title: AP3 temperature sensitive perturbation 8

status: Public on Jun 01 2012

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

description: Biological Replicate 2: several plants (approx 25-30) pooled per replicate and genotype

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization

source_name: wholeInf ap3-1 set2 27deg

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

tag: tissue

value: whole inflorescences (not in the floral induction system) up to approx. stage 10 flowers

tag: developmental stage

tag: genotype

value: 16 degrees (constant) + shifted to 27 degrees for 24 hrs

tag: genetic background

value: Ler

source_name: wholeInf AP3 set2 27deg

value: L-er wt

tag: temperature


title: Gill Bacteria Rep 2

status: Public on Aug 31 2012

type: RNA

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

country: USA

institute: Applied Food Technologies

hyb_protocol: The microarrays were hybridized in Agilent hybridization chambers and incubated overnight (17 hrs.) in a rotisserie oven (Model G2545A, Agilent) at 65°C.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and raw images were processed using Agilent’s Feature Extraction Software, Version 10.1.1.1.

data_processing: Gene Spring version GX11;  any value <1.0 was set to 1.0;  No baseline transformation. Data were normalized using LOWESS (Locally Weighted Least Squares Regression). No MTC applied.

molecule: total RNA

organism: Micropterus dolomieu

source_name: Gill

label_protocol: Total RNA samples (900 ng each) were labeled using Agilent’s Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), version 5.7, March 2008 (no. 5190-4444).

growth_protocol: Adults used

extract_protocol: RNA extractions were done with an Omega BioTek EZNA Total RNA kit, following manufacturer's instructions, with on-column DNase digestion

tag: sample id

tag: treatment

value: bacteria

tag: Sex

value: Female

organism: Micropterus salmoides

source_name: Liver (n=8 pooled sample)

tag: gender

value: Male


title: Gill Control Rep 1

value: control


title: AP3 temperature sensitive perturbation 9

description: Biological Replicate 3: several plants (approx 25-30) pooled per replicate and genotype

organism: Arabidopsis thaliana

source_name: wholeInf AP3 set3 27deg

source_name: wholeInf ap3-1 set3 27deg


title: AP3 temperature sensitive perturbation 5

description: Biological Replicate 2: several plants (approx 20-25) pooled per replicate and genotype

source_name: day6 ap3-1 set2 27deg

value: early floral stages ~ stage 6 flowers

value: 6 days after Dexamethasone treatment (early floral stages ~ stage 6 flowers)

value: FIS (ap1 cal AP1-GR); ap3-1

source_name: day6 AP3 set2 27deg

value: FIS (ap1 cal AP1-GR); wt


title: AP3 temperature sensitive perturbation 7

description: Biological Replicate 1: several plants (approx 25-30) pooled per replicate and genotype

source_name: wholeInf ap3-1 set1 27deg

source_name: wholeInf AP3 set1 27deg


title: B6_Frontal_Cortex_HIV infected

status: Public on Aug 01 2012

city: Omaha

first: Jessica

last: Winkler

address: 985800 Nebraska Medical Center- DRC I

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description:
36G758.CEL
Gene expression data from the white matter of HIV infected human brain

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Human U133 2.0 plus GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Affy package for R programming.

label: biotin

organism: Homo sapiens

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

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

tag: race

value: White

tag: age

value: male

tag: phenotype

value: HIV Infected

value: Frontal cortex


title: AP3 temperature sensitive perturbation 6

description: Biological Replicate 3: several plants (approx 20-25) pooled per replicate and genotype

source_name: day6 AP3 set3 27deg

source_name: day6 ap3-1 set3 27deg


title: AP3 temperature sensitive perturbation 1

description: Biological Replicate 1: several plants (approx 20-25) pooled per replicate and genotype

source_name: day3 ap3-1 set1 27deg

value: early floral stages ~ stage 3-4 flowers

value: 3 days after Dexamethasone treatment (early floral stages ~ stage 3-4 flowers)

source_name: day3 AP3 set1 27deg


title: AP3 temperature sensitive perturbation 4

source_name: day6 ap3-1 set1 27deg

value: 16 degrees (constant) + shifted to 27 degrees for 24 hrs

source_name: day6 AP3 set1 27deg


title: B6_white_matter_HIV infected

description:
12G756.CEL
Gene expression data from the white matter of HIV infected human brain

data_processing: Partek

value: White matter


title: B6_basal_ganglia_HIV infected

description:
60G759.CEL
Gene expression data from the white matter of HIV infected human brain

value: Basal ganglia


title: AP3 temperature sensitive perturbation 3

source_name: day3 AP3 set3 27deg

value: Ler

source_name: day3 ap3-1 set3 27deg


title: AP3 temperature sensitive perturbation 2

source_name: day3 ap3-1 set2 27deg

source_name: day3 AP3 set2 27deg


title: 4.0N (2006)

status: Public on Apr 01 2012

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All hybridizations were done for 40 hours at 20 rpm and 65C

scan_protocol: Microarray slides were scanned using an Agilent 2565C DNA scanner and images were analyzed with Agilent Feature Extraction version 10.5 using default settings

data_processing: The aCGH data from each sorted sample that passed our QC metrics were analyzed in Agilent Genomics Workbench 5.0 using the ADM2 step gram algorithm to identify genomic intervals that were significantly aberrant relative to a normal diploid genome.11 We then ranked the aberrant intervals in each cancer genome based on the relative fold change and the number of annotated genes in each interval.

molecule: genomic DNA

source_name: tumors

label_protocol: 1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).

extract_protocol: DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).

tag: disease state

value: Anal carcinoma

value: tumor

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: PI null mutant perturbation 8

description: Biological Replicate 4: several plants (approx 20-25) pooled per replicate and genotype

source_name: day2.5 PI set4

value: 2.5 days after Dexamethasone treatment (early floral stages ~ stage 3-4 flowers)

value: FIS (ap1 cal AP1-GR); pi-1 heterozygous

value: 20 degrees (constant)

source_name: day2.5 pi set4

value: FIS (ap1 cal AP1-GR); pi-1 homozygous


title: PI null mutant perturbation 11

source_name: day5 PI set2

value: 5 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 5-6 flowers)

source_name: day5 pi set2


title: PI null mutant perturbation 1

source_name: day0 pi set1

value: undifferentiated meristematic tissue

value: no Dexamethasone treatment (undifferentiated meristematic tissue)

source_name: day0 PI set1


title: PI null mutant perturbation 10

source_name: day5 pi set3

value: early-intermediate floral stage ~ stage 5-6 flowers

source_name: day5 PI set3


title: PI null mutant perturbation 5

source_name: day2.5 pi set1

value: early floral stages ~ stage 3-4 flowers

source_name: day2.5 PI set1


title: PI null mutant perturbation 9

source_name: day5 pi set1

source_name: day5 PI set1


title: PI null mutant perturbation 6

source_name: day2.5 pi set3

source_name: day2.5 PI set3


title: PI null mutant perturbation 2

source_name: day0 pi set3

source_name: day0 PI set3


title: AP3 null mutant perturbation 12

source_name: day5 AP3 set4

value: FIS (ap1 cal AP1-GR); ap3-3 heterozygous

source_name: day5 ap3 set4

value: FIS (ap1 cal AP1-GR); ap3-3 homozygous


title: 3.9N

source_name: tumors

value: Leiomyosarcoma

source_name: Reference pooled 46XX


title: PI null mutant perturbation 3

source_name: day0 PI set2

source_name: day0 pi set2


title: PI null mutant perturbation 4

source_name: day0 PI set4

source_name: day0 pi set4


title: PI null mutant perturbation 7

source_name: day2.5 PI set2

source_name: day2.5 pi set2


title: AP3 null mutant perturbation 1

source_name: day0 ap3 set1

source_name: day0 AP3 set1


title: AP3 null mutant perturbation 10

source_name: day0 AP3 set4

source_name: day0 ap3 set4


title: AP3 null mutant perturbation 4

source_name: day2.5 AP3 set2

source_name: day2.5 ap3 set2


title: PI null mutant perturbation 12

source_name: day5 PI set4

source_name: day5 pi set4


title: Liver Estradiol Rep 1

source_name: Liver

value: estradiol

value: Female

source_name: Liver (n=8 pooled sample)

value: Male


title: AP3 null mutant perturbation 3

source_name: day0 AP3 set2

value: Ler

source_name: day0 ap3 set2


title: AP3 null mutant perturbation 6

source_name: day5 ap3 set1

source_name: day5 AP3 set1


title: AP3 null mutant perturbation 7

source_name: day0 ap3 set3

source_name: day0 AP3 set3


title: AP3 null mutant perturbation 9

source_name: day5 ap3 set3

source_name: day5 AP3 set3


title: ER71 deficient Flk-1 mesoderm

status: Public on Feb 20 2012

city: St. Louis

first: Fang

last: Liu

state: MO

address: 660S Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Flk-1+ cells sorted from day3 differentiated ES cells

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChipHybridization Oven 640 for 18 hr at 45C on Exon 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000

data_processing:
Data were processed using Affymetrix Expression Console software. Gene level expression were summarized from the intensities and then normalized using the RMA algorithm.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: Biotin

organism: Mus musculus

source_name: Er71-/-, ES cell

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA

growth_protocol: Mouse ES cells were maintained on PMEF cells in DMEM with 15% pre-selected fetal calf serum (FCS), 2% LIF, 1% L-glutamine, 1% NEAA and 4.5x 10–4 M MTG. ES cells were differentiated  in IMDM containing 15% differentiation-screened FCS, 1% L-glutamine, 50  g/ml ascorbic acidand 4.5x 10–4 M MTG.

