title: HEK293 ALKBH7 uninduced replicate 1, Illumina HumanWG-6 Expression BeadChip version 3


title: 11299.p1

status: Public on Dec 01 2013

type: genomic

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

country: USA

institute: Emory University

description:
Autism: affected individual diagnosed as autistic
Autism-sib: non-affected sibling with an autistic brother
P1: label for probands (i.e. autistic individuals) as described by the Simons foundation. Please note these should all be classified as "autism"
S1: label for controls (i.e. unaffected individuals with autistic brothers), also as described by the Simons foundation. Please note these should all be classified as "autism-sib"
The sites (fl, gv, hv, kc, kr, lu, oi, ox, pb, sb, vn, xm, xx) are designators of the collection site for the Simons trial. We are currently blinded to the actual location, but we have analyzed the data with site as a covariate to adjust for any potential site-specific influences so I thought we should include it in our public data submission.
Group designates the shipment batch that we received the samples from the biobank at Rutgers where Simons houses their specimens. These groups of samples were run in multiple experiments denoted by the Experiment variable. Finally, distribution denotes the shipment from Simons to the biobank at Rutgers. All these variables are potential covariates in analysis to ensure we adjusting for batch effects.

scan_protocol: Followed the manufacturer's (Illumina) specifications on either a BeadStation 500 or an iScan

data_processing: Avg beta (β), detection value, and signal for Probe A (unmethylated) and Probe B were exported from GenomeStudio v2010.3 Methylation Module 1.8.5. The manufacturer measures methylation through the beta (β) value calculated as probe B signal / (probe A signal + probe B signal + 100). Based on better reproducibility of the controls we calculated the methylation using a metric denoted beta prime (β') which is calculated as probe B signal / (probe A signal + probe B signal).

label: biotin nucleotide or dinitrophenyl labeled

molecule: genomic DNA

organism: Homo sapiens

source_name: leukocyte

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: DNA was extracted by the Rutgers University Cell and DNA Repository RUCDR

treatment_protocol: Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

tag: sample id

tag: gender

value: Male

tag: sentrix id

tag: sentrix position

value: L

tag: experiment

tag: group

tag: family

tag: distribution

tag: site

value: oi

tag: cpea dx

tag: age at collection (months)

tag: ethnicity

value: other

tag: cell type

value: leukocyte


title: BEAS2B - EPI - 6 hours - repl. 2

type: RNA

city: Mol

first: Sylvie

last: Remy

state: Antwerp

address: Boeretang 200

country: Belgium

institute: VITO

description: Non-sensitizing irritant EPI

hyb_protocol: Equal amounts of the exposed and negative control labeled cRNA samples were competitively hybridized onto the arrays in a fully automatic HS 4800 Pro hybridization station (Tecan, Grödig/Salzburg, Austria) for 17 hours.

scan_protocol: The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Raw data feature extraction files were generated using Agilent protocol GE2-v5_95_Feb07.  Standard Agilent Feature Extraction normalization

molecule: total RNA

source_name: BEAS2B, vehicle control, 6 hours

label_protocol: 1 μg of total RNA was used in the Agilent LIRAK PLUS, two-colour Low RNA input Linear Amplification method, according to the manufacturer’s instructions.  cRNAs showing a yield >825 ng and a specific activity of 8-20 pmol/μg cRNA were selected for further processing.

growth_protocol:
BEAS-2B cells were grown in T-75 culture flasks precoated with a mixture of 10 µg/ml human plasma fibronectin (Invitrogen, Paisley, UK), 30 µg/ml PureColTM (Advance Biomatrix, USA), and 10µg/ml bovine serum albumin (Sigma–Aldrich Chemie Gmbh, Steinheim, Germany) dissolved in growth medium (BEGM, Lonza). The mixture was added at a ratio of 0.2 ml/cm2 surface area.
The cells were kept in a humidified atmosphere at 37 °C and 5% CO2. Before reaching 80% confluence, cells were subcultured using 0.25 % trypsin/0.53 mM versene (EDTA) solution (LGC Promochem) containing 0.5% polyvinylpyrrolidone (Sigma–Aldrich Chemie Gmbh). Medium was refreshed every 2–3 days and cells were subcultured every 4-5 days (1500–3000 cells/cm2).

extract_protocol: After exposure time, the supernatants was removed and the cells were lysed in the plates with 99% RLT lysis buffer (Qiagen, Hilden, Germany) and 1% 2-mercaptoethanol (Sigma–Aldrich Chemie Gmbh). Total RNA was isolated using mini RNeasy RNA isolation kits, according to the manufacturer’s specifications (Qiagen).

treatment_protocol:
BEAS-2B cells were seeded in six-well plates (6×105 cells suspended in 4 ml growth medium per well) 24 hours before exposure to the test substance.  Cells were exposed for 6, 10, and 24 hours to the selected chemicals to a concentration yielding 20% cell viability reduction (IC20). This concentration was derived from concentration-response relationships after 24 hours of exposure determined using the neutral red uptake assay.
Except for 4 chemicals (DOP, MeSA, STY, and TMA) which did not induce reduction in cell viability for concentrations ranging up to the highest soluble concentration (solved in growth medium supplemented with maximally 0.05% dimethylsulfoxide (DMSO)). These chemicals were applied at highest soluble concentration

tag: cell line

tag: treatment

value: control

source_name: BEAS2B, Non-sensitizing irritant, 6 hours

value: EPI

tag: time

value: 6 hours


title: 11520.p1

hyb_protocol: Followed the manufacturer's (Illumina) specifications

value: K

value: xm

value: white


title: BEAS2B - EPI - 6 hours - repl. 1

description: Non-sensitizing irritant EPI


title: BEAS2B - CP - 24 hours - repl. 2

description: Non-sensitizing irritant CP

source_name: BEAS2B, vehicle control, 24 hours

source_name: BEAS2B, Non-sensitizing irritant, 24 hours

value: CP

value: 24 hours


title: 11545.p1

value: F

value: kr


title: 11096.p1

value: A


title: BEAS2B - CP - 24 hours - repl. 1

description: Non-sensitizing irritant CP


title: 11216.p1

value: I

value: more-than-one-race


title: HEK293 ALKBH4 induced replicate 2, Illumina HumanWG-6 Expression BeadChip version 3

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalised in J-express

label: Biotin

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

growth_protocol: HEL293 were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza) supplemented with 10 % tetracycline-free fetal bovine serum (FBS) (Clontech), 100 U/ml penicillin (Lonza), 100 U/ml streptomycin (Lonza), 2 mM L-glutamine (Lonza), 15 μg/ml blasticidin-S (Invitrogen) and 200 μg/ml hygromycin B.), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency.

extract_protocol: RNA was isolated using the standard TRIzol procedure (Invitrogen), and further purified with an RNeasy mini column (Qiagen GmbH, Hilden, Germany), according to the manufacturers’ instructions.

treatment_protocol: Ectopic ALKBH expression was induced by addition of 2 μg/mL doxycycline to the medium.

tag: expression

value: ALKBH4 induced

value: Human Embryonic Kidney

tag: provider

value: Life Technologies

tag: catalog number


title: HEK293 ALKBH4 induced replicate 1, Illumina HumanWG-6 Expression BeadChip version 3


title: BEAS2B - CP - 10 hours - repl. 3

description: Non-sensitizing irritant CP

source_name: BEAS2B, vehicle control, 10 hours

source_name: BEAS2B, Non-sensitizing irritant, 10 hours

value: 10 hours


title: BEAS2B - CP - 24 hours - repl. 3

description: Non-sensitizing irritant CP

value: control


title: BEAS2B - CP - 10 hours - repl. 1

description: Non-sensitizing irritant CP


title: BEAS2B - CP - 10 hours - repl. 2

description: Non-sensitizing irritant CP


title: 11596.p1

tag: sample id

tag: gender

value: Male

tag: sentrix id

value: B

value: leukocyte


title: HEK293 ALKBH4 uninduced replicate 3, Illumina HumanWG-6 Expression BeadChip version 3

value: ALKBH4 uninduced


title: HEK293 ALKBH4 uninduced replicate 1, Illumina HumanWG-6 Expression BeadChip version 3


title: HEK293 ALKBH4 uninduced replicate 2, Illumina HumanWG-6 Expression BeadChip version 3


title: BEAS2B - CP - 6 hours - repl. 1

description: Non-sensitizing irritant CP

value: 6 hours


title: BEAS2B - CP - 6 hours - repl. 2

description: Non-sensitizing irritant CP

value: CP


title: BEAS2B - CP - 6 hours - repl. 3

description: Non-sensitizing irritant CP


title: Normal breast tissue 013

city: Madrid

first: Beatriz

last: Martinez

address: Calle Melchor Fernandez Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Normal breast tissue

hyb_protocol: Exiqon miRNA microarray slides containing denaturated labeled RNA in 1x hybridization buffer were hybridized at 56ºC for 16h

scan_protocol: Slides were scanned using Agilent array scanner set to 10μm wit 100PMT sensitivity in an ozone-free-environment. Fluorescence intensities on scanned images were quantified using Feature Extraction software (Agilent) using the modified Exiqon protocol

data_processing: Agilent feature extraction software (version 9.5.3) was run on all array datasets using the GE2-v5_95_Feb07 protocol.  Normexp and quantiles were applied for background correction and normalization respectively.

source_name: Normal tissue

label_protocol: 300ng of total RNA were treated for  with Calf Intestine Phosphatase and than labeled with Hy3 fluorescent dye

growth_protocol: Normal Human Mammary Epithelial Cells (HMEC) (Clonetics) were grown in MEGM, Mammary Epithelial Growth Medium (Clonetics) supplemented with growth factors SingleQuots (Clonetics) in absence of FBS and with 2%penicilin/streptomicine at 37ºC and  5% CO2 atmosphere and 80% humidity

extract_protocol: Total RNA was extracted from cell pellet using Trizol following manufacturer's recommendations

tag: sample type

value: Normal tissue


title: Normal breast tissue 007

description: Normal breast tissue


title: VB0032

value: VB

tag: sentrix position

tag: experiment

tag: group


title: P.alba_CONTROLvsUVB_T3h_rep3

city: Florence

first: Giovanni

last: Emiliani

address: via S. Bonaventura, 13

department: Dept. of Environmental and Forestry Technologies and Sciences

country: Italy

institute: University of Florence

description: Transcriptional profiling of UV-B response of Populus alba

hyb_protocol: Hybridisation was performed in an HS400 hybridisation station (Tecan, Reading, UK). The slides were washed for 1 min in pre-hybridisation buffer. The prepared probe was then added, and the slides hybridised for 16 hr at 42 °C with low agitation frequency. The slides were then washed 5 times for 1 min in each of WBI (1X SSC, 0.2% SDS), WBII (0.1X SSC, 0.1% SDS) and WBIII, and then for 1 min in H2O, and 1 min in 100% EtOH. The slides were dried with nitrogen gas

scan_protocol: The slides were scanned on a Genetix Aquire scanner (Genetix, Hampshire, UK) at 5 μm resolution. PMT settings were adjusted to equalise the channel intensities.

