title: Clinical-4 vs Bovine-biased-4

status: Public on Apr 24 2009

city: East Lansing

middle: S

last: Whittam

state: MI

address: 165 Food Safety & Tox

department: Microbiology

institute: Michigan State University

description: There are probes on the array that target three different E. coli genomes. Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5× SSC, and 1 mg/mL BSA at 42°C for 1 hour. After blocking, arrays were washed 2× 5 min in 0.1× SSC and 2× 30 s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95°C for 5 min and then mixed with 40 uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47°C for 16–18 h. After hybridization, arrays were washed in 2× SSC, 0.5% SDS 37C for 5 min, followed by 2× 5 min in 0.1× SSC, 0.1% SDS 37°C, and then 2 × 2.5 min in room temperature 0.1× SSC. Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (clinical or bovine-biased)+ sample (biological replicate) + error. Significant differences in expression due to strain were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR). SAM provided by TMEV was also used for data analysis.

source_name: clinical-4 strain grown to exponential phase of growth

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP. 30uL C. cDNA was purified using PCRreactions were incubated overnight at 42 cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

growth_protocol: TW10950 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

extract_protocol: 5 ml of the culture was mixed with 1/10V 10% phenol:ethanol buffer to stabilize the RNA, and centrifuged at 4 oC, 4300 × g for 30 min to pellet cells.  The supernatant was decanted and cell pellets were suspended in 5 ml of buffer (2 mM EDTA, 20 mM NaOAc, pH 5.2) before mixing with equal volume of hot acid-phenol:chloroform (pH 4.5 with Iso Amyl Alcohol (IAA), 125:25:1) (Ambion, Austin, TX) and incubating at 65 oC with periodic shaking for 10 min.  The samples were centrifuged at 3220 × g for 20 min and the supernatant was subjected to further extractions with phenol:chloroform and chloroform:IAA (3).  RNA was precipitated overnight at -70 oC in 2.5 volume 100% ethanol and 1/10 volume 3 M sodium acetate pH 5.2.  RNA purification and DNase treatment of RNA samples were done with the Rneasy kit (Qiagen, Valencia, CA) and RNA quality was assessed on a formaldehyde-agarose gel.

value: e. coli o157 H7 strain TW10950

tag: replicate

source_name: bovine-biased-4 strain grown to exponential phase of growth

growth_protocol: TW10957 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10957


title: WAG0_N3I5_R2

status: Public on Apr 25 2009

type: RNA

city: Le Rheu

first: Denis

last: TAGU

department: UMR 1099 BiO3P

country: France

institute: INRA Rennes

hyb_protocol: Hybridizations were performed with a Discovery XT System Hybridization Robot using the ChipMap 80 kit (Ventana Medical Systems, Tucson, AZ, USA) at INRA–SCRIBE transcriptomic facilities (IFR 140 GFAS, Rennes). Prehybridization was performed at 42°C for 1h in a 0.5% BSA, 2X SSC and 0.2% SDS prehybridization buffer. Target labelled cDNAs were mixed before hybridizations at 42°C for 6h (protocol no. 2, ALC-D60/10-H48/8, Ventana) in a ChypHybe80 (Ventana Medical Systems, Tucson, AZ, USA) hybridization buffer. Hybridized slides were washed manually with a RiboWash solution (2 times) and a 0.1X SSC solution (1 time). The 3 washes were performed at room temperature for 2 minutes.

scan_protocol: Fluorescent images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v5.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA, USA).

data_processing: Raw data were normalized by the MADSCAN software. After subtraction of the fluorescence background, a rank-invariant method and a spatial normalisation were performed before a scaling of the variance within each slide and between all the slides at the same rank. The normalized values were log-transformed and used to perform statistical analysis by Significance Analysis of Microarray (SAM). To detect genes significantly regulated, the same delta-value was applied for the 4 analyzes, which resulted in a maximum False Discovery Rate (FDR) of 6.5%.

molecule: total RNA

organism: Acyrthosiphon pisum

source_name: Heads of WAG0 pea aphid reared under 16h photoperiod

label_protocol: 1.5 µg of aRNA were labelled and purified using the ChipShot Indirect Labelling and Clean-Up System (Promega, Madison, WI, USA). Labelling was performed with the CyDye (Cy3/Cy5) Reactive (Amersham Biosciences-GE, Faifield, CT, USA).

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached adulthood 4 days later and a batch of 25 WA-G0 aphids was collected and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 generations later.

extract_protocol: RNAs were extracted from heads (after their dissection under liquid nitrogen) using SV Total RNA Isolation kit (Promega, Madison, WI, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 1 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Short night reared pea aphids

tag: strain

value: YR2 (red holocyclic clone)

tag: tissue

value: head

tag: gender

value: parthenogenetic female

tag: treatment

value: 4 days of 16h photoperiod

tag: developmental stage

value: wingless adult stage

tag: generation

tag: reproductive mode

value: female producing parthenogenetic females

source_name: Heads of WAG0 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood 4 days later.  A batch of 25 WA-G0 aphids was collected in the middle of the photophase and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

extract_protocol: RNAs were extracted from heads using SV Total RNA Isolation kit (Promega, Madison, WI, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 1 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).

treatment_protocol: Long Night reared pea aphids

value: 4 days of 12h photoperiod

value: female producing sexual individuals


title: BLASTOMERE-EMBRYO_1-cell_c (SNP)

status: Public on Apr 26 2009

type: genomic

city: Leuven

first: Thierry

last: Voet

address: Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KULeuven

hyb_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

data_processing: GeneChip Human Mapping 250K NspI technology (Affymetrix, SNP annotation 2008/01/04) was used for independent copy number determination as well as for SNP-typing and LOH-screening. Experiments were performed according to manufacturer’s instructions using 250 ng of SC amplified DNA. For SNP-copy number analysis, probe intensities were quantile normalized per cell type and compared by the ‘Copy Number Analysis Tool’ (CNAT4.0.1) to a publicly available reference pool of 41 female HapMap genomic DNA samples that were hybridized on the same platform. All user-tunable CNAT4.0.1 parameters were optimized for the detection of the known chromosome imbalances of the lymphoblastoids. Log2-ratios were Gaussian smoothed using a 16 Mb window and interpreted by a five-state Hidden Markov model with prior probabilities set equal for all five states. Standard deviation settings were 0.11 for hidden-states 0, 1, 3 and 4, while 0.08 for hidden-state 2. Transition decay was set at 4000 Mb. Outliers were allowed to be readjusted. For SNP-typing, probe intensities were analyzed by the ‘GeneChip Genotyping Analysis Software (GTYPE) version 4.1’ using the dynamic model with a stringency (P=0.12) tuned for LOH detection in hemizygous regions. Subsequently, LOH was determined using ‘Copy Number Analyzer for Genechip (CNAG) version 2.0’ by application of a likelihood threshold of 100 for blastomeres and 50 for lymphoblastoids.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blastomere

extract_protocol: Single cells were transferred to a 200 µl PCR tube containing 1.5 µl alkaline lysis buffer (ALB; 200 mM KOH and 50 mM DTT) by mouth controlled pipetting using 75 µm stripper tips (MidAtlantic Diagnostics, Mount Laurel, USA). An aliquot from the last washing droplet was taken as a negative control per cell line. The samples were stored at -20°C for at least 30 min and were further incubated for 10 min at 65°C prior to the multiple displacement amplification (MDA) reaction. Single cell DNA was amplified following an MDA-approach with Genomi Phi V2 (GE Healthcare, Piscataway, NJ). The MDA products were purified and resuspended in 50 µl of elution buffer (High Pure PCR Product Purification Kit, Roche, Basel, Switzerland). All amplification products were quantified with a spectrophotometer (Nanodrop ND-1000 spectrophotometer; Nanodrop Technologies, Rockland, DE). SC-amplifications yielding less than 2 µg DNA were not further used.