extract_protocol: Total RNA were extracted and purified by RNeasy Mini Kit (Qiagen.)  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

value: Day 3

value: embryonic stem cell


title: AP3 null mutant perturbation 5

source_name: day5 AP3 set2

source_name: day5 ap3 set2


title: AP3 null mutant perturbation 11

source_name: day2.5 AP3 set4

value: 2.5 days after Dexamethasone treatment (early floral stages ~ stage 3-4 flowers)

source_name: day2.5 ap3 set4


title: wild-type Flk-1 mesoderm

source_name: wild-type, ES cell

value: wild-type


title: AP3 null mutant perturbation 8

source_name: day2.5 ap3 set3

value: 20 degrees (constant)

source_name: day2.5 AP3 set3


title: n.i. IFN-gamma vs. T. gondii IFN-gamma

status: Public on Jan 25 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Non-infected IFN-gamma treated vs. T. gondii-infected IFN-gamma treated

hyb_protocol: Hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed; no fractionation; probes were denatured for 3 min at 98 degrees Celsius; hybridization at 65 degrees Celsius; SSPE washes as recommended; slides were dipped in acetonitril (10 s) and then dried.

scan_protocol: Scanned with a G2505B Microarray Scanner (Agilent Technologies). Quantification software: Feature Extraction 9 (Agilent Technologies).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Non-infected IFN-gamma-treated bone marrow-derived macrophages, timepoint 24h

label_protocol: The samples for hybridization were prepared from total RNA according to the Atlas SMART Fluorescent Probe Amplification Kit protocol (Clontech-Takara Bio Europe), with minor modifications: The RNA template was hydrolyzed under alkaline conditions before cDNA purification, and the PCR amplification process was monitored and stopped in the exponential phase. Quantity and Cy-dye incorporation rates of the generated target material were assessed using a NanoDrop ND-100 spectrophotometer.

growth_protocol: Primary bone marrow-derived macrophages (BMMΦ) were isolated from female BALB/c mice. Briefly, bone marrow cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated FCS, 100 U/ml penicillin, 100 µg/ml streptomycin and 20% L929-conditioned medium as a source of M-CSF. After differentiation for 6 days, adherent BMMΦ were incubated in RPMI 1640 medium (as above) devoid of L929-derived supernatant. The murine leukaemia monocyte/macrophage cell line RAW264.7 (TIB 71; ATCC, Rockville, MD) was cultured in RPMI 1640 containing 4.5 g/L glucose, 10% FCS, 1 mM sodium pyruvate, 10 mM HEPES and antibiotics. Tachyzoites of the mouse-avirulent type II strain NTE were propagated in L929 fibroblasts as described. Prior to infection of macrophages, parasites were isolated by differential centrifugation and thoroughly washed.

extract_protocol: Twenty-four hours after infection, total RNA from Toxoplasma-infected or non-infected BMMΦ that had been cultured in the presence or absence of 100 U/ml IFN-gamma was isolated using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality was assured using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) before RNAs from 4 biological replicates each were pooled and then treated with DNase I. After phenol/chloroform/isoamylalcohol extraction, isopropanol/sodium acetate precipitation and RNA quality control as above, mRNA was isolated with the Oligotex mini kit as recommended (Qiagen).

treatment_protocol: Cells were infected at parasite-host cell ratios of 6:1 for 24 hours. Infected macrophages or non-infected controls were stimulated with 100 U/ml recombinant mouse IFN-gamma (R&D Systems, Wiesbaden, Germany) starting at 2 hours.

tag: strain

value: BALB/c

value: female

value: primary bone marrow

tag: cell type

value: primary bone marrow-derived macrophages

value: IFN-gamma at timepoint 2h

tag: infection

source_name: T. gondii-infected IFN-gamma-treated bone marrow-derived macrophages, timepoint 24h

value: T.gondii at timepoint 0h


title: T. gondii Untreated vs. T. gondii IFN-gamma

description: T. gondii-infected untreated vs. T. gondii-infected IFN-gamma treated

source_name: T. gondii-infected untreated bone marrow-derived macrophages, timepoint 24h

tag: tissue

value: untreated

value: T. gondii at timepoint 0h


title: T. gondii IFN-gamma vs. n.i. Untreated

description: T. gondii-infected IFN-gamma treated vs. non-infected untreated

source_name: Non-infected untreated bone marrow-derived macrophages, timepoint 24h


title: n.i. Untreated vs. T. gondii IFN-gamma

description: Non-infected untreated vs. T. gondii-infected IFN-gamma treated


title: T. gondii IFN-gamma vs. n.i. IFN-gamma

description: T. gondii-infected IFN-gamma treated vs. non-infected IFN-gamma treated


title: n.i. IFN-gamma vs. n.i. Untreated

description: Non-infected IFN-gamma treated vs. non-infected untreated


title: n.i. Untreated vs. n.i. IFN-gamma

description: Non-infected untreated vs. non-infected IFN-gamma treated


title: T. gondii Untreated vs. n.i. Untreated

description: T. gondii-infected untreated vs. non-infected untreated


title: n.i. Untreated vs. T. gondii Untreated

description: Non-infected untreated vs. T. gondii-infected untreated


title: AP3 null mutant perturbation 2

source_name: day2.5 ap3 set1

value: early floral stages ~ stage 3-4 flowers

tag: developmental stage

value: FIS (ap1 cal AP1-GR); ap3-3 homozygous

source_name: day2.5 AP3 set1

value: FIS (ap1 cal AP1-GR); ap3-3 heterozygous


title: FTC-238/hrTPO/RSK008 treated with benzophenone Array

status: Public on Nov 09 2011

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

description: validation sample

hyb_protocol: Stratagene FairPlay III microarray labeling kit

scan_protocol: PixelSize=5 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000 ). A significance analysis of microarray (SAM) was performed for genes with significant changes in expression. Spots that were adjudged as substandard via the visual examination of each slide were flagged and excluded from further analysis. Spots that harbored dust artifacts or spatial defects were manually flagged and excluded. And in an attepmt to filter out the unreliable data, spots with signal-to-noise (signal-background-background SD) ratios below 10 were not included in the data.

source_name: FTC-238/hrTPO/RSK008 treated benzophenone labeled with Cy5

extract_protocol: TRIzol extraction

tag: cell line

source_name: FTC-238/hrTPO/RSK008 treated benzophenone labeled with Cy3


title: FTC-238/hrTPO/RSK008 treated with Dibenzo(a,h)anthracene Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated Dibenzo(a,h)anthracene labeled with Cy5

label_protocol: Stratagene FairPlay III microarray labeling kit

source_name: FTC-238/hrTPO/RSK008 treated Dibenzo(a,h)anthracene labeled with Cy3


title: T. gondii IFN-gamma vs. T. gondii Untreated

description: T. gondii-infected IFN-gamma treated vs. T. gondii-infected untreated


title: FTC-238/hrTPO/RSK008 treated with PFOS Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated PFOS labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated PFOS labeled with Cy3


title: FTC-238/hrTPO/RSK008 treated with methylmercury Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated methylmercury labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated methylmercury labeled with Cy3


title: Control Flk-1 mesoderm

source_name: Doxycycline treated iER71, ES cell

treatment_protocol: Doxycycline (1mg/ml) was added in iER71+DOX group from day 2 to 3.

tag: genotype

tag: doxycycline treated

value: yes


title: WT vs Hypomethylated DRG Gene Expression

status: Public on Dec 01 2011

city: Nara

first: Masakazu

last: Namihira

address: 8916-5 Takayama, Ikoma

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

description:
Using the cre-loxP binary gene deletion strategy, we crossed female mice homozygous for the Dnmt1 conditional allele (Dnmt12lox (Fan et al., 2001; Jackson-Grusby et al., 2001)) with male mice carrying the Wnt1-cre insertion (Wnt1-cre) to generate both control, heterozygous, and mutant offspring in expected Mendelian ratios.
RNA samples were extracted from the DRG of WT and mutant mice at the embryonic day (E) 13.5.

hyb_protocol: 1ug of RNA for each channel was labelled using Agilent Low Input Linear Amplification protocol. Labelled cRNA mixed with Agilent 10x Control targets and Agilent 25x Fragmentation Buffer. This was incubated at 37C for 30 min and the reaction was stopped by the addition of 2x Agilent hybridization buffer. This mix was hybridized to arrays for 17 hours at 65C at 4rpms. Arrays were washed as per Agilent protocol and scanned immediately to prevent ozone degradation.

scan_protocol: The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 8.5)

data_processing: Arrays were processed using Agilent Feature Extraction (Version 8.5). Log 10 ratio were calculated from processed Cy3/ processed Cy5 signals. Replicates 1 - 4 were labeled - mutant mutant with Cy3 and WT with Cy5.

source_name: DRG of E13.5 Wnt1-cre Dnmt1 mutant mice

extract_protocol: Trizol Extracted and cleaned with Qiagen RNeasy minElute column and tested the quality of the RNA on a NanoChip (Agilent).

tag: genetic background

value: Embryonic day 13.5

value: Dorsal root ganglion

value: Wnt1-cre Dnmt1 mutant

source_name: DRG of E13.5 WT mice

label_protocol: We converted the RNA into cDNA and then the cDNA into cRNA using the Agilent Low RNA Input Linear Amplification Kit (Agilent). We using a Nanodrop (Nanodrop) to quantify the labeled cRNA. Cy3 Labelled with Agilent Low Input Linear Amplification Kit.

