title: slide 5 - Hyp Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #5; dye-swap of slide #11

label_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)


title: CNS PNET34 HindIII

status: Public on Aug 22 2011

type: genomic

city: Nottingham

first: Suzanne

last: Miller

state: Nottinghamshire

address: Queen's Medical Centre

department: Human Development

country: United Kingdom

institute: Children's Brain Tumour Research Centre

description: CNS PNET34 HindIII

hyb_protocol: Affymetrix 100K Hybridisation Protocol

scan_protocol: Affymetrix 100K Scanning Protocol

data_processing: GCOS

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain Tumour, CNS PNET34 HindIII

label_protocol: Affymetrix 100K Labeling Protocol

extract_protocol: Phenol/Chloroform Isoamyl Alcohol and PLG tubes

tag: gender

value: male

tag: age

value: 107 months

tag: tumour location

value: Cerebral and Posteria Fossa

tag: metastasis


title: healthy male M(13)

city: Toronto

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: sample: M(13); age-match to F(13)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation in BeadStudio, Methylation Module 3.2

source_name: healthy male

label_protocol: Genomic sample not directly labeled. Detection involves extension of bead-bound probe with a single fluorescent nucleotide.

extract_protocol: Genomic DNA was extracted using phenol-chloroform and Phase Lock Gel according to protocol provided by Eppendorf

treatment_protocol: Genomic DNA was sodium-bisulfite treated using Epitect Bisulfite Kit according to protocol provided by Qiagen

tag: tissue

value: whole blood lymphocytes

tag: sex

tag: age (yrs)


title: slide 26 - Hyp Quin

type: RNA

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

institute: University of Ottawa

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #26

hyb_protocol: Array 900MPX™ Expression Array Detection Kit (Genisphere; see http://www.genisphere.com/array_detection_protocols.html)

scan_protocol: Microarrays were scanned at full speed 10 micron resolution using the ScanArray 5000 XL system (Packard Biosciences/PerkinElmer) using both red and blue lasers. Images were obtained with ScanArray Express software using automatic calibration sensitivity varying PMT gain (PMT starting at 65% for Cy5 and 70% for Cy3) with fixed laser power at 80% and the target intensity set for 90%.

data_processing: Microarray images were analyzed using QuantArray (Packard Biosciences/PerkinElmer) and raw signal intensity values were obtained for duplicate spots of genes. Normalization was performed using LOWESS and GPA methods.

molecule: total RNA

organism: Carassius auratus

source_name: control

extract_protocol: RNA was isolated with the TRIzol reagent (Invitrogen, Burlington, ON, Canada) per the manufacturer's protocol.  Samples were treated with DNase on-column in an RNeasy Mini Plus kit (Qiagen, Mississauga, ON, Canada).  RNA quantity was evaluated using the NanoDrop.  RNA integrity was evaluated using the BioAnalyzer (Agilent);   RIN for each sample was > 8.4.

tag: Sexually mature (mid-May) female adult goldfish received 2 injections at 5 uL/g body weight:

tag: 1) 0.1% DMSO in 0.6% saline, and;

tag: 2) 0.6% saline

tag: Hypothalamus tissue was extracted 5h post-injection.

source_name: quinpirole 2 ug/g

tag: 2) quinpirole (LY 171555) 2 ug/g in 0.6% saline


title: CNS PNET33 HindIII

description: CNS PNET33 HindIII

source_name: Brain Tumour, CNS PNET33 HindIII

value: Cerebral


title: slide 14 - Hyp Quin

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline, and;
2)  0.6% saline (control) or quinpirole (LY 171555) 2 ug/g in 0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #14


title: slide 44 - Hyp SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #44; dye-swap of slide #19

tag: 1) SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;


title: C-PTC-mut LB06-190 312186

type: other

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
C-PTC-mut.3S vs C-PTC-mut.3L
Date:2007/05/09

hyb_protocol: Agilent : 700.0 ng at 48 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : vsn, Intraslide norm. : none, Background norm. : none, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

molecule: other

label_protocol: Invitrogen - Ulysis

extract_protocol: MirVana

tag: label

tag: extract

tag: sample

tag: subject

value: Thyroid

tag: disease

value: safe (CPTC-mut)

value: lesional (CPTC-mut)


title: healthy male M(3)

description: sample: M(3); age-match to F(2)


title: slide 33 - Hyp SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #33


title: healthy male M(4)

description: sample: M(4); age-match to F(4)


title: CNS PNET31 HindIII

description: CNS PNET31 HindIII

source_name: Brain Tumour, CNS PNET31 HindIII

tag: gender

value: female

tag: age

value: 85 months

value: Frontal Lobe


title: CNS PNET36 HindIII

description: CNS PNET36 HindIII

source_name: Brain Tumour, CNS PNET36 HindIII

value: 122 months

tag: tumour location

value: Parietal Lobe

tag: metastasis


source_name: Blood, CNS PNET33 and CNS PNET34 Constitutional HindIII


title: slide 19 - Hyp SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #19


title: Flag-HA-TEAD4 Duplicate 2/2 array 2

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

hyb_protocol: 5µg of Cy3 Labeled Input DNA was combined with 5µg of Cy5 ChIP-DNA and the mix was hybridized to the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent) for 40 hours at 65 degrees in the Agilent hybridization oven rotating at 20rpm. The arrays were washed and processed according to Agilent’s Mammalian ChIP-on-chip Protocol (Version 9.1, August 2006).

scan_protocol: Arrays were scanned on at 5-micron resolution using the Agilent G2505B Scanner and data were extracted using Feature Extraction software v9.1 with ChIP-v1_95_May07 protocol.

data_processing: Raw array data were processed with Agilent's ChIP Analytics software v1.3 following Agilent G4477AA ChIP Analytics 1.3 User Guide

organism: Mus musculus

source_name: C2C12 myoblasts

label_protocol: Input DNA (4µg) was labelled with Cy3 dye and ChIP-DNA (4µg) was labelled with Cy5 using Invitrogen’s BioPrime Array CGH Genomic Labeling System (18095-012) as detailed in the Agilent Mammalian ChIP-on-chip Protocol (Version 9.1, August 2006).

growth_protocol: C2C12 cells were cultured in DMEM with 10% FCS and differentiated by replacing growth medium with differentiation medium containing 2% horse serum

extract_protocol: Cells were crosslinked with formaldehyde 0.4% for 10 min at room temperature and the reaction was stopped by adding glycine to final concentration 0.2M for 10 minutes at room temperature. Fixed cells were rinsed twice with PBS and resuspended in lysis buffer (10 mM EDTA pH 8, 50 mM Tris-HCl pH 8, SDS 1 %). Lysate was sonicated 30 min (30 sec on / 30 sec off) in Diagenode water bath-sonicator and centrifuged at 14000 rpm for 10 min. The cleared supernatant was used immediately in ChIP experiments or stored at -80°C. ChIP was performed  by standard methods as described in the publication.