treatment_protocol: Treatment protocol: Embryos were incubated briefly in Acid Tyrod (AT; pH 2.4 Sigma-Aldrich, St Louis, MO) to remove the zona pellucida (ZP) by mouth controlled pipetting using Flexipet micromanipulation pipettes (130 µm, Cook, IVF Queensland, Australia). They were then transferred to Ca2+/Mg2+ free medium (PGD biopsy Medium, GlobalLife) and 0.01% (w/v) phenol red supplemented with 4 mg/ml BSA (Sigma-Aldrich, St Louis, MO) (dissociation medium) and gently pipetted to disaggregate the individual blastomeres. Single blastomeres were washed three times in the dissociation medium.

tag: single cell from a 4-day-old human IVF embryo

tag: IVF protocol

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).

tag: Patient info

value: Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).


title: Formoterol 1H Rep 3

city: St Lucia

first: Michael

middle: Andrew

last: Pearen

state: Queensland

address: The University of Queensland

country: Australia

institute: Institute for Molecular Bioscience

description:
1512403079_C
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanned with Illumina BeadStation Scanner.

data_processing: Data was compiled using BeadStudio v1.5.1.3 (Illumina). Normalized data was produced using GeneSpring GX version 7.3.1 via normalization to control genes, where control genes were represented by all genes with an Illumina detection score equal to one in at least four out of the 16 samples (7596 control genes in total).

organism: Mus musculus

source_name: tibialis anterior

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Male C57BL/10 ScSn (wild type, 6-7 weeks old) mice were housed in the Biological Research Facility at The University of Melbourne and maintained on a 12 h-light/12 h-dark cycle, with standard mouse chow and water provided ad libitum.

extract_protocol: RNA was extracted with tri-reagent (Sigma), followed by treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100.

treatment_protocol: Mice were randomly assigned and injected with a single intraperitoneal injection of either formoterol (100 μg/kg in 0.2mL saline) or saline. Following treatment for 1 or 4 hours, mice were anesthetized and tibialis anterior muscles were surgically excised for RNA extraction.

value: C57BL/10 ScSn

value: Formoterol

tag: treatment time

value: 1 Hours


title: Clinical-4 vs Bovine-biased-3

first: Thomas

country: USA

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

organism: Escherichia coli

source_name: bovine-biased-3 strain grown to exponential phase of growth

growth_protocol: TW10948 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10948


title: Formoterol 1H Rep 4

description:
1512403079_D
Replicate 4


title: Formoterol 4H Rep 1

description:
1512403075_D
Replicate 1

value: 4 Hours


title: Formoterol 4H Rep 3

description:
1512403075_F
Replicate 3


title: Saline 1H Rep 3

description:
1512403079_A
Replicate 3

value: Saline


title: Clinical-4 vs Bovine-biased-1

data_processing: The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain as fixed factor. The linear model tested was Y (intensity) = array + dye + strain (clinical or bovine-biased)+ sample (biological replicate) + error. Significant differences in expression due to strain were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR). SAM provided by TMEV was also used for data analysis.

value: e. coli o157 H7 strain TW10950

source_name: bovine-biased-1 strain grown to exponential phase of growth

growth_protocol: TW10938 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10938


title: Clinical-4 vs Bovine-biased-2

source_name: bovine-biased-2 strain grown to exponential phase of growth

growth_protocol: TW10917 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10917


title: Clinical-3 vs Bovine-biased-3

source_name: clinical-3 strain grown to exponential phase of growth

growth_protocol: TW10915 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10915


title: Clinical-3 vs Bovine-biased-2


title: Saline 1H Rep 4

description:
1512403079_B
Replicate 4


title: Clinical-2 vs Bovine-biased-3

source_name: clinical-2 strain grown to exponential phase of growth

growth_protocol: TW10967 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10967


title: Saline 4H Rep 3

description:
1512403075_C
Replicate 3


title: Clinical-3 vs Bovine-biased-4

value: e. coli o157 H7 strain TW10957


title: Formoterol 4H Rep 2

description:
1512403075_E
Replicate 2


title: WAG0_N5I3_R1

value: YR2 (red holocyclic clone)

value: head

value: parthenogenetic female

value: 4 days of 16h photoperiod

value: wingless adult stage

value: female producing parthenogenetic females


title: Clinical-3 vs Bovine-biased-1


title: Clinical-2 vs Bovine-biased-4


title: Saline 4H Rep 2

description:
1512403075_B
Replicate 2

value: C57BL/10 ScSn


title: Formoterol 1H Rep 2

description:
1512403076_F
Replicate 2

value: Formoterol

value: 1 Hours


title: Clinical-2 vs Bovine-biased-2


title: Clinical-1 vs Bovine-biased-4

source_name: clinical-1 strain grown to exponential phase of growth

growth_protocol: TW10916 cells were grown in DMEM medium upto exponential phase (OD600~0.5, 2.5 h after inoclulation) at 37C.

value: e. coli o157 H7 strain TW10916


title: Formoterol 1H Rep 1

description:
1512403076_E
Replicate 1


title: Input-ArrayF-rep1

status: Public on Apr 23 2009

city: University of Sydney

first: Roger

last: Pamphlett

address: Blackburn Bld

institute: University of Sydney

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data INPUT DNA

hyb_protocol: Hybridization to Affymetrix GeneChip Human Tiling 2.0R arrays at 45 degrees overnight (Genpathway Inc.)

scan_protocol: Arrays were washed and scanned (Genpathway Inc.)

data_processing: Data processed using Affymetrix TAS software and Genpathway IP analysis software (Genpathway Inc.)

source_name: Genpathway Inc.

label_protocol: Amplified DNAs were fragmented and labeled using the Affymetrix DNA Terminal Labeling Kit (Genpathway Inc.)

extract_protocol: Phenol chloroform extraction of human brain tissue. Genpathway Inc performed the following: DNA (12 ug) was precleared with protein G agarose beads (Invitrogen).  Methylated DNA was detected using a sheep polyclonal antibody against 5-methyl-cytosine.  After incubation at 4C overnight, protein G agarose beads were used to isolate the immune complexes.  Complexes were washed and eluted from the beads with SDS buffer.  IP’ed DNA was purified by phenol/chloroform extraction and ethanol precipitation.

tag: Genpathway Inc.


title: Clinical-2 vs Bovine-biased-1


title: Brain-SALS19-ArrayF-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

source_name: SALS Brain (Brodmann area 46)

tag: Gender

value: male

tag: Age

tag: Phenotype

value: SALS


title: Brain-SALS15-ArrayF-rep1


title: Brain-CTRL20-ArrayF-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain

source_name: Control Brain (Brodmann area 46)

value: normal


title: Brain-CTRL12-ArrayF-rep1


title: Saline 4H Rep 1

description:
1512403075_A
Replicate 1

value: Saline

value: 4 Hours


title: Brain-CTRL16-ArrayF-rep1


title: Brain-CTRL18-ArrayF-rep1


title: Brain-CTRL14-ArrayF-rep1


title: Clinical-1 vs Bovine-biased-2

value: e. coli o157 H7 strain TW10917


title: Saline 1H Rep 2

description:
1512403076_D
Replicate 2


title: Brain-SALS11-ArrayF-rep1


title: Brain-SALS09-ArrayF-rep1


title: Saline 1H Rep 1

description:
1512403076_C
Replicate 1


title: Brain-CTRL10-ArrayF-rep1


title: Brain-SALS17-ArrayF-rep1


title: repo-GAL4/UAS-UPRT_brain_TU-tagged-VS-untagged_2

city: Eugene

last: Miller

state: OR

address: 1229 University of Oregon

department: Institute of Molecular Biology

institute: University of Oregon

description: 64h-88h repo-GAL4/UAS-UPRT larvae were feed 4-thiouracil for 8 hours.

hyb_protocol: Hybridization was done according to Agilent's Two-Color Microarray-Based Gene Expression Analysis Protocol (Version 5.5, February 2007).

scan_protocol: Scanning was done using an Axon GenePix 4000B microarray scanner.  Fluorescent ratios for each microarray element were recovered and normalized to the Median of Ratios using GenePix Pro 6.0.