data_processing: The TIFF images were analysed using GenePixPro 5.1 (Axon Instruments, Union City, California). Spots were flagged as “bad” if the median signal intensity was equal to 65535 or if less than 150 µm in diameter. Images were also checked manually and miss-called spots were manually flagged as bad. A combination of custom functions and functions from within the LIMMA package were used to produce pre- and post-normalized quality control plots to ensure data quality. Background subtraction was achieved by removing the local median background intensity from the spot foreground median intensity. Background corrected data were then normalized using a print-tip LOWESS normalization, and spots with a ‘bad’ flag had a negative weighting factor of 0.1 applied to them. A cross-slide normalization was also applied to ensure consistency of scale. Normalized data were then filtered based on A value [(log2 R + log2 G)/2] to remove spots with low intensities in both channels (the threshold value for A was set to 8.0, equating to a raw intensity of 256)

organism: Populus alba

source_name: T3h bulked leaves of control replicate 3

label_protocol: Total RNA was primed with 2 µl of anchored oligo(dt)20 primer and reverse transcribed over night at 48 ºC with the Superscript™ reverse transcriptase system (Invitrogen, Paisley, UK) (aa-dUTP:dTTP, 4:1). cDNA was purified using a Qiagen PCR purification kit according to the manufacturers instructions. 35 µl 100 mM sodium acetate (pH 5.2) was then added to each purified and this then added to an aliquot of CyDye™ ester (Amersham, Buckinghamshire, UK). Cy3 and Cy5 were added to control and treatment respectively, and for nearly 50 % of the samples this orientation was reversed to account for any dye binding bias. The samples were gently agitated and then left in the dark at room temperature for 2 hours. Dye-coupled cDNA was purified using Qiagen PCR purification kit (Qiagen, Crawley, UK). The Cy3-labelled cDNA was purified according to the manufacturer’s protocol. The Cy5-labelled sample was treated the same and eluted into the same eppendorf tube as the corresponding Cy3-labelled sample, following randomised paring between control and treated samples. The total eluate containing 200 µl of Cy3-and-Cy5 coupled cDNA was concentrated down to 25 µl in a spin concentrator (Eppendorf Concentrator 5301, Eppendorf, Cambridge, UK). The dye-labelled cDNA target (25 µl) was denatured by the addition of 50 µl formamide, 25 µl of hybridisation buffer (Amersham, Buckinghamshire, UK) was added and the sample heated at 95 ºC for 1 minute and then chilled on ice.

growth_protocol: Plants were grown in a nursery for 1 year and then acclimated in the chambers for 2 week before the start of the UVB treatment; plants were randomized inside the chamber during the experiment to exclude position effect as well as swapped between the two chambers to avoid a chamber effect.

extract_protocol: Total RNA was extracted following Chang et al., 1993

treatment_protocol: Plants were treated for 12 hours with an UVBbe (UVB biologically effective radiation, Caldwell, 1971) supplementary dose of 6 kJ/m2/day (0.15 W/m2 at 100 cm from the lamps) and allowed to recover during the night. Growing conditions were as follow: temperature 25 °C during the day and 20 °C during the night, relative humidity 60%, CO2 concentration 350 ppm.

tag: Two years old micropropagated plants, rooted and grown in nursery for 1 year before the radiation treatment

source_name: T3h bulked leaves of UV-B treated replicate 3


title: P.alba_CONTROLvsUVB_T3h_rep2

source_name: T3h bulked leaves of control replicate 2

source_name: T3h bulked leaves of UV-B treated replicate 2


title: VB0115

value: L


title: 11057.p1

value: D

tag: family

tag: distribution

tag: site

value: kr

tag: cpea dx

tag: age at collection (months)

value: white


title: VB0107

value: H

tag: cell type


title: BEAS2B - ACR - 10 hours - repl. 2

description: Non-sensitizing irritant ACR

tag: cell line

tag: treatment

value: ACR

tag: time


title: BEAS2B - ACR - 24 hours - repl. 2

description: Non-sensitizing irritant ACR

value: 24 hours


title: 11561.p1

tag: sample id

value: E

value: fl

tag: ethnicity


title: BEAS2B - ACR - 10 hours - repl. 3

description: Non-sensitizing irritant ACR

value: control

value: 10 hours


title: Embryo_Traf6.Morpholino-2_Low_rep1

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

country: Netherlands

institute: AMC

description: 1nl of Traf6 ATG morpholino 2 (0.5mM) was injected into 30% epiboly zebrafish embryos

hyb_protocol: 825 ng for each channel were combined and made to 55 μl with 10x Blocking Agent and 25x Fragmentation Buffer. 55 μl of 2x Hi-RPM Hybridization Buffer was added (Gene Expression Hybridization Kit, Agilent Technologies). 100 μl of hybridization mixture was loaded onto each array and allowed to hybridize at 65°C (10 RPM) for 17h. The slides were washed with Gene Expression Wash Buffers I and II (Gene Expression Wash Buffer Kit, Agilent Technologies).

scan_protocol: Slides were scanned in an ozone-free room with the Agilent G2565BA scanner as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis guide version 5.5 (G4140-90050, Agilent technologies).

data_processing: Data was extracted with Feature Extraction version 9.5.1.1. (Protocol GE2-v5_95)  for two-color Agilent microarrays.

organism: Danio rerio

source_name: Traf6 ATG morpholino 2 0.5mM injected replicate 1

label_protocol: 0,5 μg of total RNA was amplified with the Amino-Allyl MessageAmp II kit (Ambion) according to manufacturer’s instruction. After aRNA synthesis, samples were labeled with Cy3-NHS mono-reactive dye (GE Healthcare) for the test samples and Cy5-NHS (GE Healthcare) mono-reactive dye for the common reference (pooled aRNA).

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos of each treatment group were sampled at the 30% epiboly stage and snap frozen in liquid nitrogen. Total RNA from each sample was extracted using TRIZOL followed by a clean up procedure using the RNeasy Mini Kit (Qiagen) and removal of a residual genomic DNA by an RNase-free DNase treatment (Qiagen). RNA concentration was determined using a Nanodrop ND-1000 (Thermo Fisher Scientific) and RNA quality was assessed on a Agilent 2100 BioAnalyzer (Agilent Technologies). Total RNA samples with an RNA integrity number (RIN) >7 were used for further analysis. All assays were performed according to the manufacturer’s protocols.

treatment_protocol: Translation of traf6 was blocked by either one of two non-overlapping morpholinos (traf6 morpholino-1 and morpholino-2) specifically targeting the 5’UTR region. To be able to control for aspecific morpholino effects, a 5bp mismatch morpholino of traf6 morpholino-1 and a standard control morpholino (Gene Tools) were used. Morpholino oligonucleotides were diluted with Danieu buffer to a concentration of 0.5, 1 and 2 mM and embryos were injected at the one cell stage with 1nl of one of the above mentioned morpholinos. In addition, 1x Danieu’s buffer containing Phenol red was injected to control for the injection effect per se. All injections were performed in random order and the experiment was performed in quintuplicate.

tag: developmental stage

value: 30% epiboly

value: Traf6 ATG morpholino 2

tag: dose

value: low


title: Normal breast tissue 015

description: Normal breast tissue

tag: sample type


title: Embryo_Traf6.Morpholino-2_Low_rep2 Reference

description: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample.

source_name: Common Reference


title: BEAS2B - ACR - 24 hours - repl. 3

description: Non-sensitizing irritant ACR


title: BEAS2B - ACR - 24 hours - repl. 1

description: Non-sensitizing irritant ACR


title: P.alba_CONTROLvsUVB_T3h_rep4

source_name: T3h bulked leaves of control replicate 4

source_name: T3h bulked leaves of UV-B treated replicate 4


title: VB0057

tag: gender

value: Male

tag: sentrix id

tag: sentrix position

value: C

tag: experiment

value: leukocyte


title: Normal breast tissue 008

description: Normal breast tissue

value: Normal tissue


title: Embryo_Traf6.Morpholino-2_Low_rep2

source_name: Traf6 ATG morpholino 2 0.5mM injected replicate 2


title: Normal breast tissue 014

description: Normal breast tissue


title: 11504.p1

source_name: leukocyte

value: D

tag: group

tag: family

tag: distribution


title: Normal breast tissue 012

description: Normal breast tissue


title: 11305.s1

value: A

tag: site

value: kr

tag: cpea dx

tag: age at collection (months)


title: Embryo_Traf6.Morpholino-2_Low_rep1 Reference

tag: treatment


title: BRCAX tumor sample 021

description: BRCA1 tumor

source_name: Tumor sample

value: BRCA1 tumor


title: BEAS2B - ACR - 6 hours - repl. 3

description: Non-sensitizing irritant ACR

source_name: BEAS2B, vehicle control, 6 hours

tag: cell line

source_name: BEAS2B, Non-sensitizing irritant, 6 hours

value: ACR

tag: time

value: 6 hours


title: BRCAX tumor sample 022

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_High_rep5 Reference


title: BRCAX tumor sample 015

description: BRCA1 tumor


title: 11077.p1

tag: sample id

value: E

value: sb

tag: ethnicity

value: white

tag: cell type


title: P.alba_CONTROLvsUVB_T3h_rep1

source_name: T3h bulked leaves of control replicate 1

tag: Two years old micropropagated plants, rooted and grown in nursery for 1 year before the radiation treatment

source_name: T3h bulked leaves of UV-B treated replicate 1


title: BEAS2B - ACR - 10 hours - repl. 1

description: Non-sensitizing irritant ACR

source_name: BEAS2B, vehicle control, 10 hours

value: control

source_name: BEAS2B, Non-sensitizing irritant, 10 hours

value: 10 hours


title: BEAS2B - ACR - 6 hours - repl. 1

description: Non-sensitizing irritant ACR


title: 11285.p1.1

tag: gender

value: K

value: oi


title: BRCA2 tumor sample 008

description: BRCA1 tumor

source_name: Human mammary epithelial cells

tag: sample type

value: Human mammary epithelial cells


title: Embryo_Traf6.Morpholino-1_High_rep4

description: 1nl of Traf6 ATG morpholino 1 (2mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 1 2mM injected replicate 4

tag: developmental stage

value: 30% epiboly

value: Traf6 ATG morpholino 1

tag: dose

value: high


title: 11596.s1

value: Male

tag: sentrix id

tag: sentrix position

value: C

tag: experiment

tag: group

value: leukocyte


title: BEAS2B - ACR - 6 hours - repl. 2

description: Non-sensitizing irritant ACR


title: Embryo_Traf6.Morpholino-1_High_rep4 Reference


title: Human Mammary Epithelial Cells

description: Human Mammary Epithelial Cells

value: BRCA1 tumor


title: 11093.p1

value: F

tag: family

tag: distribution

tag: site

value: xm

tag: cpea dx


title: Embryo_Traf6.Morpholino-1_High_rep5

source_name: Traf6 ATG morpholino 1 2mM injected replicate 5

tag: treatment


title: Normal breast tissue 004

description: Normal breast tissue

source_name: Normal tissue

value: Normal tissue


title: Normal breast tissue 005

description: Normal breast tissue


title: 11031.p1

tag: sample id

value: D

value: kr

tag: age at collection (months)


title: BEAS2B - MA - 24 hours - repl. 3

description: Respiratory sensitizer MA

source_name: BEAS2B, vehicle control, 24 hours

tag: cell line

value: control

source_name: BEAS2B, respiratory sensitizer, 24 hours

value: MA

tag: time

value: 24 hours


title: 08SE272

city: Seville

first: Purificacion

last: Estevez-Garcia

state: Seville

address: Manuel Siurot avenue

department: Molecular Oncology

institute: Institute of Biomedicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC on Human Genome U133 Plus 2.0 array. GeneChips were washed and stained following manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GC3000 laser confocal scanner (Affymetrix)

data_processing: The microarray image data were analyzed using GeneChip Operating Software (GCOS 1.4 Affymetrix). Partek Genomics Suite v7.3.1 (Partek Inc; St Louis, MO, USA) was used for statistical analysis. Affymetrix default analysis settings were used and normalization was performed using the RMA (Robust Multichip Average) method.

