title: Chinese Spring control LYC-CK

description: Chinese Spring

source_name: roots water

value: tap water


title: AC_Test_15

status: Public on Jan 01 2012

type: RNA

city: London

first: Charles

middle: R. M.

last: Bangham

address: Norfolk Place

department: Immunology

country: United Kingdom

institute: Imperial College London

description: globin-reduced total RNA

hyb_protocol: Following the manufacturer’s protocol, cRNA was hybridized overnight to HumanWG6 v3 expression BeadChip arrays (Illumina, San Diego, CA, USA).

scan_protocol: Standard Illumina scanning protocol (Illumina BeadStation 500).

data_processing: Microarray signal intensity values were acquired with BeadStudio version 2.0 software (Illumina). Raw gene expression values were normalised and analysed with GeneSpring GX7.3.1 software (Agilent Technologies). Normalization followed a standard 2-step procedure for one-colour arrays: first, BeadStudio raw gene expression values were transformed by setting signal values <10 to 10, then per-gene normalisation was applied by dividing each probe’s intensity by the median intensity value for all samples.

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: The globin-depleted mRNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: RNA was extracted using the Tempus Spin Isolation kit (Applied Biosystems) and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA); all samples scored integrity values ≥9 (scale: 0-10). Globin mRNA was depleted using the GLOBIN-clearTM-Human kit (Ambion, Austin, TX, USA).

tag: gender

value: F

tag: ethnicity

value: African Caribbean

tag: age

tag: proviral load

tag: disease status

value: AC

tag: barcode


title: T5KO + FliC 3

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

country: USA

institute: Emory University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

label: biotin

organism: Mus musculus

source_name: T5KO + FliC

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

growth_protocol: Generation of WT, T5KO, N4KO and T5/N4-DKO was previously described 7. Mice were bred and maintained at Emory University and used between 6 and 8 weeks of age.

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: Flagellin (FliC) from WT Salmonella enterica serovar Typhimurium (SL3201, fljB–) was purified through sequential cation and anion-exchange chromatography and purity was verified as previously described.

tag: mouse ko type

tag: tissue type

value: Colon

tag: treatment

value: Flagelin


title: set3D LatA biological replicate 3

first: Jim

last: Karagiannis

state: Ontario

address: 1151 Richmond St. N

department: Biology

country: Canada

institute: University of Western Ontario

description: Gene expression data for LatA treated set3D strains

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

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

data_processing: Analysis was performed using Genespring GX 10.0.1 software (Agilent).  CEL files were normalized with the RMA algorithm.  The data were grouped according to: genotype, wild-type or set3D, and drug, LatA or DMSO treatment.  All of the data could thus be classified as 1) wild-type, DMSO treated, 2) wild-type, LatA treated, 3) set3D, DMSO treated, and 4) set3D, LatA treated. To identify differentially regulated genes, data for these genes were inspected and data were filtered using Volcano plot analysis employing the Benjamin-Hochberg multiple testing correction.  Genes  showing statistically significant differences (p-value <0.05) and fold changes greater than 1.5 were identified as differentially regulated.

organism: Schizosaccharomyces pombe

source_name: set3D strain, LatA treated, 0.5 mM, 3 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All strains were grown in liquid YES media with constant shaking.

extract_protocol: Total RNA extraction was performed using the Ribopure Yeast Kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Strains were treated with 0.5 mM LatA or DMSO for 3 hours prior to RNA extraction.

tag: genotype

value: set3::KanMX ura4-D18 leu1-32 ade6-216

value: LatA


title: set3D LatA biological replicate 1


title: T5KO + FliC 2


title: set3D LatA biological replicate 2


title: SA461 Parental pluripotent hESC control sample rep1

first: Nicole

middle: Margaret

last: Kane

address: 30 Guilford Street

institute: University College London

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Tests are performed between different sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: SA461 hESC cell line

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: hESC-ECs were derived from human embryonic stem cell line SA461 via a published directed differentiation protocol (Kane et al, ATVB, 2010). SA461 hESC cells were maintained under feeder-free pluripotent conditions.

extract_protocol: miRNeasy

tag: cell line

tag: developmental state

value: Parental pluripotent hESC control

tag: time

value: control


title: AC_Test_14

description: globin-reduced total RNA

value: Caucasian


title: set3D DMSO biological replicate 3

description: Gene expression data for DMSO treated set3D strains

source_name: set3D strain, DMSO treated, 3 hrs

value: DMSO


title: T5KO + FliC 1


title: set3D DMSO biological replicate 2


title: T5KO + PBS 3

source_name: T5KO + PBS

value: PBS


title: Ton1Rep1Exp2_ProcessedSignal(normalized)

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

country: Germany

hyb_protocol: following fragmentation, 600ng of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 8x15K Agilent Ustilago_v1 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 9.5.3.1 (Agilent Technologies Germany). Each target (6783) is represented by two probes (features)

data_processing: Signal intensities were normalized to the 75th percentile and normalized data were baseline transformed to the median using Gene Spring XI software (Agilent Technologies).

organism: Mycosarcoma maydis

source_name: sporidia, 2 h after transfer from AMM to -N medium

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 400ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Sporidia of the indicated U. maydis strains were grown at 28°C in ammonium minimal medium (AMM) overnight to OD~1 and washed twice with distilled water prior to transfer into nitrogen starvation medium (see below).

extract_protocol: Total RNA from sporidia harvested during the exponential growth phase was extracted using a guanidium isothiocyanate based method (as described by Chomczynski and Sacchi, 1987).

treatment_protocol: Two hours after transfer from AMM to nitrogen starvation medium (-N), sporidia grown at 28°C were harvested for total RNA extraction.

