AgNPs Replicate 6

description:
Biological replicate 1 of 6. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample17-3B


title: q064_c_18_M_41

description:
control
array: HumanHT-12 V4.0

value: whole blood


title: Control VS AgNPs Replicate 4

description:
Biological replicate 1 of 4. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample13-1B


title: Control VS AgNPs Replicate 2

description:
Biological replicate 1 of 2. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample5A-16


title: Control VS AgNPs Replicate 3

description:
Biological replicate 1 of 3. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample6A-18


title: q026_p_17_M_20

description:
patient
array: HumanHT-12 V4.0


title: q053_c_8_F_34

description:
control
array: HumanHT-12 V4.0

value: healthy control


title: 557182A01 - control_roots_1 vs pyo_roots_1

hyb_protocol: pyo_roots_1 Cy5 / controle_roots_1 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.


title: q009_p_10_M_11

description:
patient
array: HumanHT-12 V4.0

value: M


title: q054_c_20_F_35

description:
control
array: HumanHT-12 V4.0


title: Control VS AgNO3 Replicate 6

description:
Biological replicate 6 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample11-6B


title: q042_c_39_F_28

description:
mother of q_0041
array: HumanHT-12 V4.0

source_name: mother of q_0041


title: Control VS AgNPs Replicate 1

description:
Biological replicate 1 of 6. Control VS AgNPs zebrafish larvae, harvested after 15 days of exposure
Sample4A-14


title: Control VS AgNO3 Replicate 1

description:
Biological replicate 1 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample1A-8


title: Control VS AgNO3 Replicate 3

description:
Biological replicate 3 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample3A-12


title: Control VS AgNO3 Replicate 5

description:
Biological replicate 5 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample9-5B


title: Control VS AgNO3 Replicate 4

description:
Biological replicate 4 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample7-4B


title: q058_c_50_M_37

description:
father of q_0056
array: HumanHT-12 V4.0

source_name: father of q_0056


title: q071_p_44_F_7

description:
patient
array: HumanHT-12 V4.0


title: q033_c_26_F_22

description:
unrelated control
array: HumanHT-12 V4.0

source_name: unrelated control


title: q034_p_13_F_23

description:
patient
array: HumanHT-12 V4.0

source_name: patient


title: q049_c_39_F_31

description:
mother of q_0048
array: HumanHT-12 V4.0

source_name: mother of q_0048


title: q029_c_34_F_21

description:
mom of q_0029
array: HumanHT-12 V4.0

source_name: mom of q_0029


title: Control VS AgNO3 Replicate 2

description:
Biological replicate 2 of 6. Control VS AgNO3 zebrafish larvae, harvested after 15 days of exposure
Sample2A-10


title: q062_p_25_M_40

description:
patient
array: HumanHT-12 V4.0


title: Heart_CON_rep.3

description: in vivo

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Direct Hybridization Assay protocol from Illumina.

source_name: heart muscle tissue, untreated

value: male

value: heart muscle


title: q031_c_66_M_7

description:
grandfather of q_0030 and father of 90007
array: HumanHT-12 V4.0


title: q039_c_18_F_26


title: q030_p_12_M_7

description:
patient and son of 90007
array: HumanHT-12 V4.0

source_name: patient and son of 90007

value: patient

value: no


title: q032_c_adlt_M_7

description:
father of q_0030
array: HumanHT-12 V4.0

source_name: father of q_0030

value: adult


title: q040_c_11_F_27


title: q028_p_7_M_21

description:
patient
array: HumanHT-12 V4.0

value: non


title: Trastuzumab #3

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression in Trastuzumab-treated cells

hyb_protocol: Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray kit 8 x 60K ver2.0 (Agilent) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner system using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Trastuzumab-treated cells_replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: SKBR3 cells were cultivated in McCoy’s 5a medium modified (Sigma-Aldrich).

extract_protocol: RNA was prepared using the RNeasy Micro Kit (Qiagen) following the manufacturer's recommendations.

tag: treatment

value: Trastuzumab


title: Trastuzumab-NLS-L #2

description: Gene expression in Trastuzumab-NLS-L-treated cells

value: Trastuzumab-NLS-L


title: Trastuzumab-NLS-L #3


title: MRP8_4h, 2

city: Münster

first: Mona

last: Riemenschneider

address: Domagkstraße 3

institute: Genetic Epidemiology, University of Muenster

hyb_protocol: biotinylated cRNA was hybridized and stained (Cy3) according to the manufacturer´s instruction

scan_protocol: hybridized arrays were scanned using the BeadArray Reader (Illumina).