value: wild type


title: FTC-238/hrTPO/RSK008 treated with Bisphenol A Bis Ether Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated Bisphenol A Bis Ether  labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated Bisphenol A Bis Ether  labeled with Cy3


title: FTC-238/hrTPO/RSK008 treated with B(a)P Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated B(a)P labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated B(a)P labeled with Cy3


title: ER71 overexpressed Flk-1 mesoderm

source_name: No doxycycline treated iER71, ES cell

value: Day 3

value: embryonic stem cell

value: wild-type

value: no


title: yFR116_W0012_W303_Rpb3_Rep1

status: Public on Feb 01 2012

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

hyb_protocol: Hybridization: Add 110uL of hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA) to the resuspended (mixed) colored pellet. Put at 95C for 5 minutes, centrifuge briefly and transfer at 42C for 10 min (Keep samples at 42C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42C in Agilent hybridization oven at 20 rpm rotation speed.    Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.    Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1) Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Submerge the rack with slides (from 1 to 10) in stripping buffer and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2) Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations.

scan_protocol: Scanner Axon GenePix4000B and GenePix Pro (version 6.1.0.4) extraction software were used for scanning and features quantification. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0uM. Set the minimal intensity (histogram preview) to 3000-5000. Adjust PMTs so that approximately 5-10% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 (when possible).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL mQH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 400ng of DNA diluted to 40uL with mQH2O. Incubate 20 minutes at 12C. Add 12uL of a the following mix: 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -20'C for at least 30 min, then spin 20 minutes at 4C. Wash the pellet with 700uL -20'C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL mQH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice (or in cold room). Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL mQH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20'C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (visible as a smear on the side of the tube) with 700uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL mQH2O.    Labeling: Add 15uL of PCR aa-dUTP mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL mQH2O) to resuspended ligation samples. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL mQH2O)(Pause program if necessary). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C. Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also elute twice with 40uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO (Use DMSO store in vacuum with desiccant). Resuspended dyes are store in the dark at -80?C. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, elute twice in 40uL.  Speed-vac until ~10uL is left, or to dryness (corresponding Cy3 and Cy5 samples can be mixed before speed-vac in order to avoid DNA loss upon later resuspension).  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.

growth_protocol: Culture were done at 30C in YEP+2% Glucose media (50 to 200mL) inoculated at OD600 0.1 from an overnight preculture in YEP+2% Glucose media. Culture were allowed to grow until it reach OD600 0.6-1.0, poured in 50mL Falcon tubes containing 1.4mL 37% formaldehyde for crosslinking (1% final), and incubate on rotating wheel for 30 min at room temperature. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (~125mM final). Crosslinked cells were pelleted at 4 C, 3000 rpm ( in Beckman centrifuge (GS 6R Rotor 3.8)), resuspended in 40mL ice cold TBS and pelleted again. This wash was repeated a second time. Cell pellets were resuspended in the remaining liquid (~1mL) and transferred to 1.5mL screw cap tubes. Cells were pelleted by centrifugation, the supernatant removed by pipetting, and the cells snap-freeze in liquid nitrogen. Cells were store at -80 C. Ref: Bataille A.R., Robert F. Methods in Enzymology 2009

extract_protocol: Cells are thawed on ice, and resuspended in 700mL lysis buffer with protease inhibitors (50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate; 1mM PMSF; 1mM Benzamidine; 10ug/mL Aprotinin; 1ug/mL Leupeptin; 1ug/mL Pepstatin). 500uL of acid-washed glass beads (Sigma) are added, and the cells lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle and place in 2mL collection tubes to allow transfer of lysate, but not beads, with a brief centrifugation. The lysates are then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates are centrifuge for 5 min at 4 C max speed and supernatant used immediately for ChIP (or snap-freeze in liquid nitrogen and saved frozen at -80C).    For immunoprecipitation, Dynabeads (details at the end of the section) (50uL / ChIP) are washed twice with PBS + 0.5% BSA (freshly made), and resuspended in PBS + 0.5% BSA. Antibody are added (Concentration and souce at the end of the section), and incubated overnight at 4 C in haematological mixer. Beads are washed twice (with PBS/BSA or Lysis buffer), and resuspended in 30uL (PBS/BSA or Lysis buffer) / ChIP. 30uL of resuspended beads/antibody are added to 400-600uL of lysate, and incubated overnight at 4 C in haematological mixer. Beads are then washed in cold room (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors)(50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate ), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl, twice with ice cold Wash Buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA), and once with ice cold TE. Remaining liquid is removed by pipetting after 1 min centrifugation at 4 C (max speed). 50uL TE + 1% SDS is added and beads are incubated overnight at 65 C for elution and reverse crosslink. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks with the ChIP samples.  For this study the anti-myc (9E10) was a kind gift from Alain Verreault. The anti-Flag (M2) was from Sigma. The 3E8, 3E10 and 4E12 antibodies were purchased from Helmholtz Zentrum in Munich. The H5 (P-Ser2) and H14 (P-Ser5) were purchased from Covance. The anti-Rpb3 (W0012) was purchased from Neoclone Biotechnology. The 8WG16 (Ab817) antibody was purchased from Abcam.The following amounts of antibody per immunoprecipitation were used: 3E8 (5μL), 3E10 (5μL), 4E12 (5μL), 8WG16 (2μg), H14 (15μg), H5 (15μg), W0012 (3μL), 9E10 (5μg), M2 (5μg). The antibodies were coupled to Dynabeads (Invitrogen) coated with protein G (3E8, 3E10, 4E12), IgG Pan mouse antibodies (8WG16, H14, W0012, 9E10, M2) or Sheep anti-mouse IgG (H5).    To clean up the DNA, beads are spun down and supernatant is transfered to a new 1.5mL tube. 350uL of a solution of 345uL TE / 3uL RNAse A (10mg/mL) / 2uL Glycogen (20mg/mL) is added to the supernatant and samples incubated at 37C for 2 hours. 15uL of 10% SDS and 7.5uL Proteinase K are then added and the tubes incubated for another 2 hours at 37 C. The samples are then extracted twice with 400uL phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 14uL of 5M NaCl (for about 350uL of extracted sample) and 1mL of freezing 100% EtOH (-20 C). Pellets are washed with 700uL 70% EtOH (-20 C) and left to air dry for few minutes before they are resuspended in 50uL TE. Stored ChIP samples at -20 C.  Ref: Bataille A.R., Robert F. Methods in Enzymology 2009.

tag: antibody

tag: vendor

value: Neoclone Biotechnology


title: FTC-238/hrTPO/RSK008 treated with mehtimazole

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated mehtimazole labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated mehtimazole labeled with Cy3


title: FTC-238/hrTPO/RSK008 treated with Genistein Array

description: validation sample

source_name: FTC-238/hrTPO/RSK008 treated Genistein labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated Genistein labeled with Cy3


title: yFR116_W0012_W303_Rpb3_Rep2


title: T-ALL sample #56

status: Public on Nov 05 2011

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: sample collected in human clinical trial E2993 (Marks et al., 2009)

hyb_protocol: 500 ng of RNA was amplified and biotinylated using the TotalPrep RNA Amplification Kit (Ambion) and hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina)

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression profiling data from 57 adult T-ALL patients were transfomed to log2 scale and normalized using quantile normalization without background subtraction

source_name: TALL lymphoblast sample 56

label_protocol: 10ng of RNA from each T-cell subset was amplified using the Ovation® PicoSL WTA System (Nugen), labeled by the EncoreTM BiotinIL Module (Nugen)

extract_protocol: RNA isolation from lymphoblast obtained from adult T-ALL patient samples was achieved using the RNeasy plus mini kit (Qiagen) according to manufacturer's protocol

treatment_protocol: Leukemic DNA and cryopreserved lymphoblast samples were provided by the Eastern Cooperative Oncology Group (ECOG). All samples were collected in clinical trial E2993(Marks et al., 2009) and informed consent to use leftover material for research purposes was obtained from all the patients at trial entry according to the declaration of Helsinki. T-cell phenotype was confirmed by flow cytometry

value: cryopreserved lymphoblast


title: T-ALL sample #46

source_name: TALL lymphoblast sample 46


title: T-ALL sample #51

source_name: TALL lymphoblast sample 51


title: T-ALL sample #54

source_name: TALL lymphoblast sample 54


title: T-ALL sample #40

source_name: TALL lymphoblast sample 40


title: T-ALL sample #41

source_name: TALL lymphoblast sample 41


title: T-ALL sample #36

source_name: TALL lymphoblast sample 36


title: Control_2

status: Public on Nov 17 2011

city: Toronto

first: Mohamed

last: Abdelhaleem

state: Ontario

address: 555 University Avenue

department: Pediatric Laboratory Medicine

institute: Hospital for Sick Children

description: liver tissue aliquot snap frozen

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console Software version 1.1. on core probe sets using RMA. The p values for alternatively spliced transcripts (mutant versus control) were calculated by using the algorithms of Partek Genomics Suite version 6.4 (http://www.partek.com) on core probes excluding probes with signal less than 3.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1_na26_mm9

source_name: liver control

label_protocol: Samples were biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Dhx32 homozygous mutant and control were identifed by genotyping. Liver tissues were quickly removed and snap frozen in liquid nitrogen. RNA extracted by using Trizol. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: gender