treatment_protocol: C2C12 cells were infected with a retrotiviral vector expressing Flag-HA-Tagged TEAD4 or with empty control vector and selected in the continouos presence of puromycin. Infected cell populations were then differentiated for 5 days in DMEM medium with 2% horse serum and fixed in 0.4% formaldehyde.

tag: cell line

value: C2C12 cell derived myotubes

tag: sample type

value: Flag-immunoprecipitated Formaldehyde fixed chromatin

tag: antibody

value: anti-Flag

value: Formaldehyde fixed chromatin - input DNA


title: slide 9 - Hyp SKF

description:
Sexually mature female goldfish received 2 injections at 5 uL/g body weight:
1)  0.1% DMSO and 0.6% saline (control) or SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;
2)  0.6% saline
Animals were anaesthetized in MS222, and hypothalamus tissues were harvested for RNA extraction, cDNA synthesis and microarray analysis.
Slide #9

tag: Sexually mature (mid-May) female adult goldfish received 2 injections at 5 uL/g body weight:

tag: 1)  0.1% DMSO in 0.6% saline, and;

tag: 2)  0.6% saline

tag: 1)  SKF 38393 40 ug/g in 0.1% DMSO and 0.6% saline, and;


title: Flag-HA Control array 2


title: healthy female F(33)

description: sample: F(33); age-match to M(35)

source_name: healthy female

tag: tissue

tag: sex

tag: age (yrs)


title: CNS PNET31 Constitutional HindIII

description: CNS PNET31 Constitutional HindIII

source_name: Blood, CNS PNET31 Constitutional HindIII


title: CNS PNET38 HindIII

description: CNS PNET38 HindIII

source_name: Brain Tumour, CNS PNET38 HindIII

value: male

value: 141 months


title: Flag-HA-TEAD4 Duplicate 1/2 array 2


title: Eucommia-3

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

country: Japan

institute: Tokyo University of Marine Science and Technology

description: gene expression data from liver of rat fed a high-fat diet and high-fructose water with Eucommia ulmoides leaves

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized on a Whole Rat Genome Microarray 4x44K (Agilent) and wawhed according to the standard Agilent protocol.

scan_protocol: Microarrays were scanned using a DNA Microarray Scanner (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction 10.1.1.1 (Agilent Technologies) to obtain background subtracted and spatially detrended processed signal intensities.

organism: Rattus norvegicus

label_protocol: Cy3-labeled cRNA were prepared from 500 ng total RNA according to the standard Agilent protocol.

extract_protocol: RNAiso extraction (Takara Bio) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rats fed a high-fat diet and high-fructose water were orally administrated Eucommia ulmoides leaf extract as drinking water. After 5 weeks, rats were anesthetized and killed by exsanguination. Parts of liver of each rat was taken and immediately immersed in RNAlater (Applied Biosystems).

tag: strain

value: Wistar/ST

value: liver


title: healthy female F(21)

description: sample: F(21); age-match to M(19)

value: whole blood lymphocytes


title: Eucommia-4

source_name: liver of rat fed a high-fat diet and high-fructose water with Eucommia ulmoides leaves


title: healthy female F(28)

description: sample: F(28); age-match to M(26)


title: CNS PNET26 HindIII

description: CNS PNET26 HindIII

source_name: Brain Tumour, CNS PNET26 HindIII

value: 61 months


title: healthy female F(16)

description: sample: F(16); age-match to M(16)


title: CNS PNET28 HindIII

description: CNS PNET28 HindIII

source_name: Brain Tumour, CNS PNET28 HindIII

value: 71 months

value: Frontal and Parietal Lobes


title: CNS PNET26 Constitutional HindIII

description: CNS PNET26 Constitutional HindIII

source_name: Blood, CNS PNET26 Constitutional HindIII


title: Eucommia-2


title: healthy female F(15)

description: sample: F(15); age-match to M(14)

value: female


title: CNS PNET24 HindIII

description: CNS PNET24 HindIII

source_name: Brain Tumour, CNS PNET24 HindIII

value: 53 months

value: Temporal and Parietal Lobes


title: Control-4

description: gene expression data from liver of rat fed a high-fat diet and high-fructose water without Eucommia ulmoides leaves


title: Eucommia-1


title: healthy female F(10)

description: sample: F(10); age-match to M(10)


title: Control-2

source_name: liver of rat fed a high-fat diet and high-fructose water without Eucommia ulmoides leaves


title: healthy female F(13)

description: sample: F(13); age-match to M(13)


title: CNS PNET23 HindIII

description: CNS PNET23 HindIII

source_name: Brain Tumour, CNS PNET23 HindIII

value: 51 months


title: healthy female F(8)_2

description: sample: F(8)_2; age-match to M(7)_2


title: Control-3


title: Control-1


title: healthy female F(12)

description: sample: F(12); age-match to M(12)


title: healthy female F(8)_1

description: sample: F(8)_1; age-match to M(7)_1


title: CNS PNET20 HindIII

description: CNS PNET20 HindIII

source_name: Brain Tumour, CNS PNET20 HindIII

value: 32 months

value: Frontal Lobe


title: CNS PNET43 Sty1

hyb_protocol: Affymetrix 500K Hybridisation Protocol

scan_protocol: Affymetrix 500K Scanning Protocol

source_name: Brain Tumour

label_protocol: Affymetrix 500K Labelling Protocol

value: 190 months

value: Cerebral


title: CNS PNET25 HindIII

description: CNS PNET25 HindIII

source_name: Brain Tumour, CNS PNET25 HindIII

value: 59 months

value: Midline and Frontal Lobe


title: CNS PNET24 Constitutional HindIII

description: CNS PNET24 Constitutional HindIII

source_name: Blood, CNS PNET24 Constitutional HindIII


title: PB5 HindIII

description: PB5 HindIII

source_name: Brain Tumour, PB5 HindIII

value: male

value: 24 months

value: Pineal


title: healthy female F(4)

description: sample: F(4); age-match to M(4)

value: whole blood lymphocytes


title: healthy male M(26)

description: sample: M(26); age-match to F(28)

source_name: healthy male


title: Non-H2-producing_Rhodobacter_succinate_Ref_rep2

city: Madison

first: Timothy

last: Donohue

state: Wisconsin

address: 1550 Linden Drive

department: Department of Bacteriology

country: USA

institute: University of Wisconsin-Madison

hyb_protocol: Labeled cDNA samples were hybridized to Rhodobacter sphaeroides GeneChip CustomExpress microarrays (Affymetrix) following product instructions, for 16 h at 45 C on a rotisserie spindle rotating at 60 rpm.

scan_protocol: Microarrays were washed, stained, and scanned using the Pseudomonas aeruginosa midi-array hybridization with amplification protocols.