data_processing: raw data pre-processing was executed with Genome Studio (Illumina, Version 1.9.0). The data were normalised using quantile normalisation.

source_name: Monocytes, stimulated for 4 hours with 5µg/ml MRP8

label_protocol: total RNA was in vitro transcripted and amplified to biotinylated cRNA unsing the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer´s instruction

extract_protocol: total RNA from 5x10^6 MRP8 stimulated or untreated human monocytes was isolated (NucleoSpin®RNAII, Macherey-Nagel, Dueren, Germany).

value: blood


title: MRP8_4h, 1


title: Gene Expression-3h Camptothecin treated cells-Total RNA

city: Bethesda

first: Vivek

last: Sharma

state: MD

address: 41 Library Drive

department: CCR

institute: NCI

description: Human Fibroblast cells -Camptothecin treated-3hrs

hyb_protocol: Agilent 5188-5242 Gene Expression Hybridization Kit was used to prepare hybridization

scan_protocol: scanned in an Agilent C-Scanner

data_processing: The data was extracted with Agilent Feature extraction 10.7. The data were analyzed with Excel.

source_name: Human Fibroblast cells immortalised with htert

label_protocol: Two Color Labelling using, Quick Amp Labeling kit, Agilent 5190-0444

growth_protocol: Human Fibroblast cells were grown in 10 MEM supplemented with Penn/Strep and Glutamine

extract_protocol: Total RNA was extracted using the RNAeasy kit (Qiagen), Nuclear RNA was isolated using the Ambion® PARIS™ system (Life Technologies)

treatment_protocol: Cells were treated with DNA damaging reagents for 3 hours

value: hTERT immortalised

value: Untreated

value: Camptothecin


title: MRP8_4h, 3


title: Trastuzumab #1

source_name: Trastuzumab-treated cells_replicate 1


title: Trastuzumab-NLS-L #1


title: Gene Expression-3h Camptothecin treated cells-Nulcear RNA

molecule: nuclear RNA


title: Gene Expression-3h  Neocarzinostatin treated cells - TotalRNA

description: Human Fibroblast cells -Neocarzinostatin treated-3hrs

value: Neocarzinostain


title: Untreated #3

description: Gene expression in untreated cells

source_name: Untreated cells_replicate 3

value: Medium only


title: Gene Expression - 3h Etoposide treated cells-Total RNA

description: Human Fibroblast cells -Etoposide treated-3hrs

value: Etoposide


title: In-111-trastuzumab #1

description: Gene expression in In-111-trastuzumab-treated cells

value: In-111-trastuzumab, 231.25 MBq


title: Trastuzumab #2

source_name: Trastuzumab-treated cells_replicate 2


title: Gene Expression - 3h Etoposide treated cells-Nuclear RNA


title: In-111-trastuzumab-NLS-L #2

description: Gene expression in In-111-trastuzumab-NLS-L-treated cells

value: In-111-trastuzumab-NLS-L, 231.25 MBq


title: In-111-trastuzumab-NLS-L #1


title: In-111-trastuzumab-NLS-L #3


title: n_4h, 1

source_name: Monocytes; non-stimulated

value: male


title: placenta_cpi_44

city: Hamilton

first: Jefferson

last: Terry

state: Ontario

address: 1280 Main St West

institute: McMaster Universtiy

description: SS gene expn 44-Positive control 10

hyb_protocol: Samples were hybridized to the Illumina HumanHT-12 WG-DASL V4.0 according to the manufacturer’s protocol

scan_protocol: Arrays were scanned on the iScan system according to Illumina's protocol

data_processing:
Raw data pre-processing consisted of background correction using the non-genomic control probes on each chip, followed by quantile normalization and log2 transformation.
All data pre-processing was conducted in R version 3.0.1 (2013-05-16) and the neqc function in the LIMMA bioconductor package (limma_3.18.13) was implemented. The reference for the function is PMID:20929874..

source_name: FFPE placenta_CPI

label_protocol: 200ng of total RNA was reverse-transcribed and biotinylated using the Illumina WG-DASL assay according to the protocol

extract_protocol: Total RNA was isolated from five 10-micron tissue sections from 2 separate areas of placental disc (100 microns total placental tissue) using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol

value: primary placenta

tag: sample group

value: with chronic placental inflammation (CPI)


title: n_4h, 2


title: n_4h, 3


title: placenta_cpi_47

description: SS gene expn 47-Positive control 13

data_processing:
Raw data pre-processing consisted of background correction using the non-genomic control probes on each chip, followed by quantile normalization and log2 transformation.
All data pre-processing was conducted in R version 3.0.1 (2013-05-16) and the neqc function in the LIMMA bioconductor package (limma_3.18.13) was implemented. The reference for the function is PMID:20929874.


title: In-111-trastuzumab #2


title: In-111-trastuzumab #3


title: Untreated #1

description: Gene expression in untreated cells

source_name: Untreated cells_replicate 1


title: Untreated #2

description: Gene expression in untreated cells

source_name: Untreated cells_replicate 2


title: placenta_cpi_46

description: SS gene expn 46-Positive control 12


title: placenta_cpi_43

description: SS gene expn 43-Positive control 9


title: CD45+ HLA-DR+ sample from subject # 8 after allergen challenge.