value: male

value: 6-8 weeks


title: Mutant_1

description: liver tissue aliquot snap frozen

source_name: liver Dhx32-/-

value: Dhx32-/- mutant


title: T-ALL sample #38

source_name: TALL lymphoblast sample 38


title: T-ALL sample #55

source_name: TALL lymphoblast sample 55


title: T-ALL sample #43

source_name: TALL lymphoblast sample 43


title: Mutant_3

description: liver tissue aliquot snap frozen


title: T-ALL sample #35

source_name: TALL lymphoblast sample 35


title: T-ALL sample #32

source_name: TALL lymphoblast sample 32


title: Mutant_2

description: liver tissue aliquot snap frozen


title: T-ALL sample #33

source_name: TALL lymphoblast sample 33


title: T-ALL sample #50

source_name: TALL lymphoblast sample 50


title: T-ALL sample #34

source_name: TALL lymphoblast sample 34


title: T-ALL sample #37

source_name: TALL lymphoblast sample 37


title: T-ALL sample #57

source_name: TALL lymphoblast sample 57


title: T-ALL sample #39

source_name: TALL lymphoblast sample 39


title: Control_3

description: liver tissue aliquot snap frozen


title: T-ALL sample #42

source_name: TALL lymphoblast sample 42


title: Control_1

description: liver tissue aliquot snap frozen


title: T-ALL sample #27

source_name: TALL lymphoblast sample 27


title: T-ALL sample #31

source_name: TALL lymphoblast sample 31


title: T-ALL sample #29

source_name: TALL lymphoblast sample 29


title: Gill Bacteria Rep 3

source_name: Gill

tag: sample id

tag: treatment

value: bacteria

tag: Sex

value: Female

source_name: Liver (n=8 pooled sample)

value: Male


title: T-ALL sample #24

source_name: TALL lymphoblast sample 24


title: T-ALL sample #20

source_name: TALL lymphoblast sample 20


title: T-ALL sample #23

source_name: TALL lymphoblast sample 23


title: T-ALL sample #17

source_name: TALL lymphoblast sample 17


title: T-ALL sample #13

source_name: TALL lymphoblast sample 13


title: T-ALL sample #14

source_name: TALL lymphoblast sample 14


title: T-ALL sample #7

source_name: TALL lymphoblast sample 7


title: T-ALL sample #19

source_name: TALL lymphoblast sample 19


title: T-ALL sample #18

source_name: TALL lymphoblast sample 18


title: T-ALL sample #4

source_name: TALL lymphoblast sample 4


title: T-ALL sample #16

source_name: TALL lymphoblast sample 16


title: T-ALL sample #3

source_name: TALL lymphoblast sample 3


title: T-ALL sample #25

source_name: TALL lymphoblast sample 25


title: cdh17 vs lhx1a cells, biological replicate 1

status: Public on Nov 01 2011

city: SAN FRANCISCO

first: Rahul

middle: C

last: Deo

state: CA

address: 555 Mission Bay Blvd. South

department: Cardiovascular Research Institute

institute: University of California San Francisco

description: Bilogical replicate 1 of 3

hyb_protocol: The corresponding cy3 and cy5 labeled cDNAs were combined and hybridized overnight (17h, 65C) to the Agilent Whole Zebrafish Genome Oligo Microarray using Agilent's recommended hybridization chamber.

scan_protocol: Fluorescence signals were detected using Agilent's DNA microarray scanner

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. The three biological replicates were then quantile normalized using the normalizeBetweenArrays function of affy Bioconductor package in R(2.9.2).

organism: Danio rerio

source_name: distal tubule cells

label_protocol: 250ng of the relevant cDNA was labeled with Cy3 or Cy5.

extract_protocol: Zebrafish cell samples were lysed using SuperAmp (Miltenyi Biotec) Lysis Buffer and amplified via a global PCR protocol using mRNA derived cDNA

treatment_protocol: ~4000 FACS sorted cells

value: renal distal tubule cells

tag: facs marker

source_name: nephrogenic stem cells

value: nephrogenic stem cells


title: T-ALL sample #5

source_name: TALL lymphoblast sample 5


title: T-ALL sample #10

source_name: TALL lymphoblast sample 10


title: T-ALL sample #22

source_name: TALL lymphoblast sample 22


title: T-ALL sample #9

source_name: TALL lymphoblast sample 9


title: T-ALL sample #1

source_name: TALL lymphoblast sample 1


title: T-ALL sample #6

source_name: TALL lymphoblast sample 6


title: T-ALL sample #8

source_name: TALL lymphoblast sample 8


title: T-ALL sample #21

source_name: TALL lymphoblast sample 21


title: T-ALL sample #2

source_name: TALL lymphoblast sample 2


title: T-ALL sample #26

source_name: TALL lymphoblast sample 26


title: cdh17 vs lhx1a cells, biological replicate 2

description: Bilogical replicate 2 of 3


title: Gastric primary tumor sample 990017T SNP6 (correction: 990071T)

status: Public on Feb 10 2012

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

description: Hybridized to SNP6 array

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

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

data_processing: Analysis of raw cel files was performed by Affymetrix Genotyping Console 4.0 software. A reference Model File was created based on 98 non-malignant samples (included as Gastric Normal.REF in the submission). Gastric non-malignant samples and tumors samples were then processed separately using this referenece file by median normalization and GC correlation to obtain the CHP files.

source_name: Gastric primary tumor sample 990017T

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

value: Gastric primary tumor tissue


title: cdh17 vs lhx1a cells, biological replicate 3

description: Bilogical replicate 3 of 3


title: CPG-stimulated B-CLL repl 18

status: Public on Jun 30 2011

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

hyb_protocol: The fluorescent labeled samples were hybridized to the Human miRNA microarray Version 3 from the Sanger database v12.0 (Agilent Technologies)

scan_protocol: The microarray slides were analyzed with an Agilent Microarray Scanner.

data_processing: The hybridization signal values for the multiple probes for each miRNA were obtain with the use of Agilent Feature Extraction Software 10.7.3 (Agilent Technologies). The data were analyzed by R and limma packages. The  the signal is background corrected by fitting a normal-exponential convolution model to a vector of observed intensities.  The signal is normalized between arrays using the  quantile method.

source_name: CPG stimulated purified cell of  CLL

label_protocol: Samples were labeled with Cy3 dye using the miRNA Complete Labeling System & Hyb Kit (Agilent Technologies)

extract_protocol: Total RNA was extracted using the TRIZOL Reagent.

treatment_protocol: CLL cells were purified by negative selection using anti-CD3, anti-CD14 and anti-CD16 mouse monoclonal antibodies and Dynabeads coated with a pan anti-mouse IgG antibody. The purity of the CLL cells after negative selection was monitored by flow-cytometry and the percentage of CD5+/CD19+ cells exceeded 98% for each sample.CLL cells were resuspended in RPMI complete medium at a density of 2 × 105 and stimulated with 7.5 μg/ml complete phosphorothioate CpG ODN oligonucleotide 2006 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) or left unstimulated for 18 h.

value: B-CLL


title: Unstimulated B-CLL repl 17

source_name: unstimulated purified cell of  CLL


title: Unstimulated B-CLL repl 18


title: P28 primary visual cortex of monocularly deprived mice rep2

status: Public on Sep 04 2011

city: Cambridge

first: Nikolaos

last: Mellios

state: MA

address: 43 Vassar Street

institute: MIT

description: P28 primary visual cortex of monocularly deprived mice replicate 2

hyb_protocol: Microarrays were hybridized to Agilent murine miRNA arrays overnight at 64 ºC.

scan_protocol: Microarrays were scanned using an Agilent scanner.

data_processing: Data in GEO were extracted with Agilent feature extractor 10.1 with no additional processing.

label_protocol: 100ng of total RNA were labeled using the Agilent miRNA labeling system.

growth_protocol: C57BL6 mice were reared till P28.

extract_protocol: Mice were euthanized at P28 and their primary visual cortex areas were excised and subjected to RNA isolation. In the case of MD mice only the contralateral to lid suture primary visual cortex was extracted.

treatment_protocol: C57BL6 mice were reared in normal light and dark conditions (control) till P28, in complete darkness since birth (DR) till P28, or were grown in normal light/dark conditions from birth till P24 and then subjected to lid suturing of one eye till P28.

value: primary visual cortex

tag: age


title: P28 primary visual cortex of monocularly deprived mice rep3

description: P28 primary visual cortex of monocularly deprived mice replicate 3

tag: strain


title: P28 primary visual cortex of monocularly deprived mice rep1

description: P28 primary visual cortex of monocularly deprived mice replicate 1


title: HEK293T cell culture,control,biological rep 3

status: Public on Oct 05 2011

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA, and all treatments were compared to the control LA via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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


title: CPG-stimulated B-CLL repl 16


title: CPG-stimulated B-CLL repl 15


title: P28 primary visual cortex of non deprived mice rep2

description: P28 primary visual cortex of non deprived mice replicate 2


title: CPG-stimulated B-CLL repl 14


title: CPG-stimulated B-CLL repl 17


title: Unstimulated B-CLL repl 14


title: P28 primary visual cortex of non deprived mice rep3

description: P28 primary visual cortex of non deprived mice replicate 3


title: Unstimulated B-CLL repl 13


title: HEK293T cell culture,control,biological rep 2

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 2


title: CPG-stimulated B-CLL repl 13


title: Unstimulated B-CLL repl 15


title: HEK293T cell culture,control,biological rep 1

source_name: HEK293T human embryonic epithelial kidney cell culture,control,biological rep 1


title: P28 primary visual cortex of dark reared mice rep3

description: P28 primary visual cortex of dark reared mice replicate 3


title: Unstimulated B-CLL repl 12


title: CPG-stimulated B-CLL repl 12


title: Unstimulated B-CLL repl 16


title: Unstimulated B-CLL repl 10


title: CPG-stimulated B-CLL repl 11


title: Unstimulated B-CLL repl 11


title: P28 primary visual cortex of non deprived mice rep1

description: P28 primary visual cortex of non deprived mice replicate 1


title: Unstimulated B-CLL repl 9


title: CPG-stimulated B-CLL repl 9


title: Unstimulated B-CLL repl 8


title: day 2 epiblast like cells (EpiLCs), biological rep2

status: Public on Aug 05 2011

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

source_name: day 2 EpiLCs

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: ES cells were maintained with 2i+LIF, feeder free condition.  EpiLCs were induced from the ES cells.  PGCLCs were induced from day 2 EpiLCs.  EpiSCs were derived from epiblast (embryonic day 5.75).  For detail,  see Hayashi et al., Cell 2011.

