title: Exp2Rep2: 0.185 TU Flu + 0.0625 TU Pyr


title: Exp2Rep2: 0.125 TU Pyr

status: Public on Dec 31 2009

type: RNA

city: Antwerp

first: Tine

last: Vandenbrouck

address: Groenenborgerlaan 171

department: Department of Biology

country: Belgium

institute: University of Antwerp

description: Hybridization: Pyrene 0.125Tu vs Reference sample

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments).

data_processing: Prior to the actual statistical analysis, the quality of the microarray spots was assessed. Over-saturated spots and bad quality spots identified during the feature identification process (visual inspection of the slides) were excluded from further analysis. Hereafter, a local background correction was performed on these datasets (BASE). Those spots with foreground levels lower than the background levels for both channels were excluded from the analysis. Spots for which the foreground was smaller than the mean (local) background ±2 standard deviations for both channels were given a ‘weight’ of 0.1. All other included spots are given a weight of 1. Subsequently, microarray datasets were normalized using the variance stabilizing normalization (VSN) (Huber 2002). The significantly differentially expressed genes (between control and treatment) were statistically determined using LIMMA (LInear Model for Microarray Analysis) (Smyth 2004). Results were corrected for multiple testing using the false discovery rate (FDR) and differential gene expression was detected in probes with p<0.05. An additional threshold which was taken into account is the fold induction cut-off (Log2) of (-)0.85. In conclusion, genes with fold inductions outside these thresholds and p-values below 0.05 were selected as differentially expressed.

molecule: total RNA

organism: Daphnia magna

source_name: pyrene 0.125 TU

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 5µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 50 pmol labelled target was vacuum dried.

extract_protocol:
Approximately 40 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C.
All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

treatment_protocol: The organisms were exposed to two PAHs, fluoranthene and pyrene (Sigma-Aldrich, Belgium) both as single compounds and as binary mixtures. EC50 (immobility at 48h) values of the single compounds (when fed) were established to set the concentrations of the individual component exposures equal to 0; 0.062; 0.125 and 0.250 Toxic Units (TU) when one TU is defined as the EC50 (immobility at 48h) of the single compound. For the binary mixtures, concentrations for a total of 6 (to 8) combinations were determined based on a fixed ratio design. During the 96h exposure experiments, 40 Daphnia/replica were kept at a density of 1 organism/10mL OECD standard water (CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Since fluoranthene and pyrene are both poorly soluble in water, a solvent was used. The PAHs were dissolved in acetone; final solvent concentrations of 0.01% were used. Therefore besides the pure OECD water control, an additional solvent control sample was included in each test. Organisms were fed every other day – when test solutions were renewed - with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio.

tag: tissue

value: whole body extracts (40 organisms)

tag: age

value: 96h old

source_name: reference sample


title: Exp2Rep2: 0.25 TU Pyr

description: Hybridization: Pyrene 0.25Tu vs Reference sample

source_name: pyrene 0.25 TU


title: Exp1Rep1: 0.125 TU Flu + 0.125 TU Pyr

description: Hybridization: Mixture of 0.125TUFlu and 0.125TUPyr vs  Reference sample

source_name: mixture of 0.125 TU fluoranthene and 0.125 TU pyrene


title: Exp2Rep1: 0.25 TU Flu

description: Hybridization: Reference sample vs 0.25TU Fluoranthene

source_name: fluoranthene 0.25 TU


title: Exp2Rep1: Control_0 TU

description: Hybridization: Reference sample vs Control sample

source_name: control sample


title: Exp1Rep2: 0.25 TU Flu


title: Exp1Rep1: 0.0625 TU Flu + 0.185 TU Pyr

description: Hybridization: Mixture of 0.062TUFlu and 0.185TUPyr sample vs Reference sample

source_name: mixture of 0.0625 TU fluoranthene and 0.185 TU pyrene


title: Exp1Rep2: 0.0625 TU Flu

description: Hybridization: Reference sample vs 0.0625TU Fluoranthene

source_name: 0.0625 TU fluoranthene


title: Exp2Rep2: 0.125 TU Flu + 0.125 TU Pyr

description: Hybridization: Mixture of 0.125TUFlu and 0.125TUPyr vs Reference sample


title: Exp2Rep2: 0.125 TU Flu

description: Hybridization: Fluoranthene 0.125TU vs Reference sample

source_name: fluoranthene 0.125 TU


title: Exp2Rep2: 0.25 TU Flu + 0.25 TU Pyr

description: Hybridization: Mixture of 0.25TUFlu and 0.25TUPyr Vs Reference sample

source_name: mixture of 0.25 TU fluoranthene and 0.25 TU pyrene


title: Exp1Rep2: 0.0625 TU Flu + 0.0625 TU Pyr

description: Hybridization: Reference sample vs Mixture of 0.062TUFlu and 0.062TUPyr

source_name: mixture of 0.0625 TU fluoranthene and 0.0625 TU pyrene


title: Exp2Rep2: 0.18 TU Flu + 0.18 TU Pyr

description: Hybridization: Mixture of 0.187TU FLU and 0.187TU PYR Vs Reference sample

source_name: mixture of 0.187 TU fluoranthene and 0.187 TU pyrene


title: Exp1Rep2: ControlS_0 TU


title: Exp1Rep2: ControlM_0 TU


title: Exp1Rep1: ControlM_0 TU

description: Hybridization: Control sample vs Reference sample


title: Exp2Rep2: Control_0 TU

description: Hybridization: Control organisms vs Reference sample


title: Exp1Rep1: ControlS_0 TU


title: Exp1Rep1: 0.25 TU Flu

description: Hybridization: Fluoranthene 0.25TU versus Reference sample


title: Exp1Rep1: 0.125 TU Flu

description: Hybridization: Fluoranthene 0.125TU versus Reference sample


title: Exp1Rep1: 0.0625 TU Flu

description: Hybridization: Fluoranthene 0.062TU versus Reference sample

source_name: fluoranthene 0.0625 TU


title: Exp1Rep1: 0.0625 TU Flu + 0.0625 TU Pyr

description: Hybridization: Mixture of 0.062TUFlu and 0.0625TUPyr versus Reference sample


title: Exp1Rep1: 0.25 TU Pyr

description: Hybridization: Pyrene 0.25TU versus Reference sample


title: Exp1Rep1: 0.0625 TU Pyr

description: Hybridization: Pyrene 0.0625 TU versus Reference sample

source_name: pyrene 0.0625 TU


title: YJB8741_slide2_aCGH

type: genomic

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

description: second array

hyb_protocol: Slides were hybridized overnight in a 37C waterbath

scan_protocol: Slides were scanned using a ScanArray (Perkin Elmer) and accompanying ScanArray Express software.

data_processing: Data were extracted using GenePix Pro and GeneTraffic software. Global Lowess normalization.

molecule: genomic DNA

organism: Candida albicans

label_protocol: DNA was digested with HaeIII, purified, and labeled using an Invitrogen Bioprime aCGH labeling kit.

growth_protocol: DNA was isolated after minimal growth in YPAD at 30C

extract_protocol: Phenol Chloroform DNA extraction

tag: strain

source_name: SC5314 (reference)

value: SC5314 (sequenced strain)


title: Exp2Rep2: 0.0625 TU Flu + 0.0625 TU Pyr

description:
Hybridization: Mixture_0_062TUFlu_0_0625TUPyr
versus Reference sample


title: Exp2Rep2: 0.25 TU Flu

data_processing: Prior to the actual statistical analysis, the quality of the microarray spots was assessed. Over-saturated spots and bad quality spots identified during the feature identification process (visual inspection of the slides) were excluded from further analysis. Hereafter, a local background correction was performed on these datasets (BASE). Those spots with foreground levels lower than the background levels for both channels were excluded from the analysis. Spots for which the foreground was smaller than the mean (local) background ±2 standard deviations for both channels were given a ‘weight’ of 0.1. All other included spots are given a weight of 1. Subsequently, microarray datasets were normalized using the variance stabilizing normalization (VSN) (Huber 2002). The significantly differentially expressed genes (between control and treatment) were statistically determined using LIMMA (LInear Model for Microarray Analysis) (Smyth 2004). Results were corrected for multiple testing using the false discovery rate (FDR) and differential gene expression was detected in probes with p<0.05.  An additional threshold which was taken into account is the fold induction cut-off (Log2) of (-)0.85. In conclusion, genes with fold inductions outside these thresholds and p-values below 0.05 were selected as differentially expressed.

treatment_protocol: The organisms were exposed to two PAHs, fluoranthene and pyrene (Sigma-Aldrich, Belgium) both as single compounds and as binary mixtures.  EC50 (immobility at 48h) values of the single compounds (when fed) were established to set the concentrations of the individual component exposures equal to 0; 0.062; 0.125 and 0.250 Toxic Units (TU) when one TU is defined as the EC50 (immobility at 48h) of the single compound. For the binary mixtures, concentrations for a total of 6 (to 8) combinations were determined based on a fixed ratio design. During the 96h exposure experiments, 40 Daphnia/replica were kept at a density of 1 organism/10mL OECD standard water (CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Since fluoranthene and pyrene are both poorly soluble in water, a solvent was used. The PAHs were dissolved in acetone; final solvent concentrations of 0.01% were used. Therefore besides the pure OECD water control, an additional solvent control sample was included in each test. Organisms were fed every other day – when test solutions were renewed - with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio.


title: YJB8741_aCGH

description: no additional information


title: YJB8739_slide2

description: second analysis


title: YJB8739 aCGH

description:
slide 1
no additional information


title: YJB8740_aCGH

description: first array analysis


title: Exp1Rep1: 0.125 TU Pyr

description: Hybridization: Pyrene 0.125TU versus Reference sample


title: YJB8740_slide2_aCGH

description: second array analysis


title: YJB8737_slide2_aCGH

description: second array analysis


title: YJB8738_slide2_aCGH

description: second array analysis


title: SC5314_vs_SC5314_aCGH

description: Control strain SC5314 (YJB2348) hybridized against itself

hyb_protocol: Arrays were hybridized in a 37C waterbath overnight

scan_protocol: Arrays were scanned using a ScanArray scanner.

label_protocol: Labeling was done with a BioPrime aCGH kit from Invitrogen.

extract_protocol: gDNA extractions were done using the Hoffman-Winston preparation (phenol/chloroform/isoamyl alcohol and lysis buffer followed by EtOH/salt precipitation).  All gDNA is RNaseA treated.  The same gDNA prep was used to label with Cy3 for this array.