value: Ton1 deletion strain

tag: experiment

value: Experiment 2


title: AC_Test_12

description: globin-reduced total RNA


title: T5KO + PBS 2


title: Ton1RepExp2_ProcessedSignal(normalized)


title: Ton1Rep3Exp2_ProcessedSignal(normalized)


title: set3D DMSO biological replicate 1


title: AC_Test_10

description: globin-reduced total RNA


title: Luohan control CK-4-2

city: Zhengzhou

first: Yongchun

last: Li

state: Henan

address: Nongye Road No. 62

department: National Engineering Research Center for Wheat

country: China

institute: Henan Agricultural University

description: Luohan 2 cultivar

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

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Seeds were surface-sterilized in 70% alcohol for 5 min, 0.1% HgCl for 15min and washed 6 times (2 min each) in distilled water, then germinated and cultured in Petri dishes with water in a temperature-controlled cultivation chamber at 25 °C with a 14 hour photoperiod.

extract_protocol: RNA was extracted using Trizol (Invitrogen) and purified by RNeasy Mini Kit (Qiagen). Purified RNAs were labeled and prepared for hybridization according to the protocols (Section 2: Eukaryotic Sample and Array Processing) outlined in the GeneChip® Expression Analysis Technical Manual (http://www.affymetrix. com/support/technical/manual/ expression_manual.affx).

treatment_protocol: Seedlings at the two leaf stage were stressed by polyethyleneglycol (PEG) 6000 solutions and the osmotic potential is -0.49 MPa.

tag: tissue

value: roots

tag: cultivar

value: Luohan No. 2


title: Ncr1Rep2Exp2_ProcessedSignal(normalized)

value: Ncr1 deletion strain


title: WT LatA biological replicate 3

description: Gene expression data for LatA treated wild-type strains

source_name: wild-type strain, LatA treated, 0.5 mM, 3 hrs


title: AC_Test_13

description: globin-reduced total RNA

value: F


title: AC_Test_11

description: globin-reduced total RNA

value: African Caribbean


title: AC_Test_9

description: globin-reduced total RNA

value: AC


title: WT DMSO biological replicate 3

description: Gene expression data for DMSO wild-type strains

source_name: wild-type strain, DMSO treated, 3 hrs


title: WT LatA biological replicate 1


title: WT LatA biological replicate 2


title: WT + FliC 3

source_name: WT + FliC

value: WT

value: Colon


title: T5KO + PBS 1


title: WT DMSO biological replicate 2


title: AC_Test_8

description: globin-reduced total RNA


title: AC_Test_7

description: globin-reduced total RNA


title: SG200Rep2Exp2_ProcessedSignal(normalized)


title: WT + FliC 2

value: Flagelin


title: Ncr1Rep1Exp2_ProcessedSignal(normalized)


title: WT DMSO biological replicate 1


title: WT + PBS 3

source_name: WT + PBS


title: WT + PBS 2


title: AC_Test_6

description: globin-reduced total RNA


title: SG200Rep3Exp2_ProcessedSignal(normalized)


title: AC_Test_5

description: globin-reduced total RNA


title: AC_Test_16

description: globin-reduced total RNA


title: Ncr1Rep2Exp1_ProcessedSignal(normalized)

value: Experiment 1


title: WT + FliC 1


title: SG200Rep1Exp2_ProcessedSignal(normalized)


title: WT + PBS 1


title: AC_Test_4

description: globin-reduced total RNA


title: Ncr1Rep3Exp1_ProcessedSignal(normalized)


title: AC_Test_2

description: globin-reduced total RNA


title: AC_Test_3

description: globin-reduced total RNA

value: African (Uganda)


title: SG200Rep2Exp1_ProcessedSignal(normalized)


title: mefs_homz_2

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: 3649 Promenade Sir William Osler

department: Physiology

institute: McGill University

description:
5184013013_C
homz 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The array probe summaries were calculated in BeadStudio and quantile normalized.
Using limma, a linear model fit was applied and the top differentially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct the p-values.

source_name: Mouse embryonic fibroblasts, homozygous

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep-96 RNA Amplification kit (Ambion, UK) according to the manufacturer's instructions.

extract_protocol: Tissues were snap-frozen in liquid nitrogen. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. RNA samples were quantified using NanoDrop™ 1000 (Thermo Scientific), and quality-checked by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: background strain

tag: cell type

value: embryonic fibroblasts (MEFs)

value: Mysm1tma1/tm1a (homozygous)


title: AC_Test_1

description: globin-reduced total RNA

tag: gender

tag: ethnicity

value: Caucasian


title: mefs_homz_1

description:
5184013013_B
homz 1


title: Cochlea, biol rep 2

city: Portland

first: Peter

last: Gillespie

state: OR

address: L335A / 3181 SW Sam Jackson Pk Rd

department: Oregon Hearing Research Center

institute: Oregon Health & Science University

description: Gene expression data from auditory organ at E20-21

hyb_protocol: Affymetrix protocol

scan_protocol: The microarray was incubated, washed, and read by a Microcon Array imager

data_processing: GC-RMA, quantile normalization, and summarized using a linear model estimated by the median polish algorithm.

organism: Gallus gallus

source_name: Chick inner ear

label_protocol: The sample was amplified and labeled using the Ambion MessageAmp Premier RNA Amplification/Affx fragmentation (Ambion M.Amp_Affy frag) protocol. Note that a nonstandard labeling input amount of 0.08μg was used.

growth_protocol: Fertilized chicken eggs were incubated at 38°C for 20 to 21 days.

extract_protocol: Total RNA was isolated from 10-20 pooled utricle or cochlear epithelia using Trizol and RNeasy MinElute Cleanup Kit (Qiagen) using the manufacturers' instructions.

treatment_protocol: Sensory epithelia from cohclea and utricle were microdissected, leaving pure populations of hair cells and supporting cells.