data_processing: Normalized Median of Ratio values from different microarray elements that targeted the same transcript were averaged.

organism: Drosophila melanogaster

source_name: repo-GAL4/UAS-UPRT, brain, TU-tagged

label_protocol: 50 ng of TU-tagged RNA was labeled according to Agilent's Two-Color Microarray-Based Gene Expression Analysis Protocol (Version 5.5, February 2007).

extract_protocol: Larval brains were dissected out and brain RNA was extracted using Trizol.  Thio-labeled (TU-tagged) RNA was tagged and separated from untagged RNA.

tag: test cell type

value: repo-GAL4/UAS-UPRT, brain, TU-tagged

source_name: repo-GAL4/UAS-UPRT, brain, untagged

label_protocol: 200 ng of untagged RNA was labeled according to Agilent's Two-Color Microarray-Based Gene Expression Analysis Protocol (Version 5.5, February 2007).

tag: reference cell type

value: repo-GAL4/UAS-UPRT, brain, untagged


title: repo-GAL4/UAS-UPRT_brain_TU-tagged-VS-untagged_1


title: Clinical-1 vs Bovine-biased-1

tag: strain

value: e. coli o157 H7 strain TW10938

tag: replicate


title: Clinical-1 vs Bovine-biased-3

value: e. coli o157 H7 strain TW10948


title: Brain-SALS13-ArrayF-rep1


title: Saline 4H Rep 4

description:
1512403076_A
Replicate 4


title: Formoterol 4H Rep 4

description:
1512403076_B
Replicate 4


title: Brain-CTRL08-ArrayF-rep1


title: Brain-SALS07-ArrayF-rep1


title: Brain-SALS05-ArrayF-rep1


title: Brain-CTRL06-ArrayF-rep1


title: Brain-SALS01-ArrayF-rep1


title: Brain-CTRL02-ArrayF-rep1


title: Brain-CTRL04-ArrayF-rep1


title: Brain-SALS03-ArrayF-rep1


title: genomic V4-L2-F24

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
V4-L2-F24 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt's, 0.5% SDS and 100 µg herring sperm DNA/ml.The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization background subtracted.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae W303-1a.

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol).The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

growth_protocol: Exponentian growth in YPD

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267-272

tag: In vitro genomic DNA labelling with 33P-dCTP in a yeast strain exponentially growing in YPD


title: genomic V4-L2-F23

description:
V4-L2-F23 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F20

description:
V4-L2-F20 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F17

description:
V4-L2-F17 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F18

description:
V4-L2-F18 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F22

description:
V4-L2-F22 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F21

description:
V4-L2-F21 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F16

description:
V4-L2-F16 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F14

description:
V4-L2-F14 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: hog1 mutant  0.4MNaCl RA t15 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F19.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt's, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t15 rep3

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL  dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t15: 15 minutes after adding NaCl.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York


title: hog1 mutant  0.4MNaCl RA t10 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t10 rep3

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t10: 10 minutes after adding NaCl.


title: hog1 mutant  0.4MNaCl RA t6 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t6 rep3

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t6: 6 minutes after adding NaCl.


title: hog1 mutant  0.4MNaCl RA t8 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t8 rep3

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t8: 8 minutes after adding NaCl.


title: genomic V4-L2-F19

description:
V4-L2-F19 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: genomic V4-L2-F15

description:
V4-L2-F15 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: hog1 mutant  0.4MNaCl RA t10 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t10 rep2


title: hog1 mutant  0.4MNaCl RA t8 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t8 rep2


title: L4G0_N3I5_R1

source_name: Heads of L4G0 pea aphid reared under 16h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“Short night” or SN) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under SN photoperiod. This corresponds to generation G0. They reached L4-G0 stage 2 days later and a batch of 25 L4-G0 aphids was collected in the middle of the photophase and immedialtely frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in SN 2 generations later.

value: YR2 (red holocyclic clone)

tag: tissue

value: head

tag: gender

value: parthenogenetic female

tag: treatment

value: 2 days of 16h photoperiod

value: instar stage L4

source_name: Heads of L4G0 pea aphid reared under 12h photoperiod

growth_protocol: The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“Long-Night” or LN) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at LN photoperiod. This corresponds to generation G0. L3-G0 aphids reached L4-G0 stage A batch of 25 L4-G0 aphids was collected in the middle of the photophase and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in LN.

value: 2 days of 12h photoperiod

value: female producing sexual individuals


title: hog1 mutant  0.4MNaCl RA t15 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t15 rep2


title: hog1 mutant  0.4MNaCl RA t2 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t2 rep2

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t2: 2 minutes after adding NaCl.


title: hog1 mutant  0.4MNaCl RA t4 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t4 rep2

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t4: 4 minutes after adding NaCl.


title: genomic V4-L2-F12

description:
V4-L2-F12 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: hog1 mutant  0.4MNaCl RA t0 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t0 rep3

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t0: before adding NaCl.

tag: Total RNA from W303 hog1 mutant yeast strain.t0


title: hog1 mutant  0.4MNaCl RA t6 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t6 rep2


title: genomic V4-L2-F13

description:
V4-L2-F13 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.


title: hog1 mutant  0.4MNaCl RA t2 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t2 rep3


title: hog1 mutant  0.4MNaCl RA t15 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t15 rep1


title: hog1 mutant  0.4MNaCl RA t10 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t10 rep1


title: hog1 mutant  0.4MNaCl RA t8 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t8 rep1


title: hog1 mutant  0.4MNaCl RA t6 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t6 rep1


title: hog1 mutant  0.4MNaCl RA t2 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F19.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t2 rep1


title: hog1 mutant  0.4MNaCl RA t0 rep 2

description: Total RNA from W303 hog1 mutant yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F19.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t0 rep2


title: hog1 mutant  0.4MNaCl RA t4 rep 1

description: Total RNA from W303 hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t4 rep1


title: hog1 mutant  0.4MNaCl TR t15 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F19.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t15 rep3

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP.Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 Ci/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.


title: hog1 mutant  0.4MNaCl TR t10 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t10 rep2


title: hog1 mutant  0.4MNaCl RA t0 rep 1

description: Total RNA from W303 hog1 mutant yeast strain.t0: Before adding NaCl. Hybridization on macrochip V4-L2-F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t0 rep1


title: hog1 mutant  0.4MNaCl TR t8 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t8 rep3


title: hog1 mutant  0.4MNaCl TR t6 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t6 rep2


title: hog1 mutant  0.4MNaCl TR t6 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t6 rep3


title: hog1 mutant  0.4MNaCl TR t4 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t4 rep3


title: hog1 mutant  0.4MNaCl TR t2 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t2 rep3


title: hog1 mutant  0.4MNaCl TR t8 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t8 rep2


title: hog1 mutant  0.4MNaCl TR t2 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t2 rep2


title: hog1 mutant  0.4MNaCl TR t4 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t4 rep2


title: hog1 mutant  0.4MNaCl TR t15 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t15 rep2


title: hog1 mutant  0.4MNaCl TR t0 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t0 rep3


title: hog1 mutant  0.4MNaCl TR t10 rep 3

description: In vivo labeled total RNA from hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t10 rep3


title: hog1 mutant  0.4MNaCl TR t0 rep 2

description: In vivo labeled total RNA from hog1 mutant yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F19.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t0 rep2


title: hog1 mutant  0.4MNaCl TR t8 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t8: before adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t8 rep1


title: hog1 mutant  0.4MNaCl TR t15 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F24.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t15 rep1


title: hog1 mutant  0.4MNaCl TR t10 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F23.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t10 rep1


title: hog1 mutant  0.4MNaCl RA t4 rep 3

description: Total RNA from W303 hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F22.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. RA t4 rep3


title: hog1 mutant  0.4MNaCl TR t6 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F21.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t6 rep1


title: hog1 mutant  0.4MNaCl TR t2 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F19.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t2 rep1


title: W303-1a 0.4MNaCl RA t15 rep 3

description: Total RNA from W303-1a yeast strain.t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F12.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t15 rep3

tag: Total RNA from W303-1a yeast strain.t15


title: hog1 mutant  0.4MNaCl TR t4 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F20.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t4 rep1