title: Exp2Rep2: 0.0625 TU Pyr

description: Hybridization: Pyrene_0_062TU versus Reference sample


title: YJB8736_slide2_aCGH

description: second array analysis


title: Exp2Rep2: 0.0625 TU Flu + 0.185 TU Pyr

description:
Hybridization: Mixture_0_062TUFlu_0_185TUPyr
versus Reference sample


title: 24 hpf

city: Galveston

first: Saravanan

last: Thangamani

state: TX

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

description: Group 5

hyb_protocol: The OligoGEArrays were prehybridized for 2 hours at 60C with GEAhyb Hybridization Solution (SABiosciences), and then hybridized  for 14 hours at 60C with  hybridization mix containing GEAhyb Hybridization Solution (SABiosciences) and 2ug of biotin labeled cRNA.

scan_protocol: The arrays were then exposed for 1 min to a X-ray film (Kodak X-omat film) and developed.  They were then scanned using EPSON Perfection V700 (Epson).

data_processing: The scanned images were uploaded on to Superarray's GEArray Expression analysis suite 2.0  (http://geasuite.sabiosciences.com), and signal intensites were calculated according to software instructions.

label: biotin

organism: Aedes aegypti

source_name: Salivary glands

label_protocol: 200 ng of total RNA was amplified and biotin labeled  using TrueLabeling-AMP 2.0 kit (SABiosciences).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen),  and RiboPure kit (Ambion). This was followed by Dnase treatment to remove any DNA contamination. Denaturing formaldehyde agarose gel electrophoresis was performed to analyze the quality of extracted RNA. The quanity of RNA was measured using Nanodrop 1000 (ThermoScientific).

tag: gender

value: female

tag: treatment

value: 24 hours post fed mosquitoes


title: 48 hpf

description: Group 6

value: 48 hours post fed mosquitoes


title: YJB8735_slide2

description: slide2 analysis


title: 3 hpf

description: Group 3

value: 3 hours post fed mosquitoes


title: 1 hpf

description: Group 2

value: 1 hour post fed mosquitoes


title: Naïve

description: Group 1

value: unfed mosquitoes


title: 251502810579_1_1

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: HCC mouse liver hybridized with ctrl pool

hyb_protocol: Hybridisation was performed according to the manufacturer's instuctions (Agilent) at 65°C for 40 hours on a 4x44K microarray (Agilent).

scan_protocol: Scan was performed using a Agilant Scanner Control software v 7.0, with a Agilent G2565B Scanner system

data_processing: Data extraction was performed by using feature extraction software (Agilent) - and Agilents DNA analytics software

organism: Mus musculus

source_name: genomic DNA from pooled liver tissue

label_protocol: Cy3 (HCC and ctrl) or Cy5 (ctrl pool) labeling of genomic DNA was performed according to manufacturer's instructions (Agilent oligonucelotide array-based CGH for genomic DNA analysis (for FFPE samples)

extract_protocol: Genomic DNA was isolated using Qiagen genomic DNA separation columns according to the manufacturer's instuctions (Agilent and Qiagen) - DNA was heat fragmented.

value: 12 months

tag: disease state

value: tumor

source_name: genomic DNA from individual liver tissue

value: MCL1-/- knock-out


title: scr-3 vs. Col-0

city: Ikoma

first: Keiji

last: Nakajima

state: Nara

address: 8916-5 Takayama

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

hyb_protocol: Hybridization was carried out with In situ Hybridization Kit Plus (Agilent, product #5184-3568) according to the manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner at 5 micro m resolution.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: Wild-type Col-0 root tip

label_protocol: Labeling was performed with Low RNA Input Linear Amplification Kit (Agilent, product # 5184-3523) and fragmented according to the manufacturer`s instructions.

growth_protocol: Sterilized Arabidopsis seeds were plated on nutrient agar medium and grown at 23 ˚C with 16h-light/8h-dark cycle.

extract_protocol: Total RNA was extracted from about 1-cm root tip region with RNeasy  Plant Minikit (Qiagen, Valencia, CA).

tag: genotype

value: wild type

value: root tip

tag: cultivar

source_name: scr-3 root tip


title: Col-0 vs. ago1-101

source_name: ago1-101 (SALK_035319 ) root tip


title: 251502810579_1_3


title: Col-0 vs. scr-3


title: 251502810578_1_4


title: ago1-101 vs. Col-0


title: 251502810579_1_2


title: 251502810579_1_4

description: ctrl mouse liver hybridized with ctrl pool

value: healthy

value: C57BL/6, alb cre


title: 251502810578_1_2


title: 251502810578_1_3


title: brain_SLDFB3

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

description:
Atlantic salmon (Aquaculture and Catchment Management Services of the Marine Institute (Ireland) in Burrishoole, Newport, Co. Mayo)
Eight microarray hybridisations were carried out in total as part of this design. To compare brain samples total RNA from 10 individual brains (dissected of hypothalamus and pituitary) of precocious fish and 10 brains of non-precocious fish were pooled to give two pools each of five precocious (PA and PB) and non-precocious (NPA and NPB) brains. Each pool of precocious brains was compared in a dye swap experiment with each pool of non-precocious brains.

hyb_protocol: Slides were pre-hybridised in 50% formamide, 5x SSC, 0.1% SDS, 0.1 mg/ml BSA at 42 oC for 1 h, then washed twice for 5 min with 0.1x SSC and for 30 s with 18MOhm water. The slides were dried immediately by centrifugation (Eppendorf Multipuropose Centrifuge 5804) at 1500 rpm for 5 min at room temperature in a slide box lined with 3MM Whatman paper (10.8 x 7.4cm). Dust was removed from the surface of the pre-hybridised arrays using an ozone-free air duster (Kenair, UK). The purified, combined Cy5- and Cy3-labelled cDNAs (80 microlitre) were denatured at 95 C in a thermal cycler for 3 min, immediately applied to the array surface and covered with a lifter slip (Erie Scientific, USA). Each array was placed in a pre-warmed Genetix hybridisation chamber. The chamber was sealed and incubated in an oven for 16-18 h at 50 oC. Microarray wash solutions were warmed to 55 oC. All wash steps were carried out in the dark. Each array was dipped in a 50 ml Sarstedt tube filled with wash solution 1 (2X SSC, 0.1% SDS) to dislodge the coverslip. The arrays were washed twice for 5 min on a rotary table in fresh wash solution 1. The arrays were transferred to wash solution 2 (0.1X SSC) and washed twice for 1 min on a rotary table. Finally, the arrays were rinsed by immersion in RNase/DNase-free water to remove any residual salts, followed by brief immersion in 100 % isopropanol (Sigma-Aldrich) at room temperature and brief centrifugation at 1500 rpm for 2 min to dry the slides

scan_protocol: The arrays were scanned as soon as possible after washing. After hybridisation, fluorescence was measured using a confocal laser scanner (ScanArray Express HT, Perkin Elmer, USA). The high-resolution images were inspected using Genepix Pro v6.0.1.25 (Molecular Devices, USA).

data_processing: LIMMA (part of the Bioconductor R package) was applied to the design used in this experiment. The Cy5 channel signal was given the nominal label of F670 and the Cy3 channel signal was given the nominal label of F570 (and B670 and B570 for the corresponding channel backgrounds). Spots were weighted based on feature flagging in Genepix. If for any spot [% > B670+2SD2] < 50 or [% > B570+2SD2] < 50 or [Ratio of Medians (670/570)] > (10* [Rgn Ratio (670/570)]) or [Ratio of Medians (670/570)] < (0.1* [Rgn Ratio (670/570)] the spot was flagged as ‘bad’. In LIMMA this was converted to a weight of 0.1 whereas remaining good quality spots were given a weight of 1.0. Because there are two sub-arrays per slide and these are averaged, final weights can be 0.1 (both spots bad), 1.0 (both spots good) and 0.55 (one spot good and one spot bad). Median local background values were subtracted from median feature values, dye channels were swapped as appropriate and a printtiploess normalisation was applied (log2 fold ratios are given).

organism: Salmo salar

label_protocol: An indirect labelling method was used to attach Cy5 and Cy3 dyes to the cDNA. All target cDNAs were synthesised in one round. 10 Micrograms of both tester and reference total RNA was used per hybridisation. cDNA was generated by reverse transcription for 2 h at 42 oC using an anchored oligo VdT26, a random primer (V9), both at 1 micrograms/ml, and Stratascript RT enzyme (75U). Amino-allyl (aa) dUTP/dNTPs produced from a 20X stock (10 mM dCTP, dGTP, dATP and 5mM ea. of dTTP and dUTP) were incorporated into the cDNA. Contaminating enzymes and buffers were removed by purification with the Nucleospin Extract II Kit (Macherey-Nagel, Ger). Eluted cDNA was concentrated using a Vacufuge Concentrator 5301 at 42 oC (Eppendorf, Ger). The resulting cDNA pellets were resuspended in 5 microlitres of sodium bicarbonate (0.1M) (Sigma Aldrich). Cy dyes (Amersham Pharmacia Biotech, UK) were resuspended in 0.1M sodium bicarbonate and coupling to the cDNA took place in the dark for 2 h at room temperature. The labelled cDNA was again purified to remove any uncoupled Cy dye using the Nucleospin Extract II Kit.

growth_protocol: Fish were netted and transferred to an anaesthetic/sedative solution (1:1000 dilution of a stock 100 mg/ml ethyl 4-benzoate; Sigma-Aldrich). Blood samples were collected from the caudal vessels into EDTA (1.5 mg/ml blood; Sigma-Aldrich) and aprotinin (3000 KU/ml blood; Sigma-Aldrich) and fish were killed by spinal section. Fifty precocious male parr and fifty non-precocious male parr (sex determined on dissection) were sampled in January 2004. Length and weight measurements were taken. All tissues were removed to RNAlater or snap frozen in liquid nitrogen. Samples were stored at -80oC until RNA extraction.

extract_protocol: All samples were lysed and homogenized in TRIzol reagent (Invitrogen Life Technologies). Qiagen RNeasy midi columns and wash buffers were used to purify the RNA. All samples were DNase treated on-column using the Qiagen DNA-free DNase kit. The concentrations of the RNA samples were determined by UV spectrophotometry (Shimadzu UV-1601 / Eppendorf BioPhotometer) and checked for quality using the Agilent Bioanalyser-derived RNA integrity number (RIN) and by denaturing formaldehyde gel electrophoresis followed by northern blotting and subsequent analysis with a radiolabelled beta-actin probe.