value: Cochlea

tag: age

value: Embryonic day 20-21


title: Ncr1Rep1Exp1_ProcessedSignal(normalized)


title: iPS

city: Suita

first: hideshi

last: ishii

state: Osaka

address: Yamadaoka 2-2

department: Department of Gastroenterological Surgery

country: Japan

institute: Osaka University Graduate School of Medicine

description: TaqMan Array Mouse Stem Cell Pluripotency Card

hyb_protocol: not applicable

scan_protocol: using HT7900

data_processing: Reverse transcription of mRNA was performed using SuperScriptIII (Invitrogen). To confirm the PCR amplification of cDNA, 25–35 cycles of PCR were performed using a PCR kit (Takara, Kyoto, Japan) on the Geneamp PCR system 9600 (Applied Biosystems). For quantitative assessments, gene expression was evaluated by real-time RT-PCR analysis using the TaqMankit (Applied Biosystems).

source_name: iPS

label_protocol: not applicable

growth_protocol: Cultured in DMEM or ES certified medium with 10% FBS

extract_protocol: Using a RNA extraction kit (Qiagen)

value: iPS


title: CTR_Test_7

description: globin-reduced total RNA

tag: proviral load

tag: disease status

value: CTR


title: mefs_homz_3

description:
5209410040_D
homz 3


title: SG200Rep3Exp1_ProcessedSignal(normalized)


title: Utricle, biol rep 4

description: Gene expression data from vestibular organ at E20-21

value: Utricle


title: CTR_Test_8

description: globin-reduced total RNA

value: M

tag: barcode


title: Cochlea, biol rep 1


title: SG200Rep1Exp1_ProcessedSignal(normalized)


title: mefs_het_4

description:
5184013013_A
het 4

source_name: Mouse embryonic fibroblasts, heterozygous

value: Mysm1+/tm1a (heterozygous)


title: Utricle, biol rep 3


title: CTR_Test_6

description: globin-reduced total RNA

value: F

value: African Caribbean


title: Utricle, biol rep 2


title: mefs_wt_4

description:
5183977015_F
wt 4

source_name: Mouse embryonic fibroblasts, wild type

value: wild type


title: CTR_Test_5

description: globin-reduced total RNA


title: Cochlea, biol rep 4


title: esc_homz_3

description:
5183977015_E
homz 3

source_name: Mouse embryonic stem cells, homozygous

value: embryonic stem cells (MSCs)


title: CTR_Test_4

description: globin-reduced total RNA

source_name: Whole blood


title: esc_homz_2

description:
5183977015_D
homz 2


title: Utricle, biol rep 1


title: CTR_Test_2

description: globin-reduced total RNA


title: CTR_Test_3

description: globin-reduced total RNA


title: esc_het_1

description:
5183977013_F
het 1

source_name: Mouse embryonic stem cells, heterozygous


title: Cochlea, biol rep 3


title: CTR_Test_1

description: globin-reduced total RNA


title: esc_homz_1

description:
5183977015_C
homz 1


title: esc_het_3

description:
5183977015_B
het 3


title: esc_het_2

description:
5183977015_A
het 2


title: esc_wt_2

description:
5183977013_D
wt 2

source_name: Mouse embryonic stem cells, wild type


title: esc_wt_3

description:
5183977013_E
wt 3


title: SP1

city: Seoul

first: Young kee

last: shin

address: 599 Gwanakro, Gwanak-gu

department: Department of Pharmacy

country: South Korea

institute: Seoul national university

description: Biological replicate 1 of 2

hyb_protocol: Equal amounts of Cy3 and Cy5-lableled cRNA were hybridized to an Agilent Human Microarray (G4112F) for 17 h at 65°C

scan_protocol: The hybridized microarrays were washed and scanned using an Agilent G2565BA scanner

data_processing: Data were extracted from the scanned images using Agilent Feature Extraction software

source_name: intestinal-type gastric carcinoma

label_protocol: 100 ng RNA from each sample was amplified and labeled with Cy3 or Cy5 fluorescent dye

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen, Inc., Valencia)

treatment_protocol: Control or SP1 specific siRNA oligonucleotides (ON-TARGET plus Smart pool, Dharmacon, Chicago, USA) were transfected into MKN28 cells

value: SP1 siRNA

value: control siRNA


title: Control

description: Biological replicate 1 of 2


title: OS53

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

hyb_protocol: The Chemiluminescent Detection kit (Applied Biosystems) was used for the preparation of labeled cRNA, and hybridization and washing solutions. Both digoxigenin-UTP and the anti-digoxigenin -AP were provided by Roche Diagnostics (Mannheim, Germany). Digoxigenin-labeled probes were hybridized to the microarrays overnight (16 h) at 55 °C.

scan_protocol: Chemiluminescence signals were detected by using AB1700 Chemiluminescent Microarray Analyzer (Applied Biosystems). Image preparation, signal intensity quantification and initial analysis were performed by using the accompanying software from Applied Biosystems.

data_processing: The data were further processed with the R package ABarray, which is part of the Bioconductor project (http://www.R-project.org). The data were quantile normalized, log2 transformed and missing values were imputed using average values from the other arrays in the subgroup. The osteosarcoma samples were divided into two groups of primary or metastatic origin. Weakly expressed probes were filtered away by defining that a probe is only detected if it has a signal-to-noise ratio (SNR) ≥ 3 in at least 50% of the samples in either subgroup primary or metastatic.

label: Digoxigenin

label_protocol: A 1-μg of total RNA was amplified and converted to digoxigenin-labeled cRNA by using the NanoAmp RT-IVT Labeling kit (Applied Biosystems) in accordance with the manufacturer's protocol.

tag: disease state

value: osteosarcoma

tag: origin

value: Met

value: Male

tag: developed metastases

value: Yes


title: OS55

value: Prim

value: Female

value: No


title: SP1 (dye swap)

description: Biological replicate 2 of 2

tag: cell line

tag: treatment


title: OS51


title: OS50


title: 14227748 - WT rep3 vs DKO rep3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

hyb_protocol: DKO rep3 Cy5 / WT rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: DKO rep3