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

hyb_protocol: CD4 T cell samples were hybridized to Human Gene 1.0 ST microarrays and CD45+ HLA-DR+ samples were  hybridized to Human Gene 1.1 ST microarrays at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).

scan_protocol: The samples were scanned on an Affymetrix GeneChip® Scanner 3000 7G (CD4 T cell samples) or on an Affymetrix GeneTitan system (CD45+HLA-DR+ cells).

data_processing: The raw microarray data was preprocessed in R software using the Single Channel Array Normalization (SCAN) algorithm and a custom chip description file (CD4 T cell samples, hugene10sthsentrezgprobe, version 17; CD45+HLA-DR+ samples, hugene11sthsentrezgprobe, version 17)

label_protocol: The samples were processed using the NuGEN Ovation Pico WTA with the WT-Ovation Exon Module and the Encore Biotin Module at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia).

growth_protocol: A mucosal biopsy was obtained on day 0 (prior to nasal challenge) from the lower turbinate of one nostril. The other untouched nasal cavity was then challenged daily for 8 days with a solution of birch pollen extract. A mucosal biopsy was obtained on day 9 from the challenge site.

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

treatment_protocol: The biopsy specimens were immediately digested for 60 min at 37°C in DMEM medium containing 2 mg/ml Liberase TL. The samples were washed, filtered, stained with a panel of antibodies, and CD4 T cells and CD45+ HLA-DR+ cells were isolated by FACS sorting.

tag: phenotype

value: Allergic rhinitis patient

value: CD45+ HLA-DR+

tag: individual

value: subject # 8

value: after allergen challenge


title: placenta_ctrl_39

description: SS gene expn 39-Positive control 5

source_name: FFPE placenta_control

tag: tissue

value: Control (no chronic placental inflammation)


title: CD45+ HLA-DR+ sample from subject # 8 at baseline.

value: baseline


title: CD45+ HLA-DR+ sample from subject # 5 after allergen challenge.

value: subject # 5


title: 557182A06 - pyo_roots_3 vs control_roots_3

description: Analyse de l’effet d’un traitement par la pyoverdine sur les gènes liés à l’homéostasie du fer et à l’induction des réactions de défense.

hyb_protocol: controle_roots_3 Cy5 / pyo_roots_3 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.

value: Columbia (Col-0)


title: CD45+ HLA-DR+ sample from subject # 4 after allergen challenge.

value: subject # 4


title: 343754_mixPulseCy3-mixCy5

city: Groningen

first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

institute: University of Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman TG et al., 2006b

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

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

organism: Streptococcus pneumoniae D39

source_name: cells

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

growth_protocol: Cells were grown to MID-log phase in CDM with the respective sugar

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

tag: strain d39

tag: growth sugar

value: mixPulse

source_name: F635 Mean

value: mix


title: placenta_cpi_42

description: SS gene expn 42-Positive control 8


title: placenta_ctrl_38

description: SS gene expn 38-Positive control 4


title: CD45+ HLA-DR+ sample from subject # 4 at baseline.

tag: cell type


title: placenta_cpi_45

description: SS gene expn 45-Positive control 11


title: CD45+ HLA-DR+ sample from subject # 1 after allergen challenge.

value: subject # 1


title: placenta_ctrl_37

description: SS gene expn 37-Positive control 3


title: 343753_mixCy3-mixPulseCy5

description: Sample 1


title: 343757_ManCy3-ManPulseCy5

description: Sample 1

value: Man

value: ManPulse


title: 343758_ManPulseCy3-ManCy5

description: Sample 2


title: CD45+ HLA-DR+ sample from subject # 5 at baseline.


title: placenta_ctrl_36

description: SS gene expn 36-Positive control 2


title: CD45+ HLA-DR+ sample from subject # 1 at baseline.


title: CD45+ HLA-DR+ sample from subject # 3 after allergen challenge.