tag: maturation

value: non-precocious

value: Male

tag: developmental stage

value: Parr

value: Brain

value: precocious


title: brain_SLDFH3


title: brain_SLDFA3


title: 251502810578_1_1


title: brain_SLDFD3


title: brain_SLDFC3


title: brain_SLDFF3


title: FPV-infected IKK2kd-transfected HUVEC_V3

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

description: FPV-infected IKK2kd-transfected HUVEC

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Fluorescent signals were detected by the GeneChip Scanner 3000 and recorded and computed by GeneChip Operating Software (GCOS) version 1.4 (Affymetrix).

data_processing: GCOS version 1.4 (Affymetrix)

organism: Homo sapiens

source_name: FPV-infected IKK2kd-transfected HUVEC

tag: FPV-infected

tag: HUVEC monolayer


title: brain_SLDFE3


title: PR8-infected IKK2kd-transfected HUVEC_V1

description: PR8-infected IKK2kd-transfected HUVEC

source_name: PR8-infected IKK2kd-transfected HUVEC

label_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).


title: PR8-infected IKK2kd-transfected HUVEC_V2

description: PR8-infected IKK2kd-transfected HUVEC

extract_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).


title: PR8-infected IKK2kd-transfected HUVEC_V3

description: PR8-infected IKK2kd-transfected HUVEC


title: FPV-infected IKK2kd-transfected HUVEC_V2

description: FPV-infected IKK2kd-transfected HUVEC


title: PR8-infected pEGZ-transfected HUVEC_V3

description: PR8-infected pEGZ-transfected HUVEC

source_name: PR8-infected pEGZ-transfected HUVEC

tag: pEGZ-transfected (empty vector)


title: FPV-infected pEGZ-transfected HUVEC_V3

description: FPV-infected pEGZ-transfected HUVEC

source_name: FPV-infected pEGZ-transfected HUVEC


title: PR8-infected pEGZ-transfected HUVEC_V2

description: PR8-infected pEGZ-transfected HUVEC


title: GATA3siRNA-2-Cy5_2

status: Public on Dec 25 2009

city: St. Louis

first: David

middle: Michael

last: Alvarado

state: MO

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

description: GATA3 siRNA versus GFP siRNA, biological replicate number 2

hyb_protocol: cDNA populations were resuspended in 40ul hybridization buffer (0.25M NaPO4, 0.5% SDS, 1 mM EDTA, 1x SSC and 2X Denhardt's Solution). Microarray slides were hybridized at 42 degrees C for 16 hrs, washed and rehybridized with Cy3 and Cy5 dyes per manufactures recommendations

scan_protocol: Microarray chips were scanned using a GMS 418 Scanner (Affymetrix, Santa Clara, CA)

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed GATA3 siRNA signal/processed GFP siRNA signal

molecule: polyA RNA

organism: Gallus gallus

source_name: GFP control siRNA in utricle sensory epithelia

label_protocol: Purified run-off RNAs from each sample were used for indirect labeling using Genisphere 3DNA Array 50 Kit following manufacturers protocols

extract_protocol: Isolation of RNA, cDNA synthesis and amplification were carried out as described in Hawkins et al, 2003 (PMID: 12761041). Following the second round of amplification, cDNA was added to an in vitro transcription kit (Ambion) as per the manufacturers instructions

value: Utricle sensory epithelia

source_name: GATA3 siRNA in utricle sensory epithelia


title: H5N1-infected IKK2kd-transfected HUVEC_V3

description: H5N1-infected IKK2kd-transfected HUVEC

source_name: H5N1-infected IKK2kd-transfected HUVEC


title: FPV-infected pEGZ-transfected HUVEC_V1

description: FPV-infected pEGZ-transfected HUVEC


title: H5N1-infected pEGZ-transfectedHUVEC_V3

description: H5N1-infected pEGZ-transfected HUVEC

source_name: H5N1-infected pEGZ-transfected HUVEC


title: GATA3siRNA-2-Cy3_2


title: ST-1-Cy5_1

description: Striola versus extra-striola, biological replicate number 1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Striola signal/processed Extra-striola signal

source_name: Micro-dissected utricle extra-striola

source_name: Micro-dissected utricle striola


title: GATA3siRNA-2-Cy5_1


title: ST-1-Cy3_2


title: GATA3siRNA-2-Cy3_1


title: FPV-infected IKK2kd-transfected HUVEC_V1

description: FPV-infected IKK2kd-transfected HUVEC


title: FPV-infected pEGZ-transfected HUVEC_V2

description: FPV-infected pEGZ-transfected HUVEC


title: H5N1-infected pEGZ-transfectedHUVEC_V1

description: H5N1-infected pEGZ-transfected HUVEC


title: H5N1-infected pEGZ-transfectedHUVEC_V2

description: H5N1-infected pEGZ-transfected HUVEC


title: PR8-infected pEGZ-transfected HUVEC_V1

description: PR8-infected pEGZ-transfected HUVEC


title: GATA3siRNA-1-Cy3_1

description: GATA3 siRNA versus GFP siRNA, biological replicate number 1


title: H5N1-infected IKK2kd-transfected HUVEC_V2

description: H5N1-infected IKK2kd-transfected HUVEC


title: H5N1-infected IKK2kd-transfected HUVEC_V1

description: H5N1-infected IKK2kd-transfected HUVEC


title: GATA3siRNA-1-Cy5_2


title: GATA3siRNA-1-Cy3_2


title: GATA3oe-2-Cy5_2

description: GATA3 overexpression versus GFP control, biological replicate number 2

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed GATA3 signal/processed GFP signal

source_name: GFP control in dissociated utricle sensory epithelia

source_name: GATA3 overexpression in dissociated utricle sensory epithelia


title: GATA3oe-2-Cy3_2


title: GATA3siRNA-1-Cy5_1


title: GATA3oe-2-Cy5_1


title: ST-1-Cy5_2


title: GATA3oe-1-Cy3_2

description: GATA3 overexpression versus GFP control, biological replicate number 1


title: GATA3oe-1-Cy5_2


title: GATA3oe-1-Cy3_1


title: GATA3oe-2-Cy3_1


title: GATA3oe-1-Cy5_1


title: ST-2-Cy5_2

description: Striola versus extra-striola, biological replicate number 2


title: ST-2-Cy3_2


title: ST-2-Cy3_1


title: C.elegans, L1 stage, sample 61

status: Public on Dec 19 2009

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

description: C.elegans, L1 stage, sample 61

hyb_protocol: Hybridized as four (4) biological replicates onto C. elegans whole genome chips (Washington University in St Louis, MO, USA) containing 22,490 oligo features overnight.

scan_protocol: The microarrays were scanned with a ScanArray5000 scanner and ScanArrayExpress software.

data_processing: The spots with a bad flag were excluded completely from the data. Values from the accepted spots were set to have a baseline at the threshold of detection. The data was normalized per chip to the 50th percentile, and per gene to median. The over- and under-expressed genes were determined by t-test (p<0.05).

label: Cy3-dUTP (Amersham)

organism: Caenorhabditis elegans

source_name: C.elegans, L1 stage, sample 61

label_protocol: Labelled cDNA was created by adding 8 μl 5X first strand buffer (Invitrogen), 4 μl 0.1 M DTT (Invitrogen), 1 μl dNTP mix (Promega), 3 μl Cy3-dUTP (Amersham), and 2 μl SuperscriptII (Invitrogen), further incubating at 45°C for 25 min. After 1 μl of SuperscriptII was added, the reaction was incubated for additional 35 min. RNA was degraded with a solution of 0.1 M NaOH and 2 mM EDTA at 65°C for 15 min, and neutralized with 0.1 M HCl. The cDNA was purified with a CyScribe GFX purification kit.

growth_protocol: Eggs harvested, hatched on plate with E.coli and liquid, grown until L1 stage.

extract_protocol: Total RNA was isolated with a RiboPureTM kit (Ambion, Foster City, CA) according to the manufacturers protocol.


title: C.elegans, L1 stage, sample 59

description: C.elegans, L1 stage, sample 59

source_name: C.elegans, L1 stage, sample 59

treatment_protocol: Eggs harvested, hatched on plate with E.coli and liquid, grown until L1 stage.


title: C.elegans, L1 stage, sample 63

description: C.elegans, L1 stage, sample 63

source_name: C.elegans, L1 stage, sample 63


title: ahr-mutant, biological sample #62

description: C.elegans with nonfunctional ahr-gene, L1 stage, sample 62

source_name: C.elegans with nonfunctional ahr-gene, L1 stage, sample #62

value: ahr-mutant


title: CyclosporinA_day7_replicate1

status: Public on Dec 24 2009

city: Yokohama

first: Yumiko

last: Tsuji

address: 2-12-1, Fukuura, Kanazawa-ku

institute: Shiseido

description: Biological replicate 1 of 2. Day7 after Ciclosporin A treatment. Vs. ethanol treatment

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

source_name: back skin, day7 after CyclosporinA treatment

label_protocol: Double-stranded cDNA was synthesized from the 500ng of total RNA, and then cyanin3- or 5- labeled cRNA was made from the cDNA by an in vitro transcription according to the manufacturer’s instruction (Agilent Technologies, Palo Alto, California).

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

value: back skin

tag: agent

value: CyclosporinA

tag: time

value: 7 days

source_name: day7 after ethanol treatment

value: control


title: ST-2-Cy5_1


title: ahr-mutant, biological sample #54

description: C.elegans with nonfunctional ahr-gene, L1 stage, sample 54


title: ahr-mutant, biological sample #60

description: C.elegans with nonfunctional ahr-gene, L1 stage, sample 60


title: ST-1-Cy3_1


title: CyclosporinA_day4_replicate2

description: Biological replicate 1 of 2. Day4 after Ciclosporin A treatment. Vs. ethanol treatment

source_name: back skin, day4 after CyclosporinA treatment

value: 4 days

source_name: day4 after ethanol treatment


title: CyclosporinA_day4_replicate1


title: CyclosporinA_day2_replicate1

description: Biological replicate 1 of 2. Day2 after Ciclosporin A treatment. Vs. ethanol treatment

source_name: back skin, day2 after CyclosporinA treatment

value: 2 days

source_name: day2 after ethanol treatment


title: CyclosporinA_day7_replicate2


title: CyclosporinA_day2_replicate2


title: ahr-mutant, biological sample #56

description: C.elegans with nonfunctional ahr-gene, L1 stage, sample 56


title: vinyl carbamate and indole-3-carbinol treated 1

status: Public on Dec 06 2009

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

source_name: Total RNA from lung tumor of mice, vinyl carbamate and indole-3-carbinol treated

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: A/J mice are maintained in the animal facility at UMN.