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: stem - Media=SOIL hygrometry=60% for 4w followed by and 50% for 3w Temperature=22°C Light=4w at 10/14h (light/dark) at constant 200 µmol m-2 s-1 followed by 3w at 16/8h (light/dark) at constant 100 µmol m-2 s-1

extract_protocol: DKO rep3:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: columbia (col-0)

value: boyes:6.10 (boyes et al. plant cell 2001)

tag: genotype/variation

value: DKO mutant (lacking 2 monolignol exporter proteins)

value: 7-weeks old

value: stem

source_name: WT rep3

extract_protocol: WT rep3:10ug. (Qiagen_RNeasy.pdf)


title: 14227749 - DKO rep3 vs WT rep3

hyb_protocol: WT rep3 Cy5 / DKO rep3 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.

tag: tissue


title: esc_wt_1

description:
5183977013_C
wt 1

tag: genotype


title: Control (dye swap)

description: Biological replicate 2 of 2


title: 14227747 - fca2 rep3 vs WT rep3

hyb_protocol: WT rep3 Cy5 / fca2 rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: fca2 rep3

extract_protocol: fca2 rep3:10ug. (Qiagen_RNeasy.pdf)

value: fca2 mutant (expressing a hydroxycinnamoyl-CoA hydratase/lyase)


title: 14227745 - DKO rep2 vs WT rep2

hyb_protocol: WT rep2 Cy5 / DKO rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT rep2

extract_protocol: WT rep2:10ug. (Qiagen_RNeasy.pdf)

value: wild type

source_name: DKO rep2

extract_protocol: DKO rep2:10ug. (Qiagen_RNeasy.pdf)


title: OS32


title: mefs_het_2

description:
5183977025_E
het 2

tag: background strain

value: embryonic fibroblasts (MEFs)

value: Mysm1+/tm1a (heterozygous)


title: 14227743 - fca2 rep2 vs WT rep2

hyb_protocol: WT rep2 Cy5 / fca2 rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: fca2 rep2

extract_protocol: fca2 rep2:10ug. (Qiagen_RNeasy.pdf)


title: mefs_het_1

description:
5183977025_D
het 1

tag: cell type


title: mefs_het_3

description:
5183977025_F
het 3


title: OS30

tag: gender


title: OS48


title: OS41

value: Not available


title: 14227746 - WT rep3 vs fca2 rep3

hyb_protocol: fca2 rep3 Cy5 / WT rep3 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: mefs_wt_2

description:
5183977025_B
wt 2


title: OS29

value: osteosarcoma


title: 14227739 - fca2 rep1 vs WT rep1

hyb_protocol: WT rep1 Cy5 / fca2 rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT rep1

extract_protocol: WT rep1:10ug. (Qiagen_RNeasy.pdf)

source_name: fca2 rep1

extract_protocol: fca2 rep1:10ug. (Qiagen_RNeasy.pdf)


title: mefs_wt_3

description:
5183977025_C
wt 3


title: OS23

value: Met


title: marrow_homz_3

description:
4797045035_C
homz 3

source_name: Mouse bone marrow, homozygous

value: bone marrow

value: Mysm1tma1/tm1a (homozygous)


title: OS47

value: Prim

value: Male

value: Yes


title: marrow_homz_2

description:
4797045035_B
homz 2


title: 14227741 - DKO rep1 vs WT rep1

hyb_protocol: WT rep1 Cy5 / DKO rep1 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)

source_name: DKO rep1

extract_protocol: DKO rep1:10ug. (Qiagen_RNeasy.pdf)


title: OS20

value: Female


title: OS21


title: OS25


title: marrow_het_3

description:
4797045024_F
het 3

source_name: Mouse bone marrow, heterozygous


title: marrow_homz_1

description:
4797045035_A
homz 1


title: 14227742 - WT rep2 vs fca2 rep2

hyb_protocol: fca2 rep2 Cy5 / WT rep2 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: boyes:6.10 (boyes et al. plant cell 2001)


title: mefs_wt_1

description:
5183977025_A
wt 1

source_name: Mouse embryonic fibroblasts, wild type


title: 14227740 - WT rep1 vs DKO rep1

hyb_protocol: DKO rep1 Cy5 / WT rep1 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: DKO mutant (lacking 2 monolignol exporter proteins)

value: 7-weeks old


title: OS19

value: No


title: 14227736 - WT rep1 vs fca2 rep1

hyb_protocol: fca2 rep1 Cy5 / WT rep1 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: fca2 mutant (expressing a hydroxycinnamoyl-CoA hydratase/lyase)

value: stem

value: wild type


title: OS18


title: 14090062 - Cord+glc+ABA_3 vs Cord_3

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

description: Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms

hyb_protocol: Cord_3 Cy5 / Cord+glc+ABA_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: whole plant - 5 days in 0.3% Glc MS/2 media at 22°C under continue light; 1 day in MS/2 without Glc; treatments on the 7th day

extract_protocol: Cord_3:15.74ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: harvest date


title: OS17

tag: age


title: marrow_wt_3

description:
4797045024_C
wt 3

hyb_protocol: Standard Illumina hybridization protocol.

source_name: Mouse bone marrow, wild type


title: marrow_het_2

description:
4797045024_E
het 2

value: Mysm1+/tm1a (heterozygous)


title: 14090060 - Cord+glc+ABA_2 vs Cord_2

hyb_protocol: Cord_2 Cy5 / Cord+glc+ABA_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.

extract_protocol: Cord_2:21.68ug. (Qiagen_RNeasy.pdf)


title: marrow_wt_2

description:
4797045024_B
wt 2


title: OS14

value: osteosarcoma


title: 14090056 - Cord_1 vs Cord+glc+ABA_1

hyb_protocol: Cord+glc+ABA_1 Cy5 / Cord_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.