label: biotin

source_name: colorectal cell fraction

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: All colorectal tissue samples were maintained at -80ºC until RNA extraction and grinded under liquid nitrogen. Homogenization was achieved using QIAshredder homogenizers and total RNA was extracted using RNeasy Mini kit (both kits from Qiagen Inc; Valencia, CA, USA).

tag: disease state

value: metastatic colorectal cancer (mCRC)

tag: response to chemotherapy

value: YES


title: Embryo_Traf6.Morpholino-1_High_rep3 Reference

source_name: Common Reference

tag: developmental stage

value: 30% epiboly


title: BEAS2B - MA - 10 hours - repl. 2

description: Respiratory sensitizer MA

source_name: BEAS2B, respiratory sensitizer, 10 hours

value: 10 hours


title: BEAS2B - MA - 24 hours - repl. 2

description: Respiratory sensitizer MA


title: BEAS2B - MA - 24 hours - repl. 1

description: Respiratory sensitizer MA


title: Embryo_Traf6.Morpholino-1_High_rep2 Reference


title: BEAS2B - MA - 10 hours - repl. 3

description: Respiratory sensitizer MA


title: 08SE269


title: Embryo_Traf6.Morpholino-1_High_rep3

source_name: Traf6 ATG morpholino 1 2mM injected replicate 3

value: Traf6 ATG morpholino 1

tag: dose

value: high


title: BRCAX tumor sample 012

description: BRCA1 tumor

source_name: Tumor sample

tag: sample type


title: 08SE270

value: NO


title: BRCAX tumor sample 010

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_High_rep2

source_name: Traf6 ATG morpholino 1 2mM injected replicate 2


title: 08SE267


title: 08SE263


title: Embryo_Traf6.Morpholino-1_High_rep1

source_name: Traf6 ATG morpholino 1 2mM injected replicate 1


title: BRCAX tumor sample 014

description: BRCA1 tumor


title: BRCAX tumor sample 020

description: BRCA1 tumor


title: BEAS2B - MA - 6 hours - repl. 2

description: Respiratory sensitizer MA

source_name: BEAS2B, vehicle control, 6 hours

source_name: BEAS2B, respiratory sensitizer, 6 hours

value: 6 hours


title: 08SE265


title: BRCAX tumor sample 011

description: BRCA1 tumor

value: BRCA1 tumor


title: 08SE261


title: BRCAX tumor sample 018

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_High_rep1 Reference


title: Embryo_Traf6.Morpholino-1_Medium_rep5

description: 1nl of Traf6 ATG morpholino 1 (1mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 1 1mM injected replicate 5

value: medium


title: Embryo_Traf6.Morpholino-1_Medium_rep5 Reference


title: 08SE259


title: Embryo_Traf6.Morpholino-1_Medium_rep4 Reference


title: BRCAX tumor sample 017

description: BRCA1 tumor


title: BEAS2B - MA - 6 hours - repl. 3

description: Respiratory sensitizer MA


title: 08SE257


title: Embryo_Traf6.Morpholino-1_Medium_rep3 Reference


title: Embryo_Traf6.Morpholino-1_Medium_rep4

source_name: Traf6 ATG morpholino 1 1mM injected replicate 4


title: BEAS2B - MA - 6 hours - repl. 1

description: Respiratory sensitizer MA


title: BRCAX tumor sample 019

description: BRCA1 tumor


title: 08SE244


title: 08SE253


title: BEAS2B - MA - 10 hours - repl. 1

description: Respiratory sensitizer MA

source_name: BEAS2B, vehicle control, 10 hours


title: BEAS2B - HDI - 24 hours - repl. 3

description: Respiratory sensitizer HDI

value: HDI


title: BRCAX tumor sample 016

description: BRCA1 tumor


title: BEAS2B - HDI - 24 hours - repl. 1

description: Respiratory sensitizer HDI


title: BEAS2B - HDI - 24 hours - repl. 2

description: Respiratory sensitizer HDI


title: BEAS2B - HDI - 10 hours - repl. 3

description: Respiratory sensitizer HDI


title: Embryo_Traf6.Morpholino-1_Medium_rep3

source_name: Traf6 ATG morpholino 1 1mM injected replicate 3


title: BRCAX tumor sample 009

description: BRCA1 tumor


title: BEAS2B - HDI - 10 hours - repl. 2

description: Respiratory sensitizer HDI


title: BEAS2B - HDI - 10 hours - repl. 1

description: Respiratory sensitizer HDI


title: 08SE255


title: 08SE240


title: BEAS2B - HDI - 6 hours - repl. 3

description: Respiratory sensitizer HDI


title: 08SE231


title: BRCA1 tumor sample 001

description: BRCA1 tumor


title: BRCAX tumor sample 013

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_Medium_rep2

source_name: Traf6 ATG morpholino 1 1mM injected replicate 2


title: 08SE229


title: 08SE239


title: Embryo_Traf6.Morpholino-1_Medium_rep1 Reference


title: BEAS2B - HDI - 6 hours - repl. 2

description: Respiratory sensitizer HDI


title: 08SE223


title: Normal breast tissue 001

description: Normal breast tissue

source_name: Normal tissue

value: Normal tissue


title: 08SE225


title: BRCA1 tumor sample 003

description: BRCA1 tumor


title: BEAS2B - HCPt - 24 hours - repl. 2

description: Respiratory sensitizer HCPt

source_name: BEAS2B, vehicle control, 24 hours

value: HCPt


title: BEAS2B - HCPt - 24 hours - repl. 3

description: Respiratory sensitizer HCPt

source_name: BEAS2B, respiratory sensitizer, 24 hours


title: Normal breast tissue 002

description: Normal breast tissue


title: BRCA2 tumor sample 004

description: BRCA1 tumor


title: 08SE233

source_name: colorectal cell fraction


title: 08SE251


title: BRCA2 tumor sample 007

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_Low_rep5

description: 1nl of Traf6 ATG morpholino 1 (0.5mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 1 0.5mM injected replicate 5

value: low


title: Embryo_Traf6.Morpholino-1_Low_rep5 Reference

source_name: Common Reference


title: BRCA2 tumor sample 006

description: BRCA1 tumor


title: Embryo_Traf6.Morpholino-1_Low_rep4

source_name: Traf6 ATG morpholino 1 0.5mM injected replicate 4


title: BRCA1 tumor sample 002

description: BRCA1 tumor

source_name: Tumor sample


title: BEAS2B - HCPt - 10 hours - repl. 3

description: Respiratory sensitizer HCPt

value: control

source_name: BEAS2B, respiratory sensitizer, 10 hours


title: BRCA2 tumor sample 005

description: BRCA1 tumor


title: 08SE247


title: Normal breast tissue 006

description: Normal breast tissue


title: Embryo_Traf6.Morpholino-1_Medium_rep2 Reference


title: Embryo_Traf6.Morpholino-1_Medium_rep1

source_name: Traf6 ATG morpholino 1 1mM injected replicate 1


title: 08SE249


title: BEAS2B - HCPt - 6 hours - repl. 3

description: Respiratory sensitizer HCPt

source_name: BEAS2B, vehicle control, 6 hours


title: Embryo_Traf6.Morpholino-1_Low_rep4 Reference


title: BEAS2B - HCPt - 24 hours - repl. 1

description: Respiratory sensitizer HCPt


title: BEAS2B - HCPt - 10 hours - repl. 1

description: Respiratory sensitizer HCPt


title: Embryo_Traf6.Morpholino-1_Low_rep1

source_name: Traf6 ATG morpholino 1 0.5mM injected replicate 1


title: Embryo_Traf6.Morpholino-1_Low_rep1 Reference


title: Embryo_Control.Morpholino_High_rep5

description: 1nl of control morpholino (2mM) was injected into 30% epiboly zebrafish embryos

source_name: Control morpholino 2mM injected replicate 5

value: Control  morpholino


title: BEAS2B - HDI - 6 hours - repl. 1

description: Respiratory sensitizer HDI

source_name: BEAS2B, respiratory sensitizer, 6 hours


title: BEAS2B - HCPt - 6 hours - repl. 2

description: Respiratory sensitizer HCPt


title: 08SE242


title: Embryo_Traf6.Morpholino-1_Low_rep2

source_name: Traf6 ATG morpholino 1 0.5mM injected replicate 2


title: 08SE221


title: Embryo_Control.Morpholino_High_rep5 Reference


title: Embryo_Control.Morpholino_High_rep4

source_name: Control morpholino 2mM injected replicate 4


title: 08SE246


title: BEAS2B - 7-ACA - 24 hours - repl. 3

description: Respiratory sensitizer 7-ACA

value: 24 hours


title: BEAS2B - HCPt - 10 hours - repl. 2

description: Respiratory sensitizer HCPt

source_name: BEAS2B, vehicle control, 10 hours


title: BEAS2B - HCPt - 6 hours - repl. 1

description: Respiratory sensitizer HCPt


title: 08SE237

value: metastatic colorectal cancer (mCRC)