data_processing: Microarray data sets were normalized by Robust Multichip Average (RMA) with background adjustment and quantile normalization.  Statistical analysis of normalized data to identify differentially expressed genes used the limma package.  Correction for multiple testing was done using Benjamini-Hochberg correction.  Differentially expressed genes were defined as those having an adjusted p-value ≤ 0.01 and a fold-change ≥ 2 with respect to those in the reference data sets.  All analyses were conducted in the R statistical programming environment (http://www.R-project.org).

label: biotin

organism: Cereibacter sphaeroides

source_name: Non-H2-producing R. sphaeroides provided succinate & NH4+

label_protocol: Fragmented cDNA was end-labeled with biotin-16-ddUTP using Terminal Transferase for 2 hr at 37 C.

growth_protocol: R. sphaeroides cultures were grown photoheterotrophically in Sistrom's Minimal Medium (with succinate replaced by the indicated organic substrate, and NH4+ replaced by glutamate where indicated) at a temperature of 28-30 C and a light intensity of 10 W/m2.

extract_protocol: Cells were lysed by addition of 1/10 v 10% SDS at 64 C for 2 min.  1/10 v 1 M Na acetate (pH 5.2), then equal volume of H2O-saturated phenol, were added.  Samples were incubated at 64 C for 6 min, with mixing every 30 s, then chilled on ice before centrifugation (16,000 X g for 10 min at 4 C).  The aqueous phase was removed and extracted with equal volumes of phenol, then chloroform, then precipitated (1/10 v 3 M Na acetate, 1 mM EDTA, 2 volumes cold ethanol).

treatment_protocol: Cell culture was transferred to an ice-cold conical tube containing 1/8 volume of 5% water-saturated phenol in ethanol.  Cells were collected by centrifugation (5,000 X g for 5 min at 4 C); cell pellets were frozen in dry ice/ethanol and stored at -80 C.

tag: organic substrate

value: succinate

tag: nitrogen source

tag: cell density, in klett units (1 ku ~10^7 cells/ml)

tag: growth stage

value: early post-exponential


title: CNS PNET35 HindIII

description: CNS PNET35 HindIII

source_name: Brain Tumour, CNS PNET35 HindIII

tag: gender

tag: age

value: 122 months

tag: tumour location

value: Parietal Lobe


title: Hypothalamus_WildType_6weeks_rep5

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

institute: British Columbia Cancer Agency

description: WTMH C72

hyb_protocol: Hybridized for 17 h to the Mouse 1.0 ST Array chip in the GeneChip Hybridization Oven 640 using the GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Before scanning the chip on the GeneChip Scanner 3000 7G, each chip was run through the GeneChip Fluidics Station 450 for washing and staining with Streptavidin Phycoerythrin (SAPE). When the sample yielded a concentration less than required for subsequent steps in the protocol, the process was started over again and resulting volumes amalgamated (and in some instances vacuum centrifuged to increase the concentration) before moving forward to the next step.

data_processing:
CEL files were processed using ArrayAssist 5.0. Raw intensity calls were normalized using quantile normalization (Bolstad, 2003) and probeset summarization undertaken with gc-rma (Wu, 2004). Outliers and probesets with greater than 1.5 fold change between genotypes and level of significance p < 0.05 were selected for further analysis by quantitative PCR (Q-PCR). A complete data matrix of ArrayAssist 5.0 quantile normalized data not provided due to the following reason: "We had a license for ArrayAssist back in 2007, and unfortunately at that time I did not save complete matrix output. The files from the Affy Exon chips were so large (1.6 million rows of data for probeset level exon data) that no software we had could process or display the data for our biologists - only filtered lists of significant results were manageable outside of software such as ArrayAssist.  We no longer have an ArrayAssist license, so I am unable to generate the complete data matrix. We now have computers capable of handling larger sets of data and R/Bioconductor software for processing. I suspect that anyone wanting to use this data would not use ArrayAssist 5.0 or the older analytical methods implemented therein, but will want to operate directly with the CEL files."
Significant genes list can be found on GSE28383.xls file.
probe group file: ArrayAssist 5.0 internal affy pgf
meta-probeset file: ArrayAssist 5.0 internal affy mps

source_name: WT6 biological rep 5, Affy processing batch 3

label_protocol: 5.5 μg of single stranded cDNA was fragmented with Uracil DNA Glycosylase (UDG) and APE 1 then labeled with biotin allonamide triphosphate (TdT) using the GeneChip Whole Transcript Terminal Labeling Kit before being hybridized.

growth_protocol: Microdissected hypothalamic tissue from KISS1-/- mutant, GPR54-/- mutant, and wild type mice.  Male 129S6/Sv/Ev wildtype, 129S6/Sv/Ev Gpr54- or 129S6/Sv/Ev Kiss1- knockout mice were housed under conditions of 12 hours of light with ad libitum access to food and water.

extract_protocol: After removal of the brain, the meninges and optic chiasm were discarded and the hypothalamus was isolated. The external limits for this dissection were: lateral, the external border of the medial preoptic area and more caudally, the lateral borders of the mammillary nucleus; dorsal, 1.5 mm depth; anterior, the anterior limit of the nucleus of the vertical limb of the diagonal band (bregma + 1.34 mm); and posterior, the posterior limit of the mammillary nucleus (bregma – 3.40 mm). The whole hypothalamus contained at least the following main hypothalamic nuclei: arcuate nucleus (ARC), anteroventral periventricular nucleus (AVPV), anterodorsal preoptic nucleus (ADP), magnocellular  nucleus (MA), supraoptic (SON) and paraventricular (PVN) nuclei, medial preoptic area (MPO) and the diagonal band of Broca (DBB). Immediately after dissection, hypothalami samples were placed in 600 μl 21 of RNAlater (Applied Biosystems, UK) and kept at 4°C for 24 h and then stored at -20°C until RNA extraction.

treatment_protocol: Not applicable.

tag: genotype

value: WT

value: 6 weeks old


title: Non-H2-producing_Rhodobacter_succinate_Ref_rep1


title: healthy female F(2)

description: sample: F(2); age-match to M(3)