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t4: 4 minutes after adding NaCl


title: Brain-CTRL16-ArrayA-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain

source_name: Control Brain (Brodmann area 46)

value: male


title: Brain-CTRL20-ArrayA-rep1


title: Input-ArrayA-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data INPUT DNA

source_name: Genpathway Inc.


title: Brain-CTRL18-ArrayA-rep1


title: Brain-SALS17-ArrayA-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

source_name: SALS Brain (Brodmann area 46)

value: SALS


title: BLASTOMERE-EMBRYO_1-cell_b (SNP)

scan_protocol: according to Affymetrix GeneChip Mapping 500K Assay Manual

source_name: blastomere

tag: single cell from a 4-day-old human IVF embryo

tag: IVF protocol

value: controlled ovarian hyperstimulation was performed using a “long protocol” as follows.  In the previous cycle an oral contraceptive pill was given for 25 days (Cilest®, Janssen-Cilag), followed by pituitary downregulation with bucerelin acetate (Suprefact®, Hoechst, Frankfurt, Germany; 600 µg daily) from day 21 onwards. Human menopausal gonadotropins or human recombinant gonadotrophins  (Humegon® or Puregon, Organon, Oss, The Netherlands; Gonal F, Merck Serono, Geneva, Switzerland) were started on the second day after the subsequent menstruation while ovulation was induced with 10000 IU HCG (Pregnyl®, Organon, Oss, The Netherlands) when at least 3 follicles with a diameter of at least 17 mm were observed at gynecological ultrasound. Ultrasound guided oocyte aspiration was performed 36 hours later. Luteal supplementation was given by vaginal progesterone (600 mg/day, Utrogestan®, Piette International, Drogenbos, Belgium). Subsequently, oocytes were fertilized using conventional IVF (n=8) or ICSI (n=1) with ejaculated sperm. Embryos were cultured in Global Medium (GlobalLife) and the morphology was daily assessed. Only genetically normal embryos of good morphology (with compaction or blastocyst formation) were transferred on day 4 or 5. Supernumerary genetically normal embryos of good morphology were frozen at day 4 or 5. Day 3 (evening) or day 4 (morning) embryos diagnosed with a microdeletion or with a normal sex but not suitable for transfer due to a familial genetic reason were used for this study if fulfilling all inclusion criteria (see patient info).

value: Couples entering the IVF-PGD-program for sex selection due to X-linked disorders or BRCA mutations or for familial microdeletion syndromes were asked to participate. Inclusion criteria were:(1) written informed consent from each couple, (2) maternal and paternal age ≤ 35 years, (3) normal karyotype for both partners, (4) a maternal body mass index of 18-30 kg/m², (5) initial normal semen parameters according to WHO regulation, (6) good quality embryos:2-5 blastomeres on day 2, 6-10 blastomeres on day 3, <20% fragmentation, equal sized blastomeres, (7) no recurrent miscarriages. The study was approved by the Ethical Committee of the University Hospital (registration number NCT00614367).


title: W303-1a 0.4MNaCl RA t10 rep 3

description: Total RNA from W303-1a yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F11.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t10 rep3


title: W303-1a 0.4MNaCl RA t8 rep 3

description: Total RNA from W303-1a yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t8 rep3

tag: Total RNA from W303-1a yeast strain. t8


title: W303-1a 0.4MNaCl RA t6 rep 3

description: Total RNA from W303-1a yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t6 rep3

tag: Total RNA from W303-1a yeast strain. t6


title: Brain-SALS13-ArrayA-rep1

tag: Gender


title: W303-1a 0.4MNaCl RA t4 rep 3

description: Total RNA from W303-1a yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t4 rep3

tag: Total RNA from W303-1a yeast strain. t4


title: Brain-CTRL14-ArrayA-rep1

tag: Age

tag: Phenotype

value: normal


title: W303-1a 0.4MNaCl RA t2 rep 3

description: Total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t2 rep3

tag: Total RNA from W303-1a yeast strain. t2


title: hog1 mutant  0.4MNaCl TR t0 rep 1

description: In vivo labeled total RNA from hog1 mutant yeast strain. t0: before adding NaCl. Hybridization on macrochip F18.

source_name: Saccharomyces cerevisiae W303 hog1 mutant. Osmotic stress 0.4M NaCl. TR t0 rep1


title: W303-1a 0.4MNaCl RA t10 rep 2

description: Total RNA from W303-1a yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t10 rep2


title: W303-1a 0.4MNaCl RA t8 rep 2

description: Total RNA from W303-1a yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t8 rep2


title: Brain-SALS19-ArrayA-rep1


title: W303-1a 0.4MNaCl RA t15 rep 2

description: Total RNA from W303-1a yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F11

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t15 rep2


title: W303-1a 0.4MNaCl RA t0 rep 3

description: Total RNA from W303-1a yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F13

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t0 rep3

tag: Total RNA from W303-1a yeast strain. t0


title: W303-1a 0.4MNaCl RA t6 rep 2

description: Total RNA from W303-1a yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t6 rep2


title: Brain-SALS15-ArrayA-rep1


title: Brain-SALS07-ArrayA-rep1


title: Brain-CTRL10-ArrayA-rep1


title: Brain-SALS09-ArrayA-rep1


title: Brain-CTRL08-ArrayA-rep1


title: Brain-SALS05-ArrayA-rep1


title: Brain-SALS11-ArrayA-rep1


title: Brain-CTRL06-ArrayA-rep1


title: W303-1a 0.4MNaCl RA t4 rep 2

description: Total RNA from W303-1a yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t4 rep2


title: W303-1a 0.4MNaCl RA t2 rep 2

description: Total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F13

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t2 rep2


title: W303-1a 0.4MNaCl RA t0 rep 2

description: Total RNA from W303-1a yeast strain. t0: 1Before adding NaCl. Hybridization on macrochip V4-L2-F12

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t0 rep2


title: Brain-CTRL04-ArrayA-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain

source_name: Control Brain (Brodmann area 46)


title: W303-1a 0.4MNaCl RA t15 rep 1

description: Total RNA from W303-1a yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t15 rep1


title: W303-1a 0.4MNaCl RA t8 rep 1

description: Total RNA from W303-1a yeast strain.t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t8 rep1

tag: Total RNA from W303-1a yeast strain.t8


title: Brain-SALS03-ArrayA-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

source_name: SALS Brain (Brodmann area 46)


title: W303-1a 0.4MNaCl RA t10 rep 1

description: Total RNA from W303-1a yeast strain.t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t10 rep1

tag: Total RNA from W303-1a yeast strain. t10


title: W303-1a 0.4MNaCl RA t6 rep 1

description: Total RNA from W303-1a yeast strain.t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t6 rep1

tag: Total RNA from W303-1a yeast strain.t6


title: Brain-SALS01-ArrayA-rep1


title: Brain-CTRL02-ArrayA-rep1


title: Input-ArrayD-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data INPUT DNA

source_name: Genpathway Inc.

tag: Genpathway Inc.


title: Brain-SALS19-ArrayD-rep1


title: Brain-CTRL20-ArrayD-rep1


title: Brain-CTRL18-ArrayD-rep1


title: W303-1a 0.4MNaCl TR t6 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t6 rep3


title: Brain-SALS17-ArrayD-rep1


title: W303-1a 0.4MNaCl RA t0 rep 1

description: Total RNA from W303-1a yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F11.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t0 rep1

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).