title: Normal breast tissue 009

description: Normal breast tissue

source_name: Normal tissue


title: Embryo_Control.Morpholino_High_rep4 Reference


title: 08SE235

value: YES


title: Normal breast tissue 003

description: Normal breast tissue


title: 08SE219


title: Normal breast tissue 010

description: Normal breast tissue


title: Normal breast tissue 011

description: Normal breast tissue


title: 08SE217


title: BEAS2B - 7-ACA - 24 hours - repl. 1

description: Respiratory sensitizer 7-ACA

source_name: BEAS2B, vehicle control, 24 hours


title: 08SE213


title: Embryo_Control.Morpholino_High_rep3

source_name: Control morpholino 2mM injected replicate 3

value: 30% epiboly


title: 08SE209

source_name: colorectal cell fraction


title: 08SE211


title: Embryo_Control.Morpholino_High_rep3 Reference


title: BEAS2B - 7-ACA - 10 hours - repl. 2

description: Respiratory sensitizer 7-ACA

value: 10 hours


title: Embryo_Control.Morpholino_High_rep2

source_name: Control morpholino 2mM injected replicate 2


title: BEAS2B - 7-ACA - 6 hours - repl. 2

description: Respiratory sensitizer 7-ACA


title: BEAS2B - 7-ACA - 24 hours - repl. 2

description: Respiratory sensitizer 7-ACA

source_name: BEAS2B, respiratory sensitizer, 24 hours


title: 08SE215


title: 08SE205


title: BEAS2B - 7-ACA - 6 hours - repl. 3

description: Respiratory sensitizer 7-ACA


title: Embryo_Traf6.Morpholino-1_Low_rep2 Reference

source_name: Common Reference


title: Embryo_Control.Morpholino_High_rep2 Reference


title: BEAS2B - 7-ACA - 10 hours - repl. 3

description: Respiratory sensitizer 7-ACA


title: Embryo_Control.Morpholino_High_rep1 Reference


title: 08SE203


title: Embryo_Control.Morpholino_High_rep1

source_name: Control morpholino 2mM injected replicate 1


title: Embryo_Control.Morpholino_Medium_rep5

description: 1nl of control morpholino (1mM) was injected into 30% epiboly zebrafish embryos

source_name: Control morpholino 1mM injected replicate 5


title: Treated vs untreated at 72 h Replicate2

city: Miami

first: Subbarayan

middle: R.

last: Pochi

state: FL

department: Medicine

institute: University of Miami

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

scan_protocol: The microarrays were scanned at 5 mm resolution using a GenePix 4000B scanner (Molecular Devices, USA).

data_processing: The scanned images were analyzed with GenePix Pro 6.1 the software package provided by Molecular Devices, USA. Data extracted from the images were transferred to the software package Acuity 4.0 (Molecular Devices, USA) for quality control. Only features that passed all quality control criteria in all micro arrays were analyzed further. To identify significantly expressed genes the R package 'limma' was used. 'Within array' normalization was carried out with Lowess method, and 'between arrays' normalization with 'quantile' algorithm in the 'limma' package. Features that did not pass the quality control criteria in all arrays were given weight of 0 and were excluded from the analysis.

source_name: MIA PaCa-2_treated

label_protocol: Target RNA was amplified using Amino Allyl Message Amp kit (Ambion, USA). Amplified RNA was labeled with Cy-3 or with Cy-5 dye (Amersham, USA) according to the design of the experiment.

growth_protocol: The human pancreatic cancer cell line MIA PaCa-2 (CRL-1420) was maintained in RPMI 1640 medium supplemented with 10% FBS (Invitrogen, USA) at 37C in a humidified 5% CO2 atmosphere.

extract_protocol: Cells were directly lysed in TriReagent (Sigma, USA) for total RNA isolation according to the manufacturer instructions

treatment_protocol: Overnight cultures were exposed to 34 µg/ml of LE for 24, 48 and 72 hours respectively. Two percent methanol exposed cells served as control

value: MIA PaCa-2 (CRL-1420)

tag: cell type

value: human pancreatic cancer cells

tag: time point

value: 72 hours

tag: treated with

value: 34 µg/ml A.aspera leaves extract in 2% methyl alcohol

source_name: MIA PaCa-2_untreated

tag: treated

value: 2% methyl alcohol (control)


title: Embryo_Control.Morpholino_Medium_rep5 Reference


title: BEAS2B - 7-ACA - 10 hours - repl. 1

description: Respiratory sensitizer 7-ACA

source_name: BEAS2B, respiratory sensitizer, 10 hours


title: BEAS2B - 7-ACA - 6 hours - repl. 1

description: Respiratory sensitizer 7-ACA

source_name: BEAS2B, vehicle control, 6 hours

value: 6 hours


title: Treated vs untreated at 72 h Replicate1


title: Embryo_Control.Morpholino_Medium_rep4 Reference


title: Treated vs untreated at 48 h Replicate4

value: 48 hours


title: 08SE199

value: NO


title: Treated vs untreated at 48 h Replicate3


title: 08SE197


title: Embryo_Control.Morpholino_Medium_rep4

source_name: Control morpholino 1mM injected replicate 4

value: medium


title: Treated vs untreated at 48 h Replicate1


title: Embryo_Control.Morpholino_Medium_rep3 Reference


title: Embryo_Control.Morpholino_Medium_rep2

source_name: Control morpholino 1mM injected replicate 2


title: Treated vs untreated at 48 h Replicate2


title: Maver-1 NIKsh#1 0ng/ml DOX 7d

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

description: Gene expression data from Maver-1 NIKsh#1 cells treated with 0ng/ml DOX for 7 days

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: Maver-1 NIKsh#1 cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: Z-138 and Maver-1 cells were cultured in 10% FBS RPMI with 0.5ug/ml Puromycin (selection marker for shRNAs)

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 1 million cells were resuspended in 3ml of fresh media in 6 well dishes in the presence or absence of 100ng/ml DOX.  Cells were diluted into fresh media with or without doxycycline every 3 days.

tag: nik pathway mutation

value: TRAF3 deletion

value: 0ng/ml DOX

tag: knockdown

value: NIK


title: Maver-1 NIKsh#1 100ng/ml DOX 7d

description: Gene expression data from Maver-1 NIKsh#1 cells treated with 100ng/ml DOX for 7 days

value: 100ng/ml DOX


title: Embryo_Control.Morpholino_Low_rep5

description: 1nl of control morpholino (0.5mM) was injected into 30% epiboly zebrafish embryos

source_name: Control morpholino 0.5mM injected replicate 5

value: Control  morpholino

value: low


title: Embryo_Control.Morpholino_Medium_rep3

source_name: Control morpholino 1mM injected replicate 3

value: 30% epiboly


title: Treated vs untreated at 24 h Replicate6

value: 24 hours


title: Treated vs untreated at 24 h Replicate4

value: MIA PaCa-2 (CRL-1420)


title: Embryo_Control.Morpholino_Medium_rep1 Reference


title: Maver-1 NIKsh#2 100ng/ml DOX 7d

description: Gene expression data from Maver-1 NIKsh#2 cells treated with 100ng/ml DOX for 7 days

source_name: Maver-1 NIKsh#2 cells


title: Treated vs untreated at 24 h Replicate2

value: human pancreatic cancer cells


title: Maver-1 NIKsh#2 0ng/ml DOX 7d

description: Gene expression data from Maver-1 NIKsh#2 cells treated with 0ng/ml DOX for 7 days


title: Treated vs untreated at 24 h Replicate5


title: Treated vs untreated at 24 h Replicate3


title: Maver-1 NTC 0ng/ml DOX 7d

description: Gene expression data from Maver-1 NTC cells treated with 0ng/ml DOX for 7 days

source_name: Maver-1 NTC cells

value: control


title: Z-138 NIKsh#2 100ng/ml DOX 7d

description: Gene expression data from Z-138 NIKsh#2 cells treated with 100ng/ml DOX for 7 days

source_name: Z-138 NIKsh#2 cells

value: TRAF2 nonsense


title: Maver-1 NTC 100ng/ml DOX 7d

description: Gene expression data from Maver-1 NTC cells treated with 100ng/ml DOX for 7 days


title: Embryo_Control.Morpholino_Medium_rep1

source_name: Control morpholino 1mM injected replicate 1


title: Embryo_Control.Morpholino_Medium_rep2 Reference


title: Treated vs untreated at 24 h Replicate1

value: 2% methyl alcohol (control)

value: 34 µg/ml A.aspera leaves extract in 2% methyl alcohol


title: Embryo_Control.Morpholino_Low_rep5 Reference


title: Z-138 NIKsh#2 0ng/ml DOX 7d

description: Gene expression data from Z-138 NIKsh#2 cells treated with 0ng/ml DOX for 7 days


title: Embryo_Control.Morpholino_Low_rep4 Reference


title: Z-138 NIKsh#1 100ng/ml DOX 7d

description: Gene expression data from Z-138 NIKsh#1 cells treated with 100ng/ml DOX for 7 days

source_name: Z-138 NIKsh#1 cells


title: Z-138 NIKsh#1 0ng/ml DOX 7d

description: Gene expression data from Z-138 NIKsh#1 cells treated with 0ng/ml DOX for 7 days


title: Z-138 NTC 100ng/ml DOX 7d

description: Gene expression data from Z-138 NTC cells treated with 100ng/ml DOX for 7 days

source_name: Z-138 NTC cells


title: Embryo_Control.Morpholino_Low_rep4

source_name: Control morpholino 0.5mM injected replicate 4


title: Control vs Tamoxifen treated Akt3 overr-expressing MCF-7 cells (AC vs AT)

city: Stockton

first: Jesika

last: Faridi

state: California

address: 751 Brookside Road

department: Physiology & Pharmacology

institute: University of the Pacific

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers (part number G2534A) containing 750 ng of cyanine 3-labeled and 750 ng of cyanine 5-labeled cRNA per hybridization. Color swaps were performed as follows: four replicate hybridization reactions with cyanine 3-FH versus cyanine 5-AH (designated as polarity +1) and four replicate color swap reactions with cyanine 3-AH versus cyanine 5-FH (designated as polarity -1), resulting in a total of 16 microarray hybridizations to test both protocols. The hybridization reactions with the Legacy/SSPE Version 2.1 protocol were performed at 60°C for 17 hours using Agilent’s In Situ Hybridization Kit Plus (part number 5184-3568), following procedures as described in the Agilent 60-mer Oligo Microarray SureHyb Enabled/SSPE Wash (Version 2.1, April 2004) protocol. The In Situ Hybridization Kit Plus includes a tube of 10x control targets. The 10x control targets in this kit are formulated with both the blocking agents and a TAMRA labeled control oligonucleotide that hybridizes to the positive control features on the microarrays. The hybridization reactions with the higher stringency Version 4.0 protocol were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit (part number 5188-5242), following procedures as described in the Agilent Two-Color Microarray Based Gene Expression Analysis (Version 4.0, December 2005, publication number G4140-90050) protocol. The Gene Expression Hybridization Kit includes a tube of 10x blocking agent that is no longer formulated with the TAMRA-labeled control oligonucleotide.