source_name: healthy female

value: female


title: CNS PNET22 HindIII

description: CNS PNET22 HindIII

source_name: Brain Tumour, CNS PNET22 HindIII

value: 37 months

value: Temporal Lobe

tag: metastasis


title: CNS PNET41 Sty1

value: 144 months


title: H2-producing_Rhodobacter_glycerol_rep2

source_name: H2-producing R. sphaeroides provided glycerol & glutamate

value: glycerol

value: glutamate


title: Hypothalamus_WildType_6weeks_rep3

source_name: WT6 biological rep 3, Affy processing batch 1


title: PB6 HindIII

description: PB6 HindIII

source_name: Brain Tumour, PB6 HindIII


title: CNS PNET18 HindIII

description: CNS PNET18 HindIII

source_name: Brain Tumour, CNS PNET18 HindIII


title: CNS PNET15 HindIII

description: CNS PNET15 HindIII

source_name: Brain Tumour, CNS PNET15 HindIII

value: 20 months

value: Frontal Lobe


title: CNS PNET30 Sty1

value: male

value: 84 months


title: CNS PNET15 Constitutional HindIII

description: CNS PNET15 Constitutional HindIII

source_name: Blood, CNS PNET15 Constitutional HindIII


title: Hypothalamus_WildType_6weeks_rep1

source_name: WT6 biological rep 1, Affy processing batch 2


title: CNS PNET21 Sty1

source_name: Brain Tumour

value: 36 months

value: Temporal and Parietal Lobes


title: Hypothalamus_WildType_6weeks_rep2

source_name: WT6 biological rep 2, Affy processing batch 2


title: CNS PNET37 Sty1

value: 127 months


title: H2-producing_Rhodobacter_xylose_rep3

source_name: H2-producing R. sphaeroides provided xylose & glutamate

value: xylose

value: early post-exponential


title: H2-producing_Rhodobacter_xylose_rep4


title: CNS PNET32 Sty1

value: 91 months


title: CNS PNET29 Sty1

value: 77 months


title: CNS PNET19 Sty1

value: female

value: 26 months

value: Cerebral


title: H2-producing_Rhodobacter_glycerol_rep1


title: H2-producing_Rhodobacter_xylose_rep2


title: CNS PNET17 Sty1

value: 23 months

value: Temporal Lobe


title: CNS PNET16 Sty1

value: 22 months


title: CNS PNET27 Sty1

value: 61 months


title: CNS PNET43 Nsp1

value: 190 months


title: Hypothalamus_WildType_6weeks_rep4

source_name: WT6 biological rep 4, Affy processing batch 3

value: WT

value: male

value: 6 weeks old


title: CNS PNET14 HindIII

description: CNS PNET14 HindIII

source_name: Brain Tumour, CNS PNET14 HindIII

value: 19 months

value: Frontal and Temporal Lobes


title: CNS PNET11 Sty1

value: 14 months


title: CNS PNET13 HindIII

description: CNS PNET13 HindIII

source_name: Brain Tumour, CNS PNET13 HindIII


title: Hypothalamus_WildType_3weeks_rep2

source_name: WT3 biological rep 2, Affy processing batch 1

value: 3 weeks old


title: CNS PNET37 Nsp1

value: 127 months

value: Parietal Lobe


title: Hypothalamus_KISS1-/-_mutant_rep5

description: KKOMH KB16

source_name: KKO biological rep 5, Affy processing batch 3

value: KISS1-/- mutant


title: H2-producing_Rhodobacter_xylose_rep1

value: xylose

value: glutamate

value: early post-exponential


title: H2-producing_Rhodobacter_glucose_rep4

source_name: H2-producing R. sphaeroides provided glucose & glutamate

value: glucose


title: H2-producing_Rhodobacter_glucose_rep2


title: Hypothalamus_KISS1-/-_mutant_rep4

description: KKOMH KB15

source_name: KKO biological rep 4, Affy processing batch 3


title: CNS PNET41 Nsp1

value: female

value: 144 months

value: Cerebral


title: Hypothalamus_KISS1-/-_mutant_rep3

description: KKOMH CKB5

source_name: KKO biological rep 3, Affy processing batch 3


title: V583_0.05mM_Cu_rep3ds

city: Oeiras

first: Marta

middle: Coelho

last: Abrantes

address: Av. da República - EAN

country: Portugal

institute: ITQB-UNL

description: Dye-swap of biological replicate 3

hyb_protocol: Labelled cDNA was mixed and hybridized on glass slides. Hybridization was performed at 45ºC for 16h, with Ambion Slide Hyb #1 hybridization buffer

scan_protocol: Slides were scanned in a GeneTac LS IV confocal laser scanner

data_processing: Slide images were analyzed using GenePix Pro 6.0 software. Processing and normalization (LOWESS spotpin-based) was done with MicroPrep software

organism: Enterococcus faecalis

source_name: E. faecalis V583 cells

label_protocol: cDNA synthesis and indirect labelling with Cy-3-dCTP and Cy-5-dCTP were performed as described elsewhere (Kloosterman et al. 2006)

growth_protocol: E. faecalis V583 cultures were grown until mid-exponential phase in GM17 or GM17 + 0.4mM MnSO4

extract_protocol: Initial steps of RNA isolation were performed as described elsewhere (Kloosterman et al. 2006). Isolation was completed with Roche High Pure RNA isolation kit, following the manufacturer's instructions.