extract_protocol: total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction

tag: cell type

value: epiblast like cells (EpiLCs)

tag: amplification


title: day 3 epiblast like cells (EpiLCs), biological rep1

source_name: day 3 EpiLCs


title: day 3 epiblast like cells (EpiLCs), biological rep2


title: day 2 epiblast like cells (EpiLCs), biological rep1


title: Unstimulated B-CLL repl 7


title: CPG-stimulated B-CLL repl 7


title: Unstimulated B-CLL repl 5


title: Unstimulated B-CLL repl 6


title: CPG-stimulated B-CLL repl 6


title: CPG-stimulated B-CLL repl 5


title: Unstimulated B-CLL repl 4


title: CPG-stimulated B-CLL repl 4


title: Unstimulated B-CLL repl 2


title: Unstimulated B-CLL repl 1


title: CPG-stimulated B-CLL repl 3


title: CPG-stimulated B-CLL repl 10


title: CPG-stimulated B-CLL repl 2


title: CPG-stimulated B-CLL repl 1


title: CPG-stimulated B-CLL repl 8


title: Skin_DHT_3

status: Public on Jun 03 2011

city: Duarte

first: jeremy

last: jones

address: 1500 E Duarte Rd

institute: City of Hope

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

data_processing: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent). This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A one-way ANOVA linear model was fit to the comparison to estimate the mean M values and calculated moderated t-statistic, B statistic, false discovery rate, and p-value for each gene for the comparison of interest. Adjusted p-values were produced by the method proposed by Holm. All procedures were carried out using functions in the R package limma in Bioconductor. For most analyses, the B statistic was least stringent and was used to compile lists of candidate androgen-regulated genes for each tissue.

organism: Rattus norvegicus

source_name: Skin_10mg/kg DHT_16hrs

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

extract_protocol: RNA was extracted within an hour of sacrifice using an RNAEasy kit (Qiagen), according to manufacturer’s protocol.

treatment_protocol: Male animals were castrated, then three days later, treated with a single IP dose of 10mg/kg DHT or vehicle for 16hrs. Intace females were treated with a single IP dose of 10mg/kg DHT or vehicle for 16hrs.

tag: breed

value: Sprague-Dawley

value: 12 weeks

tag: castrate/intact

value: castrate


title: Prostate_DHT_3

description: 335 P6

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent)

source_name: Prostate_10mg/kg DHT_16hrs


title: Forebrain_DHT_3

description: 335 FB6

source_name: Forebrain_10mg/kg DHT_16hrs


title: Ovary_DHT_2

description: 335 O5

source_name: Ovary_10mg/kg DHT_16hrs

value: female

value: intact


title: Ovary_DHT_3

description: 335 O6


title: Forebrain_DHT_2

description: 335 FB5

value: male


title: Skin_DHT_2


title: Prostate_DHT_2

description: 335 P5


title: Ovary_DHT_1

description: 335 O4


title: Prostate_DHT_1

description: 335 P4


title: Skin_DHT_1


title: Forebrain_DHT_1

description: 335 FB4


title: Skin_Vehicle_3


title: Forebrain_Vehicle_3

description: 335FB3, the array data did not meet quality control standards, therefore excluded from normalization processing


title: Prostate_Vehicle_3

description: 335 P3


title: Skin_Vehicle_2


title: Ovary_Vehicle_2

description: 335 O2


title: Prostate_Vehicle_2

description: 335 P2


title: Ovary_Vehicle_1

description: 335 O1


title: Forebrain_Vehicle_2


title: Skin_Vehicle_1


title: LSD1 knock-down ESC line overexpressing wild type LSD1 - replicate 2

status: Public on May 27 2011

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

hyb_protocol: Labeled cRNA was hybridized to the Agilent SurePrint G3 Human gene expression 8x60K microarray according to the manufacturer's protocol.

scan_protocol: The arrays were scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 um resolution.

data_processing: Intensity data was extracted using the Feature Extraction software (Agilent).

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions.

growth_protocol: The human embryonic stem cell line ES[4] was grown in matrigel coated plates and in the presence of irradiated MEFs conditioned media supplemented with FGF.

extract_protocol: RNA was extracted using miRNeasy Mini Kit (Qiagen).

tag: cell line

tag: replicate


title: Prostate_Vehicle_1

description: 335 P1


title: LSD1 knock-down ESC line overexpressing mutant (K661A) LSD1


title: Ovary_Vehicle_3

description: 335 O3


title: LSD1 knock-down ESC line overexpressing wild type LSD1 - replicate 1


title: Control ESC line treated with DMSO - replicate 2

source_name: ES line transfected with control short hairpin, treated with DMSO

tag: modification


title: LSD1 knock-down ESC line treated with BMP pathway inhibitor - replicate 1

source_name: ES line transfected with LSD1 short hairpin, treated with BMP pathway inhibitor


title: LSD1 knock-down ESC line treated with DMSO - replicate 1

source_name: ES line transfected with LSD1 short hairpin, treated with DMSO


title: Control ESC line treated with BMP2 - replicate 2

source_name: ES line transfected with control short hairpin, treated with BMP2


title: LSD1 knock-down ESC line treated with BMP pathway inhibitor - replicate 2

value: transfected with LSD1 short hairpin, treated with BMP pathway inhibitor


title: Control ESC line treated with BMP2 - replicate 1

value: transfected with control short hairpin, treated with BMP2


title: Control ESC line - replicate 2

source_name: ES line transfected with control short hairpin

value: transfected with control short hairpin


title: LSD1 knock-down ESC line - replicate 1

source_name: ES line transfected with LSD1 short hairpin

value: transfected with LSD1 short hairpin


title: Forebrain_Vehicle_1

description: 335 FB1


title: LSD1 knock-down ESC line - replicate 2


title: LSD1 knock-down ESC line treated with DMSO - replicate 2

value: transfected with LSD1 short hairpin, treated with DMSO


title: Control ESC line treated with DMSO - replicate 1

value: transfected with control short hairpin, treated with DMSO


title: Control ESC line - replicate 1


title: PAE-iPS-11_p18_1

status: Public on Mar 07 2011

city: Tsukuba

first: Makoto

last: Asashima

state: Ibaraki

address: 1-1-1 Higashi

department: Tsukuba Central 4

institute: National Institute of Advanced Industrial Science Technology (AIST)

description: Gene expression in human iPS cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PAE-iPS-11, passage 18

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using ISOGEN (Nippon Gene, Toyama, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Human iPS cells were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: PAE-iPS-11, passage 18

tag: provenance somatic cell

value: human placental artery-derived endothelial (hPAE) cell

tag: iPS cell-line name

tag: passage number


title: UtE_p8_1

description: Gene expression in human somatic cell

source_name: human uterine endometrium (hUtE) cell, passage 8


title: UtE-iPS-4_p18_2

description: Gene expression in human iPS cell

source_name: UtE-iPS-4, passage 18

value: UtE-iPS-4, passage 18

value: human uterine endometrium (hUtE) cell


title: UtE-iPS-4_p18_3

description: Gene expression in human iPS cell


title: AM_p13_1

description: Gene expression in human somatic cell

source_name: human amniotic ectoderm and mesoderm layer (hAM) cell, passage 13


title: AM-iPS-7 (Marry)_p19_1

description: Gene expression in human iPS cell

source_name: AM-iPS-7 (Marry), passage 19

value: AM-iPS-7 (Marry), passage 19

value: human amniotic ectoderm and mesoderm layer (hAM) cell

value: AM-iPS-7 (Marry)


title: PAE-iPS-11_p18_3

description: Gene expression in human iPS cell


title: PAE-iPS-11_p18_2

description: Gene expression in human iPS cell


title: AM-iPS-8 (Thyme)_p16_1

description: Gene expression in human iPS cell

source_name: AM-iPS-8 (Thyme), passage 16

value: AM-iPS-8 (Thyme), passage 16

value: AM-iPS-8 (Thyme)