scan_protocol: Microarrays were scanned using the Agilent DNA Microarray Scanner (part number G2565BA). The microarray images generated by the scanner were analyzed with Agilent Feature Extraction Software (Version 8.5, part number G4148AA) using the GE2_22K_1205 FE extraction protocol. The Feature Extraction files were imported into Microsoft Access, Microsoft Excel, and Spotfire DecisionSite for further data analysis. T-tests comparing the two protocols were performed on filtered data

data_processing: Data was extracted using Agilent Feature Extraction 9.1 Software and analyzed using Agilent GeneSpring GX version 9.0.  Following removal of flagged values, a volcano plot was generated using a fold change cutoff value of > or < than 3 and a p value cutoff value of > or < than 0.01 to generate a differentially expressed gene list of interest.   Other QCmetric were applied such as hierarchical clustering, Box and Whisker, and PCA plots to make sure that replicate arrays had similar Gene expression profiles and no outliers were present.  Finally, self-self hybidization analysis identified less than 1% of differentially expressed genes.

source_name: Tamoxifen treated Akt3 over-expressing MCF-7 cells

label_protocol: Briefly, 250ng of either control or treated total RNA was labeled with the Quick Amp Two Color Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA p/n 5190-0445) in the presence of Spike A and B Mix in a dye-swap experiment prior to hybridizing for 17 hours at 65oC.

extract_protocol: Total RNA was isolated using RNeasy according to manufacturer’s protocol (Qiagen, Valencia, CA). The concentration and A260/A280 ratio were measured by UV absorbance. Quality was also determined on an ethidium bromide (Sigma, St. Louis, MO) stained 1.5% agarose gel (Invitrogen, Carlsbad, CA), and Kodak 1D Image Analysis Software (CareStream Health, Rochester, NY) was used to determine the intensity and ratio of the 28S to 18S ribosomal RNA bands.

value: Akt3 over-expressing MCF-7 cells

value: Tamoxifen

source_name: Control treated Akt3 over-expressing MCF-7 cells

value: Control


title: JVM-13 AFN700 5uM AFN700 20hr

description: Gene expression data from JVM-13 cells treated with 5uM AFN701

source_name: JVM-13 cells

growth_protocol: Granta-519 were cultured in 10% FBS DMEM.  All other cell lines were cultured in 10% FBS RPMI.

treatment_protocol: 3 million cells were resuspended in 3ml of fresh media in 6 well dishes and DMSO or AFN700 was added for 20hrs.

tag: stn/ibrutinib sensitivity

value: insensitive

value: 5uM AFN701

value: JVM-13 cells


title: Embryo_Control.Morpholino_Low_rep3 Reference

description: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample.

source_name: Common Reference

tag: treatment


title: Embryo_Control.Morpholino_Low_rep2 Reference


title: JVM-13 DMSO 0.025% DMSO 20hr

description: Gene expression data from JVM-13 cells treated with DMSO


title: Embryo_Control.Morpholino_Low_rep2

source_name: Control morpholino 0.5mM injected replicate 2


title: JVM-2 AFN700 5uM AFN700 20hr

description: Gene expression data from JVM-2 cells treated with 5uM AFN700

source_name: JVM-2 cells

value: 5uM AFN700

value: JVM-2 cells


title: Embryo_Control.Morpholino_Low_rep3

source_name: Control morpholino 0.5mM injected replicate 3

value: Control  morpholino

value: low


title: Tamoxifen treated MCF-7 cells vs Tamoxifen treated Akt3 over-expressing MCF-7 (MT vs AT)

source_name: tamoxifen treated MCF-7 cells


title: JVM-2 DMSO 0.025% DMSO 20hr

description: Gene expression data from JVM-2 cells treated with DMSO


title: Control vs Estrogen treated MCF-7 cells (MC vs ME)

source_name: Estrogen treated MCF-7 Cells

value: Estrogen

source_name: Control Treated MCF-7 cells


title: control vsTamoxifen treated MCF-7 cells (MC vs MT)


title: Embryo_Mismatch.Morpholino_High_rep4 Reference

value: 30% epiboly


title: Z-138 NTC 0ng/ml DOX 7d

description: Gene expression data from Z-138 NTC cells treated with 0ng/ml DOX for 7 days

value: 0ng/ml DOX


title: Embryo_Control.Morpholino_Low_rep1 Reference


title: Embryo_Mismatch.Morpholino_High_rep5 Reference


title: Embryo_Control.Morpholino_Low_rep1

source_name: Control morpholino 0.5mM injected replicate 1


title: Z-138 AFN700 5uM AFN700 20hr

description: Gene expression data from Z-138 cells treated with 5uM AFN700

source_name: Z-138 cells

value: Z-138 cells


title: Control treated MCF-7 cells vs Control treated Akt3 over-expressing MCF-7 cells (MC vs AC)

value: Akt3 over-expressing MCF-7


title: Embryo_Mismatch.Morpholino_High_rep5

description: 1nl of mismatch morpholino (2mM) was injected into 30% epiboly zebrafish embryos

source_name: Mismatch morpholino 2mM injected replicate 5

value: Mismatch morpholino

value: high


title: Maver-1 AFN700 5uM AFN700 20hr

description: Gene expression data from Maver-1 cells treated with 5uM AFN700

source_name: Maver-1 cells

value: Maver-1 cells


title: Z-138 DMSO 0.025% DMSO 20hr

description: Gene expression data from Z-138 cells treated with DMSO


title: NFP2_CSCCOSM_DP7_24 with array type Medicago from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description:
medicago truncatula (a17)  - harvest date: 31-01-12
Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: roots - - In vitro conditions on liquid M medium - 16h light 8h dark 22°C

treatment_protocol: Name:A17_NFP2_CSCCOSMEAN_DP7 - compound based treatment - compound addition,csc cos mean dp7:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-2 A17 were grown in vitro on liquid M medium. The roots were then treated with CSC COS mean DP7 and then harvested after 4 hours of incubation.

tag: genotype/variation

value: nfp-2 mutant

value: CSCCOS


title: Maver-1 DMSO 0.025% DMSO 20hr

description: Gene expression data from Maver-1 cells treated with DMSO

value: insensitive


title: A17_NFP1_MOCK_12 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_NFP1_MOCK - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-1 A17 were grown in vitro on liquid M medium. The roots were then treated with sterile water and then harvested after 4 hours of incubation.

value: nfp-1 mutant

value: mock


title: A17_NFP1_MOCK_11 with array type Medicago from Affymetrix

description:
medicago truncatula (a17)  - harvest date: 24-01-12
Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants.


title: Estrogen treated MCF-7 cells vs Estrogen treated Akt3 over-expressing MCF-7 cells (ME vs AE)

value: Akt3 over-expressing cells

source_name: Estrogen treated MCF-7 cells


title: NFP2_CSCCOSM_DP7_23 with array type Medicago from Affymetrix


title: Embryo_Mismatch.Morpholino_High_rep4

source_name: Mismatch morpholino 2mM injected replicate 4


title: Embryo_Mismatch.Morpholino_High_rep3

source_name: Mismatch morpholino 2mM injected replicate 3


title: Granta-519 AFN700 5uM AFN700 20hr

description: Gene expression data from Granta-519 cells treated with 5uM AFN700

source_name: GRANTA-519 cells

value: 5uM AFN700

value: GRANTA-519 cells


title: Granta-519 DMSO 0.025% DMSO 20hr

description: Gene expression data from Granta-519 cells treated with DMSO


title: Hbl-2 DMSO 0.025% DMSO 20hr

description: Gene expression data from Hbl-2 cells treated with DMSO

source_name: HBL-2 cells

value: HBL-2 cells


title: SP49 AFN700 5uM AFN700 20hr

description: Gene expression data from SP49 cells treated with 5uM AFN700

source_name: SP49 cells

value: sensitive

value: SP49 cells


title: A17_WTA_ECP2F1_8 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_WTA_ECP2_F1 - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old WT A17 were grown in vitro on liquid M medium. The roots were then treated with CSC COS mean DP7 and then harvested after 4 hours of incubation.

value: WT


title: Embryo_Mismatch.Morpholino_High_rep3 Reference

source_name: Common Reference

value: 30% epiboly


title: A17_WTM_3 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_WT_MOCK - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old WT A17 were grown in vitro on liquid M medium. The roots were then treated with sterile water and then harvested after 4 hours of incubation.


title: NFP2_CSCCOSM_DP7_22 with array type Medicago from Affymetrix

description:
medicago truncatula (a17)  - harvest date: 17-01-12
Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants.


title: SP49 DMSO 0.025% DMSO 20hr

description: Gene expression data from SP49 cells treated with DMSO


title: Rec-1 DMSO 0.025% DMSO 20hr

description: Gene expression data from Rec-1 cells treated with DMSO

source_name: REC-1 cells

value: REC-1 cells


title: Embryo_Mismatch.Morpholino_Medium_rep5 Reference

description: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample.


title: Hbl-2 AFN700 5uM AFN700 20hr

description: Gene expression data from Hbl-2 cells treated with 5uM AFN700


title: A17_WTA_ECP2F1_7 with array type Medicago from Affymetrix

growth_protocol: roots - In vitro conditions on liquid M medium - 16h light 8h dark 22°C


title: NFP2_MOCK_21 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_NFP2_MOCK - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-2 A17 were grown in vitro on liquid M medium. The roots were then treated with sterile water and then harvested after 4 hours of incubation.


title: Embryo_Mismatch.Morpholino_High_rep1

source_name: Mismatch morpholino 2mM injected replicate 1

value: Mismatch morpholino


title: Embryo_Mismatch.Morpholino_High_rep2 Reference


title: Embryo_Mismatch.Morpholino_High_rep1 Reference


title: Rec-1 AFN700 5uM AFN700 20hr

description: Gene expression data from Rec-1 cells treated with 5uM AFN700


title: Embryo_Mismatch.Morpholino_Medium_rep5

description: 1nl of mismatch morpholino (1mM) was injected into 30% epiboly zebrafish embryos

source_name: Mismatch morpholino 1mM injected replicate 5

value: medium


title: Embryo_Mismatch.Morpholino_High_rep2

description: 1nl of mismatch morpholino (2mM) was injected into 30% epiboly zebrafish embryos

source_name: Mismatch morpholino 2mM injected replicate 2

value: high


title: NFP2_MOCK_20 with array type Medicago from Affymetrix

value: nfp-2 mutant


title: A17_NFP2A_ECP2F1_27 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_NFP2A_ECP2F1 - compound based treatment - compound addition,a. euteiches chitosaccharides p2f1:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-2 A17 were grown in vitro on liquid M medium. The roots were then treated with A. euteiches chitosaccharides P2F1 and then harvested after 4 hours of incubation.


title: A17_WTCSC_CM_DP7_6 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_WT_CSC_COSMEAN_DP7 - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old WT A17 were grown in vitro on liquid M medium. The roots were then treated with CSC COS mean DP7 and then harvested after 4 hours of incubation.