extract_protocol: Cord_1:18.3ug. (Qiagen_RNeasy.pdf)


title: 14090058 - Cord_2 vs Cord+glc+ABA_2

hyb_protocol: Cord+glc+ABA_2 Cy5 / Cord_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: 14090057 - Cord+glc+ABA_1 vs Cord_1

hyb_protocol: Cord_1 Cy5 / Cord+glc+ABA_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: 14090061 - Cord_3 vs Cord+glc+ABA_3

hyb_protocol: Cord+glc+ABA_3 Cy5 / Cord_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: marrow_wt_1

description:
4797045024_A
wt 1


title: OS15

hyb_protocol: The Chemiluminescent Detection kit (Applied Biosystems) was used for the preparation of labeled cRNA, and hybridization and washing solutions. Both digoxigenin-UTP and the anti-digoxigenin -AP were provided by Roche Diagnostics (Mannheim, Germany). Digoxigenin-labeled probes were hybridized to the microarrays overnight (16 h) at 55 °C.


title: OS04

value: Met


title: brain_homz_1

description:
4797045023_D
homz 1

source_name: Mouse brain, homozygous

value: brain


title: OS11


title: brain_homz_2

description:
4797045023_E
homz 2

value: Mysm1tma1/tm1a (homozygous)


title: 14090044 - Cord+glc_2 vs Cord+mannitol_2

hyb_protocol: Cord+mannitol_2 Cy5 / Cord+glc_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.

extract_protocol: Cord+glc_2:23.06ug. (Qiagen_RNeasy.pdf)


title: 14090043 - Cord+mannitol_2 vs Cord+glc_2

hyb_protocol: Cord+glc_2 Cy5 / Cord+mannitol_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: brain_het_3

description:
4797045023_C
het 3

source_name: Mouse brain, heterozygous

extract_protocol: Tissues were snap-frozen in liquid nitrogen. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol. RNA samples were quantified using NanoDrop™ 1000 (Thermo Scientific), and quality-checked by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies).


title: 14090045 - Cord+mannitol_3 vs Cord+glc_3

hyb_protocol: Cord+glc_3 Cy5 / Cord+mannitol_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.

extract_protocol: Cord+glc_3:20.75ug. (Qiagen_RNeasy.pdf)


title: OS12


title: 14090046 - Cord+glc_3 vs Cord+mannitol_3

hyb_protocol: Cord+mannitol_3 Cy5 / Cord+glc_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: marrow_het_1

description:
4797045024_D
het 1

value: bone marrow


title: brain_homz_3

description:
4797045023_F
homz 3


title: OS03

value: Male


title: IgM-treated Ramos replicate 3 Cy3

city: Newbury Park

first: Chetan

last: Deshpande

state: CA

address: One Amgen Center Dr

department: Molecular Sciences

institute: Amgen Inc

description: 071207_251485017114_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt

hyb_protocol: Each labeled treated sample was hybridized against its corresponding untreated sample in fluor-reversed pairs of arrays to an Agilent 4x44K Whole Human Genome Microarray.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner

data_processing: The data were extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol (GE2-v5_95_Feb07_Feature_Extraction) except with Lowess normalization.

source_name: Ramos Cells_treated_IgM

label_protocol: Labeled cRNA was generated using 200ng of total RNA from each sample and the Agilent Low RNA Input Linear Amplification labeling kit.

growth_protocol: Ramos cells were grown in RPMI supplemented with 10% fetal bovine serum, non-essential amino acids, and antibiotics.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, then cleaned using the Qiagen RNeasy kit

treatment_protocol: Ramos cells were treated with 20uM etoposide or 10ug/ml anti-IgM for 6 hours.

value: Ramos germinal center B cells

value: Burkitt's lymphoma cell line

source_name: Ramos Cells_untreated

value: Untreated-3 (30287)


title: Etoposide-treated Ramos replicate 3 Cy3

description: 071207_251485017114_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt

source_name: Ramos Cells_treated_Etoposide

value: Etoposide3 (30291)


title: brain_het_2

description:
4797045023_B
het 2


title: brain_het_1

description:
4797045023_A
het 1


title: 14090042 - Cord+glc_1 vs Cord+mannitol_1

hyb_protocol: Cord+mannitol_1 Cy5 / Cord+glc_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.

extract_protocol: Cord+glc_1:15.71ug. (Qiagen_RNeasy.pdf)


title: 14090038 - Cord+ABA_2 vs Cord_2

hyb_protocol: Cord_2 Cy5 / Cord+ABA_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.

extract_protocol: Cord+ABA_2:14.03ug. (Qiagen_RNeasy.pdf)


title: IgM-treated Ramos replicate 3 Cy5

description: 071207_251485017114_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: 14090039 - Cord_3 vs Cord+ABA_3

hyb_protocol: Cord+ABA_3 Cy5 / Cord_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.

extract_protocol: Cord+ABA_3:12.82ug. (Qiagen_RNeasy.pdf)


title: brain_wt_3

description:
4797045022_F
wt 3

source_name: Mouse brain, wild type


title: 14090040 - Cord+ABA_3 vs Cord_3

hyb_protocol: Cord_3 Cy5 / Cord+ABA_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: prostatecancer_xenograft_MDAPCa170

type: genomic

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

hyb_protocol: Agilent Version 5.0  post processing steps:

scan_protocol: Agilent G2505B; software- Agilent Scan Control; version 3.0 @ 5uM resolution, Feature Extraction 9.5.3.1

data_processing: Between array normalization: normalizeBetweenArrays function in limma R package with method=Rquantile. This method ensures that the red (reference) channel has the same empirical distribution across arrays, leaving the log-ratios unchanged.