title: W303-1a 0.4MNaCl RA t2 rep 1

description: Total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F12.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t2 rep1


title: Brain-CTRL16-ArrayD-rep1


title: W303-1a 0.4MNaCl RA t4 rep 1

description: Total RNA from W303-1a yeast strain.t4: 4 minutes after adding NaCl.Hybridization on macrochip V4-L2-F13.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. RA t4 rep1

tag: Total RNA from W303-1a yeast strain.t4


title: Brain-SALS15-ArrayD-rep1


title: W303-1a 0.4MNaCl TR t8 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t8 rep3


title: W303-1a 0.4MNaCl TR t15 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F12.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t15 rep3


title: W303-1a 0.4MNaCl TR t10 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F11.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t10 rep3


title: W303-1a 0.4MNaCl TR t2 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t2 rep3


title: W303-1a 0.4MNaCl TR t4 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t4 rep3


title: Brain-CTRL12-ArrayA-rep1


title: W303-1a 0.4MNaCl TR t15 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F11.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t15 rep2


title: W303-1a 0.4MNaCl TR t0 rep 3

description: In vivo labeled total RNA from W303-1a yeast strain. t0: before adding NaCl. Hybridization on macrochip V4-L2-F13.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t0 rep3


title: Brain-SALS13-ArrayD-rep1


title: Brain-CTRL12-ArrayD-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain

source_name: Control Brain (Brodmann area 46)


title: W303-1a 0.4MNaCl TR t8 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t8 rep2


title: Brain-CTRL14-ArrayD-rep1


title: W303-1a 0.4MNaCl TR t10 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t10 rep2


title: Brain-SALS11-ArrayD-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

source_name: SALS Brain (Brodmann area 46)


title: W303-1a 0.4MNaCl TR t6 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t6 rep2


title: Yeast_yap1deletion_0.1mMH2O2_rep4

city: La Jolla

first: Ryan

last: Kelley

state: CA

address: 9500 Gilman Drive

department: Bioinformatics

institute: UCSD

description: Yap1 deletion mutants treated with 0.1 mM H2O2 compared to untreated cells

hyb_protocol: Cy-3 and Cy-5 labeled samples were mixed with hybridization buffer (Agilent In Situ Hybridization Kit) and co-hybridized to the Yeast Oligo Microarray. Slides were hybridized for 17h at 60 degree Celcius in a rotating oven, and washed

scan_protocol: Arrays were scanned using a GenePix 4000A or PerkinElmer Scanarray Lite microarray scanner at 10.0 uM and quantified with the GenePix 6.0 software package.

data_processing: Value is the log ratio of the foreground mean of the treated channel versus the foreground mean of the background channel

molecule: polyA RNA

label_protocol: Purified mRNA from the control experiments was labeled with dUTP incorporating either Cy3 or Cy5 dye (CyScribe First-Strand cDNA labeling kit, Amersham Biosciences).

extract_protocol: RNA from each sample was isolated via phenol extraction followed by mRNA purification [Poly(A)Purist, Ambion, Catalog # 1916].

tag: Yap1 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with 0.1 mM H2O2 for 45 minutes

source_name: Untreated

tag: Yap1 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with sham dose for 45 minutes


title: Yeast_yap1deletion_0.1mMH2O2_rep3


title: W303-1a 0.4MNaCl TR t4 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t4 rep2


title: Brain-CTRL10-ArrayD-rep1


title: Brain-CTRL08-ArrayD-rep1


title: W303-1a 0.4MNaCl TR t2 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F13.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t2 rep2


title: Yeast_rox1deletion_0.1mMH2O2_rep4

description: Rox1 deletion mutants treated with 0.1 mM H2O2 compared to untreated cells

tag: Rox1 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with 0.1 mM H2O2 for 45 minutes

tag: Rox1 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with sham dose for 45 minutes


title: Brain-SALS07-ArrayD-rep1


title: Yeast_rox1deletion_0.1mMH2O2_rep1


title: Yeast_yap1deletion_0.1mMH2O2_rep1


title: Yeast_mga2deletion_0.1mMH2O2_rep4

description: Mga2 deletion mutants treated with 0.1 mM H2O2 compared to untreated cells

tag: Mga2 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with 0.1 mM H2O2 for 45 minutes

tag: Mga2 deletion mutant cells in BY4741 background grown to OD600 0.6 and treated with sham dose for 45 minutes


title: W303-1a 0.4MNaCl TR t15 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t15: 15 minutes after adding NaCl. Hybridization on macrochip V4-L2-F17.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t15 rep1


title: Yeast_rox1deletion_0.1mMH2O2_rep2


title: Brain-CTRL06-ArrayD-rep1

tag: Gender


title: W303-1a 0.4MNaCl TR t0 rep 2

description: In vivo labeled total RNA from W303-1a yeast strain. t0: before adding NaCl. Hybridization on macrochip V4-L2-F12.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t0 rep2


title: Yeast_yap1deletion_0.1mMH2O2_rep2


title: Brain-SALS05-ArrayD-rep1


title: Brain-SALS09-ArrayD-rep1


title: W303-1a 0.4MNaCl TR t8 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t8: 8 minutes after adding NaCl. Hybridization on macrochip V4-L2-F15.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t8 rep1


title: Yeast_mga2deletion_0.1mMH2O2_rep3


title: W303-1a 0.4MNaCl TR t10 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t10: 10 minutes after adding NaCl. Hybridization on macrochip V4-L2-F16.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t10 rep1


title: Yeast_rox1deletion_0.1mMH2O2_rep3


title: Yeast_0.4mMH2O2_rep4

description: Yeast cells treated with 0.4 mM H2O2 compared to untreated cells

tag: BY4741 yeast cells grown to OD600 0.6 and treated with 0.4 mM for 1 hour

tag: BY4741 yeast cells grown to OD600 0.6 and treated with sham dose for 1 hour


title: Yeast_mga2deletion_0.1mMH2O2_rep1


title: Yeast_mga2deletion_0.1mMH2O2_rep2


title: Yeast_0.4mMH2O2_rep2


title: W303-1a 0.4MNaCl TR t6 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t6: 6 minutes after adding NaCl. Hybridization on macrochip V4-L2-F14.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t6 rep1


title: Brain-CTRL04-ArrayD-rep1

tag: Age

tag: Phenotype


title: Yeast_0.1mM+0.4mMH2O2_rep2

description: Yeast cells treated with 0.1mM and 0.4 mM H2O2 compared to untreated cells

tag: BY4741 yeast cells grown to OD600 0.6 and treated with 0.1 mM H2O2 for 45 minutes and then 0.4 mM for 1 hour

tag: BY4741 yeast cells grown to OD600 0.6 and treated with sham dose for 45 minutes and then shame dose for 1 hour


title: W303-1a 0.4MNaCl TR t4 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t4: 4 minutes after adding NaCl. Hybridization on macrochip V4-L2-F13.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t4 rep1

growth_protocol: Osmotic stress conditions were created by addition of NaCl at 0.4M. Experiments were initiated on exponential cultures growing in YPD. t4: 4 minutes after adding NaCl..


title: Yeast_0.1mM+0.4mMH2O2_rep4


title: Yeast_0.4mMH2O2_rep1


title: Brain-SALS03-ArrayD-rep1


title: Yeast_0.1mM+0.4mMH2O2_rep3


title: Brain-CTRL02-ArrayD-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain


title: W303-1a 0.4MNaCl TR t0 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t0: Before adding NaCl. Hybridization on macrochip V4-L2-F11.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t0 rep1

label_protocol: In vivo labeling by run-on (GRO) using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo  transcription. After spinning down cells, they were washed in cold water  and the cell pellet was resuspended in 900 µl of sterile cold water  (final volume 950 µl). Then, the cell suspension was transferred to a  fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells  were incubated for 20 minutes on ice. After the permeabilization step,  cells were recovered by low-speed centrifugation and the supernatant was  removed. In vivo transcription was performed by resuspending cells in  120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl,  80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of  DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 μCi/µL). Cells  were maintained on ice at all times. The final volume was adjusted to  300 µl with distilled water and the mix was incubated for 5 minutes at  30ºC to allow transcription elongation. The reaction was stopped by  adding 1 ml of cold distilled water to the mix.