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from lung tissue.

treatment_protocol: Female A/J mice were injected i.p. with two doses of VC (0.32 mg per mouse) dissolved in isotonic saline, 1 week apart, and then randomized into treatment groups. One week after the second injection of carcinogen, 15 mice were fed I3C-supplemented AIN-93G/M diet (Harlan Teklad, Madison, WI) for 15 weeks. Carcinogen controls (20 mice) and vehicle controls (10 mice) were injected with the carcinogen in isotonic saline or isotonic saline, respectively, and maintained on non-supplemented AIN-93G/M diet until the end of the study.

value: miRNAs and control RNAs from 293T cells

tag: sample

value: A/J

value: lung tumor

value: vinyl carbamate and indole-3-carbinol

label: Alexa Fluor® 647

molecule: other

source_name: synthetic DNA

value: synthetic DNA oligos corrresponding to human miRNAs


title: Benzoate 30 mM rep 3

status: Public on Dec 01 2009

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

description: Gene expression profiles of Bacillus subtilis AG174 were compared as a function of presence or absence of benzoate in the growth medium. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM MOPS at pH 7.0. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 220 rpm, incubated at 37 °C to an optical density at 600 nm of 0.2. Four cultures were grown in the presence of 30 mM benzoate and four cultures were grown in the absence of benzoate. One sample was taken from each of four replicate cultures of 0 mM benzoate and 30 mM benzoate.

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: Affymetrix GCOS software

organism: Bacillus subtilis

source_name: Bacillus subtilis AG174

label_protocol: Labeled cDNA was prepared and hybridized to Affymetrix Antisense Bacillus subtilis arrays by standard procedures.

growth_protocol: Bacillus subtilis strain AG174 was diluted 500-fold in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM MOPS at pH 7.0. The cultures were rotated at 220 rpm at 37 ºC. Cultures were grown to an optical density at 600 nm of 0.2. Four cultures were grown in the presence of 30 mM benzoate and four cultures were grown in the absence of benzoate. One sample was taken from each of four replicate cultures of 0 mM benzoate and 30 mM benzoate.

extract_protocol: RNA was isolated using 10% saturated phenol-ethanol solution and the RNeasy Kit.

treatment_protocol: Growth at pH 7.0

tag: Bacillus subtilis AG174


title: Benzoate 0 rep 4


title: Control replicate 2

source_name: Total RNA from lung tumor of mice, control treated

tag: tissue


title: Benzoate 30 mM rep 2


title: Control replicate 3


title: Benzoate 30 mM rep 1


title: vinyl carbamate treated 4

source_name: Total RNA from lung tumor of mice, vinyl carbamate treated

value: vinyl carbamate


title: vinyl carbamate treated 1


title: vinyl carbamate treated 3


title: vinyl carbamate treated 2


title: Control replicate 1


title: Benzoate 30 mM rep 4


title: Benzoate 0 rep 2


title: Benzoate 0 rep 3


title: Benzoate 0 rep 1


title: DLL4_3

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgU133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgU133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).

data_processing: Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.

source_name: lymphatic endothelial cells (pSin-DLL4 co-culture)

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand synthesis, in vitro transcription was carried out with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf).

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC specific marker, and cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C in fibronectin-coated plates. KSHV microRNA Cluster transfected LEC were grown under the same conditions. All cells were mycoplasma free.

extract_protocol: Qiazol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was used per Affymetrix chip.

tag: co-culture

value: lymphatic endothelial cells

tag: co-culture vector


title: DLL4_1


title: JAG1_1

source_name: lymphatic endothelial cells (pSin-JAG1 co-culture)


title: JAG1_3


title: JAG1_2


title: DLL4_2


title: pSin_1

source_name: lymphatic endothelial cells (pSin co-culture)

value: pSin


title: pSin_2


title: Control 96 hours comparing with heat shock 96 hours after dormancy release Series C

city: Bet-Dagan

first: Ron

last: Ophir

address: POB 6

department: Fruit Tree Sciences

country: Israel

institute: Agricultire Research Organization

description: Due to the small number of replicates, biological-comparison variance was then corrected by empirical Bayesian method to obtain moderated t-statistics (Smyth, 2004) and multiple comparison correction (Benjamini and Hochberg, 1995) was applied. Statistical test of the difference in expression signal between each treatment and control (adjusted p-value < 0.05) was calculated separately for each clone at each time point analyzed.

hyb_protocol: For each microarray hybridization, a pair of Cy3- and Cy5-labeled targets, for comparison according to the hybridization plan, were mixed. Microarray cross-linking, hybridization and washing procedures were carried out as detailed at http://ag.arizona.edu/microarray/Microarraymethod1

scan_protocol: Arrays were scanned with a GenePix Microarray scanner (Molecular Devices, Sunnyvale, CA) and quantified with GenePix Pro 5.0 software to extract the median signal and background intensities for each spot for both channels on the microarray.

data_processing: Differentially expressed genes were selected using the Linear Models for Microarray (LIMMA) package which is part of the Bioconductor project (Gentleman et al., 2004). Although it is a dual-channel platform, we analyzed each channel separately as described in chapter 9 of the LIMMA user's guide and presented at the 55th Session of the International Statistics Institute (Smyth, 2005). First, we weighted bad spots by 0.1 and subtracted the local background measurement. This was followed by a per-tip LOWESS normalization within slides (Yang et al., 2002) and variance stabilization normalization (VSN) (Huber et al., 2002) between slides. Technical replicates were averaged and then we estimated the intra-spot correlation between the two channels of the same RNA sample and as weighting for further fitting. This technique is equivalent to a randomized block-over-dye effect within spots (Smyth, 2005).

organism: Vitis vinifera

source_name: Control 96 hours after dormancy release

label_protocol: Direct labeling of the resultant aRNA by random priming was then used for the production of Cy3 and Cy5 probes.A total of 150 µg of aRNA was incubated with 3 µL dNTP (10 mM), 2 µL Cy3 or Cy5-dUTP (1 mM) and 2 µL random hexamer (0.5 µg/µL) in a total volume of 26 µL at 65oC for 5 min.Following the heating step, 8 µL of 5X first-strand buffer, 4 µL of DTT (0.1 M), 1 µL of RNase inhibitor (Invitrogen, Carlsbad , CA) and 2 µL of Power Script (Invitrogen) were added and the reaction was incubated for 2 h at 42oC.Products were purified using RNeasy MinElute columns (Qiagen, Carlsbad, CA) and kept protected from light at -80oC.

extract_protocol: Total RNA samples were extracted separately from each pool according to Or et al.(2000), and PolyA RNA preparations were purified using Dynabeads Oligo (dT)25 (Dynal Biotech, Oslo, Norway) according to the manufacturer's instructions.PolyA RNA samples were then used as templates for amplification reactions using MessageAmpTM II aRNA kit (Ambion, Austin, TX), following the manufacturer's instructions.

treatment_protocol:
Hydrogen cyanamide (HC): 5% Dormex.
Heat shock (HS): Incubation for 1 h in 50oC water.
Vitis vinefera buds were pooled from multiple single-node cuttings at six time points (3, 6, 12, 24, 48 and 96 h) after control, HS and HC treatments and frozen.

value: grape bud

source_name: Heat shock 96 hours after dormancy release


title: Control 12 hours comparing with heat shock 12 hours after dormancy release Series C

source_name: Control 12 hours after dormancy release

source_name: Heat shock 12 hours after dormancy release


title: Heat shock 24 hours comparing with Heat shock 48 hours after dormancy release Series C

source_name: Heat shock 24 hours after dormancy release


title: Control 24 hours comparing with control 48 hours after dormancy release Series C

source_name: Control 24 hours after dormancy release

source_name: Control 48 hours after dormancy release


title: Heat shock 12 hours comparing with Heat shock 24 hours after dormancy release Series C


title: Control 24 hours comparing with heat shock 24 hours after dormancy release Series C


title: Heat shock 48 hours comparing with Heat shock 96 hours after dormancy release Series C

source_name: Heat shock 48 hours after dormancy release


title: Control 6 hours comparing with heat shock 6 hours after dormancy release Series C

source_name: Control 6 hours after dormancy release

source_name: Heat shock 6 hours after dormancy release


title: Heat shock 6 hours comparing with Heat shock 12 hours after dormancy release Series C


title: Heat shock 3 hours comparing with Heat shock 6 hours after dormancy release Series C

source_name: Heat shock 3 hours after dormancy release


title: Control 3 hours comparing with heat shock 3 hours after dormancy release Series C

source_name: Control 3 hours after dormancy release


title: Control 48 hours comparing with control 96 hours after dormancy release Series C


title: Hydrogen cyanamide 96 hours comparing with Hydrogen cyanamide 48 hours after dormancy release Series F

source_name: Hydrogen cyanamide 96 hours after dormancy release


title: Heat shock 96 hours comparing with Heat shock 3 hours after dormancy release Series C


title: Control 12 hours comparing with control 24 hours after dormancy release Series C


title: Control 3 hours comparing with control 6 hours after dormancy release Series C


title: Hydrogen cyanamide 48 hours comparing with Hydrogen cyanamide 24 hours after dormancy release Series F

source_name: Hydrogen cyanamide 48 hours after dormancy release


title: Hydrogen cyanamide 6 hours comparing with Hydrogen cyanamide 96 hours after dormancy release Series F

source_name: Hydrogen cyanamide 6 hours after dormancy release


title: Control 48 hours comparing with heat shock 48 hours after dormancy release Series C


title: Hydrogen cyanamide 12 hours comparing with Hydrogen cyanamide 6 hours after dormancy release Series F

source_name: Hydrogen cyanamide 12 hours after dormancy release


title: Control 6 hours comparing with control 12 hours after dormancy release Series C


title: Hydrogen cyanamide 24 hours comparing with Hydrogen cyanamide 12 hours after dormancy release Series F