molecule: genomic DNA

source_name: a pool of healthy male volunteer peripheral blood mononuclear cells

label_protocol: Protocol from Agilent Oligonucleotide Array-Based aCGH for Genomic DNA Analysis

extract_protocol: DNAs were isolated using standard protocol using proteinase K digestion followed by phenol-chloroform extraction, and ethanol precipitation

tag: sample type

value: reference

value: peripheral blood mononuclear cells

source_name: xenografted prostate cancer grown subcutaneously in the flanks of CB17 SCID intact mice

growth_protocol: tumors were grown subcutaneously in the flanks of CB17 SCID intact mice

tag: tumor tissue

value: castrate-resistant prostate cancer (CRPC)

tag: histology

value: adenocarcinoma


title: brain_wt_1

description:
4797045022_D
wt 1

hyb_protocol: Standard Illumina hybridization protocol.


title: IgM-treated Ramos replicate 2 Cy5

description: 051607_251485014106_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt

value: Untreated2 (29613)


title: 14090041 - Cord+mannitol_1 vs Cord+glc_1

hyb_protocol: Cord+glc_1 Cy5 / Cord+mannitol_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: IgM-treated Ramos replicate 2 Cy3

description: 051607_251485014106_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt


title: brain_wt_2

description:
4797045022_E
wt 2

value: wild type


title: Etoposide-treated Ramos replicate 3 Cy5

description: 071207_251485017114_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt


title: liver_homz_2

description:
4797045022_B
homz 2

source_name: Mouse liver, homozygous

value: liver


title: IgM-treated Ramos replicate 1 Cy3

description: 051607_251485014106_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt

value: Untreated1 (29612)


title: 14090037 - Cord_2 vs Cord+ABA_2

hyb_protocol: Cord+ABA_2 Cy5 / Cord_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: prostatecancer_xenograft_MDAPCa180-30


title: prostatecancer_xenograft_MDAPCa146-10

value: small cell carcinoma


title: liver_homz_3

description:
4797045022_C
homz 3


title: prostatecancer_xenograft_MDAPCa155-2


title: IgM-treated Ramos replicate 1 Cy5

description: 051607_251485014106_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt


title: 14090036 - Cord+ABA_1 vs Cord_1

hyb_protocol: Cord_1 Cy5 / Cord+ABA_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.

extract_protocol: Cord+ABA_1:7.26ug. (Qiagen_RNeasy.pdf)


title: 14227744 - WT rep2 vs DKO rep2

hyb_protocol: DKO rep2 Cy5 / WT rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: DKO rep2

extract_protocol: DKO rep2:10ug. (Qiagen_RNeasy.pdf)

value: columbia (col-0)

value: boyes:6.10 (boyes et al. plant cell 2001)

value: DKO mutant (lacking 2 monolignol exporter proteins)

value: 7-weeks old

value: stem

source_name: WT rep2

extract_protocol: WT rep2:10ug. (Qiagen_RNeasy.pdf)


title: prostatecancer_xenograft_MDAPCa144-13


title: prostatecancer_xenograft_MDAPCa144-4

value: large cell neuroendocrine carcinoma


title: 14090035 - Cord_1 vs Cord+ABA_1

hyb_protocol: Cord+ABA_1 Cy5 / Cord_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: liver_homz_1

description:
4797045022_A
homz 1

value: Mysm1tma1/tm1a (homozygous)


title: 14090024 - Cord_3 vs Cord+glc_3

hyb_protocol: Cord+glc_3 Cy5 / Cord_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: liver_het_3

description:
4797045011_F
het 3

source_name: Mouse liver, heterozygous

value: Mysm1+/tm1a (heterozygous)


title: Patient 2 : 2521469334205_Processed

city: Gosselies (Charleroi)

first: Bernard

last: Grisart

address: Avenue Georges Lemaitre,25

department: Centre de génétique humaine

country: Belgium

institute: Institut de pathologie et de génétique

description: CGH analysis using standard Agilent hybridization procedure as recommended by Agilent : G4410-90010

hyb_protocol: Labelled DNA was hybridized according to manufactured instruction (Agilent G4410-90010) with Cot-1 DNA from Roche (11 581 074 001), 2µg.

scan_protocol: Scanned on an upgraded Agilent Scanner G2539A

data_processing: Extraction of data from scanned tiff files (Agilent type C scanner : upgraded scanner G2539A) was performed using feature extraction software (version 10.7.3.1) with an hg19 annotated design file (014693_D_F_20101001) and a modified Agilent provided extraction protocol (CGH_107_Sep09 ; "linear and lowess" normalization was used instead of linear normalization only as in the Agilent provided protocol).  Visualisation of the data (log2ratio) and aberration calling were performed using Genomic Work Bench (v.6.5.0.58).

source_name: DNA from a female patient with Kabuki phenotype

label_protocol: Patient and reference DNA was labeled by random priming using BioPrime Array CGH Genomic Labeling System (Invitrogen, 18095-012).  Patient DNA (2 µgr) was labeled with Cyanine-5 dCTP (Amersham, PA55021) and reference DNA (2 µg of a pool of 7 sex-matched DNA) was labeled with Cyanine-3 dCTP (Amersham, PA53021).  Labeled DNA were pooled and were purified by ethanol precipitation and hybridized on Agilent 244K whole genome array for 24h using procedure recommended by Agilent (G4410-90010).

growth_protocol: No growth ; DNA directly extrated from blood of patients

extract_protocol: genomic DNA was extracted using QiaAmp DNA blood extraction kit (Ref 51106) from Qiagen using 200 µl of fresh blood according to Agilent recommendations (G4410-90010 : Agilent Oligonucleotide array-based CGH for genomic analysis).