value: subject # 3


title: 343755_GlcNacPulseCy3-GlcNacCy5

description: Sample 1

value: GlcNacPulse

value: GlcNac


title: 343756_GlcNacCy3-GlcNacPulseCy5

description: Sample 2


title: GSC35

city: Austin

first: Brian

middle: D

last: Vaillant

state: TX

department: Neurology

institute: Seton Brain and Spine Institute

hyb_protocol: Performed by Expression Analysis (Durham, NC)

data_processing: Affymetrix data processed in R using a custom CDF from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp   ; package 'affy' from Bioconductor suite, robust multi-array average (rma) data processing

source_name: Glioma Stem Cells isolated from glioblastoma

growth_protocol: Neural basal media supplemented with bFGF and EGF

extract_protocol: Whole RNA extraction kit from ABI

value: brain

value: glioma stem cells


title: 343751_glucoseCy3-mannoseCy5

description: Sample 1

value: glucose

value: mannose


title: GSC34

scan_protocol: Performed by Expression Analysis (Durham, NC)


title: GSC38

label_protocol: Performed by Expression Analysis (Durham, NC)


title: GSC28


title: 343752_mannoseCy3-glucoseCy5

description: Sample 2


title: GSC46


title: GSC37


title: GSC30


title: GSC42


title: 344304_galactoseCy3-glucoseCy5

description: Sample 2

value: galactose


title: placenta_ctrl_40

description: SS gene expn 40-Positive control 6

value: primary placenta

value: Control (no chronic placental inflammation)


title: 343750_glucoseCy3-GlcNacCy5

description: Sample 2


title: 344305_GlcNacCy3-glucoseCy5

description: Sample 1


title: GSC13


title: GSC16


title: genomic_DNA_from_contol_brain_BS_rep1

type: genomic

city: Setagaya-ku

first: Keiko

last: Matsubara

state: Tokyo

department: Department of Molecular Endocrinology

institute: National Research Institute for Child Health and Development

description:
control_brain_BS_rep1
control_brain

hyb_protocol: Oxidative bisulfite and bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from LBC samples of KOS14 and normal controls using Qiagen Gentra Puregene Blood Kit according to standard instructions. Brain gDNA was purchased  from BioChain (catalogue #D1234035, lot #B801123) .

tag: gender

value: Male

tag: disease state

value: normal

tag: dna conversion protocol

value: BS


title: 343760_GalPulseCy3-GalCy5

description: Sample 2

value: GalPulse

value: Gal


title: 344303_glucoseCy3-galactoseCy5

description: Sample 1


title: 343759_GalCy3-GalPulseCy5

description: Sample 1


title: GSC7-2


title: GSC6-27


title: GSC23


title: GSC20


title: genomic_DNA_from_control_brain_BS_rep2

description:
control_brain_BS_rep2
control_brain


title: genomic_DNA_from_control_brain_oxBS_rep1

description:
control_brain_oxBS_rep1
control_brain

value: oxBS


title: GSC11


title: genomic_DNA_from_control_brain_oxBS_rep2

description:
control_brain_oxBS_rep2
control_brain


title: GSC2


title: CD4 T cell sample from subject # 8 at baseline.

value: Allergic rhinitis patient

value: CD4 T cell

value: subject # 8

value: baseline


title: CD4 T cell sample from subject # 8 after allergen challenge.

value: after allergen challenge


title: CD4 T cell sample from subject # 6 at baseline.

value: subject # 6


title: CD4 T cell sample from subject # 5 after allergen challenge.

value: subject # 5


title: GSC17

value: brain

value: glioma stem cells


title: genomic_DNA_from_KOS14_patient3_BS_rep1

description:
KOS14_patient3_BS_rep1
KOS14_patients_blood

value: patient 3

value: Female

value: peripheral blood


title: genomic_DNA_from_KOS14_patient3_BS_rep2

description:
KOS14_patient3_BS_rep2
KOS14_patients_blood


title: CD4 T cell sample from subject # 5 at baseline.


title: genomic_DNA_from_KOS14_patient2_BS_rep1

description:
KOS14_patient2_BS_rep1
KOS14_patients_blood

value: patient 2

value: Male


title: CD4 T cell sample from subject # 4 after allergen challenge.

value: subject # 4


title: genomic_DNA_from_control_blood_oxBS_rep2

description:
control_blood_oxBS_rep2
control_blood

value: Pooled male and female

value: normal


title: CD4 T cell sample from subject # 4 at baseline.