title: UtE_p8_2

description: Gene expression in human somatic cell

value: human uterine endometrium (hUtE) cell, passage 8


title: UtE-iPS-4_p27_1

description: Gene expression in human iPS cell

source_name: UtE-iPS-4, passage 27

value: UtE-iPS-4, passage 27


title: UtE-iPS-4_p27_2

description: Gene expression in human iPS cell


title: PAE_p16_1

description: Gene expression in human somatic cell

source_name: human placental artery-derived endothelial (hPAE) cell, passage 16


title: AM_p13_2

description: Gene expression in human somatic cell

value: human amniotic ectoderm and mesoderm layer (hAM) cell, passage 13


title: UtE_p8_3

description: Gene expression in human somatic cell


title: UtE-iPS-4_p27_3

description: Gene expression in human iPS cell


title: AM-iPS-7 (Marry)_p20_2

description: Gene expression in human iPS cell

source_name: AM-iPS-7 (Marry), passage 20

value: AM-iPS-7 (Marry), passage 20


title: AM-iPS-8 (Thyme)_p16_2

description: Gene expression in human iPS cell


title: PAE_p16_3

description: Gene expression in human somatic cell

value: human placental artery-derived endothelial (hPAE) cell, passage 16


title: PAE_p16_2

description: Gene expression in human somatic cell


title: AM-iPS-7 (Marry)_p20_1

description: Gene expression in human iPS cell


title: AM-iPS-8 (Thyme)_p16_3

description: Gene expression in human iPS cell


title: AM_p10_1

description: Gene expression in human somatic cell

source_name: human amniotic ectoderm and mesoderm layer (hAM) cell, passage 10


title: UtE-iPS-4_p18_1

description: Gene expression in human iPS cell


title: AM-iPS-7 (Marry)_p15_3

description: Gene expression in human iPS cell

source_name: AM-iPS-7 (Marry), passage 15

value: AM-iPS-7 (Marry), passage 15


title: AM-iPS-7 (Marry)_p15_1

description: Gene expression in human iPS cell


title: AM-iPS-7 (Marry)_p15_2

description: Gene expression in human iPS cell


title: Unstimulated B-CLL repl 3

source_name: unstimulated purified cell of  CLL

value: B-CLL


title: MDS tumor cells patient 101

status: Public on Jan 30 2011

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description:
Agilent Feature Extraction file: sample_101.txt
MDS tumor cells

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

source_name: MDS tumor cells, patient 101

label_protocol: Protocol Version 5.0, June 2007, Agilent.Same gender reference/control DNA was purchased from Promega as pool.

growth_protocol: Bone marrow cells were cultured unstimulated 24, 48 or 72 hrs in RPMI or Marrow Max Medium and 10% FCS. Colcemid was used to arrest cell cycle in metaphases.

extract_protocol:
For samples marked Qiagen: DNA was extracted from methanol-acetic acid fixed cells with QIAamp DNA Blood Midi Kit (Qiagen).
For samples marked PC: DNA was extracted from methanol-acetic acid fixed cells with Proteinase K, SDS and Phenol-Chloroform.

treatment_protocol: Hypotonic treatment to eliminate red blood cells and fixation with methanol-acetic acid (3:1) of white blood cells.

tag: gender

value: M

tag: International Prognostic Scoring System (IPSS)

tag: extract protocol

value: Qiagen

source_name: control DNA

tag: reference

value: Pooled, same gender reference/control DNA (Promega)


title: MDS tumor cells patient 102

description:
Agilent Feature Extraction file: sample_102.txt
MDS tumor cells

hyb_protocol: Protocol Version 5.0, June 2007, Agilent.

source_name: MDS tumor cells, patient 102


title: MDS tumor cells patient 99

description:
Agilent Feature Extraction file: sample_99.txt
MDS tumor cells

source_name: MDS tumor cells, patient 99


title: MDS tumor cells patient 97

description:
Agilent Feature Extraction file: sample_97.txt
MDS tumor cells

source_name: MDS tumor cells, patient 97

value: F


title: AM-iPS-20 (Lovage)_p9_2

description: Gene expression in human iPS cell

source_name: AM-iPS-20 (Lovage), passage 9

value: AM-iPS-20 (Lovage), passage 9

value: AM-iPS-20 (Lovage)


title: AM-iPS-5 (Chives)_p8_1

description: Gene expression in human iPS cell

source_name: AM-iPS-5 (Chives), passage 8

value: AM-iPS-5 (Chives), passage 8

value: human amniotic ectoderm and mesoderm layer (hAM) cell

value: AM-iPS-5 (Chives)


title: AM-iPS-5 (Chives)_p7_1

description: Gene expression in human iPS cell

source_name: AM-iPS-5 (Chives), passage 7

value: AM-iPS-5 (Chives), passage 7


title: AM-iPS-20 (Lovage)_p9_1

description: Gene expression in human iPS cell


title: AM-iPS-5 (Chives)_p7_2

description: Gene expression in human iPS cell


title: P28 primary visual cortex of dark reared mice rep1

description: P28 primary visual cortex of dark reared mice replicate 1

tag: tissue

value: primary visual cortex


title: AM-iPS-20 (Lovage)_p8_1

description: Gene expression in human iPS cell

source_name: AM-iPS-20 (Lovage), passage 8

value: AM-iPS-20 (Lovage), passage 8


title: MDS tumor cells patient 85

description:
Agilent Feature Extraction file: sample_85.txt
MDS tumor cells

source_name: MDS tumor cells, patient 85


title: MDS tumor cells patient 66

description:
Agilent Feature Extraction file: sample_66.txt
MDS tumor cells

source_name: MDS tumor cells, patient 66


title: MDS tumor cells patient 87

description:
Agilent Feature Extraction file: sample_87.txt
MDS tumor cells

source_name: MDS tumor cells, patient 87


title: AM-iPS-20 (Lovage)_p12_3

description: Gene expression in human iPS cell

source_name: AM-iPS-20 (Lovage), passage 12

value: AM-iPS-20 (Lovage), passage 12


title: MRC-iPS-25 (Tic)_p22_3

description: Gene expression in human iPS cell

source_name: MRC-iPS-25 (Tic), passage 22

value: MRC-iPS-25 (Tic), passage 22

value: MRC-iPS-25 (Tic)


title: AM-iPS-3 (Sage)_p7_2

description: Gene expression in human iPS cell

source_name: AM-iPS-3 (Sage), passage 7

value: AM-iPS-3 (Sage), passage 7

value: AM-iPS-3 (Sage)


title: MDS tumor cells patient 44

description:
Agilent Feature Extraction file: sample_44.txt
MDS tumor cells

source_name: MDS tumor cells, patient 44


title: AM-iPS-3 (Sage)_p7_1

description: Gene expression in human iPS cell


title: AM-iPS-3 (Sage)_p7_3

description: Gene expression in human iPS cell


title: MRC-iPS-25 (Tic)_p22_1

description: Gene expression in human iPS cell


title: P28 primary visual cortex of dark reared mice rep2

description: P28 primary visual cortex of dark reared mice replicate 2

tag: age


title: MRC-5_3

description: Gene expression in human somatic cell


title: MRC-5_1

description: Gene expression in human somatic cell


title: MRC-iPS-25 (Tic)_p22_2

description: Gene expression in human iPS cell


title: AM-iPS-20 (Lovage)_p12_1

description: Gene expression in human iPS cell


title: MDS tumor cells patient 39

description:
Agilent Feature Extraction file: sample_39.txt
MDS tumor cells

source_name: MDS tumor cells, patient 39

value: M


title: MRC-5_2

description: Gene expression in human somatic cell


title: MDS tumor cells patient 34

description:
Agilent Feature Extraction file: sample_34.txt
MDS tumor cells

source_name: MDS tumor cells, patient 34

value: Qiagen


title: MDS tumor cells patient 13

description:
Agilent Feature Extraction file: sample_13.txt
MDS tumor cells

source_name: MDS tumor cells, patient 13

source_name: control DNA

value: Pooled, same gender reference/control DNA (Promega)


title: MDS tumor cells patient 23

description:
Agilent Feature Extraction file: sample_23.txt
MDS tumor cells

source_name: MDS tumor cells, patient 23

value: F


title: MDS tumor cells patient 9

description:
Agilent Feature Extraction file: sample_9.txt
MDS tumor cells

source_name: MDS tumor cells, patient 9


title: MDS tumor cells patient 10

description:
Agilent Feature Extraction file: sample_10.txt
MDS tumor cells

source_name: MDS tumor cells, patient 10


title: MDS tumor cells patient 15

description:
Agilent Feature Extraction file: sample_15.txt
MDS tumor cells

source_name: MDS tumor cells, patient 15


title: MDS tumor cells patient 12

description:
Agilent Feature Extraction file: sample_12.txt
MDS tumor cells

source_name: MDS tumor cells, patient 12


title: 20020945

status: Public on Dec 31 2010

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

institute: F. Hoffmann-La Roche Ltd.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added,

scan_protocol: Hybridized slides were scanned on an Agilent DNA Microarray Scanner

data_processing: Images were extracted using Agilent Feature Extraction software(9.1.3). Data was analyzed using Agilent CGH Analytics software (v.3.5)

label_protocol: Gastric genomic DNA were hybed with Cy3-dUTP, and the control human spleen DNA were labeled with Cy5-dUTP.

extract_protocol: Total DNA extacted using Qiagen DNA extraction kit.

value: gastric tumor tissue 20020945

source_name: control human spleen genomic DNA

value: spleen


title: 20020876

value: gastric tumor tissue 20020876


title: 20021007

value: gastric tumor tissue 20021007


title: 37175329

value: gastric tumor tissue 37175329


title: 20021013

value: gastric tumor tissue 20021013


title: 20021031

value: gastric tumor tissue 20021031


title: 90929219

value: gastric tumor tissue 90929219


title: 73499279

value: gastric tumor tissue 73499279


title: 20020859

value: gastric tumor tissue 20020859


title: 77482608

value: gastric tumor tissue 77482608


title: 20021048

value: gastric tumor tissue 20021048


title: 55761861

value: gastric tumor tissue 55761861


title: 54119380

value: gastric tumor tissue 54119380


title: 80903789

value: gastric tumor tissue 80903789


title: MDS tumor cells patient 4

description:
Agilent Feature Extraction file: sample_4.txt
MDS tumor cells

source_name: MDS tumor cells, patient 4

value: M

value: Qiagen

value: Pooled, same gender reference/control DNA (Promega)


title: 73499299

value: gastric tumor tissue 73499299

value: spleen


title: 42761681

value: gastric tumor tissue 42761681


title: 37357120

value: gastric tumor tissue 37357120


title: 20020756

value: gastric tumor tissue 20020756


title: 20020838

value: gastric tumor tissue 20020838


title: AM-iPS-20 (Lovage)_p12_2

description: Gene expression in human iPS cell

value: AM-iPS-20 (Lovage), passage 12

value: human amniotic ectoderm and mesoderm layer (hAM) cell

value: AM-iPS-20 (Lovage)


title: 20020457

value: gastric tumor tissue 20020457


title: 20020700

value: gastric tumor tissue 20020700


title: M14_GFP_3D

status: Public on Jan 14 2011

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

description: For 3D embedded growth, 6 well plates were coated with 1ml/well of 80-100% growth factor-reduced Matrigel (BD Biosciences, Bedford, MA) which was allowed to set, and then 3x105 cells suspended in 1ml of 40% growth factor-reduced Matrigel diluted in 10% FBS-supplemented medium were seeded on top.  After setting, 10% FBS-supplemented medium (1ml) containing 500mg/ml G418 was added and the medium changed every 2d until harvest.