tag: growth medium

value: GM17 + 0.05mM CuSO4


title: V583_0.05mM_Cu_rep2

description: Biological replicate 2 of 3


title: CNS PNET12 HindIII

description: CNS PNET12 HindIII

source_name: Brain Tumour, CNS PNET12 HindIII

value: male

value: Cerebral and Posteria Fossa


title: PB4 HindIII

description: PB4 HindIII

source_name: Brain Tumour, PB4 HindIII

value: 15 months

value: Pineal


title: Hypothalamus_KISS1-/-_mutant_rep2

source_name: KKO biological rep 2, Affy processing batch 1


title: H2-producing_Rhodobacter_glucose_rep1


title: PB3 HindIII

description: PB3 HindIII

source_name: Brain Tumour, PB3 HindIII

value: 13 months


title: PB3 Constitutional HindIII

description: PB3 Constitutional HindIII

source_name: Blood, PB3 Constitutional HindIII


title: PB4 Constitutional HindIII

description: PB4 Constitutional HindIII

source_name: Blood, PB4 Constitutional HindIII


title: V583_0.05mM_Cu_rep1

description: Biological replicate 1 of 3


title: Hypothalamus_GPR54-/-_mutant_rep4

description: GKOMH C70

source_name: GKO biological rep 4, Affy processing batch 3

value: GPR54-/- mutant


title: V583_0.4mM_Mn_rep3ds

description: Dye-swap of biological replicate 3

value: GM17 + 0.4mM MnSO4


title: CNS PNET32 Nsp1

source_name: Brain Tumour

value: 91 months

value: Frontal Lobe


title: PB2 HindIII

description: PB2 HindIII

source_name: Brain Tumour, PB2 HindIII

value: 12 months


title: CNS PNET10 HindIII

description: CNS PNET10 HindIII

source_name: Brain Tumour, CNS PNET10 HindIII

value: 10 months


title: H2-producing_Rhodobacter_succinate_rep3

source_name: H2-producing R. sphaeroides provided succinate & glutamate

value: succinate

value: glutamate

value: early post-exponential


title: CNS PNET30 Nsp1

value: 84 months

value: Parietal Lobe


title: H2-producing_Rhodobacter_succinate_rep2


title: Hypothalamus_GPR54-/-_mutant_rep3

description: GKOMH C35

source_name: GKO biological rep 3, Affy processing batch 3


title: V583_0.4mM_Mn_rep2

description: Biological replicate 2 of 3


title: H2-producing_Rhodobacter_succinate_rep1


title: Hypothalamus_WildType_3weeks_rep3

source_name: WT3 biological rep 3, Affy processing batch 1

value: WT

value: 3 weeks old


title: V583_0.4mM_Mn_rep1

description: Biological replicate 1 of 3


title: CNS PNET27 Nsp1

value: male

value: 61 months

value: Temporal Lobe


title: H2-producing_Rhodobacter_lactate_rep3

source_name: H2-producing R. sphaeroides provided lactate & glutamate

value: lactate


title: Hypothalamus_WildType_3weeks_rep1

source_name: WT3 biological rep 1, Affy processing batch 2


title: Hypothalamus_GPR54-/-_mutant_rep2

description: GKOMH C34

source_name: GKO biological rep 2, Affy processing batch 3

value: GPR54-/- mutant


title: CNS PNET21 Nsp1

value: female

value: 36 months

value: Temporal and Parietal Lobes


title: Hypothalamus_GPR54-/-_mutant_rep1

description: GKO 8

source_name: GKO biological rep 1, Affy processing batch 1


title: Hypothalamus_KISS1-/-_mutant_rep1

source_name: KKO biological rep 1, Affy processing batch 2

value: KISS1-/- mutant


title: H2-producing_Rhodobacter_glucose_rep3

source_name: H2-producing R. sphaeroides provided glucose & glutamate

value: glucose


source_name: Blood, CNS PNET9 and CNS PNET10 Constitutional HindIII

value: 10 months


title: PB1 HindIII

description: PB1 HindIII

source_name: Brain Tumour, PB1 HindIII

value: 6 months

value: Pineal


title: V583_4mMZn_rep2ds

description: Dye-swap of biological replicate 2

source_name: E. faecalis V583 cells

growth_protocol: E. faecalis V583 cultures were grown until mid-exponential phase in GM17 or GM17 + 4mM ZnSO4

value: GM17 + 4mM ZnSO4


title: H2-producing_Rhodobacter_lactate_rep1

value: glutamate

value: early post-exponential


title: CNS PNET29 Nsp1

value: 77 months


title: CNS PNET17 Nsp1

value: 23 months


title: H2-producing_Rhodobacter_lactate_rep2


title: cwinv4-1a, lateral nectaries, rep1

city: minneapolis

first: wayne

last: xu

state: MN

address: 117 Pleasant ST

department: supercomputing Institute

institute: university of minnesota

description:
cwINV1
Gene expression data from pooled Stage 14-15 lateral nectaries

hyb_protocol: Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.

scan_protocol: GeneChips were scanned using a GeneChip 3000 scanner at the University of Minnesota Microarray Facility.

data_processing: The probe level signals were summarized into expression indexes using MAS5 algorithm and were further linear scaled up to a media of 500 by the Expressionist (Genedata, Basel, Switzerland) Refiner module.  Scaling median to 500, PM/MM pvalue passes 0.05 as valid probesets. Invalid sets are null.

organism: Arabidopsis thaliana

source_name: lateral nectaries from stage 14-15 flowers, cwinv4-1 mutant

label_protocol: RNA was processed using the MessageAmp™ II-Biotin Enhanced Kit (Ambion, Austin, TX) for a single round of RNA amplification as described by the manufacturer. Briefly, 250-500 ng of total RNA (500 ng from lateral nectaries; 250 ng from median nectaries due to extremely small size) was used in a reverse transcription reaction to generate first-strand cDNA. Following second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotin-labeled, amplified RNA (aRNA). aRNA size distribution was evaluated by conventional denaturing agarose gel analysis according to manufacturer’s instructions (Ambion, Austin, TX). An aRNA fragmentation reaction, employing metal-induced hydrolysis, was used to fragment aRNA as described by the manufacturer (Ambion, Austin, TX).

growth_protocol: Plants were grown in individual pots on a peat-based growth medium with vermiculite and perlite (Pro-Mix BX; Premier Horticulture, Rivière-du-Loup, Quebec, Canada). All plant growth was performed in Percival AR66LX environmental chambers with settings of: 16 hr day/8hr night cycle, photosynthetic photon flux of 150 µmol m-2 s-1, 50% humidity and temperature of 21C.  All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 30-35 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4-8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at +4°C prior to RNA extraction. Up to two nectaries were collected per flower, with approximately 250-300 nectaries being processed as a single RNA sample.

extract_protocol: RNA was extracted from floral nectariferous tissue by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Denaturing agarose gel electrophoresis (Applied Biosystems, 2008) and UV spectrophotometry were used to assess RNA quality for all samples.

tag: ecotype

tag: genotype/variation

value: cwinv4-1 mutant

value: 30-35 day-old

tag: organ

value: pooled lateral nectaries from stage 14-15 flowers


title: Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 4

status: Public on Aug 21 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: The GeneChip HT MG-430 PM 24 Array Plate consists of 24 single MG-430 PM arrays arranged into standard 96 well plate format. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations on a GeneTitan Instrument.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated using RMA in Bioconductor.

source_name: Adipose tissue from male wild-type animal (C57/Bl6 background)

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430 PM arrays.

growth_protocol: Male wild-type (control) (C57/BL6 background) and ASC-/- and Casp1-/- mice (C57/BL6 background), aged 8-12 weeks at the start of the intervention, were maintained on a high fat diet (45 energy% of fat) for 16 weeks. After the diet intervention, mice were killed and the adipose tissue was removed.

extract_protocol: Total RNA was prepared from mouse adipose tissue using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: White adipose tissue was dissected from all 3 genotypes after 16 weeks of high fat diet-feeding. Adipose tissue RNA samples from 3-4 mice per experimental group were used for microarray analysis.

value: wild-type

value: male

tag: tissue

value: epididymal white adipose tissue


title: cwinv4-1, lateral nectaries, rep2

description:
cwINV2
Gene expression data from pooled Stage 14-15 lateral nectaries


title: wild-type, lateral nectary, rep1

description:
WT4
Gene expression data from pooled Stage 14-15 lateral nectaries

source_name: lateral nectaries from stage 14-15 flowers, wild-type


title: Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 1


title: V583_4mMZn_rep1

description: Biological replicate 1 of 2


title: CNS PNET16 Nsp1

source_name: Brain Tumour

value: 22 months

value: Cerebral


title: CNS PNET19 Nsp1

value: female

value: 26 months


title: V583_4mMZn_rep2

description: Biological replicate 2 of 2


title: CNS PNET9 HindIII

description: CNS PNET9 HindIII

source_name: Brain Tumour, CNS PNET9 HindIII

value: 10 months

value: Parietal Lobe


title: Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 2


title: Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 3

source_name: Adipose tissue from male ASC-/- animal (C57/Bl6 background)