value: Allergic rhinitis patient


title: Sample7-DN T-cells

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: not provided

scan_protocol: not provided

data_processing: BeadStudio

source_name: DN T cells

label_protocol: not provided

growth_protocol: n/a (isolated cell populations)

extract_protocol: Double negative T cells and autologous CD4+ and CD8+ T cells were isolated using the T cell isolation protocol (see overall design). RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) and RNeasy kits (Qiagen, Valencia, CA). RNA was then purified from DNA contaminants using a Turbo DNA-free kit (Ambion, Austin, TX) as per manufacturer’s instructions, and RNA concentration was measured with a Nanodrop 2000 Spectrophotometer (Thermo Scientific, Wilmington, DE). Purified RNA was then used for the RT-PCR quantification of DNA methyltransferases DNMT1, DNMT3A, and DNMT3B, relative to ACTB (β actin), using a ViaA 7 Real-Time PCR System (Applied Biosystems, Carlsbad, CA) and a Power SYBR Green RNA-to-CT 1-Step kit (Applied Biosystems, Carlsbad, CA) with 10μL reaction mixtures and PCR conditions suggested by the manufacturer.

treatment_protocol: T cells were sorted into TCRαβ+ CD4+ T cells, TCRαβ+ CD8+ T cells, and TCRαβ+ DN T cell subsets by flow cytometry.

tag: age

tag: cell population

value: TCRαβ+ DN T cells


title: genomic_DNA_from_KOS14_patient3_oxBS_rep2

description:
KOS14_patient3_oxBS_rep2
KOS14_patients_blood

value: oxBS


title: genomic_DNA_from_control_blood_BS_rep2

description:
control_blood_BS_rep2
control_blood

value: BS


title: CD4 T cell sample from subject # 3 after allergen challenge.

value: CD4 T cell

value: subject # 3

value: after allergen challenge


title: genomic_DNA_from_KOS14_patient1_oxBS_rep2

description:
KOS14_patient1_oxBS_rep2
KOS14_patients_blood

value: patient 1


title: genomic_DNA_from_KOS14_patient2_BS_rep2

description:
KOS14_patient2_BS_rep2
KOS14_patients_blood


title: genomic_DNA_from_KOS14_patient1_BS_rep2

description:
KOS14_patient1_BS_rep2
KOS14_patients_blood


title: genomic_DNA_from_KOS14_patient2_oxBS_rep2

description:
KOS14_patient2_oxBS_rep2
KOS14_patients_blood


title: Sample3-DN T-cells


title: Sample4-DN T-cells


title: genomic_DNA_from_control_blood_BS_rep1

description:
control_blood_BS_rep1
control_blood


title: genomic_DNA_from_KOS14_patient1_oxBS_rep1

description:
KOS14_patient1_oxBS_rep1
KOS14_patients_blood


title: KO5

city: Boston

first: Sarah

last: Morton

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: miRNA profiling

data_processing:
LC Biosciences protocol done at their facility
Signals <500 considered unreliable.

source_name: Quadriceps, day 7

growth_protocol: Routine mouse care

extract_protocol: miRvana

tag: strain

tag: genotype/variation

value: cofilin-2 null

value: quadriceps


title: KO4

description: miRNA profiling

hyb_protocol: LC Biosciences protocol done at their facility


title: KO3

description: miRNA profiling

scan_protocol: LC Biosciences protocol done at their facility


title: CD45+ HLA-DR+ sample from subject # 3 at baseline.

value: CD45+ HLA-DR+

value: baseline


title: genomic_DNA_from_KOS14_patient2_oxBS_rep1

description:
KOS14_patient2_oxBS_rep1
KOS14_patients_blood

value: patient 2

value: peripheral blood


title: genomic_DNA_from_KOS14_patient1_BS_rep1

description:
KOS14_patient1_BS_rep1
KOS14_patients_blood

value: Male


title: Sample6-DN T-cells

value: Female


title: Sample5-DN T-cells


title: KO6

description: miRNA profiling

label_protocol: LC Biosciences protocol done at their facility


title: KO1

description: miRNA profiling


title: WT6

description: miRNA profiling

value: wildtype


title: KO2

description: miRNA profiling


title: WT5

description: miRNA profiling


title: Sample2-DN T-cells


title: Sample1-DN T-cells


title: WT4

description: miRNA profiling


title: CAF__3

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description:
cancer associated fibroblasts
US11103886_253575810003_S01_miRNA_107_Sep09_2_4

hyb_protocol: hybridization for 20 h at 55°C

scan_protocol: scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: One to 4 different probes can target each miRNA and each probe is spotted 10 to 40 times on the array. The total gene signal for each miRNA was obtained by summing the probe signals derived with the Agilent Feature Extraction software. Each probe was defined as detected if its value is greater than 3 times its standard error, and each miRNA was defined as detected if at least one of the probes was detected Data were log2 transformed and normalized using the Robust Spline Normalization algorithm. Only human (“hsa”) miRNAs detected in at least two samples were selected for downstream analyses.