source_name: Hydrogen cyanamide 24 hours after dormancy release


title: Hydrogen cyanamide 6 hours comparing with control 6 hours after dormancy release Series F


title: Hydrogen cyanamide 12 hours comparing with control 12 hours after dormancy release Series F


title: Heat shock 96 hours comparing with hydrogen cyanamide 96 hours after dormancy release Series F


title: Heat shock 24 hours comparing with hydrogen cyanamide 24 hours after dormancy release Series F


title: Heat shock 12 hours comparing with hydrogen cyanamide 12 hours after dormancy release Series F


title: Heat shock 6 hours comparing with hydrogen cyanamide 6 hours after dormancy release Series F


title: Heat shock 48 hours comparing with hydrogen cyanamide 48 hours after dormancy release Series F


title: Heat shock 48 hours comparing with Heat shock 24 hours after dormancy release Series F


title: Heat shock 24 hours comparing with Heat shock 12 hours after dormancy release Series F


title: Heat shock 6 hours comparing with Heat shock 96 hours after dormancy release Series F


title: Heat shock 96 hours comparing with Heat shock 48 hours after dormancy release Series F


title: Hydrogen cyanamide 24 hours comparing with control 24 hours after dormancy release Series F


title: Heat shock 24 hours comparing with control 24 hours after dormancy release Series F


title: Control 48 hours comparing with control 24 hours after dormancy release Series F


title: Hydrogen cyanamide 48 hours comparing with control 48 hours after dormancy release Series F


title: Hydrogen cyanamide 96 hours comparing with control 96 hours after dormancy release Series F

source_name: Control 96 hours after dormancy release


title: Heat shock 48 hours comparing with control 48 hours after dormancy release Series F


title: Control 96 hours comparing with control 48 hours after dormancy release Series F


title: Heat shock 6 hours comparing with control 6 hours after dormancy release Series F


title: Heat shock 12 hours comparing with Heat shock 6 hours after dormancy release Series F


title: Heat shock 96 hours comparing with control 96 hours after dormancy release Series F

source_name: Heat shock 96 hours after dormancy release


title: Control 6 hours comparing with control 96 hours after dormancy release Series F


title: Heat shock 12 hours comparing with control 12 hours after dormancy release Series F

source_name: Control 12 hours after dormancy release


title: Control 24 hours comparing with control 12 hours after dormancy release Series F


title: Control 12 hours comparing with control 6 hours after dormancy release Series F


title: Hydrogen cyanamide 6 hours comparing with Hydrogen cyanamide 12 hours after dormancy release Series A


title: Control 96 hours comparing with Hydrogen cyanamide 96 hours after dormancy release Series A


title: Control 48 hours comparing with Hydrogen cyanamide 48 hours after dormancy release Series A


title: Control 3 hours comparing with Hydrogen cyanamide 3 hours after dormancy release Series A


title: Hydrogen cyanamide 48 hours comparing with Hydrogen cyanamide 96 hours after dormancy release Series A


title: Control 48 hours comparing with control 24 hours after dormancy release Series A


title: Hydrogen cyanamide 12 hours comparing with Hydrogen cyanamide 24 hours after dormancy release Series A


title: Hydrogen cyanamide 24 hours comparing with Hydrogen cyanamide 48 hours after dormancy release Series A


title: Control 24 hours comparing with Hydrogen cyanamide 24 hours after dormancy release Series A


title: Hydrogen cyanamide 3 hours comparing with Hydrogen cyanamide 6 hours after dormancy release Series A

source_name: Hydrogen cyanamide 3 hours after dormancy release


title: Control 6 hours comparing with control 3 hours after dormancy release Series A


title: Control 96 hours comparing with control 48 hours after dormancy release Series A


title: Control 3 hours comparing with control 96 hours after dormancy release Series A


title: Control 12 hours comparing with Hydrogen cyanamide 12 hours after dormancy release Series A


title: Control 6 hours comparing with Hydrogen cyanamide 6 hours after dormancy release Series A


title: Control 12 hours comparing with control 6 hours after dormancy release Series A


title: Hydrogen cyanamide 96 hours comparing with Hydrogen cyanamide 3 hours after dormancy release Series A


title: Control 24 hours comparing with control 12 hours after dormancy release Series A


title: NCAM wild-type +/+ 2

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: male, 2 months

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MG_U74Av2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

label: Biotinylated Nucleotides

source_name: Mus Musculus (C57BL/6J), total brain, adult

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 rev 1, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Following cleanup according to Qiagen Rneasy Mini Kit Protocol.

treatment_protocol: dissection after cervical dislocation

value: none (wild-type, same genetic background)

tag: gender

value: male

tag: age

value: 2 months

value: brain


title: NCAM deificient -/- 3

description: male, 3 months

value: constitutive knock-out of Ncam gene (Cremer et al., Nature 367 (1994), 455-459)

value: 3 months


title: NCAM deificient -/- 2

description: male, 2 months


title: NCAM wild-type +/+ 3

description: male, 3 months


title: NCAM wild-type +/+ 1

description: male, 2 months


title: NCAM deificient -/- 1

description: male, 2 months


title: Cardiac GATA-4 overexpression, 9

city: University of OULU

first: Jaana

last: Rysä

address: PO BOX 5000

department: Pharmacology and toxicology

institute: University of Oulu

description:
Gene expression profiles three days after GATA-4 gene transfer were compared with those of Lac Z –treated animals by screening Affymetrix Rat Expression Set 230_2.0 Arrays (there are 5 samples in both group).
For additional information: Rysa J, Leskinen H, Ilves M, Ruskoaho H.  Hypertension. 2005;45:927-933.

hyb_protocol: Wash A1 Recovery Mixes: 0 Wash A1 Temperature (C): 30 Number of Wash A1 Cycles: 10 Mixes per Wash A1 Cycle: 2 Wash B Recovery Mixes: 0 Wash B Temperature (C): 50 Number of Wash B Cycles: 6 Mixes per Wash B Cycle: 15 Stain Temperature (C): 35 First Stain Time (seconds): 300 Wash A2 Recovery Mixes: 0 Wash A2 Temperature (C): 30 Number of Wash A2 Cycles: 10 Mixes per Wash A2 Cycle: 4 Second Stain Time (seconds): 300 Third Stain Time (seconds): 300 Wash A3 Recovery Mixes: 0

scan_protocol: GeneChip Scanner 3000 with GeneChip Operating Software (GCOS) v. 1.2 (Affymetrix) was used in scanning.

organism: Rattus norvegicus

source_name: Left ventricular gene expression 3 days after GATA-4 gene transfer

label_protocol: After hybridization GeneChips were washed and stained with streptavidin-phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and second staining with streptavidin-phycoerythrin by using Affymetrix Fluidics station according the standard protocol.

extract_protocol: Total RNA from left ventricular samples was isolated by the guanidine thiocyanate-CsCl method.

tag: strain

value: Sprague-Dawley

value: Male

tag: weight

value: left ventricle


title: 10-11 dpa pistil Replicate 1 Technical Replicate B

status: Public on Nov 30 2009

city: Valencia

first: Pablo

middle: A

last: Carbonell

state: Valencia

address: Ingeniero Fausto Elio

country: Spain

institute: IBMCP-CSIC

description: 10-11 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5

hyb_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

scan_protocol: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than twice the median signal background were removed as low-signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

data_processing: Linear normalized log2 ratio (test/reference). VALUEs for the technical replicates Bs have been dye-swap corrected at Matrix sheets.

source_name: reference mix

label_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydration was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem) during 16 h. Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

extract_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy3 or Cy5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

treatment_protocol: Total RNA was extracted from frozen pistils (50-100 mg per sample) using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

tag: equimolar mix of amplifyed RNA from the seven stages of replicate 1

source_name: 10-11 dpa unfertilized pistils

tag: 10-11 dpa cer6-2 Ler unfertilized pistils


title: Cardiac GATA-4 overexpression, 5

data_processing: GeneChip Operating Software (GCOS) v. 1.2

source_name: Left ventricular gene expression 3 days after LacZ gene transfer


title: Cardiac GATA-4 overexpression, 8


title: Cardiac GATA-4 overexpression, 10


title: 12-14 dpa pistil Replicate 2 Technical Replicate B

description: 12-14 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5

tag: equimolar mix of amplifyed RNA from the seven stages of replicate 2

source_name: 12-14 dpa unfertilized pistils

tag: 12-14 dpa cer6-2 Ler unfertilized pistils


title: 8-9 dpa pistil Replicate 2 Technical Replicate B

description: 8-9 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5

source_name: 8-9 dpa unfertilized pistils

tag: 8-9 dpa cer6-2 Ler unfertilized pistils


title: 10-11 dpa pistil Replicate 2 Technical Replicate B

description: 10-11 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5


title: Cardiac GATA-4 overexpression, 7


title: Cardiac GATA-4 overexpression, 2


title: Cardiac GATA-4 overexpression, 4


title: 12-14 dpa pistil Replicate 1 Technical Replicate B

description: 12-14 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5


title: Cardiac GATA-4 overexpression, 1


title: 10-11 dpa pistil Replicate 2 Technical Replicate A

description: 10-11 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: 12-14 dpa pistil Replicate 2 Technical Replicate A

description: 12-14 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: Cardiac GATA-4 overexpression, 6


title: Cardiac GATA-4 overexpression, 3


title: Control 96 hours comparing with control 3 hours after dormancy release Series C

source_name: Control 3 hours after dormancy release


title: 6-7 dpa pistil Replicate 2 Technical Replicate B

description: 6-7 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5

source_name: 6-7 dpa unfertilized pistils

tag: 6-7 dpa cer6-2 Ler unfertilized pistils


title: 8-9 dpa pistil Replicate 1 Technical Replicate A

description: 8-9 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: 8-9 dpa pistil Replicate 2 Technical Replicate A

description: 8-9 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: 8-9 dpa pistil Replicate 1 Technical Replicate B

description: 8-9 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5


title: 6-7 dpa pistil Replicate 2 Technical Replicate A

description: 6-7 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: 4-5 dpa pistil Replicate 1 Technical Replicate B