value: ASC1 null


title: Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 3

source_name: Adipose tissue from male Casp1-/- animal (C57/Bl6 background)

value: Caspase 1 null


title: Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 2


title: Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 3


title: CNS PNET11 Nsp1

value: 14 months


title: UL3 Bare, repeat 2

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

description: MNase digested bare DNA from UL3 cells (sample 2)

hyb_protocol: Hybridization was performed by Nimblegen accoring to standard procedures

scan_protocol: Scanning was performed by Nimblegen using Nimblescan version 2.4.27

data_processing: For each position, two forward and two reverse oliogs were tiled on the array. Data for each set of oligos (nucleosomal & bare) were normalized to 1.0, and the ratio of nucl/(average bare 1 & bare2) determined. The median nucl/bare values for all 4 oligos were then quantile normalized for comparisons between conditions. The data was then locally smoothed by a combination of exponential smoothing of oligos within +/-40 bp (*0.5^(BP/10)) and by down-weighting positions where the deviation from the median value for F1,F2,R1 & R2 oligos was greater than average (*0.5^(deviation/avg_deviation)). Data processing was performed using custom PERL programs.

source_name: Mononucleosomal MNase fragments from UL3 cells, bare DNA

label_protocol: 1 to 4 micrograms of each mononcleosomal sample were labeled with Cy3 or Cy5 by Nimblegen services, according to their standard procedures

extract_protocol: Chromatin was extracted from cells using NP40 lysis, digested with micrococcal nuclease (MNase) to ~70% mononucleosomes and mononucleosomes isolated by PAGE and elution

treatment_protocol: no treatment (control)

tag: cell line

value: UL3 (U20S w/ GR and MMTV-luc)


title: Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 1


title: tumor sample 746-1

city: Iowa City

first: Adam

last: Dupuy

address: 51 Newton Road

institute: University of Iowa

description:
probe_group_file:  MoEx-1_0-st-v1.r2
meta-probeset_file:  MoEx-1_0-st-v1.na27.mm9.transcript

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse Exon 1.0 ST Arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing: Data were processed using Partek Genomics Suite software. Corrected intensities were RMA normalized.

source_name: thymic lymphoma

label_protocol: Four ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Samples were snap frozen in liquid N2. All samples were prepared using Qiagen RNAeasy protocol and quality verified by Agilent Bioanalyzer. Briefly, 50 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.

value: Vav-SB

tag: disease state

value: thymic lymphoma


title: UL3 Bare, repeat 1

description: MNase digested bare DNA from UL3 cells (sample 1)


title: tumor sample 740-3

tag: strain


title: tumor sample 711-3


title: tumor sample 744-2


title: tumor sample 801-1


title: tumor sample 633-5


title: tumor sample 633-4


title: tumor sample 690-5


title: Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 2


title: tumor sample 633-1


title: tumor sample 558-2


title: tumor sample 518-3


title: tumor sample 546-1


title: Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 1


title: HL60 -DMSO

description: Mononucleosomal MNase fragments from untreated HL60 cells treated +1.5% DMSO for 5 days

treatment_protocol: 1.5% DMSO for 5 days


title: UL3 +Dex 1hr, repeat 2

description: Mononucleosomal MNase fragments from UL3 cells treated with 10nM dexamethasone for 1 hr (sample 2)

treatment_protocol: 10 nM dexamethasone for 1 hr


title: P0*200_GPL96

status: Public on Aug 20 2011

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: Gene expression data from myeloma patient before DEXA treatment

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human myeloma cell  P0*200_GPL96

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol

extract_protocol: RNeasy Mini Kit(50)

tag: human myeloma cell  P0*200_GPL96


title: P0*871_GPL96

source_name: human myeloma cell  P0*871_GPL96

tag: human myeloma cell  P0*871_GPL96


title: P0*9_GPL96

source_name: human myeloma cell  P0*9_GPL96

tag: human myeloma cell  P0*9_GPL96


title: HL60 +DMSO

description: Mononucleosomal MNase fragments from HL60 cells treated +1.5% DMSO for 5 days


title: P0*15_GPL96

source_name: human myeloma cell  P0*15_GPL96

tag: human myeloma cell  P0*15_GPL96


title: tumor sample 490-3


title: P0*894_GPL96

source_name: human myeloma cell  P0*894_GPL96

tag: human myeloma cell  P0*894_GPL96


title: UL3 +Dex 1hr, repeat 1

description: Mononucleosomal MNase fragments from UL3 cells treated with 10nM dexamethasone for 1 hr (sample 1)


title: P0*896_GPL96

source_name: human myeloma cell  P0*896_GPL96

tag: human myeloma cell  P0*896_GPL96


title: UL3 +Dex 4hr

description: Mononucleosomal MNase fragments from UL3 cells treated with 10nM dexamethasone for 4 hrs

treatment_protocol: 10 nM dexamethasone for 4 hrs


title: P0*842_GPL96

source_name: human myeloma cell  P0*842_GPL96

tag: human myeloma cell  P0*842_GPL96


title: P0*867_GPL96

source_name: human myeloma cell  P0*867_GPL96

tag: human myeloma cell  P0*867_GPL96


title: P0*877_GPL96

source_name: human myeloma cell  P0*877_GPL96

tag: human myeloma cell  P0*877_GPL96


title: P0*892_GPL96

source_name: human myeloma cell  P0*892_GPL96

tag: human myeloma cell  P0*892_GPL96


title: P0*868_GPL96

source_name: human myeloma cell  P0*868_GPL96

tag: human myeloma cell  P0*868_GPL96


title: P0*875_GPL96

source_name: human myeloma cell  P0*875_GPL96

tag: human myeloma cell  P0*875_GPL96


title: UL3 BRG1 kd +Dex 1hr

description: Mononucleosomal MNase fragments from UL3 cells with siRNA-mediated knock down of BRG1, treated with 10 nM dexamethasone for 1 hr

treatment_protocol: BRG1 knock down, 10 nM dexamethasone for 1 hr


title: P0*845_GPL96

source_name: human myeloma cell  P0*845_GPL96

tag: human myeloma cell  P0*845_GPL96


title: P0*2_GPL96

source_name: human myeloma cell  P0*2_GPL96

tag: human myeloma cell  P0*2_GPL96


title: P0*864_GPL96

source_name: human myeloma cell  P0*864_GPL96

tag: human myeloma cell  P0*864_GPL96


title: UL3 -Dex, repeat 2

description: Mononucleosomal MNase fragments from UL3 cells, untreated control (sample 2)

tag: cell line


title: P0*846_GPL96

source_name: human myeloma cell  P0*846_GPL96

tag: human myeloma cell  P0*846_GPL96


title: tumor sample 490-1

source_name: thymic lymphoma

label_protocol: Four ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

tag: strain

tag: disease state


title: UL3 BRG1 kd -Dex

description: Mononucleosomal MNase fragments from UL3 cells with siRNA-mediated knock down of BRG1, untreated control