value: CSCCOS


title: Co-cultured_human_OTSCC_cells_rep2

city: Oulu

first: Jussi

last: Vuoristo

address: Aapistie 5

department: Biocenter Oulu

country: Finland

institute: University of Oulu

hyb_protocol: A hybridization cocktail was prepared that contains the fragmented cRNA, probe array controls, BSA, and herring sperm DNA. The cRNA is hybridized to the oligonucleotide probes on the array for 16 hours at 45C.

scan_protocol: Arrays were scanned on the GeneChip Scanner 3000 7G

data_processing: dChip, Model-based expression, Normalization probe selecting method: invariant set

source_name: human oral tongue squamous cell carcinoma (OTSCC) cells, co-cultured with human bone marrow-derived multipotent mesenchymal stromal cells

label_protocol: Affymetrix 3' IVT Express Kit

extract_protocol: Qiagen Rneasy Mini Kit

tag: cell

value: cancer cell co-culture


title: Co-cultured_human_OTSCC_cells_rep1


title: Embryo_Traf6.Morpholino-2_High_rep5

description: 1nl of Traf6 ATG morpholino 2 (2mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 2 2mM injected replicate 5

value: Traf6 ATG morpholino 2


title: NFP2_MOCK_19 with array type Medicago from Affymetrix

value: mock


title: Embryo_Traf6.Morpholino-2_High_rep5 Reference


title: A17_NFP1_MOCK_10 with array type Medicago from Affymetrix

value: nfp-1 mutant


title: A17_NFP1A_ECP2F1_18 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_NFP1A_ECP2F1 - compound based treatment - compound addition,a. euteiches chitosaccharides p2f1:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-1 A17 were grown in vitro on liquid M medium. The roots were then treated with A. euteiches chitosaccharides P2F1 and then harvested after 4 hours of incubation.


title: Embryo_Traf6.Morpholino-2_High_rep3 Reference


title: Maver-1 0.025% DMSO 3h rep2

growth_protocol: Jeko-1 and Mino cells were cultured in 20% FBS RPMI; Z-138 and Maver-1 cells were cultured in 10% FBS RPMI.

treatment_protocol: 3 million cells were resuspended in 3ml of fresh media in 6 well dishes.  The next day, DMSO or Sotrastaurin was added for 3hrs.

tag: mantle cell lymphoma (mcl) line

tag: stn sensitivity

value: insensitive

tag: agent


title: Embryo_Traf6.Morpholino-2_High_rep2 Reference


title: Embryo_Traf6.Morpholino-2_High_rep3

source_name: Traf6 ATG morpholino 2 2mM injected replicate 3


title: Maver-1 0.025% DMSO 3h rep1


title: Control vs Estrogen treated Akt3 over-expressing MCF-7 cells (AC vs AE)

tag: cell line

value: Akt3 over-expressing MCF-7 cells

value: Estrogen

source_name: Control treated Akt3 over-expressing MCF-7 cells

value: Akt-3 over-expressing MCF-7 cells

value: Control


title: Embryo_Traf6.Morpholino-2_High_rep4

source_name: Traf6 ATG morpholino 2 2mM injected replicate 4

tag: developmental stage


title: A17_NFP1A_ECP2F1_17 with array type Medicago from Affymetrix


title: Embryo_Traf6.Morpholino-2_High_rep1

source_name: Traf6 ATG morpholino 2 2mM injected replicate 1

tag: dose


title: Monocultured_human_OTSCC_cells_rep1

source_name: human oral tongue squamous cell carcinoma (OTSCC) cells, monoculture

value: cancer cell monoculture


title: Maver-1 2.5uM AEB071  3h rep2

description: Gene expression data from Maver-1 cells treated with 2.5uM Sotrastaurin

source_name: Maver-1 cells

value: 2.5uM Sotrastaurin


title: Embryo_Traf6.Morpholino-2_High_rep4 Reference

value: 30% epiboly


title: A17_NFP2A_ECP2F1_25 with array type Medicago from Affymetrix


title: Maver-1 2.5uM AEB071  3h rep1


title: Z138 0.025% DMSO 3h rep2

description: Gene expression data from Z-138 cells treated with DMSO

source_name: Z-138 cells


title: A17_WTCSC_CM_DP7_4 with array type Medicago from Affymetrix

value: WT


title: A17_WTCSC_CM_DP7_5 with array type Medicago from Affymetrix


title: Embryo_Traf6.Morpholino-2_High_rep1 Reference


title: Embryo_Traf6.Morpholino-2_High_rep2

source_name: Traf6 ATG morpholino 2 2mM injected replicate 2


title: Z138 2.5uM AEB071  3h rep1

description: Gene expression data from Z-138 cells treated with 2.5uM Sotrastaurin


title: A17_WTM_2 with array type Medicago from Affymetrix

description:
medicago truncatula (a17)  - harvest date: 24-01-12
Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants.


title: Z138 2.5uM AEB071  3h rep2


title: A17_NFP2A_ECP2F1_26 with array type Medicago from Affymetrix


title: Embryo_Traf6.Morpholino-2_Medium_rep5 Reference


title: A17_WTA_ECP2F1_9 with array type Medicago from Affymetrix

description:
medicago truncatula (a17)  - harvest date: 31-01-12
Aphanomyces euteiches is a major legume parasite related to S. parasitica. Analysis of its cell wall showed the presence of an unsusual high content in GlcNAc, representing 10% of the total carbohydrates. Interestingly, this compound does not form crystalline chitin, but amorphous chitosaccharides. The aim goal of this study is to compare the response to a preparation of crab shell chitin chitooligosaccharides with a mean DP of 7 and to A.euteiches chitosaccharides at a transcriptomic level. This comparison will be done on Medicago truncatula wild type compared to the nfp-1 and nfp-2 mutants.


title: A17_WTM_1 with array type Medicago from Affymetrix


title: A17_NFP1A_ECP2F1_16 with array type Medicago from Affymetrix


title: A17_NFP1_CSCCOSM_DP7_13 with array type Medicago from Affymetrix

treatment_protocol: Name:A17_NFP1_CSCCOSMEAN_DP7 - compound based treatment - compound addition,mock:time 4hour . Reference protocol or description Sample treatment protocol : Nine 7-day-old nfp-1 A17 were grown in vitro on liquid M medium. The roots were then treated with CSC COS mean DP7 and then harvested after 4 hours of incubation.


title: Mino 0.025% DMSO 3h rep2

description: Gene expression data from Mino cells treated with DMSO

source_name: Mino cells

value: Mino

value: sensitive


title: Embryo_Traf6.Morpholino-2_Medium_rep4

description: 1nl of Traf6 ATG morpholino 2 (1mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 2 1mM injected replicate 4

value: medium


title: Embryo_Traf6.Morpholino-2_Medium_rep3 Reference

source_name: Common Reference


title: Z138 0.025% DMSO 3h rep1


title: A17_NFP1_CSCCOSM_DP7_14 with array type Medicago from Affymetrix

value: CSCCOS


title: Mino 2.5uM AEB071  3h rep1

description: Gene expression data from Mino cells treated with 2.5uM Sotrastaurin


title: A17_NFP1_CSCCOSM_DP7_15 with array type Medicago from Affymetrix


title: Embryo_Traf6.Morpholino-2_Medium_rep4 Reference


title: Mino 0.025% DMSO 3h rep1


title: Embryo_Traf6.Morpholino-2_Medium_rep2 Reference


title: Jeko-1  2.5uM AEB071  3h rep1

description: Gene expression data from Jeko-1 cells treated with 2.5uM Sotrastaurin

source_name: Jeko-1 cells


title: Embryo_Traf6.Morpholino-2_Medium_rep3

source_name: Traf6 ATG morpholino 2 1mM injected replicate 3


title: Embryo_Traf6.Morpholino-2_Medium_rep2

source_name: Traf6 ATG morpholino 2 1mM injected replicate 2


title: wt_G0_1day_rep2

city: Onna-son

first: Mizuki

last: Shimanuki

state: Okinawa

department: Research Support Division

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

description:
071005_wt-G0
PolyA RNA
Gene expression profile under 24 hours nitrogen-starved condition in EMM2-N medium at 26ºC.

hyb_protocol: Labeled targets were hybridized with the probes at 45˚C, while rotating at 60 rpm, for 16 hours, in GeneChip® Hybridization Oven 640.

scan_protocol: Microarrays were washed, stained and scanned using GeneChip® Fluidics Station 450 and GeneChip® Scanner 3000 according to the Affymetrix standard protocol.

data_processing: Results were quantified and analyzed using MicroArray Suite 5.0 and GCOS software.

organism: Schizosaccharomyces pombe

source_name: wild type cells at 1 day in G0 phase

label_protocol: The poly-A RNA (2mg) was labeled by GeneChip® One-CycleTarget Labeling and Control Reagents, according to the Affymetrix sample processing protocol.

growth_protocol:
Proliferating condition: A single colony of S. pombe cells on a YE plate was inoculated into EMM2 liquid medium to grow to 2x10^6 cell/ml at 26˚C.
Quiescent condition: After the same procedures for the proliferating condition, cells were washed twice in EMM2-N (EMM2 depleted of nitrogen sources), transferred to EMM2-N with the concentration of 2x10^7 cell/ml and further incubated at 26˚C for 24 hr.

extract_protocol: Total RNA was isolated by acid phenol methods described in http://www.sanger.ac.uk/PostGenomics/S_pombe/, and then polyA-RNA was purified by Oligotex-dT30<super>mRNA purification kit (Takara).

tag: strain/background

value: wild type

tag: mating type

value: h-

tag: cell cycle phase

tag: medium


title: Jeko-1  0.025% DMSO 3h rep2

description: Gene expression data from Jeko-1 cells treated with DMSO


title: klf1_G0_1day_rep2

description:
071005_klf1-G0
PolyA RNA
Gene expression profile under 24 hours nitrogen-starved condition in EMM2-N medium at 26ºC.

source_name: klf1 gene deletion mutant cells at 1 day in G0 phase


title: wt_VE_rep1

description:
070809_wt-VE
PolyA RNA
Gene expression profile under exponentially growing in EMM2 medium at 26ºC.

source_name: wild type cells in vegetative cell cycle

value: vegetative


title: wt_VE_rep2

description:
071005_wt-VE
PolyA RNA
Gene expression profile under exponentially growing in EMM2 medium at 26ºC.


title: Jeko-1  2.5uM AEB071  3h rep2


title: Embryo_Traf6.Morpholino-2_Medium_rep1

source_name: Traf6 ATG morpholino 2 1mM injected replicate 1

value: Traf6 ATG morpholino 2


title: klf1_VE_rep2

description:
071005_klf1-VE
PolyA RNA
Gene expression profile under exponentially growing in EMM2 medium at 26ºC.