value: whole blood

source_name: Pool of DNA from 7 normal female individuals


title: Etoposide-treated Ramos replicate 2 Cy5

description: 051607_251485014105_S01_GE2-v5_95_Feb07_Feature_Extraction_1_4.txt

value: Ramos germinal center B cells

value: Burkitt's lymphoma cell line

value: Etoposide2 (29609)


title: liver_het_1

description:
4797045011_D
het 1


title: Etoposide-treated Ramos replicate 1 Cy5

description: 051607_251485014105_S01_GE2-v5_95_Feb07_Feature_Extraction_1_2.txt

value: Etoposide1 (29608)


title: 14090020 - Cord_1 vs Cord+glc_1

hyb_protocol: Cord+glc_1 Cy5 / Cord_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: liver_wt_3

description:
4797045011_C
wt 3

source_name: Mouse liver, wild type

value: wild type


title: liver_het_2

description:
4797045011_E
het 2

value: liver


title: 14090023 - Cord+glc_2 vs Cord_2

hyb_protocol: Cord_2 Cy5 / Cord+glc_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: 14090022 - Cord_2 vs Cord+glc_2

hyb_protocol: Cord+glc_2 Cy5 / Cord_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: Left ventricle_high-responder_sedentary_5

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

institute: NTNU

description:
.The laboratory animals included in this study consists of rats (N:NIH outbred rat stock) selectively breed for low and high response to exercise based on their change in maximal treadmill running capacity, as estimated before and after 8 weeks of exercise training.  This process has generated rat models with inherited differences for the adaptation component of aerobic capacity. The founder population, the N:NIH stock of rats, was developed in 1979 as a genetic resource of a heterogeneous population from the intentional outcross breeding of eight inbred strains, representing the broadest phylogenetic spectrum of laboratory rats available:  Maudsely Reactor (MR/N), Wistar (WN/N), Wistar Kyoto (WKY/N), Marshall 520 (M520), Fischer (F344), Ax C 9935 Irish (ACI), Brown Norway (BN/SsN), and Buffalo (BUF/N).  The resultant stock has wide genetic heterogeneity and is a superior choice as a starting population for artificial selection.
.

hyb_protocol: Samples were hybridized to Applied Biosystems Rat Genome Survey chips v.1.0. The samples were hybridised over two days. The biological groups were balanced between the two hybridisation batches and the samples randomly distributed within this format. Samples were analyzed by the Applied Biosystems 1700 Array Expression System.

data_processing: The data files from the AB 1700 Chemiluminescent Microarray Analyzer Software were processed using J-Express Pro v.2.8. The signal intensity values were extracted per spot, and all flagged and control spots were filtered out. Before compiled into an expression profile data matrix, all arrays were quantile normalized to be comparable. Genes with at most 20% missing values were allowed in the final dataset. The signal intensities in the dataset were further log transformed, and missing values were replaced using the method LSimpute Adaptive. The search for differentially expressed genes was performed both on a single gene and gene set level. Rank Product was used to look for differentially expressed genes on a gene by gene basis, while Gene Set Enrichment Analysis (GSEA) was used to look for sets of genes sharing common characteristics that were differentially expressed between the classes examined.

label: Biotin

organism: Rattus norvegicus

label_protocol: All samples were labeled at the same time and according to manufactures protocol

extract_protocol: Left ventricle tissue was snap-frozen in liquid nitrogen and stored at -80oC. RNA was isolated from the left ventricle (20 mg) with the mirVana RNA isolation kit (Ambion) according to the manufacturer's instructions. RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, US) and Nanodrop (NanoDrop Technologies, Baltimore, US). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies, Santa Clara, US). Only samples with a 260/280-ratio of more than 1.8, and RNA integrity number (RIN) value above 8 was analyzed.

value: female

value: Left ventricle cardiac tissue

value: 12 months

tag: strain

value: generation 7 of HRT (see description for additional details)


title: liver_wt_1

description:
4797045011_A
wt 1


title: Patient 1 : 2521469334204_Processed


title: 14090052 - wt glucose 3 vs abi4 glucose 3

hyb_protocol: abi4 glucose 3 Cy5 / wt glucose 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.

source_name: abi4 glucose 3

growth_protocol: whole plant - grown 5 days in MS/2 plus 0,3% glucose, 1 day in MS/2 without glucose and treatments 2% glucose, 2% mannose and 2% mannitol

extract_protocol: abi4 glucose 3:11.14ug. (Qiagen_RNeasy.pdf)

source_name: wt glucose 3

extract_protocol: wt glucose 3:17.19ug. (Qiagen_RNeasy.pdf)


title: 14090025 - Cord+glc_3 vs Cord_3

hyb_protocol: Cord_3 Cy5 / Cord+glc_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.

extract_protocol: Cord_3:15.74ug. (Qiagen_RNeasy.pdf)


title: Etoposide-treated Ramos replicate 1 Cy3

description: 051607_251485014105_S01_GE2-v5_95_Feb07_Feature_Extraction_1_1.txt

hyb_protocol: Each labeled treated sample was hybridized against its corresponding untreated sample in fluor-reversed pairs of arrays to an Agilent 4x44K Whole Human Genome Microarray.

value: Untreated1 (29612)


title: Immunoprecipitated chromatin, antibody 1, replicate 1 Set 2

description: 103007_251470710707_S01_CGH-v4_91_Amgen_082406.txt

hyb_protocol: The purified enriched and control DNA were hybridized to an Agilent 244K Human Promoter ChIP-on-chip Microarray Set (Agilent Technologies, Palo Alto, CA) using Maui AO (BioMicro Systems, Salt Lake City, UT). The microarrays were hybridized at 60º in a MAUI hybridization station on setting B (12spotMAUI) for 18 hours and then washed using Agilent aCGH wash buffers following the provided protocols.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray scanner, and data were extracted from images using the Agilent Feature Extraction (version 9.5.1.1) software.

data_processing: The data were extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol with Lowess normalization.