description: 4-5 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5

source_name: 4-5 dpa unfertilized pistils

tag: 4-5 dpa cer6-2 Ler unfertilized pistils


title: 6-7 dpa pistil Replicate 1 Technical Replicate B

description: 6-7 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5


title: 4-5 dpa pistil Replicate 2 Technical Replicate B

description: 4-5 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5


title: 2-3 dpa pistil Replicate 2 Technical Replicate B

description: 2-3 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5

source_name: 2-3 dpa unfertilized pistils

tag: 2-3 dpa cer6-2 Ler unfertilized pistils


title: 4-5 dpa pistil Replicate 2 Technical Replicate A

description: 4-5 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: 0-1 dpa pistil Replicate 2 Technical Replicate A

description: 0-1 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3

source_name: 0-1 dpa unfertilized pistils

tag: 0-1 dpa cer6-2 Ler unfertilized pistils


title: 2-3 dpa pistil Replicate 1 Technical Replicate B

description: 2-3 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5


title: 2-3 dpa pistil Replicate 2 Technical Replicate A

description: 2-3 dpa unfertilized pistils, replica 2 labelled with Cy5 compared with reference mix labelled with Cy3


title: 0-1 dpa pistil Replicate 1 Technical Replicate B

description: 0-1 dpa unfertilized pistils, replica 1 labelled with Cy3 compared with reference mix labelled with Cy5


title: 12-14 dpa pistil Replicate 1 Technical Replicate A

description: 12-14 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: 0-1 dpa pistil Replicate 2 Technical Replicate B

description: 0-1 dpa unfertilized pistils, replica 2 labelled with Cy3 compared with reference mix labelled with Cy5


title: 6-7 dpa pistil Replicate 1 Technical Replicate A

description: 6-7 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: 4-5 dpa pistil Replicate 1 Technical Replicate A

description: 4-5 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: 10-11 dpa pistil Replicate 1 Technical Replicate A

description: 10-11 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: 2-3 dpa pistil Replicate 1 Technical Replicate A

description: 2-3 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: rat-liver-han/wistar-rep4 [RMA-GPL8627]

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: Raw data file RAE2230A_070303_IM02T_LH.CEL provided as supplementary file on Series record.

hyb_protocol: Microarray labeling, hybridization, and scanning was performed at The Centre for Applied Genomics (Toronto, Canada) according to manufacturer's recommended protocols.

data_processing: Raw data (CEL files) were read into the R statistical environment (v2.8.1) using the affy package (v1.20.2) of the BioConductor open-source project. Pre-processing was performed using the MAS5 and RMA algorithms implemented in the affy package and the GCRMA algorithm implemented in the GCRMA package (v2.14.1). In all cases both default CDFs and alternative CDFs mapping probes to unique Entrez Gene IDs were used.

source_name: rat liver, han/wistar

growth_protocol: Rats were obtained from breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland. All animals were males 10-12 weeks old.

extract_protocol: Total RNA was extracted using Qiagen Rneasy kits according to the manufacturer's instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyze (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver was harvested between 8:30 and 11:00 from rats treated by gavage with corn oil vehicle 19 hours earlier.

value: 10-12 weeks

value: Han/Wistar

tag: animal id


title: HFC_A3 versus HFR pool

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: Biological replicate

hyb_protocol: 1µg of labelled nucleic acid was hybridized at 67 degree_C during 17 hours

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using Genepix pro 6.0

data_processing: Lowess normalization. Only spots with SNR > 2 were considered

source_name: HFR pool

label_protocol: One microgram of total RNA was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 5 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes, following a dye switch experimental plan.  Fluorescent probes were purified using Rneasy minikit (Qiagen)

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

tag: Tissue

value: Liver


title: HFC_A8 versus HFR pool

description: Biological replicate


title: HFC_A9 versus HFR pool

description: Biological replicate


title: HFC_A4 versus HFR pool

description: Biological replicate


title: rat-liver-han/wistar-rep2 [RMA-GPL8627]

description: Raw data file RAE2230A_060403_IM04T_LH.CEL provided as supplementary file on Series record.

scan_protocol: Microarray labeling, hybridization, and scanning was performed at The Centre for Applied Genomics (Toronto, Canada) according to manufacturer's recommended protocols.


title: rat-liver-han/wistar-rep1 [RMA-GPL8627]

description: Raw data file RAE2230A_043003_IM04T_LH.CEL provided as supplementary file on Series record.

label_protocol: Microarray labeling, hybridization, and scanning was performed at The Centre for Applied Genomics (Toronto, Canada) according to manufacturer's recommended protocols.


title: 0-1 dpa pistil Replicate 1 Technical Replicate A

description: 0-1 dpa unfertilized pistils, replica 1 labelled with Cy5 compared with reference mix labelled with Cy3


title: rat-liver-lineC-rep3 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM10T_LH.CEL provided as supplementary file on Series record.

source_name: rat liver, lineC

value: Line-C


title: rat-liver-lineC-rep4 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM11T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep4 [RMA-GPL8627]

description: Raw data file RAE2230A_060403_IM03T_LH.CEL provided as supplementary file on Series record.

source_name: rat liver, long-evans

value: Long-Evans


title: HFC_A6 versus HFR pool

description: Biological replicate


title: rat-liver-long-evans-rep2 [RMA-GPL8627]

description: Raw data file RAE2230A_060403_IM02T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep1 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM08T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineA-rep4 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM04T_LH.CEL provided as supplementary file on Series record.

source_name: rat liver, lineA

value: Line-A


title: rat-liver-lineC-rep2 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM09T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineA-rep3 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM03T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep3 [RMA-GPL8627]

description: Raw data file RAE2230A_043003_IM02T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineA-rep2 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM02T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep4 [RMA-GPL341]


title: rat-liver-lineA-rep1 [RMA-GPL8627]

description: Raw data file RAE2230A_102803_IM01T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep3 [RMA-GPL341]

description: Raw data file RAE2230A_060403_IM05T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep1 [RMA-GPL8627]

description: Raw data file RAE2230A_060403_IM01T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep1 [RMA-GPL341]


title: rat-liver-han/wistar-rep2 [RMA-GPL341]


title: rat-liver-han/wistar-rep3 [RMA-GPL8627]


title: rat-liver-long-evans-rep4 [RMA-GPL341]


title: rat-liver-han/wistar-rep4 [MAS5-GPL8627]

description: Raw data file RAE2230A_070303_IM02T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep4 [MAS5-GPL8627]


title: rat-liver-long-evans-rep3 [RMA-GPL341]


title: rat-liver-long-evans-rep3 [MAS5-GPL8627]


title: rat-liver-han/wistar-rep3 [MAS5-GPL8627]


title: rat-liver-han/wistar-rep2 [MAS5-GPL8627]

description: Raw data file RAE2230A_060403_IM04T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep1 [MAS5-GPL8627]

description: Raw data file RAE2230A_043003_IM04T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep2 [RMA-GPL341]


title: rat-liver-lineA-rep4 [RMA-GPL341]


title: rat-liver-lineA-rep3 [RMA-GPL341]


title: rat-liver-long-evans-rep1 [RMA-GPL341]


title: rat-liver-lineC-rep4 [RMA-GPL341]


title: rat-liver-long-evans-rep2 [MAS5-GPL8627]


title: rat-liver-long-evans-rep2 [RMA-GPL341]


title: rat-liver-lineC-rep3 [RMA-GPL341]


title: rat-liver-lineA-rep2 [RMA-GPL341]


title: rat-liver-lineC-rep1 [RMA-GPL341]


title: rat-liver-han/wistar-rep4 [MAS5-GPL341]


title: rat-liver-han/wistar-rep3 [MAS5-GPL341]


title: rat-liver-long-evans-rep1 [MAS5-GPL8627]


title: rat-liver-lineC-rep3 [MAS5-GPL8627]


title: rat-liver-lineC-rep4 [MAS5-GPL8627]


title: rat-liver-lineC-rep2 [MAS5-GPL8627]


title: rat-liver-han/wistar-rep1 [MAS5-GPL341]


title: rat-liver-han/wistar-rep2 [MAS5-GPL341]


title: rat-liver-long-evans-rep4 [MAS5-GPL341]


title: rat-liver-long-evans-rep3 [MAS5-GPL341]


title: rat-liver-lineC-rep1 [MAS5-GPL8627]


title: rat-liver-long-evans-rep2 [MAS5-GPL341]


title: rat-liver-lineC-rep3 [MAS5-GPL341]


title: rat-liver-lineC-rep2 [MAS5-GPL341]


title: rat-liver-lineC-rep4 [MAS5-GPL341]


title: rat-liver-lineC-rep1 [MAS5-GPL341]


title: rat-liver-lineA-rep2 [MAS5-GPL341]


title: rat-liver-lineA-rep3 [MAS5-GPL341]


title: rat-liver-lineA-rep3 [MAS5-GPL8627]


title: rat-liver-lineA-rep4 [MAS5-GPL8627]


title: rat-liver-lineA-rep2 [MAS5-GPL8627]


title: rat-liver-long-evans-rep1 [MAS5-GPL341]


title: rat-liver-lineA-rep1 [MAS5-GPL341]


title: rat-liver-lineA-rep1 [RMA-GPL341]


title: rat-liver-han/wistar-rep4 [GCRMA-GPL341]


title: rat-liver-lineA-rep4 [MAS5-GPL341]


title: rat-liver-han/wistar-rep3 [GCRMA-GPL341]


title: rat-liver-lineA-rep1 [MAS5-GPL8627]


title: rat-liver-han/wistar-rep1 [GCRMA-GPL341]


title: rat-liver-han/wistar-rep2 [GCRMA-GPL341]


title: rat-liver-han/wistar-rep4 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep3 [GCRMA-GPL341]


title: rat-liver-long-evans-rep4 [GCRMA-GPL8627]


title: rat-liver-han/wistar-rep3 [GCRMA-GPL8627]


title: rat-liver-lineC-rep4 [GCRMA-GPL8627]


title: rat-liver-lineA-rep1 [GCRMA-GPL341]


title: rat-liver-lineC-rep2 [GCRMA-GPL341]


title: rat-liver-lineC-rep4 [GCRMA-GPL341]


title: rat-liver-han/wistar-rep1 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep4 [GCRMA-GPL341]


title: rat-liver-lineC-rep3 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep1 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep1 [GCRMA-GPL341]


title: rat-liver-han/wistar-rep2 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep3 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep2 [GCRMA-GPL8627]


title: rat-liver-lineA-rep3 [GCRMA-GPL341]


title: rat-liver-lineC-rep3 [GCRMA-GPL341]


title: rat-liver-lineC-rep1 [GCRMA-GPL341]


title: rat-liver-long-evans-rep2 [GCRMA-GPL341]


title: rat-liver-lineA-rep2 [GCRMA-GPL341]


title: rat-liver-lineA-rep4 [GCRMA-GPL341]


title: rat-liver-lineC-rep1 [GCRMA-GPL8627]


title: rat-liver-lineC-rep2 [GCRMA-GPL8627]


title: rat-liver-lineA-rep4 [GCRMA-GPL8627]


title: rat-liver-lineA-rep1 [GCRMA-GPL8627]


title: rat-liver-lineA-rep2 [GCRMA-GPL8627]


title: rat-liver-long-evans-rep2 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO12_LE55.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep1 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO11_LE52.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep3 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO7_LC29.CEL provided as supplementary file on Series record.