treatment_protocol: BRG1 knock down


title: UL3 -Dex, repeat 1

description: Mononucleosomal MNase fragments from UL3 cells, untreated control (sample 1)


title: P0*822_GPL96

source_name: human myeloma cell  P0*822_GPL96

tag: human myeloma cell  P0*822_GPL96


title: P0*804_GPL96

source_name: human myeloma cell  P0*804_GPL96

tag: human myeloma cell  P0*804_GPL96


title: P0*772_GPL96

source_name: human myeloma cell  P0*772_GPL96

tag: human myeloma cell  P0*772_GPL96


title: P0*807_GPL96

source_name: human myeloma cell  P0*807_GPL96

tag: human myeloma cell  P0*807_GPL96


title: P0*770_GPL96

source_name: human myeloma cell  P0*770_GPL96

tag: human myeloma cell  P0*770_GPL96


title: P0*769_GPL96

source_name: human myeloma cell  P0*769_GPL96

tag: human myeloma cell  P0*769_GPL96


title: P0*806_GPL96

source_name: human myeloma cell  P0*806_GPL96

tag: human myeloma cell  P0*806_GPL96


title: P0*830_GPL96

source_name: human myeloma cell  P0*830_GPL96

tag: human myeloma cell  P0*830_GPL96


title: P0*9_GPL97

source_name: human myeloma cell  P0*9_GPL97

tag: human myeloma cell  P0*9_GPL97


title: P0*774_GPL96

source_name: human myeloma cell  P0*774_GPL96

tag: human myeloma cell  P0*774_GPL96


title: P0*797_GPL96

source_name: human myeloma cell  P0*797_GPL96

tag: human myeloma cell  P0*797_GPL96


title: P0*894_GPL97

source_name: human myeloma cell  P0*894_GPL97

tag: human myeloma cell  P0*894_GPL97


title: P0*200_GPL97

source_name: human myeloma cell  P0*200_GPL97

tag: human myeloma cell  P0*200_GPL97


title: P0*2_GPL97

source_name: human myeloma cell  P0*2_GPL97

tag: human myeloma cell  P0*2_GPL97


title: P0*871_GPL97

source_name: human myeloma cell  P0*871_GPL97

tag: human myeloma cell  P0*871_GPL97


title: P0*779_GPL96

source_name: human myeloma cell  P0*779_GPL96

tag: human myeloma cell  P0*779_GPL96


title: P0*775_GPL96

source_name: human myeloma cell  P0*775_GPL96

tag: human myeloma cell  P0*775_GPL96


title: P0*875_GPL97

source_name: human myeloma cell  P0*875_GPL97

tag: human myeloma cell  P0*875_GPL97


title: P0*877_GPL97

source_name: human myeloma cell  P0*877_GPL97

tag: human myeloma cell  P0*877_GPL97


title: P0*896_GPL97

source_name: human myeloma cell  P0*896_GPL97

tag: human myeloma cell  P0*896_GPL97


title: P0*867_GPL97

source_name: human myeloma cell  P0*867_GPL97

tag: human myeloma cell  P0*867_GPL97


title: P0*766_GPL96

source_name: human myeloma cell  P0*766_GPL96

tag: human myeloma cell  P0*766_GPL96


title: P0*777_GPL96

source_name: human myeloma cell  P0*777_GPL96

tag: human myeloma cell  P0*777_GPL96


title: P0*15_GPL97

source_name: human myeloma cell  P0*15_GPL97

tag: human myeloma cell  P0*15_GPL97


title: P0*868_GPL97

source_name: human myeloma cell  P0*868_GPL97

tag: human myeloma cell  P0*868_GPL97


title: P0*798_GPL96

source_name: human myeloma cell  P0*798_GPL96

tag: human myeloma cell  P0*798_GPL96


title: P0*782_GPL96

source_name: human myeloma cell  P0*782_GPL96

tag: human myeloma cell  P0*782_GPL96


title: P0*778_GPL96

source_name: human myeloma cell  P0*778_GPL96

tag: human myeloma cell  P0*778_GPL96


title: P0*789_GPL96

source_name: human myeloma cell  P0*789_GPL96

tag: human myeloma cell  P0*789_GPL96


title: P0*892_GPL97

source_name: human myeloma cell  P0*892_GPL97

tag: human myeloma cell  P0*892_GPL97


title: P0*834_GPL96

source_name: human myeloma cell  P0*834_GPL96

tag: human myeloma cell  P0*834_GPL96


title: P0*768_GPL96

source_name: human myeloma cell  P0*768_GPL96

tag: human myeloma cell  P0*768_GPL96


title: P0*767_GPL96

source_name: human myeloma cell  P0*767_GPL96

tag: human myeloma cell  P0*767_GPL96


title: P0*864_GPL97

source_name: human myeloma cell  P0*864_GPL97

tag: human myeloma cell  P0*864_GPL97


title: P0*845_GPL97

source_name: human myeloma cell  P0*845_GPL97

tag: human myeloma cell  P0*845_GPL97


title: P0*842_GPL97

source_name: human myeloma cell  P0*842_GPL97

tag: human myeloma cell  P0*842_GPL97


title: P0*846_GPL97

source_name: human myeloma cell  P0*846_GPL97

tag: human myeloma cell  P0*846_GPL97


title: P0*740_GPL96

source_name: human myeloma cell  P0*740_GPL96

tag: human myeloma cell  P0*740_GPL96


title: P0*733_GPL96

source_name: human myeloma cell  P0*733_GPL96

tag: human myeloma cell  P0*733_GPL96


title: P0*830_GPL97

source_name: human myeloma cell  P0*830_GPL97

tag: human myeloma cell  P0*830_GPL97


title: P0*741_GPL96

source_name: human myeloma cell  P0*741_GPL96

tag: human myeloma cell  P0*741_GPL96


title: P0*822_GPL97

source_name: human myeloma cell  P0*822_GPL97

tag: human myeloma cell  P0*822_GPL97


title: P0*834_GPL97

source_name: human myeloma cell  P0*834_GPL97

tag: human myeloma cell  P0*834_GPL97


title: P0*804_GPL97

source_name: human myeloma cell  P0*804_GPL97

tag: human myeloma cell  P0*804_GPL97


title: P0*772_GPL97

source_name: human myeloma cell  P0*772_GPL97

tag: human myeloma cell  P0*772_GPL97


title: P0*731-2_GPL96

source_name: human myeloma cell  P0*731-2_GPL96

tag: human myeloma cell  P0*731-2_GPL96


title: P0*807_GPL97

source_name: human myeloma cell  P0*807_GPL97

tag: human myeloma cell  P0*807_GPL97


title: P0*734_GPL96

source_name: human myeloma cell  P0*734_GPL96

tag: human myeloma cell  P0*734_GPL96


title: P0*730_GPL96

source_name: human myeloma cell  P0*730_GPL96