source_name: Ramos cells, nonIP, control

label_protocol: 500ng of the control and ChIP-enriched genomic DNA was heat fragmented at 95C for 30’. The heat fragmented DNA was labeled using BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA) with some modifications.

extract_protocol: 2x10^8 cells were pelleted, washed with PBS, and lysed with hypotonic buffer on ice for 10 minutes to release the cytoplasm.  Nuclei were pelleted at 4 degrees C and lysed with ice-cold nuclear lysis buffer supplemented with protease inhibitor, on ice for 10 minutes.  Chromatin was sheared by sonication, using 5 pulses of 30 seconds each, separated by 1-minute rests.  DNA size was analyzed on a 2% agarose gel, and appeared as a smear ranging from 0.5-1 kb.

treatment_protocol: Untreated cells were used for chromatin isolation.

tag: antibody

source_name: Ramos cells, immunoprecipitataed, test

value: Ab1 = Cell Signaling #3826


title: Left ventricle_high-responder_sedentary_2

description: .The laboratory animals included in this study consists of rats (N:NIH outbred rat stock) selectively breed for low and high response to exercise based on their change in maximal treadmill running capacity, as estimated before and after 8 weeks of exercise training.  This process has generated rat models with inherited differences for the adaptation component of aerobic capacity. The founder population, the N:NIH stock of rats, was developed in 1979 as a genetic resource of a heterogeneous population from the intentional outcross breeding of eight inbred strains, representing the broadest phylogenetic spectrum of laboratory rats available:  Maudsely Reactor (MR/N), Wistar (WN/N), Wistar Kyoto (WKY/N), Marshall 520 (M520), Fischer (F344), Ax C 9935 Irish (ACI), Brown Norway (BN/SsN), and Buffalo (BUF/N).  The resultant stock has wide genetic heterogeneity and is a superior choice as a starting population for artificial selection.

scan_protocol: Samples were analyzed by the Applied Biosystems 1700 Array Expression System.


title: Left ventricle_high-responder_sedentary_3


title: Immunoprecipitated chromatin, antibody 2, replicate 2 Set 2

description: 112707_251470711232_S01_CGH-v4_91_Amgen_082406.txt

value: Ab2 = EMD Biosciences #ST1099


title: Immunoprecipitated chromatin, antibody 2, replicate 2 Set 1

description: 112707_251470611232_S01_CGH-v4_91_Amgen_082406.txt


title: Etoposide-treated Ramos replicate 2 Cy3

description: 051607_251485014105_S01_GE2-v5_95_Feb07_Feature_Extraction_1_3.txt

value: Untreated2 (29613)


title: liver_wt_2

description:
4797045011_B
wt 2


title: 14090021 - Cord+glc_1 vs Cord_1

description: Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms

hyb_protocol: Cord_1 Cy5 / Cord+glc_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.

extract_protocol: Cord_1:18.3ug. (Qiagen_RNeasy.pdf)


title: Immunoprecipitated chromatin, antibody 2, replicate 1 Set 2

description: 103007_251470710710_S01_CGH-v4_91_Amgen_082406.txt


title: 14090084 - wt mannitol 1 vs wt mannose 1

hyb_protocol: wt mannose 1 Cy5 / wt mannitol 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.

source_name: wt mannose 1

extract_protocol: wt mannose 1:19.1ug. (Qiagen_RNeasy.pdf)

source_name: wt mannitol 1

extract_protocol: wt mannitol 1:13.56ug. (Qiagen_RNeasy.pdf)


title: Left ventricle_high-responder_sedentary_1


title: 14090051 - abi4 glucose 3 vs wt glucose 3

hyb_protocol: wt glucose 3 Cy5 / abi4 glucose 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: Immunoprecipitated chromatin, antibody 1, replicate 2 Set 1

description: 112707_251470611231_S01_CGH-v4_91_Amgen_082406.txt


title: EpCAM+ cells from DDB1homozygous mutant mouse

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

source_name: EpCAM+ cells from 4 wks DDB1F/F;Alb-Cre+/+

label_protocol: As suggested by illumina

growth_protocol: Generated DDB1F/F;Alb-Cre+/+ mouse, DDB1F/F;Mx1-Cre+/-. Oval cells (EpCAM positive cells) from these mouse models were compared with a conventional chemical injury model for oval cellsproliferation, mice treated with diet containing 3,5-diethoxycarbonyl-1,4-dihydro-collidine (DDC).

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

treatment_protocol: Liver cells were isolated using a standard three-step protocol. Cells were centrifuged at least twice at 2000 rpm for 5 minutes and the pellets were suspended in ice-cold PBS containing 10% FBS and used as non-parenchymal cells. Cells were then incubated with fluorescence-conjugated EpCAM antibody in 3% BSA/PBS for 30 minutes on ice, sorted using FACSVantageSE DiVa.

value: mixed C57BL/6 x 129

value: mammary


title: EpCAM+ cells from DDB1hemizygous mutant mouse

source_name: EpCAM+ cells from 6 wks DDB1F/F;Alb-Cre+/-


title: Left ventricle_high-responder_training_5


title: EpCAM+ cells from MX1

source_name: EpCAM+ cells from DDB1F/F;MX1-Cre+/-


title: 14090076 - wt mannose 3 vs abi4 mannose 3

hyb_protocol: abi4 mannose 3 Cy5 / wt mannose 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.

source_name: abi4 mannose 3

extract_protocol: abi4 mannose 3:16.82ug. (Qiagen_RNeasy.pdf)

source_name: wt mannose 3

extract_protocol: wt mannose 3:19.04ug. (Qiagen_RNeasy.pdf)


title: Immunoprecipitated chromatin, antibody 1, replicate 2 Set 2

description: 112707_251470711231_S01_CGH-v4_91_Amgen_082406.txt


title: Left ventricle_high-responder_training_3