source_name: patient-derived fibroblasts

label_protocol: Two μg of RNA were labeled and processed according to the manufacturer’s recommended protocol

growth_protocol: Human prostate fibroblasts, HPFs and CAFs, were isolated from healthy and intratumoral regions, respectively, of the prostate of PCa-bearing patients. Tissues were digested overnight in DMEM supplemented with 5% fetal bovine serum and 1X Collagenase-Hyaluronidase Solution (STEMCELLTM Technologies Inc.). Cell suspension was centrifuged at 1,500 g for 5 minutes. The resulting fibroblast-rich pellet was suspended and plated in DMEM containing 10% fetal bovine serum and 4 mM L-Glutammine.

extract_protocol: Total RNA from cells was extracted using TRIzol® reagent (Life Technologies), according to the manufacturer’s instructions.

treatment_protocol: HPFs were grown to sub-confluence and treated for 48 h with 10 ng/ml rTGFβ1 or 50 ng/ml IL6.

value: cancer associated fibroblasts

tag: replicate


title: HPF_IL6_3

description:
human prostate fibroblasts IL6
US11103886_253575810003_S01_miRNA_107_Sep09_2_3

value: prostate fibroblasts


title: CD4 T cell sample from subject # 3 at baseline.

value: Allergic rhinitis patient


title: HPF__3

description:
human prostate fibroblasts
US11103886_253575810003_S01_miRNA_107_Sep09_2_1


title: HPF_TGFbeta_3

description:
human prostate fibroblasts TGFb
US11103886_253575810003_S01_miRNA_107_Sep09_2_2

value: TGFbeta


title: WT3

description: miRNA profiling


title: WT2

description: miRNA profiling


title: genomic_DNA_from_KOS14_patient3_oxBS_rep1

description:
KOS14_patient3_oxBS_rep1
KOS14_patients_blood

value: patient 3

value: oxBS


title: CAF__2

description:
cancer associated fibroblasts
US11103886_253575810003_S01_miRNA_107_Sep09_1_4


title: WT1

description: miRNA profiling


title: genomic_DNA_from_control_blood_oxBS_rep1

description:
control_blood_oxBS_rep1
control_blood

value: Pooled male and female

value: normal


title: Sample5-CD8+ T-cells

source_name: CD8+ T cells

value: TCRαβ+ CD8+ T cells


title: two days after akinete induction

city: Northridge

first: Michael

middle: L.

last: Summers

state: California

address: 18111 Nordhoff St

department: Dept. of Biology

institute: California State University Northridge

description: Analysis used RNA of a zwf mutant as control samples for comparison to the experimental samples contining RNA from a zwf/sigG mutant two days after akinete induction

hyb_protocol: Single and double mutant samples were combined, concentrated by vacuum centrifugation, dissolved in 1X GeneFrames hybridization buffer, and applied to spotted array slides.  Hybridization was conducted for 16 hours at 50°C using a Tecan 480 hybridization station.  Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.5x SSC each at 37 °C using a 1 minute soak and 1 minute wash for each prior to drying and scanning.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and GenePix Pro-6.0 software (Molecular Devices)

data_processing: Spot analyis s for each slide was conducted using the GenePix Pro software after manually confirming/editing automated spot alignments.  The resulting .gpr files were normalized and statistically analyzed using R and LIMA GUI packages as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256).  Loess was used for within array normalization and aquantile was used for between array normalization.

label: Alexa555, Alexa647

organism: Nostoc punctiforme

source_name: zwf mutant control samples grown with ammonia/nitrate 2 days after akinete induction

label_protocol: Fifteen micrograms of total RNA were used for cDNA synthesis using SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen).  The resulting cDNA was labeled with either Alexa Flouor 555 or 647 using an Invitrogen Reactive Dye Module.

growth_protocol: For vegetative growth comparisons zwf and zwf sigG strains were grown as 50 ml liquid cultures in 125 ml erylemyer flasks with cotton stoppers.  Flasks contained AA/4 media supplemented with ammonia/nitrate/fructose (2.5, 5.0, 50 mM, respectively).  Cultures were harvested in the exponential growth phase shaking at 100 rpm under ~15 PFD at 25°C.  To compare gene expression following akinete induction, flasks containing similarly grown exponential cultures were covered with foil at time zero to initiate darkness and RNA harvested after 48 hours.

extract_protocol: RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)

treatment_protocol: No treatment was given to the vegetative grown cultures.  Akinete induced culture flasks were wrapped in aluminum foil and a second piece of foil was loosely draped over the top of the flask to allow gas exchange but stop the entry of light.