source_name: rat liver, line-C


title: rat-liver-lineC-rep2 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO6_LC28.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep1 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO5_LC27.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep2 [MAS5-GPL7598]

description: Raw data file RAE2302_041609H_AO10_WW50.CEL provided as supplementary file on Series record.


title: rat-liver-lineA-rep4 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO4_LA20.CEL provided as supplementary file on Series record.

source_name: rat liver, line-A


title: rat-liver-lineA-rep3 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO3_LA19.CEL provided as supplementary file on Series record.


title: rat-liver-lineA-rep3 [GCRMA-GPL8627]

description: Raw data file RAE2230A_102803_IM03T_LH.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep4 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO8_LC30.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep2 [RMA-GPL7598]


title: rat-liver-lineA-rep2 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO2_LA18.CEL provided as supplementary file on Series record.


title: rat-liver-han/wistar-rep1 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO9_WW49.CEL provided as supplementary file on Series record.


title: rat-liver-long-evans-rep1 [MAS5-GPL7598]


title: rat-liver-lineA-rep1 [RMA-GPL7598]

description: Raw data file RAE2302_041609H_AO1_LA17.CEL provided as supplementary file on Series record.


title: rat-liver-lineC-rep1 [MAS5-GPL7598]


title: rat-liver-han/wistar-rep1 [MAS5-GPL7598]


title: rat-liver-long-evans-rep2 [MAS5-GPL7598]


title: rat-liver-lineA-rep4 [MAS5-GPL7598]


title: rat-liver-lineC-rep3 [MAS5-GPL7598]


title: rat-liver-lineC-rep4 [MAS5-GPL7598]


title: rat-liver-lineC-rep2 [MAS5-GPL7598]


title: rat-liver-lineA-rep3 [MAS5-GPL7598]


title: rat-liver-lineA-rep2 [MAS5-GPL7598]


title: rat-liver-long-evans-rep2 [GCRMA-GPL7598]


title: rat-liver-lineC-rep4 [GCRMA-GPL7598]


title: rat-liver-han/wistar-rep2 [GCRMA-GPL7598]


title: rat-liver-lineA-rep1 [GCRMA-GPL7598]


title: rat-liver-lineC-rep3 [GCRMA-GPL7598]


title: rat-liver-lineC-rep2 [GCRMA-GPL7598]


title: rat-liver-lineA-rep3 [GCRMA-GPL7598]


title: rat-liver-lineA-rep2 [GCRMA-GPL7598]


title: rat-liver-long-evans-rep1 [GCRMA-GPL7598]


title: rat-liver-han/wistar-rep1 [GCRMA-GPL7598]


title: rat-liver-han/wistar-rep1 [RMA-GPL1355]


title: rat-liver-long-evans-rep2 [RMA-GPL1355]


title: rat-liver-lineA-rep1 [MAS5-GPL7598]


title: rat-liver-lineC-rep4 [RMA-GPL1355]


title: rat-liver-lineA-rep4 [GCRMA-GPL7598]


title: rat-liver-long-evans-rep1 [RMA-GPL1355]


title: rat-liver-lineC-rep3 [RMA-GPL1355]


title: rat-liver-lineA-rep2 [RMA-GPL1355]


title: rat-liver-han/wistar-rep2 [RMA-GPL1355]


title: rat-liver-lineA-rep1 [RMA-GPL1355]


title: rat-liver-lineA-rep3 [RMA-GPL1355]


title: rat-liver-lineA-rep4 [RMA-GPL1355]


title: rat-liver-lineC-rep1 [MAS5-GPL1355]


title: rat-liver-lineC-rep4 [MAS5-GPL1355]


title: rat-liver-han/wistar-rep2 [MAS5-GPL1355]


title: rat-liver-lineC-rep1 [GCRMA-GPL7598]


title: rat-liver-lineC-rep3 [MAS5-GPL1355]


title: rat-liver-lineC-rep2 [MAS5-GPL1355]


title: rat-liver-lineC-rep2 [RMA-GPL1355]


title: rat-liver-han/wistar-rep1 [MAS5-GPL1355]


title: rat-liver-lineC-rep1 [RMA-GPL1355]


title: rat-liver-lineA-rep3 [MAS5-GPL1355]


title: rat-liver-lineA-rep4 [MAS5-GPL1355]


title: rat-liver-lineA-rep1 [MAS5-GPL1355]


title: rat-liver-han/wistar-rep2 [GCRMA-GPL1355]


title: rat-liver-han/wistar-rep1 [GCRMA-GPL1355]


title: rat-liver-long-evans-rep1 [MAS5-GPL1355]


title: rat-liver-long-evans-rep2 [MAS5-GPL1355]


title: rat-liver-long-evans-rep1 [GCRMA-GPL1355]


title: rat-liver-lineC-rep1 [GCRMA-GPL1355]


title: ShamC-60, biological rep 2

status: Public on Nov 01 2009

city: stockholm

first: Jesper

last: Ryge

address: retziusvag 8

department: neuroscience

country: Sweden

institute: karolinska institutet

description: Gene expression data from motor neurons of the sacral rat spinal cord 60 days post sham operation

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45 °C on Affymetrix Rat Genome 230 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated using R and Bioconductor. RMA expression summaries were calculated based on PM intensity values that were normalised (linear quantile plus quantile projection) and background subtracted (global minimization) (Ryge et al, Plos One, 2008). The genes were filtered prior to analysis such that only probe sets annotated in the Ensembl database was included (using biomaRt bioconductor package), so the probe set was reduced from 31099 to 12919.

source_name: 100-200 motor neurons, sacral spinal cord, 60 days post sham opration

label_protocol: Motor neurons retrogradely labelled with flourogold injected into the muscle and intra peritoneally 5-7 days prior to cell extraction.

extract_protocol: Spinal cords were snap frozen in liquid nitrogen, cryosectioned into 10 micro meter slices, which were mounted onto POL-membrane metal frame slides (Leica) and fluorescently identied motor neurons were laser microdissected into a collector tube. Total RNA was extrated using the Picopure RNA isolation kit (Arcturus), which were then subject to a two round amplification using the RiboAmp HS RNA amplification kit (Arcturus) according to manufactors instructions. A DNAse treatment was included in the isolation protocol.

treatment_protocol: Injury: Laminectomy of lumbar vertebra L2-L3, spinal cord transect at S2 and 1-2mm of spinal cord tissue removed. Wound closed suturing muscles, muscle fascia and skin separately. Sham opration: laminectomy with intact dura. Wound closed. Pain relieved with buprenorfin the first 48 hours.

tag: injury stage

value: Sham 60 days

value: Wistar


title: rat-liver-lineA-rep3 [GCRMA-GPL1355]


title: rat-liver-lineC-rep3 [GCRMA-GPL1355]


title: rat-liver-lineA-rep2 [GCRMA-GPL1355]


title: ShamC-21, biological rep 4

description: Gene expression data from motor neurons of the sacral rat spinal cord 21 days post sham operation

source_name: 100-200 motor neurons, sacral spinal cord, 21days post sham opration

value: Sham 21 days


title: ShamC-60, biological rep 3

value: male


title: rat-liver-lineA-rep4 [GCRMA-GPL1355]


title: rat-liver-lineC-rep4 [GCRMA-GPL1355]


title: rat-liver-lineA-rep2 [MAS5-GPL1355]


title: rat-liver-lineC-rep2 [GCRMA-GPL1355]


title: rat-liver-long-evans-rep2 [GCRMA-GPL1355]


title: ShamC-21, biological rep 3


title: Spi-60, biological rep 7

description: Gene expression data from motor neurons of the sacral rat spinal cord 60 days post transection

source_name: 100-200 motor neurons, sacral spinal cord, 60 days post injury

value: Spinal 60 days


title: Spi-60, biological rep 8


title: ShamC-21, biological rep 5


title: Spi-60, biological rep 6


title: ShamC-60, biological rep 4


title: ShamC-60, biological rep 5


title: rat-liver-lineA-rep1 [GCRMA-GPL1355]


title: ShamC-21, biological rep 1


title: ShamC-21, biological rep 2


title: ShamC-21, biological rep 6


title: Spi-60, biological rep 5


title: Spi-60, biological rep 3


title: Spi-60, biological rep 2


title: Spi-60, biological rep 4


title: ShamC-60, biological rep 1


title: Spi-60, biological rep 1


title: Spi-21, biological rep 5

description: Gene expression data from motor neurons of the sacral rat spinal cord 21 days post transection

source_name: 100-200 motor neurons, sacral spinal cord, 21 days post injury

value: Spinal 21 days


title: Spi-21, biological rep 4


title: Spi-21, biological rep 3


title: Spi-21, biological rep 8


title: Spi-21, biological rep 6


title: Spi-21, biological rep 2


title: Spi-21, biological rep 7


title: Spi-21, biological rep 1


title: EW vs LW from 14 yrs old of tree 1

status: Public on Oct 31 2009

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

description: Either EW or LW can be the experimental sample while the other as control sample.

hyb_protocol: Labelled cDNA was hybridised using the radiata pine 18K cDNA microarrays developed in CSIRO Plant Industry. Slides were placed in water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS) at 42 °C, 0.1x SSC (+0.1 % SDS), 0.1x SSC and 0.01x SSC at room temperature, each for 5 min prior to drying and scanning.

scan_protocol: Hybridized microarray slides were scanned using GenePix Personal 4100A microarray scanner (Axon Instruments, CA). Image pre-processing was performed using GenePix® Pro 4.0 and Acuity software (Axon Instruments, CA).