title: Yeast_0.1mMH2O2_rep1

description: Yeast cells treated with 0.1 mM H2O2 compared to untreated cells

tag: BY4741 yeast cells grown to OD600 0.6 and treated with 0.1 mM H2O2 for 45 minutes

tag: BY4741 yeast cells grown to OD600 0.6 and treated with sham dose for 45 minutes


title: Yeast_0.1mM+0.4mMH2O2_rep1


title: W303-1a 0.4MNaCl TR t2 rep 1

description: In vivo labeled total RNA from W303-1a yeast strain. t2: 2 minutes after adding NaCl. Hybridization on macrochip V4-L2-F12.

source_name: Saccharomyces cerevisiae W303-1a. Osmotic stress 0.4M NaCl. TR t2 rep1

value: 2 minutes after adding NaCl. Hybridization on macrochip F12.


title: Input-ArrayB-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data INPUT DNA

source_name: Genpathway Inc.

tag: Genpathway Inc.


title: Input-ArrayE-rep1


title: Brain-SALS01-ArrayD-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain


title: Yeast_0.1mMH2O2_rep2


title: Yeast_0.1mMH2O2_rep4

description: Yeast cells treated with 0.1mM H2O2 compared to untreated cells


title: genomic V4-L2-F11

description:
V4-L2-F11 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.
Genomic DNA hybridization used for normalization.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt's, 0.5% SDS and 100 Âµg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65C. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ÂºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ÂºC for 30 min in 0.2XSSC, 0.1% SDS.

source_name: Saccharomyces cerevisiae W303-1a.

extract_protocol: Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267–272

tag: In vitro genomic DNA labelling with 33P-dCTP in a yeast strain exponentially growing in YPD


title: Brain-SALS19-ArrayB-rep1


title: W46-2

description: Genomic hibridization of W46 hybrid, replicate 2

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhart's, 0.5% SDS and 100 µg herring sperm DNA/ml.The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h  at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

source_name: Yeast W27 hybrid growing in YPD

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [ÃŽÂ±-33P] dCTP (2500 Ci/mmol).The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.


title: Brain-CTRL18-ArrayE-rep1

source_name: Control Brain (Brodmann area 46)


title: Brain-SALS19-ArrayE-rep1

source_name: SALS Brain (Brodmann area 46)


title: Brain-CTRL20-ArrayB-rep1


title: Yeast_0.1mMH2O2_rep3


title: pifQ dark over Col-0 dark replicate 1

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

description: Biological replicate 1 of 3

hyb_protocol: Fragmented target was used for hybridization of Agilent oligo microarray. Fragmented target was added into 2X hybridization buffer from In situ Hybridization kit of Agilent. Hybridization solution was applied onto Agilent oligo microarray, and then microarray was hybridized for 16hr at 60°C. Microarray was washed with wash solution I (6X SSC, 0.00005% Triton-X 102) for 10min at room temperature, and then microarray was washed with wash solution II (0.1X SSC, 0.00005% Triton-X 102) for 10min at 4°C.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner and image files were processed using the Axon GenePix Pro 6.0 software

data_processing: Background correction was performed using the normexp method in LIMMA and intensity data were normalized using LOWESS method

organism: Arabidopsis thaliana

source_name: DD-grown pifQ seedlings

label_protocol: 2ug of total RNA were primed with T7 oligo dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of SuperscriptTM II RNase H– reverse transcriptase (200 U/µl) 400 U SuperScript II RTase (Invitrogen). To synthesize second-strand cDNA, 10ul of 10X second-strand buffer, 63ul of nuclease free water, 4ul of 5mM dNTP mix, 2ul of DNA polymerase mix (20U/ul) and 1ul of RNase H (2U/ul) were added into the mixture of 20ul. The reaction mixture was incubated for 2hr at 16°C. The dsDNA was purified and then we adjusted the volume of dsDNA solution using drying the solution or adding the nuclease free water to make a final volume of 14ul. 4ul of 10X reaction buffer, 12ul of ATP, CTP, GTP mix (25mM), 3ul of UTP (50mM), 3ul of amino allyl UTP and 4ul of T7 enzyme mix were added into 14ul of dsDNA solution for the IVT (in vitro transcription). The reaction mix was incubated for 14hr at 37°C and then cRNA was purified. cRNA yield was quantified by measuring the UV absorbance at 260nm, and 3ug of cRNA for each sample was coupled with Cy-dye (Amersham Pharmacia, Uppsala, Sweden). Cy-dye labeled cRNA (target) was fragmented for hybridization. Fragmentation resulted typically in a fragmented target with a size range between 100 and 200 bases.

growth_protocol: Surface sterilized seeds were plated on 1/2 MS (containing 1% of sucrose) agarose medium and imbibed for 3 days at 4°C in the dark. After germination was induced by white light (6 h at 100 μmol·m^-2·s^-1), plates were incubated for 60 hours either in the dark or in the continuous red light.

extract_protocol: Total RNA was extracted from the seedlings using SpectrumTM Plant Total RNA Kit(Sigma, www.sigma-aldrich.com), according to the manufacturer’s instructions.

treatment_protocol: The plants were grown under darkness or irradiated with continuous red light(24 μmol·m^-2·s^-1).

tag: pifQ mutant

source_name: DD-grown Col-0 seedlings

tag: Wild-type Col-0


title: Yeast_0.4mMH2O2_rep3

source_name: Untreated


title: Brain-CTRL20-ArrayE-rep1


title: W27-3

description: Genomic hibridization of W27 hybrid, replicate 3


title: pifQ dark over Col-0 dark replicate 2

description: Biological replicate 2 of 3


title: W46-1

description: Genomic hibridization of W46 hybrid, replicate 1

source_name: Yeast W46 hybrid growing in YPD


title: pifQ dark over Col-0 dark replicate 3

description: Biological replicate 3 of 3


title: W27-2

description: Genomic hibridization of W27 hybrid, replicate 2


title: Brain-CTRL18-ArrayB-rep1


title: Col-0 red light over Col-0 dark replicate 3

description: Biological replicate 3 of 3

source_name: Rc-grown Col-0 seedlings


title: Col-0 red light over Col-0 dark replicate 2

description: Biological replicate 2 of 3


title: Brain-SALS17-ArrayB-rep1


title: SPG1691-3

description: Genomic hybridization of SPG1691 hybrid, replicate 3

source_name: Yeast SPG1691 hybrid exponentially growing in YPD


title: Col-0 red light over Col-0 dark replicate 1

description: Biological replicate 1 of 3


title: Brain-SALS15-ArrayE-rep1


title: Brain-CTRL16-ArrayB-rep1


title: Brain-CTRL14-ArrayE-rep1


title: Brain-SALS17-ArrayE-rep1


title: Brain-SALS15-ArrayB-rep1


title: Brain-SALS13-ArrayE-rep1


title: Brain-CTRL12-ArrayE-rep1


title: Brain-SALS11-ArrayE-rep1


title: Brain-CTRL16-ArrayE-rep1


title: Brain-CTRL14-ArrayB-rep1


title: Brain-CTRL12-ArrayB-rep1


title: Brain-SALS09-ArrayE-rep1


title: Brain-CTRL10-ArrayE-rep1


title: Brain-SALS13-ArrayB-rep1


title: Brain-SALS05-ArrayE-rep1


title: Brain-SALS07-ArrayE-rep1


title: Brain-CTRL06-ArrayE-rep1


title: Brain-CTRL04-ArrayE-rep1


title: Brain-CTRL02-ArrayE-rep1


title: Brain-SALS11-ArrayB-rep1


title: Brain-SALS03-ArrayE-rep1


title: Brain-SALS01-ArrayE-rep1


title: Brain-CTRL10-ArrayB-rep1


title: Input-ArrayG-rep1


title: Brain-CTRL08-ArrayE-rep1


title: Brain-SALS19-ArrayG-rep1


title: Brain-SALS19-ArrayG-rep2

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain (replicate)