value: zwf mutant (CTL)

source_name: zwf/sigG double mutant experiental samples grown with ammonia/nitrate 2 days after akinete induction

value: zwf/sigG mutant (EXP)


title: CD4 T cell sample from subject # 6 after allergen challenge.

value: CD4 T cell

value: subject # 6

value: after allergen challenge


title: OA3

city: strasbourg

first: philippe

last: georgel

address: 1 Place de l'Hopital

institute: strasbourg university

description: RNA isolated FLS from OA patient 3

data_processing:
Qiagen proprietary software, normalization with the most invariant housekeeping small RNAs
OA samples as controls

label: SYBR Green

source_name: FLS from OA patient 3

label_protocol: sybr green

growth_protocol: cells were grown for 4 passages

extract_protocol: Trizol according manufacturer's instructions

value: FLS cultured from a synovial biopsy


title: vegetative growth

description: Analysis used vegetatively grown steady state RNA of a zwf mutant as control samples for comparison to the experimental samples contining RNA from a zwf/sigG mutant

source_name: steady state vegetative zwf mutant control samples grown with ammonia/nitrate

source_name: steady state vegetative zwf/sigG double mutant experiental samples grown with ammonia/nitrate


title: HPF_IL6_2

description:
human prostate fibroblasts IL6
US11103886_253575810003_S01_miRNA_107_Sep09_1_3


title: Sample3-CD8+ T-cells

value: Female


title: CAF__1

description:
cancer associated fibroblasts
US11103886_253575810002_S01_miRNA_107_Sep09_2_4


title: HPF_IL6_1

description:
human prostate fibroblasts IL6
US11103886_253575810002_S01_miRNA_107_Sep09_2_3


title: Sample1-CD8+ T-cells


title: OA4

description: RNA isolated FLS from OA patient 4

source_name: FLS from OA patient 4


title: Sample2-CD8+ T-cells


title: HPF_TGFbeta_1

description:
human prostate fibroblasts TGFb
US11103886_253575810002_S01_miRNA_107_Sep09_2_2


title: HPF__2

description:
human prostate fibroblasts
US11103886_253575810003_S01_miRNA_107_Sep09_1_1


title: HPF__1

description:
human prostate fibroblasts
US11103886_253575810002_S01_miRNA_107_Sep09_2_1


title: Sample7-CD8+ T-cells


title: OA2

description: RNA isolated FLS from OA patient 2

source_name: FLS from OA patient 2


title: HPF_TGFbeta_2

description:
human prostate fibroblasts TGFb
US11103886_253575810003_S01_miRNA_107_Sep09_1_2


title: Sample5-CD4+ T-cells

source_name: CD4+ T cells

value: TCRαβ+ CD4+ T cells


title: Sample4-CD8+ T-cells


title: RA3

description: RNA isolated from FLS from RA patient 3

source_name: FLS from RA patient 3


title: RA4

description: RNA isolated from FLS from RA patient 4

source_name: FLS from RA patient 4


title: OA1

description: RNA isolated FLS from OA patient 1

source_name: FLS from OA patient 1


title: RA2

description: RNA isolated from FLS from RA patient 2

source_name: FLS from RA patient 2


title: RA1

description: RNA isolated from FLS from RA patient 1

source_name: FLS from RA patient 1


title: Sample6-CD4+ T-cells


title: Sample3-CD4+ T-cells


title: WholeFish_4.84 ug/L_rep12C3

city: Davis

first: Ken

last: Jeffries

address: One Shields Avenue

institute: UC Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >13.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2.5 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Hypomesus transpacificus

source_name: Whole Fish, 4.84 ug/L

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrophotometer.

growth_protocol: Hypomesus transpacificus were allowed 24 hours to acclimatize to holding conditions at the Aquatic Toxicology Laboratory at the University of California Davis.

extract_protocol: At the termination of the 96 hour exposure period, fish were sacrificed by a lethal dose of MS-222 and whole fish were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Whole fish from the exposures were homogenized using a pestle in 1 ml of Trizol reagent following manufacturer’s protocols, which was followed by RNA Cleanup using RNeasy columns (Qiagen) with on-column DNAse digestion. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrophotometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Hypomesus transpacificus were exposed for 96 hours to measured concentrations of 0.69, 1.37, 2.56, 4.84 ug/L of permethrin, along with a control group handled identically to the other treatments.