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99oC for 5 min and hybridized for 16h at 45oC to Affymetrix U133_Plus_2 gene chip microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3mm resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All signal values from one microarray were then multiplied by the appropriate scaling factor.

label: biotinylated CTP and UTP

source_name: Empty vector transfected line, 3D culture

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. 8mg of total RNA was converted to first-strand cDNA using Superscript II Reverse Transcriptase (Invitrogen) primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript. The resulting cRNA was used as template for random-primed cDNA synthesis and a second round of in vitro transcription, which incorporated biotinylated CTP and UTP.

growth_protocol: M14 cells were cultured in DMEM containing 10% fetal bovine serum (FBS) at 37oC in a 5% carbon-dioxide containing incubator without antibiotics or anti-fungal agents.

extract_protocol: 5ml of Trizol reagent (Invitrogen) was added to 2D and 3D cultures of M14 transfectants. The lyzed cells were drawn through a 21G needle several times and allowed to stand at room temperature for 5min in a 15ml sterile plastic tube. 1.3ml of chloroform was then added and the mixture shaken vigorously. The sample was then centrifuged at 11,000rpm (at 4oC) for 30min and the upper (aqueous) layer transferred to a sterile siliconized 15ml glass tube. 2.5ml of isopropanol was then added and the mixture cooled at -20oC for at least 20min. The mixture was then centrifuged at 11,000rpm (4oC) for 30min and the RNA pellet washed thoroughly with 75% ethanol in DEPC-treated sterile water. RNA was then resuspended in DEPC-treated sterile water.  RNA integrity was determined using a Bioanalyzer (Agilent).

treatment_protocol: Human ARHGAP8 coding region (minus exon 5 variant) was PCR amplified from a commercially obtained cDNA clone (GenBank Accession No. BQ109505) using forward primer 5' CC ACGCGT ATG GCT GGC CAG GAT CCT 3' paired with reverse primer 5' CC ACGCGT CTA GAG ACG TCT TCT GGC 3', both containing MluI restriction sites.  The product was subcloned into the MluI site of pEF-BOS_Flag vector in frame with the FLAG epitope at the N terminus.  FLAG-tagged ARHGAP8 containing a Kozak consensus sequence and 3 in-frame stop codons was released with NheI and subcloned into the NheI site of pIRES2-eGFP (Clontech, Mountain View, CA).  M14 cells were transfected using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) and stable cells selected by treatment with G418 sulfate (1mg/ml) followed by sorting for eGFP-positivity by flow cytometry.

tag: cancer type

value: melanoma

tag: culture condition

tag: expression plasmid

value: empty vector control (pIRES2)


title: 20020849

value: gastric tumor tissue 20020849


title: M14_ARHGAP8_2D

description: For 2D culture, plastic tissue culture plates were coated with bovine dermal type I collagen (60mg/ml) (Advanced BioMatrix Inc., San Diego, CA) and allowed to air-dry before addition of medium. M14 transfectants were cultured for 4 days in the presence of 500mg/ml G418 and harvested while still pre-confluent.