title: Brain-CTRL20-ArrayG-rep1


title: Brain-CTRL18-ArrayG-rep1


title: Brain-CTRL16-ArrayG-rep1


title: Brain-CTRL08-ArrayB-rep1


title: Brain-SALS07-ArrayB-rep1


title: Brain-CTRL06-ArrayB-rep1


title: Brain-SALS15-ArrayG-rep1


title: Brain-SALS17-ArrayG-rep1


title: Brain-SALS05-ArrayB-rep1


title: Brain-SALS09-ArrayB-rep1


title: Brain-CTRL14-ArrayG-rep1


title: Brain-CTRL04-ArrayB-rep1


title: Brain-CTRL12-ArrayG-rep1


title: Brain-SALS13-ArrayG-rep1


title: Brain-SALS11-ArrayG-rep1


title: Brain-SALS03-ArrayB-rep1


title: Brain-CTRL10-ArrayG-rep1


title: Brain-SALS07-ArrayG-rep1


title: Brain-SALS01-ArrayB-rep1


title: Brain-CTRL08-ArrayG-rep1


title: Brain-CTRL02-ArrayB-rep1


title: Brain-SALS09-ArrayG-rep1


title: Brain-CTRL06-ArrayG-rep1


title: Brain-SALS05-ArrayG-rep1


title: Input-ArrayC-rep1


title: Brain-CTRL20-ArrayC-rep1


title: Brain-CTRL04-ArrayG-rep1


title: Brain-SALS03-ArrayG-rep1


title: Brain-CTRL02-ArrayG-rep1


title: Brain-SALS19-ArrayC-rep1


title: W27-1

description: Genomic hibridization of W27 hybrid, replicate 1


title: Brain-SALS01-ArrayG-rep1


title: FY1679-3

description: Genomic hibridization of FY1679, replicate 3

source_name: Saccharomyces cerevisiae FY1679 laboratory strain exponentialyy growing in YPD


title: 441-3

description: Genomic hybridization of 441 hybrid, replicate 2

source_name: Yeast 441 hybrid exponentially growing in YPD


title: FY1679-2

description: Genomic hibridization of FY1679, replicate 2

source_name: Saccharomyces cerevisiae FY1679 laboratory strain growing exponentially in YPD


title: FY1679-1

description: Genomic hibridization of FY1679, replicate 1

label_protocol: Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α-33P] dCTP (2500 Ci/mmol). The mixture was incubated at 37ºC for 1-2 h. In order to eliminate non-incorporated components, Probe Quant G-50 columns (Amersham Biosciences) were used.

growth_protocol: Exponential growth in YPD

tag: In vivo labeled total RNA from W303-1a yeast strain. t0

value: before adding NaCl. Hybridization on macrochip F11.


title: 441-2


title: SPG1691-1

description: Genomic hybridization of SPG1691 hybrid, replicate 1


title: 441-1

description: Genomic hybridization of 441 hybrid, replicate 1


title: W46-3

description: Genomiv hybridization of W46 yeast hybrid, replicate 3

source_name: Yeast W46 hybrid growing exponentially in YPD


title: Normal irradiated 6

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

description: colon normal irradiated rep6

hyb_protocol: Ten micrograms of labelled DIG-cRNA was injected into each microarray hybridization chamber, hybridized at 55C for 16 hours, and visualized using the Applied Biosystems Chemiluniescence Detection Kit and as decribed bu the manufacturer's protocol.

scan_protocol: The signals were detected by the Applied Biosystems 1700 Chemiluninescent Microarray Analyzer. The Human Genome Survey Microarray v.2.0 (Applied Biosystems Inc., USA) with 32,878 probes for the interrogation of 29,098 genes was used for microarray analysis.

data_processing: The features were extracted from the arrays using the ABI1700 software. Normalization was carried out using quantile normalization (Bolstad et al. 2003).  For the purpose  of finding differentially expressed genes, we applied an empirical Bayes analysis using the LIMMA package (Smyth 2004), and significance was determined at the 0.05 level corrected for false discovery rate (FDR) using the Benjamini-Hochberg method (Benjamini & Hochberg 1995). Principal component analysis (PCA) and Partial least squares (PLS) and were carried out on the data in order to visualize the data structure and look for potential outlier samples (Gidsehaug et al. 2004).

label: DIG

source_name: colon rectum

label_protocol: Total RNA samples were processed into digoxigenin (DIG)- labelled cRNA using the Applied Biosystems Chemiluminescent NanoAmp RT-IVT Labeling Kit (Applied Biosystems Inc., USA) and as described in the manufacturer's protocol.

growth_protocol: The patient group for this study consisted of 10 patients with an operable adenocarcinoma of the rectum. Tissue specimens were taken form both normal and tumor tissue of the rectum before and after  therapy and were kept in RNA storage buffer (RNA stabilization reagent, Qiagen GMBH, Germany) and stored at -70°C prior to downstream analyses.

extract_protocol: Disruption and homogenization of tissue specimens were performed in lysis buffer using the MagNa Lyser Instrument (Roche Applied Science, Germany) and according to the manufacturer’s protocol. Subsequently, total RNA was isolated with the MagNa Pure Compact Instrument and the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science, Germany) as previously described (Paulssen et al. 2006). RNA was quantified by measuring absorbance at 260 nm, and RNA purity was determined by the ratios OD260nm/280nm and OD230/280nm using the NanoDrop instrument (NanoDrop® ND-1000, Wilmington, USA). The RNA integrity was determined by electrophoresis using the BioRad Experion Bioanalyzer (Data not shown). RNA samples with 16S/28S ratios of >1.4 were used for further analysis.

treatment_protocol: Each patient received 50 Gy (delivered as fractions of 2 Gy 25 times) during 5 weeks. In addition, patients received Capecitabine (Xeloda®, Roche) 2500 mg/ml daily during the whole period. Resection of the rectum was performed four to six weeks after preoperative radiation therapy.

tag: tissue

value: normal tissue

tag: treatment

value: irradiated


title: Normal irradiated 5

description: colon normal irradiated rep5


title: Normal irradiated 7

description: colon normal irradiated rep7


title: Brain-CTRL18-ArrayC-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain


title: leaf_3% light_rep2

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

institute: CSIRO Plant Industry

hyb_protocol: The pre-hybridisation of the microarray slides, hybridisation of the target cDNA and subsequent washing of the slides to remove unbound target was performed following the protocol for the CMT-GAPS-coated microscope slides provided by the manufacturer (Corning, USA).

scan_protocol: The slides were scanned with a GenePix 4000 A microarray scanner (Axon Instruments, Union, Calif.). The features were analysed using the GENEPIX PRO 4 software, and unsatisfactorily segmented features were either manually adjusted or discarded to ensure the integrity of the data obtained.

data_processing: The analysis of the microarray data files was carried out using functions contained in the TRMA statistical pack- age. These functions operate as part of a statistical software package called R (http://www.r-project.org/). A detailed description of TRMA (tools for R microarray analysis; Wilson et al. 2003) is available online (http:// www.csiro.au/gena/trma). The data sets generated from the GENEPIX software were loaded into TRMA using the LOADGENEPIXFILE function. Normalisation of log2 ratio values was performed using the SPATIALLYNORMALISE function. This method of normalisation corrected for spatial and intensity-dependent effects of fluorescence across the microarray slide (Wilson et al. 2003). In addition, the possible biases in fluorescence due to differences in the efficiency of incorporation of the two dyes and unequal loading of cDNA samples were also corrected. Using the median values of the normalised log ratios for each gene in each replicate, we determined differentially expressed genes using the FINDDIFFEXPGENES function. Differentially expressed genes are selected as outliers in a Gaussian distribution of the entire data set. Therefore, a ratio cut-off was empirically computed from the normalised log2 ratio data, which were rescaled and centred in order to make direct comparisons between replicates. The COMPAREINTERESTINGGENES function was used to compare the differentially expressed genes among the replicates. The stringency was set to 100%—i.e. only those genes differentially expressed in all of the replicates tested, with a consistent direction of expression were selected.