value: 4.84 ug/L permetrhin


title: Sample7-CD4+ T-cells


title: WholeFish_2.56 ug/L_rep11D1

source_name: Whole Fish, 2.56 ug/L

value: 2.56 ug/L permetrhin


title: Sample6-CD8+ T-cells


title: WholeFish_4.84 ug/L_rep12A2


title: WholeFish_2.5mg/L_repD4

description: Sample name: D4 - 2.5

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 80 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Menidia beryllina

source_name: Whole fish, 2.5 mg/L ibuprofen exposure

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Menidia beryllina were allowed four days to acclimatize to holding conditions at the Aquatic Toxicology Laboratory at the University of California Davis.

extract_protocol: At the termination of the 14 d exposure period, fish were sacrificed by a lethal dose of MS-222 and whole fish were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Whole fish from the 14 d exposures were homogenized using a pestle in 1 ml of Trizol reagent following manufacturer’s protocols. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Menidia beryllina were exposed for 14 d to nominal concentrations of 0.025, 0.25 and 2.5 mg/L of ibuprofen, along with a control group handled identically to the other treatments.

value: ibuprofen

tag: treatment dose

value: whole fish


title: WholeFish_2.5mg/L_repD1

description: Sample name: D1 - 2.5

tag: treatment


title: WholeFish_4.84 ug/L_rep12B4


title: WholeFish_2.56 ug/L_rep11B2


title: WholeFish_2.5mg/L_repB5

description: Sample name: B5 - 2.5


title: WholeFish_2.56 ug/L_rep11A3


title: WholeFish_2.56 ug/L_rep11C4


title: WholeFish_2.5mg/L_repB8

description: Sample name: B8 - 2.5


title: WholeFish_2.5mg/L_repC6

description: Sample name: C6 - 2.5


title: WholeFish_2.5mg/L_repB1

description: Sample name: B1 - 2.5


title: Sample4-CD4+ T-cells


title: Sample1-CD4+ T-cells


title: Sample2-CD4+ T-cells


title: siNS2,Biological Replicate2

description: Gene expression data upon transcfection with siNS

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files from Affymetrix were imported into Partek Genomics Suite (Partek Incorporated) and RMA normalized.  Differentially expressed genes (DEG) were defined as genes having ≥ 1.5-fold change of expression in pair-wise comparison P value <0.05, unless otherwise stated (unadjusted p value).

source_name: hTERT immortalised Human Fibroblast cells

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen)

treatment_protocol: hTERT immotalised Human Fibroblast cells were transfected a non specific siRNA or siRNA against DDSR1,72 hours post transfection RNA was isolated and process for Microarray

tag: cell line

value: hTERT immortalised

tag: transfection

value: non specific siRNA


title: WholeFish_0.25mg/L_repB5

description: Sample name: B5 - 0.25

source_name: Whole fish, 0.25 mg/L ibuprofen exposure


title: WholeFish_1.37 ug/L_rep10D2

source_name: Whole Fish, 1.37 ug/L

value: 1.37 ug/L permetrhin


title: WholeFish_1.37 ug/L_rep10A2


title: WholeFish_0.25mg/L_repB1

description: Sample name: B1 - 0.25


title: WholeFish_0.69 ug/L_rep9D1

source_name: Whole Fish, 0.69 ug/L

value: 0.69 ug/L permetrhin


title: WholeFish_1.37 ug/L_rep10C4


title: WholeFish_0.25mg/L_repA8

description: Sample name: A8 - 0.25


title: WholeFish_1.37 ug/L_rep10B3


title: Cortex Replicate 1

city: Montreal

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

description: Biological replicate 1 of 3. Naive mice

hyb_protocol: All the steps of hybridization, washing, scanning and feature extraction were performed following the Agilent protocols for methylated DNA immunoprecipitation analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B. Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: The extracted intensities were then analyzed using the R software environment for statistical computing (R Development Core Team, 2007). Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization (Bolstad et al., 2003) under the assumption that all samples have identical overall methylation levels.

source_name: pooled DNA of frontal cortex

label_protocol: The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP respectively using the SureTag Complete DNA Labeling Kit (Agilent) following the manufacturer’s instructions.

growth_protocol: Naïve male C57BL/6 mice of 2 months old

extract_protocol: Triplicates of 2μg of frontal cortex DNA pools of 3 mice were sonicated. Methylated DNA was then immunoprecipitated with 10 μg of anti-5methylCytosine antibody (Eurogentec, Cat. # BI-MECY) that does not recognize DNA hydroxymethylation. The DNA-antibody complex was immuno-precipitated with 50 ul of protein G. The input and bound fractions were then purified and amplified using the Whole Genome Amplification kit (Sigma).

tag: Sex

value: male

value: 2 months

value: frontal cortex

tag: molecule subtype

value: input DNA

value: immunoprecipitated DNA


title: WholeFish_0.69 ug/L_rep9B3