source_name: klf1 gene deletion mutant cells in vegetative cell cycle


title: Jeko-1  0.025% DMSO 3h rep1


title: Embryo_Traf6.Morpholino-2_Medium_rep5

source_name: Traf6 ATG morpholino 2 1mM injected replicate 5


title: Embryo_Traf6.Morpholino-2_Medium_rep1 Reference

description: The  CR (common reference) was composed by combining 1 ug of cRNA from each sample.


title: klf1_VE_rep1

description:
070809_klf1D-VE
PolyA RNA
Gene expression profile under exponentially growing in EMM2 medium at 26ºC.


title: Embryo_Traf6.Morpholino-2_Low_rep5 Reference


title: Embryo_Traf6.Morpholino-2_Low_rep4 Reference


title: Mino 2.5uM AEB071  3h rep2


title: ML_NF6

city: Sheffield

first: Johanna

last: Thurlow

address: Addison Bldg, Western Bank

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from fibroblasts

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix U133 plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix 3000 Scanner

data_processing: CEL file data was normalized using Robust Multichip Average expression summary (RMAexpress; http://rmaexpress.bmbolstad.com/)

source_name: normal fibroblasts (monolayer culture)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2005-2009 Affymetrix)

growth_protocol: Primary cells derived from patients / healthy volunteers after informed consent were maintained in 3D collagen I biomatrices or as monlayers in DMEM with 5% FCS

extract_protocol: RNA was isolated using RNA STAT (Biogenesis) according to the manufacturer's instructions

tag: tissue

value: normal

tag: site

value: alveolar mucosa retromolar area

tag: age

tag: Sex

value: male


title: Meis1-WT LSK 2

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

hyb_protocol: 1.5 ug of Cy3-labelled cDNA was hybridized to Agilent Whole Mouse Genome Oligo Microarrays (4 x 44K) 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: KSL cells from wild type 2

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 10 ng RNA using the WT-Ovation Pico RNA Amplification System (Agilent) and Genomic Enzymatic Labeling kit (Agilent) according to the manufacturer's instructions.

extract_protocol: KSL cells were sorted using FACSAreaII and antibodies. Total RNA was isolated using the Qiagen RNeasy micro kit (Qiagen, Hilden, Germany) according to manufacturer's protocol.

treatment_protocol: Mx1-Cre positive Meis1fl/fl and Nx1-Cre negative Meis1fl/fl mice mice at the age of 4-8 weeks were injected i.p. with 1.5 ug/g of poly(I:C) 4 times at 1-day interval to activate interferon gene.

tag: genotype

tag: cell type

value: KSL hematopoietic cells

tag: genetic background


title: Embryo_Traf6.Morpholino-2_Low_rep5

description: 1nl of Traf6 ATG morpholino 2 (0.5mM) was injected into 30% epiboly zebrafish embryos

source_name: Traf6 ATG morpholino 2 0.5mM injected replicate 5

tag: treatment

value: low


title: Meis1-WT LSK 1

source_name: KSL cells from wild type 1


title: klf1_G0_1day_rep1

description:
070809_klf1D-G0
PolyA RNA
Gene expression profile under 24 hours nitrogen-starved condition in EMM2-N medium at 26ºC.

tag: genotype/variation


title: FLU  100µM sample of Hepatocytes in microfluidic biochip - 27

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Rat Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were RMA normalized  and  analysed with Partek Genomic Suit

organism: Rattus norvegicus

source_name: FLU  100µM sample of Hepatocytes

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Freshly isolated hepatocytes were cultured in first 24 hours in a seeding medium composed of William’s E GLutamax medium (Fisher Scientific, Illkirch, France) supplemented with bovine insulin (5µg/ml, Sigma-Aldrich, Saint-Quentin Fallavier, France) and bovine fetal  serum (10%). To enhance cell adhesion, the inner surface of the biochips were coated with rat tail type 1 (0.3mg/ml, BD Biosciences) prepared in phosphate-buffered saline (PBS) for 1 hour at 37°C in a humidiﬁed atmosphere supplied with 5% CO2. After washing with seeding medium, the cells were inoculated inside the biochips at 0.5×106 cells per biochip (i.e 0.25×106 per cm²).

extract_protocol: Total RNAs were extracted using the Nucleospin® RNA XS isolation kit (Macherey-Nagel EURL, Hoerdt, France). The quantity and quality of RNAs were evaluated using th a Nanodrop ND-1000 spectrophotometer (Nyxor Biotech,Paris, France) and the Agilent 2100 Bioanalyzer (using the Agilent RNA 6000 Nano and Pico kits), respectively. All RNA samples had an RNA Integrity Number of more than 8 (between 9.3 and 10). cDNA were synthesized from 500ng of total RNA with oligodT Primer, using SuperScript II (Life Technologies), according to the manufacturer’s protocol.

treatment_protocol: After the 24h adhesion period, cells were cultured in DMEM-F12 medium (Fisher Scientific) supplemented with 15mM Hepes , 1.2g/L sodium bicarbonate in (Sigma-Aldrich), 6.25µg/ml insulin-transferrin-selenium solution (Becton Dickinson, Biosciences, Le Pont de Claix, France), 100units/ml penicillin and 100mg/ml streptomycin (Fisher Scientific,). IDCCM is prepared for the perfusion phase. Medium reservoirs at the entrance and outlet were filled with a volume of 2mL of culture medium to ensure the correct medium supply during dynamic culture resulting in a total volume of 4mL for each biochip. Tflutamide were loaded at 10 and 100µM. Then, the polytetrafluoroethylene (PTFE) tubes were connected to the fluidic cover of the IDCCM box and to the peristaltic pump. PTFE tubes were used to prevent as much as possible the loss of chemical compounds through diffusion or adsorption to the tubing used in the fluidic circuit. The entire system (pump and IDCCM box with the biochips) was placed into the incubator (32°C, 5% CO2) and the perfusion started (25µl/min flow rate).

value: Hepatocytes


title: wt_G0_1day_rep1

description:
070809_wt-G0
PolyA RNA
Gene expression profile under 24 hours nitrogen-starved condition in EMM2-N medium at 26ºC.


title: Monocultured_human_OTSCC_cells_rep2

source_name: human oral tongue squamous cell carcinoma (OTSCC) cells, monoculture

tag: cell

value: cancer cell monoculture


title: ML_CAF4

description: Gene expression data from fibroblasts

source_name: cancer associated fibroblasts (monolayer culture)

value: oral squamous cell carcinoma

value: lingual mucosa


title: Embryo_Traf6.Morpholino-2_Low_rep4

source_name: Traf6 ATG morpholino 2 0.5mM injected replicate 4

value: 30% epiboly


title: CAF7

description: Gene expression data from fibroblasts

source_name: cancer associated fibroblasts (3D culture)

value: retromolar / base of tongue


title: Meis1-KO LSK 2

source_name: KSL cells from Meis1 KO 2

value: Meis1 KO


title: ML_NF5

description: Gene expression data from fibroblasts


title: CAF6

description: Gene expression data from fibroblasts


title: Meis1-KO LSK 1

source_name: KSL cells from Meis1 KO 1


title: ML_CAF3

description: Gene expression data from fibroblasts

value: alveolar mucosa / floor of mouth

value: female


title: CAF4

description: Gene expression data from fibroblasts


title: FLU  100µM sample of Hepatocytes in microfluidic biochip - 26


title: FLU  100µM sample of Hepatocytes in microfluidic biochip - 16


title: CAF3

description: Gene expression data from fibroblasts


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 24

source_name: FLU  10µM sample of Hepatocytes


title: 546693A11 - myb118_BR2 vs col_BR2

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: What are the genes over expressed or down regulated in seeds in response to a myb118 mutation?

hyb_protocol: col_BR2 Cy5 / myb118_BR2 Cy3 : 30pmol.

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

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

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media=Soil hygrometry=variable (greenhouse)  Temperature=18°C night/21°C day Light=16h/8h light/dark

extract_protocol: col_BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: wild type

tag: harvest date

extract_protocol: myb118_BR2:10ug. (Qiagen_RNeasy.pdf)

value: myb118 mutant


title: DF3

description: Gene expression data from fibroblasts

source_name: dysplasia fibroblasts (3D culture)

value: dysplasia

value: lateral border tongue


title: Ctrl DMSO sample of Hepatocytes in microfluidic biochip - 22

source_name: Ctrl DMSO sample of Hepatocytes


title: CAF5

description: Gene expression data from fibroblasts

value: male


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 25


title: NF5

description: Gene expression data from fibroblasts

source_name: normal fibroblasts (3D culture)

value: normal

value: alveolar mucosa retromolar area


title: CAF2

description: Gene expression data from fibroblasts

value: buccal mucosa


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 14

value: Hepatocytes


title: 546693A10 - col_BR2 vs myb118_BR2

hyb_protocol: myb118_BR2 Cy5 / col_BR2 Cy3 : 30pmol.


title: 546693A05 - col_BR1 vs T16_BR1

hyb_protocol: T16_BR1 Cy5 / col_BR1 Cy3 : 30pmol.

extract_protocol: T16_BR1:10ug. (Qiagen_RNeasy.pdf)

value: myb118 antisense line T16

extract_protocol: col_BR1:10ug. (Qiagen_RNeasy.pdf)


title: FLU  100µM sample of Hepatocytes in microfluidic biochip - 15


title: 546693A06 - T16_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / T16_BR1 Cy3 : 30pmol.


title: Ctrl DMSO sample of Hepatocytes in microfluidic biochip - 21


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 23


title: DF2

description: Gene expression data from fibroblasts

value: lingual mucosa


title: 546693A07 - col_BR2 vs T16_BR2

hyb_protocol: T16_BR2 Cy5 / col_BR2 Cy3 : 30pmol.

extract_protocol: T16_BR2:10ug. (Qiagen_RNeasy.pdf)


title: CAF1

description: Gene expression data from fibroblasts

value: oral squamous cell carcinoma


title: DF1

description: Gene expression data from fibroblasts


title: DF4

description: Gene expression data from fibroblasts

value: floor of mouth


title: 546693A08 - T16_BR2 vs col_BR2

hyb_protocol: col_BR2 Cy5 / T16_BR2 Cy3 : 30pmol.


title: 550542A12 - myb118_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / myb118_BR1 Cy3 : 30pmol.

extract_protocol: myb118_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 546693A04 - OE3_BR2 vs col_BR2

hyb_protocol: col_BR2 Cy5 / OE3_BR2 Cy3 : 30pmol.