data_processing: Data analysis was carried out using GEPAS v3.1. The mean values from each channel were log2 transformed and normalized using print-tip lowess and slide scale normalization.

label: Alexa Fluor 647, Alexa Fluor 555

organism: Pinus radiata

source_name: LW from 14 yrs old  tree 1

label_protocol: Equal amounts of total RNA (20 or 30 µg) of the two samples to be compared were reversely transcribed using Superscript reverse transcriptase, and generated fluorescently labelled cDNA using Alexa Fluor® 555-aha-dUTP and Alexa Fluor® 647-aha-dUTP, following the protocol of the SuperScriptTM Plus Direst cDNA Labelling System (Invitrogen, CA).

growth_protocol: Three sampling trees each at juvenile (5 yrs), transition (9 yrs) and mature (14 yrs) ages (based on the wood rings at breast height) were selected from a plantation forest of radiata pine at Bondo, NSW , Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The sampling trees at juvenile and mature ages were grown within 50 m distance and under similar environment. Two sampling trees at rotation age (30 yrs) were chosen at Yarralumla, ACT, Australia (35° 18′ 27″ S, 149° 7′ 27.9″ E).

extract_protocol: Developing xylem tissues were ground and total RNA was extracted using the method of Chang et al (1993) with a slight modification

treatment_protocol: For the sampling with trees at juvenile and mature ages, the same dates on November 23, 2005 (late spring) and on March 23, 2006 (early autumn) were arranged to collect earlywood and latewood, respectively. Sample collections at slightly different dates in middle spring (October 15 and 27) and middle autumn (April 13 and 16) in 2005 and 2004 were arranged for rotation and transition ages, respectively. Developing xylem samples were collected by scraping a thin surface layer on the exposed xylem tissue at breast height after freshly debarking the sampling area. Each sampling tree was used to collect developing xylem samples for earlywood in spring and latewood in autumn. In order to minimize environmental effect in the comparisons between earlywood and latewood, we carefully arranged sampling area based on the direction of sunlight and wind, and took samples just opposite in the trunk at about breast height. The sampled tissues were immediately placed into liquid nitrogen in the field, and then stored in the lab at -80 oC for late RNA extraction.

tag: developmental stage

value: latewood

value: 14 yrs old

tag: tissue

value: xylem

label: Alexa Fluor 555, Alexa Fluor 647

source_name: EW from 14 yrs old  tree 1

value: earlywood


title: EW vs LW from 14 yrs old of tree 2

source_name: LW from 14 yrs old  tree 2

tag: age

source_name: EW from 14 yrs old  tree 2


title: EW vs LW from 30 yrs old of tree 1

source_name: LW from 30 yrs old  tree 1

value: 30 yrs old

source_name: EW from 30 yrs old  tree 1


title: EW vs LW from 9 yrs old of tree 1

source_name: LW from 9 yrs old  tree 1

value: 9 yrs old

source_name: EW from 9 yrs old  tree 1


title: EW vs LW from 9 yrs old of tree 2

source_name: LW from 9 yrs old  tree 2

source_name: EW from 9 yrs old  tree 2


title: EW vs LW from 5 yrs old of tree 2

source_name: LW from 5 yrs old  tree 2

value: 5 yrs old

source_name: EW from 5 yrs old  tree 2


title: EW vs LW from 14 yrs old of tree 3

source_name: LW from 14 yrs old  tree 3

source_name: EW from 14 yrs old  tree 3


title: EW vs LW from 9 yrs old of tree 3

source_name: LW from 9 yrs old  tree 3

source_name: EW from 9 yrs old  tree 3


title: EW vs LW from 30 yrs old of tree 2

source_name: LW from 30 yrs old  tree 2

source_name: EW from 30 yrs old  tree 2


title: EW vs LW from 5 yrs old of tree 3

source_name: LW from 5 yrs old  tree 3

source_name: EW from 5 yrs old  tree 3


title: PK15, biological rep 3

status: Public on Oct 30 2009

city: Urbana

first: Gail

last: Scherba

state: IL

address: 2001 S. Lincoln Street

department: Pathobiology

institute: University of Illinois

description: gene expression detection of a porcine somatic cell background

hyb_protocol: 10 µg of biotinylated cRNA was hybridized on each Affymetrix GeneChip® Porcine Genome Expression Array according to the manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The hybridization signal intensities on each GeneChip were determined by using a GeneChip® Scanner 3000 (Affymetrix, Inc.).

data_processing: Each probe set was categorized as present, marginal or absent (PMA calls) on each array based on the Affymetrix detection call algorithm (Liu et al., 2002) as implemented in the Affy package (Gautier et al., 2004) from the Bioconductor project (Gentlemen et al., 2004). The default values were used for threshold Tau (0.015) and p-value cut-offs for absent (p > 0.06), marginal (p < 0.06) and present (p < 0.04). Although intensity values per probe set are given in the normalized data file, they were not used to assess expression differences between OBGF400 and PK15 cell lines because there were confounding batch effects. Submission of intensity values is required to submit the PMA calls, which are what were used to assess OBGF400-specific expression.

organism: Sus scrofa

source_name: PK15 (non-neuronal, epithelial origin) cell culture

label_protocol: Biotinylated cRNA was prepared from 8 μg of total cellular RNA from each pooled sample using the GeneChip® Expression 3’-Amplification Reagents One-Cycle Target Labeling and Control Reagents kit as well as the GeneChip® Sample Cleanup Module according to the manufacturer’s instructions.

growth_protocol: OBGF400 cells were maintained in Dulbecco’s modified Eagle medium (DMEM)/F12/ HAM (Sigma) supplemented with 10% bovine calf serum (Hyclone, Logan, UT), 100 U/ml penicillin, 0.1 mg/ml streptomycin and 0.05 mg/ml gentamicin (Sigma). PK15 cells were propagated in minimum essential medium (Sigma) supplemented with 10% bovine calf serum (Hyclone, Logan, UT), 100 U/ml penicillin (Sigma), 0.1 mg/ml streptomycin (Sigma), 0.05 mg/ml gentamicin (Sigma) and 0.0025 mg/ml amphotericin B (Sigma). All cell cultures were incubated at 37˚C in a 5% CO2 atm.

extract_protocol: Total RNA was independently isolated from each monolayer of OBGF400 and PK15 cell cultures by using a RNeasy Mini kit (Qiagen, Valencia, CA) as recommended by the manufacturer. After RNA extraction, all samples were DNase-treated at 37°C for 20 min with TURBO DNase (Ambion, Austin, TX). In lieu of the DNase inactivation step, immediate sample purification and concentration was performed with RNeasy Clean-Up Columns (Qiagen).

treatment_protocol: The OBGF400 and PK15 cells were not treated.

tag: cell line


title: OBGF400, biological rep 3

description: gene expression detection of a novel porcine olfactory bulb neuroblast cell line

source_name: OBGF400 (neuroblasts) cell culture


title: EW vs LW from 5 yrs old of tree 1

source_name: LW from 5 yrs old  tree 1

source_name: EW from 5 yrs old  tree 1


title: PK15, biological rep 1


title: Endometrium_UIS_P2

status: Public on Oct 17 2009

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

institute: iGenomix

hyb_protocol: All samples were hybridized onto the Whole Human Genome Oligo Microarray (Agilent technologies, Madrid, Spain) encompassing more than 44,000 human DNA probes. Fragmented cRNA samples (1.65 µg) were hybridized onto chips through 17 h of incubation at 65 ºC with constant rotation (10 rpm).

scan_protocol: Hybridized microarrays were scanned in a Axon 4100A scanner (Molecular Devices, Sunnyvale, CA, USA) with a resolution of 5 um per pixel and data extracted with GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
GenePix Pro 6.0 software was used for array image analysis and the calculation of spot intensity measurements which are considered to be raw data.
Spot intensities (means) with background subtraction (median of the background) were transformed to the log2 scale. Previously the obtained negative data were imputed with the value 2 and then were quantile normalized.
Then, the replicates by gene symbol where merged and the data were filtered in order to delete the unknown sequences or probes without gene description.

source_name: Endometrial biopsy, experimental group

label_protocol: The protocols for sample preparation and hybridization of the endometrial samples were adapted from the Agilent Technical Manual. In short, first strand cDNA was transcribed from 1 ug of total RNA using T7-Oligo(dT) Promotor Primer. Samples were in vitro transcribed and Cy-3 labelled (all with the Quick-AMP labelling kit (Agilent technologies, Madrid, Spain). The cRNA synthesis typically yielded between 10 and 15 µg. Following a further clean-up round (QIAGEN, Barcelona, Spain), cRNA was fragmented into pieces ranging from 35 to 200 bases which were confirmed using Agilent 2100 Bioanalyzer technology.

extract_protocol: Endometrial biopsies were collected with Pipelle catheters under sterile conditions from the uterine fundus. A portion (one half) of each sample was snap-frozen in liquid nitrogen and stored at -70 ºC until further processing. Total RNA was extracted using the ‘TRIzol method’ according to the protocol recommended by the manufacturer (Life Technologies, Inc., Gaithersburg, MD). In short, homogenized biopsies (1 ml TRIzol reagent/75mg tissue) were incubated at room temperature for 5 min, chloroform (0.2 volumes of TRIzol) was then added and samples incubated for 2.5 min at room temperature. Thereafter, the said samples were centrifuged for 15 min at 12 000 g (4 ºC). The aqueous phase was precipitated with an equal volume of 2-propanol, stored in ice for 5 min and centrifuged for 30 min at 12,000 g (4 ºC). The pellet was washed with 75% ethanol and dissolved in DEPC-treated water. The integrity of the RNA samples (RNA quality control procedure) was assessed by using the 2100 bioanalyzer (Agilent technologies, Madrid, Spain), running an aliquot of the RNA samples on the RNA 6000 Nano LabChip (Agilent technologies, Madrid, Spain).

value: endometrium

tag: phase

value: mid-secretory phase (LH+7)

tag: group

value: infertile

tag: sample type

value: experimental


title: Endometrium_UIS_P1


title: Endometrium_UIS_P4


title: PK15, biological rep 2


title: OBGF400, biological rep 2


title: Endometrium_UIS_C5

source_name: Endometrial biopsy, control group

value: fertile

value: control


title: Endometrium_UIS_C3


title: OBGF400, biological rep 1


title: Endometrium_UIS_C1


title: Endometrium_UIS_C2


title: Endometrium_UIS_P3


title: Endometrium_UIS_C4