organism: Hordeum vulgare

source_name: Wild type grown 3% light

label_protocol: For the labelling procedure, 50 µg of total RNA was used for both the Cy3 and Cy5 dyes (Amersham Pharmacia, UK), following the two-step labelling method of Schenk et al. (2000) Proc.Natl Acad Sci USA 97:11655–11660.

growth_protocol: Barley plants were grown under glasshouse conditions with a 16 hours light, 21oC /8 hours dark, 16oC growth regime. Plants grown under 30% and 3% light were grown under 1 or 3 layers of 70% shade cloth, respectively. Light titration experiments were undertaken in growth cabinets with incident light (umol m-2 s-1) measured at the soil surface.

extract_protocol: Total RNA was isolated from leaf tissue using TRIzol reagent (Gibco BRL) and precipitated with isopropanol then resuspended in water.

tag: Barley cultivar Golden promise

source_name: Uros III mutant grown 3% light

tag: Barley cultivar Golden promise Uros III mutant


title: Normal irradiated 1

description: colon normal irradiated rep1


title: Normal irradiated 9

description: colon normal irradiated rep9


title: Normal irradiated 4

description: colon normal irradiated rep4


title: Normal irradiated 10

description: colon normal irradiated rep10


title: SPG1691-2

description: Genomic hybridization of SPG1691 hybrid, replicate 2


title: Normal irradiated 3

description: colon normal irradiated rep3


title: Normal irradiated 2

description: colon normal irradiated rep2


title: Brain-SALS17-ArrayC-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

tag: Gender


title: leaf_3% light_rep1


title: Brain-CTRL16-ArrayC-rep1


title: Brain-CTRL14-ArrayC-rep1


title: leaf_30% light_rep1

source_name: Uros III mutant grown 30% light

source_name: Wild type grown 30% light


title: Brain-SALS15-ArrayC-rep1


title: W1118_2-3hr_vs_W1118_Stage_14_13433151

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

hyb_protocol: see flyarrays website

scan_protocol: as previously described (Neal et al., 2003), using a PerkinElmer/GSI ScanArray 4000 scanner and the ScanArray software. The 16 bit TIFF image files were quantified using QuantArray Version 3 (PerkinElmer) using the adaptive quantification algorithm (www.flyarrays.com)

data_processing: Quantified data was analyzed using GeneTraffic Duo 3.2 (Iobion Informatics/Stratagene) after normalization to the known stable transcripts for CG10122, CG12261, CG2960, CG4207, CG5317, CG5827, CG6764, CG6779, CG7434, CG7494, CG7726, CG7939, CG8470, CG8495 and CG8922. Values represent normalized log2 ratios

label: Alexa Fluor 647

label_protocol: Followed Canadian Drosophila Microarray Centre indirect labelling protocol (www.flyarrays.com). Dye = Alexa Fluor 647

extract_protocol: Canadian Drosophila Microarray Centre (RNA isolation file - www.flyarrays.com)

tag: 60ug of total RNA from the 2-3hours embryo of w1118 was labeled with Dye Alexa Fluor 647 (Cy5) by using the CDMC indirect lebeling protocol

label: Alexa Fluor 555 (Cy3)

label_protocol: Followed Canadian Drosophila Microarray Centre indirect labelling protocol (www.flyarrays.com). Dye = Alexa Fluor 555

tag: 60ug of total RNA from the stage 14 oocytes of W1118 was labeled with Dye Alexa Fluor 555 (Cy3) by using the CDMC indirect lebeling protocol


title: Brain-SALS13-ArrayC-rep1

tag: Age

tag: Phenotype


title: Brain-SALS11-ArrayC-rep1


title: Brain-CTRL12-ArrayC-rep1

source_name: Control Brain (Brodmann area 46)


title: Brain-CTRL10-ArrayC-rep1


title: leaf_30% light_rep2


title: Tumour irradiated 7

description: colon tumour irradiated rep7

value: tumour tissue


title: Tumour irradiated 9

description: colon tumour irradiated rep9


title: W1118_2-3hr_vs_W1118_Stage_14_13433145

tag: 60ug of total RNA from the 2-3hours embryo of w1118 was labeled with Dye Alexa Fluor 647 (Cy5) by using the CDMC indirect lebeling protoco


title: W1118_2-3hr_vs_W1118_Stage_14_13433150


title: SMG4_vs_w1118_Stage_14_13433825

source_name: SMGoverDf  2-3hs 60ug 647(Cy5)

tag: 60ug of total RNA from the 2-3hours embryo of SMGoverDf was labeled with Dye Alexa Fluor 647 (Cy5) by using the CDMC indirect lebeling protocol


title: SMG3_vs_w1118_Stage_14_13433152

tag: 60ug of total RNA from the 2-3hours embryoes of W1118 or SMG#Df was labeled with Dye Alexa Fluor 647 (Cy5) by using the CDMC indirect lebeling protocol


title: Gene expression in PLN vs MLN (NOD)

city: Stanford

first: Remi

middle: J

last: Creusot

address: 269 Campus Dr, CCSR 2240

department: Medicine

institute: Stanford University

description: No additional information.

hyb_protocol: Two color microarrays were performed using the whole mouse genome Oligo microarray kit (Agilent, series 2512694).  Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels.  Data was extracted using Feature Extraction software.

data_processing: Data was processed using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled PLN sample were divided by the Cy3-labelled MLN sample to obtain ratios shown in the "PRE_VALUE" column.

source_name: NOD PLN

label_protocol: RNA was amplified, labeled with Cy5 and combined with spike B using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).

extract_protocol: Pancreatic lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

tag: strain

value: NOD

tag: sample

value: Pooled tissue from 5 mice

value: pancreatic lymph nodes

source_name: NOD MLN

label_protocol: RNA was amplified, labeled with Cy3 and combined with spike A using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).

extract_protocol: Mesenteric lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: mesenteric lymph nodes


title: Brain-SALS09-ArrayC-rep1

source_name: SALS Brain (Brodmann area 46)

label_protocol: Amplified DNAs were fragmented and labeled using the Affymetrix DNA Terminal Labeling Kit (Genpathway Inc.)


title: Tumour irradiated 3

description: colon tumour irradiated rep3


title: Tumour irradiated 5

description: colon tumour irradiated rep5


title: Brain-CTRL08-ArrayC-rep1


title: Brain-SALS07-ArrayC-rep1


title: SMG2_vs_w1118_Stage_14_13433147

data_processing: Quantified data was analyzed using GeneTraffic Duo 3.2 (Iobion Informatics/Stratagene) after normalization to the known stable transcripts for CG10122, CG12261, CG2960, CG4207, CG5317, CG5827, CG6764, CG6779, CG7434, CG7494, CG7726, CG7939, CG8470, CG8495 and CG8922. Values represent normalized log2 ratios.


title: Tumour irradiated 6

description: colon tumour irradiated rep6


title: Brain-CTRL06-ArrayC-rep1


title: Gene expression in PLN vs MLN (NOD.B10)

description: No additional information.

source_name: NOD.B10 PLN

source_name: NOD.B10 MLN


title: Normal irradiated 8

description: colon normal irradiated rep8


title: Tumour irradiated 8

description: colon tumour irradiated rep8


title: Normal 10

description: colon normal rep10

value: non-irradiated


title: Brain-SALS05-ArrayC-rep1


title: Tumour irradiated 4

description: colon tumour irradiated rep4


title: Brain-CTRL04-ArrayC-rep1


title: Gene expression in PLN vs ILN (NOD.B10)

description: No additional information.

data_processing: Data was processed using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled PLN sample were divided by the Cy3-labelled ILN sample to obtain ratios shown in the "PRE_VALUE" column.

source_name: NOD.B10 ILN

extract_protocol: Inguinal lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: inguinal lymph nodes


title: Gene expression in PLN vs ILN (NOD)

description: No additional information.

source_name: NOD ILN


title: Normal 9

description: colon normal rep9