extract_protocol: OE3_BR2:10ug. (Qiagen_RNeasy.pdf)

value: myb118 antisense line 0E3


title: Ctrl DMSO sample of Hepatocytes in microfluidic biochip - 20


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 13


title: NF3

description: Gene expression data from fibroblasts


title: Ctrl DMSO sample of Hepatocytes in microfluidic biochip - 11


title: FLU  10µM sample of Hepatocytes in microfluidic biochip - 12


title: Ctrl DMSO sample of Hepatocytes in microfluidic biochip - 10


title: NF4

description: Gene expression data from fibroblasts


title: 546693A09 - col_BR1 vs myb118_BR1

hyb_protocol: myb118_BR1 Cy5 / col_BR1 Cy3 : 30pmol.


title: 546693A03 - col_BR2 vs OE3_BR2

hyb_protocol: OE3_BR2 Cy5 / col_BR2 Cy3 : 30pmol.


title: NF2

description: Gene expression data from fibroblasts


title: 546693A02 - OE3_BR1 vs col_BR1

hyb_protocol: col_BR1 Cy5 / OE3_BR1 Cy3 : 30pmol.

extract_protocol: OE3_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 546693A01 - col_BR1 vs OE3_BR1

hyb_protocol: OE3_BR1 Cy5 / col_BR1 Cy3 : 30pmol.


title: NF1

description: Gene expression data from fibroblasts

value: palatal mucosa


title: HiPS-GM00285#3

status: Public on Nov 26 2013

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

hyb_protocol: The labeled DNA is prepared for hybridization with human Cot1 DNA and placed on the Sureprint G3 human CGH + SNP 4x180k microarray and hybridized at 65ºC for ~ 24hours.

scan_protocol: The arrays are washed and scanned at 3μM resolution on an Agilent G2565CA High Resolution Scanner.

data_processing: Data was processed through Agilent’s Feature Extraction software version 11.0.1.1 using the protocol CGH_1100_Jul11 and the 029830_D_F_20100916 grid file.

label_protocol: One μg of DNA is fragmented with restriction enzymes and the test DNA labeled with Cyanine 5dUTP and reference DNA with Cyanine 3-dUTP by ExoKlenow fragment. Labeled DNA is then purified using Millipore Amicon Ultracel-30 filters and the labeling efficiency determined by the NanoDrop spectrophotometer (see Table 2).

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from GM00285 and GM05563 fibroblasts and iPSCs using the Qiagen QIAmp DNA micro Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: karyotype

value: Uniparental Disomy 13

source_name: Control-Male 4

value: Normal


title: Glioblastoma gbm-0547

status: Public on Nov 07 2013

city: Beijing

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Data were acquired using the Agilent G2565BA Microarray Scanner System and Agilent Feature Extraction Software (version 9.1).

data_processing: Probe intensities were normalized using GeneSpring GX 11.0.

source_name: Human glioblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA from frozen tumor samples was extracted using the mirVana miRNA Isolation kit (Ambion) according to the manufacturers protocol. RNA concentration and quality were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

tag: individual

value: Chinese patient

value: brain tumor

tag: tumor grade

value: WHO grade 4

tag: disease state

value: glioblastoma

tag: patient age

tag: patient gender


title: Glioblastoma gbm-0593

tag: tissue

value: male


title: H3K79me3 (Abcam ab2621 lot1) Kc167 D.melanogaster Input Rep2

status: Public on Oct 31 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: H3K79me3 (Abcam ab2621 lot1) Kc Input expt.1776 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: embryo-derived cell-line

tag: developmental stage

value: late embryonic stage

value: se/e

value: Female


title: Glioblastoma gbm-0439

value: female


title: HiPS-GM05563#1

source_name: Control-Male 5


title: Glioblastoma gbm-0557


title: Glioblastoma gbm-0311


title: HiPS-GM00285#1

source_name: Control-Male 3


title: HDF-GM00285

value: Ring chromosome 13

source_name: Control-Male 1


title: HDF-GM05563

source_name: Control-Male 2


title: Glioblastoma gbm-0444


title: Glioblastoma gbm-0401


title: Glioblastoma gbm-0380


title: Glioblastoma gbm-0168


title: Glioblastoma gbm-0225


title: H3K79me3 (Abcam ab2621 lot1) Kc167 D.melanogaster ChIP Rep2

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K79me3 (Abcam ab2621 lot 1);target name: H3K79me3;host: Rabbit;antigen: synthetic peptide containing the tri-methylated K79 residue of Histone H3.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab2621;reference: http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab2621.html;short description: Rabbit polyclonal antibody raised against a synthetic peptide containing the tri-methylated K79 residue of Histone H3.;channel ch1 is input DNA;

source_name: H3K79me3 (Abcam ab2621 lot1) Kc ChIP expt.2052 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

tag: genotype

tag: Sex


title: control group

status: Public on Nov 05 2013

city: Haidian District

first: Zhongquan

last: Dai

state: Beijing

address: No. 26 Beiqing Road

institute: Astronaut Research and training Center

description: Gene expression data from rat soleus muscle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rattus Norvegicus Genome Array. GeneChips were washed and stained in the Wash and Stain Kit of Affymetrix, P/N 900720.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner Scanner 3000: Affymetrix, P/N 00-00212.

data_processing:
Use the free miRNA QC Tool software for data summarization, normalization, and quality control.
miRNA QC Tool software

source_name: Soleus muscle at 7 days of control group

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

growth_protocol: All animal procedures were carried out in accordance with the Guidelines for Animal Care and Experimentation of the Astronaut Research and Training Center.Feed rats normally.

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

treatment_protocol: Briefly, the rats were suspended at an approximately 30° angle by taping the tail to mimic unloading condition.

value: control

tag: time

value: soleus muscle

value: white and Sprague-Dawley rats

tag: age

value: 8 weeks of age


title: H3K79me3 (Abcam ab2621 lot1) Kc167 D.melanogaster Input Rep1

description: channel ch1 is input DNA;

source_name: H3K79me3 (Abcam ab2621 lot1) Kc Input expt.1756 channel_1


title: Glioblastoma gbm-0419


title: Glioblastoma gbm-0366


title: H3K79me3 (Abcam ab2621 lot1) Kc167 D.melanogaster ChIP Rep1

source_name: H3K79me3 (Abcam ab2621 lot1) Kc ChIP expt.2051 channel_1


title: Glioblastoma gbm-0308


title: Glioblastoma gbm-0346


title: Glioblastoma gbm-0011


title: Glioblastoma gbm-0203


title: Glioblastoma gbm-0156


title: Glioblastoma gbm-0126


title: Glioblastoma gbm-0255


title: Glioblastoma gbm-0178


title: Genomic DNA from brain metastasis 8

status: Public on Sep 19 2013

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
MBM-8
Melanoma brain metastasis-8
Cell line derived from patient.

hyb_protocol: Sodium bisulfite modification (SBM) was performed on 1µg of gDNA using the Zymo EZ DNA methylation kit (Zymo Research). An aliquot of SBM-gDNA was analyzed by MethyLight-based quality control to test bisulfite completeness. After correction of SBM-gDNA amount, 200 ng of SBM-gDNA was whole-genome amplified and enzymatically fragmented. Finally, the gDNA was hybridized to Infinium Human Methylation 450K BeadChips.

scan_protocol: The chips were scanned with Illumina iScan using the manufacturer's recommended settings.

data_processing: Data was extracted using the R package methylumi on Bioconductor.

label: Cy5 and Cy3

source_name: Melanoma brain metastasis

label_protocol: Standard Illumina Protocol, run at USC core services.

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 (Life Technologies-Bethesda Research Laboratories) supplemented with 10% fetal bovine serum.

extract_protocol: gDNA was extracted from cell lines via the Qiagen DNeasy Kit according to standard instructions and from tissue after microdissection from 10 μm-thick paraffin-embedded archival tissue using Qiagen DNeasy Kit according to standard instructions.

value: melanoma brain metastasis

tag: disease

value: melanoma

tag: clinical stage

value: IV


title: Genomic DNA from brain metastasis 10

description:
MBM-10
Melanoma brain metastasis-10
Tissue


title: Genomic DNA from brain metastasis 5

description:
MBM-5
Melanoma brain metastasis-5
Cell line derived from patient.


title: Genomic DNA from brain metastasis 16

description:
MBM-16
Melanoma brain metastasis-16
Tissue


title: Genomic DNA from brain metastasis 11

description:
MBM-11
Melanoma brain metastasis-11
Tissue


title: Genomic DNA from brain metastasis 2

description:
MBM-2
Melanoma brain metastasis-2
Cell line derived from patient.


title: Genomic DNA from brain metastasis 14

description:
MBM-14
Melanoma brain metastasis-14
Tissue


title: Genomic DNA from lymph node metastasis 4

description:
LNM-4
Melanoma lymph node metastasis-4
Cell line derived from patient.

source_name: Melanoma lymph node metastasis

value: melanoma lymph node metastasis

value: III


title: Genomic DNA from brain metastasis 13

description:
MBM-13
Melanoma brain metastasis-13
Tissue


title: Genomic DNA from lymph node metastasis 12

description:
LNM-12
Melanoma lymph node metastasis-12
Cell line derived from patient.


title: Genomic DNA from brain metastasis 6

description:
MBM-6
Melanoma brain metastasis-6
Cell line derived from patient.


title: Genomic DNA from lymph node metastasis 6

description:
LNM-6
Melanoma lymph node metastasis-6
Cell line derived from patient.


title: Genomic DNA from lymph node metastasis 16

description:
LNM-16
Melanoma lymph node metastasis-16
Tissue


title: Genomic DNA from lymph node metastasis 7

description:
LNM-7
Melanoma lymph node metastasis-7
Cell line derived from patient.


title: Genomic DNA from brain metastasis 7

description:
MBM-7
Melanoma brain metastasis-7
Cell line derived from patient.


title: Genomic DNA from lymph node metastasis 14

description:
LNM-14
Melanoma lymph node metastasis-14
Tissue


title: Genomic DNA from lymph node metastasis 13

description:
LNM-13
Melanoma lymph node metastasis-13
Cell line derived from patient.


title: Genomic DNA from brain metastasis 1

description:
MBM-1
Melanoma brain metastasis-1
Tissue


title: Genomic DNA from lymph node metastasis 8

description:
LNM-8
Melanoma lymph node metastasis-8
Cell line derived from patient.


title: Genomic DNA from brain metastasis 9

description:
MBM-9
Melanoma brain metastasis-9
Tissue


title: Genomic DNA from lymph node metastasis 10

description:
LNM-10
Melanoma lymph node metastasis-10
Tissue


title: Genomic DNA from lymph node metastasis 17

description:
LNM-17
Melanoma lymph node metastasis-17
Tissue


title: Genomic DNA from lymph node metastasis 11

description:
LNM-11
Melanoma lymph node metastasis-11
Cell line derived from patient.


title: Genomic DNA from brain metastasis 12

description:
MBM-12
Melanoma brain metastasis-12
Tissue


title: Genomic DNA from brain metastasis 15

description:
MBM-15
Melanoma brain metastasis-15
Tissue