source_name: ARHGAP8 transfected line, 2D culture

value: FLAG tagged ARHGAP8 in pIRES2


title: M14_GFP_2D

source_name: Empty vector transfected line, 2D culture


title: M14_ARHGAP8_3D

source_name: ARHGAP8 transfected line, 3D culture


title: 20020448

value: gastric tumor tissue 20020448


title: 20020361

value: gastric tumor tissue 20020361


title: 20020135

value: gastric tumor tissue 20020135


title: 20020447

value: gastric tumor tissue 20020447

value: spleen


title: 20020164

value: gastric tumor tissue 20020164


title: 20020159

value: gastric tumor tissue 20020159


title: 20020563

value: gastric tumor tissue 20020563


title: 20020065

value: gastric tumor tissue 20020065


title: 2001320

value: gastric tumor tissue 2001320


title: 20020070

value: gastric tumor tissue 20020070


title: 20020148

value: gastric tumor tissue 20020148


title: 2001271

value: gastric tumor tissue 2001271


title: 9874831

value: gastric tumor tissue 9874831


title: 2001140

value: gastric tumor tissue 2001140


title: 2001098

value: gastric tumor tissue 2001098


title: 20020032

value: gastric tumor tissue 20020032


title: 20020011

value: gastric tumor tissue 20020011


title: 2001120

value: gastric tumor tissue 2001120


title: 2001272

value: gastric tumor tissue 2001272


title: 2000762

value: gastric tumor tissue 2000762


title: 2000778

value: gastric tumor tissue 2000778

value: spleen


title: 2001123

value: gastric tumor tissue 2001123


title: 2000763

value: gastric tumor tissue 2000763


title: 2001319

value: gastric tumor tissue 2001319


title: 2000710

value: gastric tumor tissue 2000710


title: 2001094

value: gastric tumor tissue 2001094


title: 2000639

value: gastric tumor tissue 2000639


title: 2000525

value: gastric tumor tissue 2000525


title: 2000563

value: gastric tumor tissue 2000563


title: 2000510

value: gastric tumor tissue 2000510


title: 2000441

value: gastric tumor tissue 2000441


title: 2000169

value: gastric tumor tissue 2000169


title: 2000433

value: gastric tumor tissue 2000433


title: 990436

value: gastric tumor tissue 990436


title: 2000088

value: gastric tumor tissue 2000088


title: 990428

value: gastric tumor tissue 990428


title: 2000137

value: gastric tumor tissue 2000137


title: 990488

value: gastric tumor tissue 990488

value: spleen


title: 990515

value: gastric tumor tissue 990515


title: 990203

value: gastric tumor tissue 990203


title: 990424

value: gastric tumor tissue 990424


title: 990187

value: gastric tumor tissue 990187


title: 990231

value: gastric tumor tissue 990231


title: 2000038

value: gastric tumor tissue 2000038


title: 990286

value: gastric tumor tissue 990286


title: 990474

value: gastric tumor tissue 990474


title: 990172

value: gastric tumor tissue 990172


title: 990275

value: gastric tumor tissue 990275


title: 990221

value: gastric tumor tissue 990221


title: 990205

value: gastric tumor tissue 990205


title: 2000721

value: gastric tumor tissue 2000721


title: 990060

value: gastric tumor tissue 990060


title: 990129

value: gastric tumor tissue 990129


title: 990170

value: gastric tumor tissue 990170


title: 990020

value: gastric tumor tissue 990020

value: spleen


title: 990005

value: gastric tumor tissue 990005


title: 980447

value: gastric tumor tissue 980447


title: 980417

value: gastric tumor tissue 980417


title: 980305

value: gastric tumor tissue 980305


title: 980444

value: gastric tumor tissue 980444


title: 980324

value: gastric tumor tissue 980324


title: 980255

value: gastric tumor tissue 980255


title: 980212

value: gastric tumor tissue 980212


title: 980138

value: gastric tumor tissue 980138


title: 980211

value: gastric tumor tissue 980211


title: 980063

value: gastric tumor tissue 980063


title: 980151

value: gastric tumor tissue 980151


title: 980204

value: gastric tumor tissue 980204


title: 980125

value: gastric tumor tissue 980125


title: 980024

value: gastric tumor tissue 980024


title: 980028

value: gastric tumor tissue 980028


title: 99069

value: gastric tumor tissue 99069

value: spleen


title: 980048

value: gastric tumor tissue 980048


title: 99098

value: gastric tumor tissue 99098


title: 99071

value: gastric tumor tissue 99071


title: 980021

value: gastric tumor tissue 980021


title: 2000484

value: gastric tumor tissue 2000484


title: MKN74

value: gastric cancer cell line MKN74


title: 2000344

value: gastric tumor tissue 2000344


title: 980453

value: gastric tumor tissue 980453


title: 980001

value: gastric tumor tissue 980001


title: SCH

source_name: SCH

value: gastric cancer cell line SCH


title: 99046

value: gastric tumor tissue 99046


title: Ist-1

value: gastric cancer cell line Ist-1


title: YCC-3

value: gastric cancer cell line YCC-3


title: YCC-2

value: gastric cancer cell line YCC-2


title: YCC-9

value: gastric cancer cell line YCC-9


title: YCC-16

value: gastric cancer cell line YCC-16


title: YCC-6

value: gastric cancer cell line YCC-6

value: spleen


title: 980040

value: gastric tumor tissue 980040


title: SNU1

value: gastric cancer cell line SNU1


title: SNU5

value: gastric cancer cell line SNU5


title: SNU16

value: gastric cancer cell line SNU16


title: NCI-N87

value: gastric cancer cell line NCI-N87


title: KatoIII

source_name: KatoIII

value: gastric cancer cell line KatoIII


title: YCC-1

value: gastric cancer cell line YCC-1


title: FU-97

value: gastric cancer cell line FU-97


title: YCC-7

value: gastric cancer cell line YCC-7


title: MKN7

value: gastric cancer cell line MKN7


title: YCC-10

value: gastric cancer cell line YCC-10


title: MKN28

value: gastric cancer cell line MKN28


title: 2000617

value: gastric tumor tissue 2000617


title: Hs 746T

source_name: Hs 746T

value: gastric cancer cell line Hs 746T


title: MKN45

value: gastric cancer cell line MKN45


title: AZ-521

value: gastric cancer cell line AZ-521


title: AGS

source_name: AGS

value: gastric cancer cell line AGS

value: spleen


title: MKN1-NCC

value: gastric cancer cell line MKN1-NCC


title: IM95

value: gastric cancer cell line IM95


title: YCC-11

value: gastric cancer cell line YCC-11


title: Arabidopsis incubated with E. coli

status: Public on Dec 01 2010

city: Brisbane

first: chanyarat

last: Paungfoo-Lonhienne

state: QLD

address: The University of Queensland

department: Science

institute: The University of Queensland

description: Represents three arrays based on biological replicates (3 E.coli, 3 control)

hyb_protocol: standard protocols by AGRF, Australia

scan_protocol: Scanned on an Agilent Technologies DNA Microarray Scanner and the program associated with it was Agilent Scan Control. Images were quantified using Agilent Feature Extraction v. 10.1.1.1.

data_processing: Partek Genomics suite was used for background subtraction and quantile normalization.  Final ratio of normalized log10 ratio (Cy3/Cy5) representing test(3 reps)/reference(3 reps)/was calculated.

source_name: root

label_protocol: standard protocols by AGRF,Australia

growth_protocol: Arabidopsis plant were grown axenically in hydroponic culture for 4 weeks before E. coli was added into the medium solution.  Control received no E. coli. After 24 h, plant roots were harvested.

extract_protocol: Total RNA of Arabidopsis roots grown in hydroponic culture were extracted using NucleoSpin® Plant Kits (BD Biosciences Clontech, Japan).

tag: cultivar

value: Columbia

tag: culture

value: hydroponic

value: 5 weeks

tag: treatment

value: incubated with E. coli for 24 h

label_protocol: standard protocols by AGRF, Australia

value: no incubation with E. coli


title: Uremic Diet vrs Reversibility Rats

status: Public on May 11 2010

city: Jerusalem

first: Mony

last: Shuvy

address: Ein-Karem

department: Cardiology

country: Israel

institute: Hadassah Hospital

description: Technical Replicate 1 of 2

hyb_protocol: Equal amounts of Cy3 or Cy5 labeled cRNA were hybridized to the 4 X 44K Agilent Whole Rat Genome Oligo-Microarray (Agilent Technologies, USA) for 17 hours at 60°c in an Agilent DNA-Microarray Hybridization Oven. The arrays were later washed using Gene Expression Wash Buffer Kit from Agilent.

scan_protocol: The Microarray was scanned using the GenePix4000B Scanner (Axon) and the data was extracted from the resulting images using GenePix Pro 4.1 software (Axon).

data_processing: The resultant files (gpr) produced by GenePix have been analyzed utilizing LIMMA package of the R software. The Cy5 and Cy3 intensities within each array were normalized using the print-tip locally weighted scatter plot smoothing (LOESS) function, while no background correction was applied. To identify differentially expressed genes, a parametric empirical Bayesian approach implemented in LIMMA was used. A moderated t test was performed in parallel, with the use of a false discovery rate correction for multiple testing. LIMMA calculated an emission intensity A value [A = (log2(Cy5) × Cy3)/2] where Cy5 and Cy3 are the normalized emission intensities of each feature. P value < 0.05 confidence level has been used to pinpoint those significantly differentiated genes. Genes had to have an A-value (average expression level for the gene across all arrays and channels) of more than 8.5, thus avoiding faint emissions.

source_name: Rat Aortic valves_Uremic diet 9 weeks_Normal Diet 10 weeks

label_protocol: One microgram of total RNA was amplified and labeled with a fluorescent dye (either Cy3 or Cy5), using the Low RNA Input Linear Amplification & Labeling kit (Agilent Technologies, Palo Alto, CA, USA). The amount and quality of the resulting labeled cRNA was measured using the ‘micro-array measurement mode’ of the Nanodrop (ND-1000) spectrophotometer (NanoDrop Technologies Wilmintog, Delaware, USA).

growth_protocol: Sixty one Sprague-Dawley female rats, 8 weeks old, each weighing about 250 g, were used for the study. The protocol was approved by the Hebrew University Ethics Committee.

extract_protocol: Sample preparation:1. Homogenize tissue samples in TRI REAGENT (1ml per 50-100 mg of tissue) 2. Add 200ul of chloroform per ml of TRI REAGENT used. Cover the sample tightly, shake vigorously for 15 seconds and allow to stand for 2-15 minutes at room temperature. Centrifuge the resulting mixture at 12,000xg for 15 minutes at 4 C .RNA Isolation:  1. Transfer the aqueous phase to a fresh tube and add 0.5ml of isopropanol per ml of TRI REAGENT used in sample preparation. Allow the sample stand for 5-10 minutes at room temperature. Centrifuge at 12,000 g for 10 min at 4C . The RNA precipitate will form pellet on the side and bottom of the tube. 2. Remove the supernatant and wash the RNA pellet by adding 1 ml (minimum) of 75% ethanol per 1ml of TRI REAGENT used in sample preparation, step 1. Vortex the sample and then centrifuge at 7,500 x g for 5 min at 4C. 3. Briefly dry the RNA pellet for 5-10 min by air drying or under vacuum. Add an appropriate volume of water.To facilitate dissolution, mix by repeated pipetting with a micropipette at 55-60C for 10 min.       Sample preparation:1. Homogenize tissue samples in TRI REAGENT (1ml per 50-100 mg of tissue) 2. Add 200ul of chloroform per ml of TRI REAGENT used. Cover the sample tightly, shake vigorously for 15 seconds and allow to stand for 2-15 minutes at room temperature. Centrifuge the resulting mixture at 12,000xg for 15 minutes at 4 C .RNA Isolation:  1. Transfer the aqueous phase to a fresh tube and add 0.5ml of isopropanol per ml of TRI REAGENT used in sample preparation. Allow the sample stand for 5-10 minutes at room temperature. Centrifuge at 12,000 g for 10 min at 4C . The RNA precipitate will form pellet on the side and bottom of the tube. 2. Remove the supernatant and wash the RNA pellet by adding 1 ml (minimum) of 75% ethanol per 1ml of TRI REAGENT used in sample preparation, step 1. Vortex the sample and then centrifuge at 7,500 x g for 5 min at 4C. 3. Briefly dry the RNA pellet for 5-10 min by air drying or under vacuum. Add an appropriate volume of water.To facilitate dissolution, mix by repeated pipetting with a micropipette at 55-60C for 10 min.

treatment_protocol: Aortic valves samples were obtained from 3 groups: a Uremic-diet group, a reversibility group and a control group (n=7 each). The rats in the Uremic-diet and the reversibility group were fed exclusively with a uraemia induced high-adenine (0.75%), high-phosphate diet (1.5%). The control group received normal rat chow with no treatment. After 9 weeks, rats in the Uremic-diet group and in the control were anaesthetized using ketamine/xylazine and sacrificed; the rats in the reversibility group were kept alive for an additional 10 weeks, on a normal rat chow, and then sacrificed.

tag: strain

value: Sprague-Dawley

tag: sex

value: Female

tag: feed

value: Uremic Diet + Normal Diet

tag: feeding time

value: 9 weeks +10 weeks

source_name: Rat Aortic valves_Uremic Diet_9 weeks

value: Uremic diet

value: 9 weeks


title: Reversibility vrs control Rats

description: Technical Replicate 1 of 2

source_name: Rat Aortic valves_Normal Diet_9 weeks

value: Normal Diet

value: 9 weeks + 10 weeks


title: At-LAP2-1

status: Public on Jun 02 2010

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Manual: Agilent Technologies

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1 (lowess and rank consistency)

source_name: WT Control Cy3

label_protocol: Kit: Low RNA Input Linear Amplification kit

growth_protocol: All plants were grown in soil or onto Murashige and Skoog (MS) standard medium pH 5.7 containing 0.8 g/L phytoagar at ~100-120 umol m-2 sec-1 for a 16-h photoperiod at 22°C

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: control

tag: ecotype

tag: genotype

value: wild type

source_name: LAP2-1 mutant Cy5

treatment_protocol: mutant

value: LAP2-1 mutant


title: At-LAP2-2

description: Manual: Agilent Technologies

source_name: LAP2-1 mutant Cy3

source_name: WT Control Cy5


title: Uremic Diet vrs Control rats replicate 2

description: Technical Replicate 2 of 2


title: TMK1

tag: cell line

value: gastric cancer cell line TMK1

source_name: control human spleen genomic DNA

value: spleen