tag: human myeloma cell  P0*730_GPL96


title: P0*705_GPL96

source_name: human myeloma cell  P0*705_GPL96

tag: human myeloma cell  P0*705_GPL96


title: P0*712_GPL96

source_name: human myeloma cell  P0*712_GPL96

tag: human myeloma cell  P0*712_GPL96


title: P0*774_GPL97

source_name: human myeloma cell  P0*774_GPL97

tag: human myeloma cell  P0*774_GPL97


title: P0*727_GPL96

source_name: human myeloma cell  P0*727_GPL96

tag: human myeloma cell  P0*727_GPL96


title: P0*806_GPL97

source_name: human myeloma cell  P0*806_GPL97

tag: human myeloma cell  P0*806_GPL97


title: P0*725_GPL96

source_name: human myeloma cell  P0*725_GPL96

tag: human myeloma cell  P0*725_GPL96


title: P0*770_GPL97

source_name: human myeloma cell  P0*770_GPL97

tag: human myeloma cell  P0*770_GPL97


title: P0*695_GPL96

source_name: human myeloma cell  P0*695_GPL96

tag: human myeloma cell  P0*695_GPL96


title: P0*723_GPL96

source_name: human myeloma cell  P0*723_GPL96

tag: human myeloma cell  P0*723_GPL96


title: P0*766_GPL97

source_name: human myeloma cell  P0*766_GPL97

tag: human myeloma cell  P0*766_GPL97


title: P0*775_GPL97

source_name: human myeloma cell  P0*775_GPL97

tag: human myeloma cell  P0*775_GPL97


title: P0*724_GPL96

source_name: human myeloma cell  P0*724_GPL96

tag: human myeloma cell  P0*724_GPL96


title: P0*713_GPL96

source_name: human myeloma cell  P0*713_GPL96

tag: human myeloma cell  P0*713_GPL96


title: P0*769_GPL97

source_name: human myeloma cell  P0*769_GPL97

tag: human myeloma cell  P0*769_GPL97


title: P0*707_GPL96

source_name: human myeloma cell  P0*707_GPL96

tag: human myeloma cell  P0*707_GPL96


title: P0*782_GPL97

source_name: human myeloma cell  P0*782_GPL97

tag: human myeloma cell  P0*782_GPL97


title: P0*718_GPL96

source_name: human myeloma cell  P0*718_GPL96

tag: human myeloma cell  P0*718_GPL96


title: P0*678_GPL96

source_name: human myeloma cell  P0*678_GPL96

tag: human myeloma cell  P0*678_GPL96


title: P0*681_GPL96

source_name: human myeloma cell  P0*681_GPL96

tag: human myeloma cell  P0*681_GPL96


title: P0*702_GPL96

source_name: human myeloma cell  P0*702_GPL96

tag: human myeloma cell  P0*702_GPL96


title: P0*778_GPL97

source_name: human myeloma cell  P0*778_GPL97

tag: human myeloma cell  P0*778_GPL97


title: P0*797_GPL97

source_name: human myeloma cell  P0*797_GPL97

tag: human myeloma cell  P0*797_GPL97


title: P0*779_GPL97

source_name: human myeloma cell  P0*779_GPL97

tag: human myeloma cell  P0*779_GPL97


title: P0*698_GPL96

source_name: human myeloma cell  P0*698_GPL96

tag: human myeloma cell  P0*698_GPL96


title: P0*684_GPL96

source_name: human myeloma cell  P0*684_GPL96

tag: human myeloma cell  P0*684_GPL96


title: P0*692_GPL96

source_name: human myeloma cell  P0*692_GPL96

tag: human myeloma cell  P0*692_GPL96


title: P0*647_GPL96

source_name: human myeloma cell  P0*647_GPL96

tag: human myeloma cell  P0*647_GPL96


title: P0*768_GPL97

source_name: human myeloma cell  P0*768_GPL97

tag: human myeloma cell  P0*768_GPL97


title: P0*691_GPL96

source_name: human myeloma cell  P0*691_GPL96

tag: human myeloma cell  P0*691_GPL96


title: P0*777_GPL97

source_name: human myeloma cell  P0*777_GPL97

tag: human myeloma cell  P0*777_GPL97


title: P0*798_GPL97

source_name: human myeloma cell  P0*798_GPL97

tag: human myeloma cell  P0*798_GPL97


title: P0*689_GPL96

source_name: human myeloma cell  P0*689_GPL96

tag: human myeloma cell  P0*689_GPL96


title: P0*789_GPL97

source_name: human myeloma cell  P0*789_GPL97

tag: human myeloma cell  P0*789_GPL97


title: P0*767_GPL97

source_name: human myeloma cell  P0*767_GPL97

tag: human myeloma cell  P0*767_GPL97


title: P0*734_GPL97

source_name: human myeloma cell  P0*734_GPL97

tag: human myeloma cell  P0*734_GPL97


title: P0*731-2_GPL97

source_name: human myeloma cell  P0*731-2_GPL97

tag: human myeloma cell  P0*731-2_GPL97


title: P0*522_GPL96

source_name: human myeloma cell  P0*522_GPL96

tag: human myeloma cell  P0*522_GPL96


title: P0*686_GPL96

source_name: human myeloma cell  P0*686_GPL96

tag: human myeloma cell  P0*686_GPL96


title: P0*510_GPL96

source_name: human myeloma cell  P0*510_GPL96

tag: human myeloma cell  P0*510_GPL96


title: P0*730_GPL97

source_name: human myeloma cell  P0*730_GPL97

tag: human myeloma cell  P0*730_GPL97


title: P0*741_GPL97

source_name: human myeloma cell  P0*741_GPL97

tag: human myeloma cell  P0*741_GPL97


title: P0*740_GPL97

source_name: human myeloma cell  P0*740_GPL97

tag: human myeloma cell  P0*740_GPL97


title: P0*733_GPL97

source_name: human myeloma cell  P0*733_GPL97

tag: human myeloma cell  P0*733_GPL97


title: P0*655_GPL96

source_name: human myeloma cell  P0*655_GPL96

tag: human myeloma cell  P0*655_GPL96


title: P0*511_GPL96

source_name: human myeloma cell  P0*511_GPL96

tag: human myeloma cell  P0*511_GPL96


title: P0*517_GPL96

source_name: human myeloma cell  P0*517_GPL96

tag: human myeloma cell  P0*517_GPL96


title: P0*723_GPL97

source_name: human myeloma cell  P0*723_GPL97

tag: human myeloma cell  P0*723_GPL97


title: P0*503_GPL96

source_name: human myeloma cell  P0*503_GPL96

tag: human myeloma cell  P0*503_GPL96


title: P0*695_GPL97

source_name: human myeloma cell  P0*695_GPL97

tag: human myeloma cell  P0*695_GPL97


title: P0*707_GPL97

source_name: human myeloma cell  P0*707_GPL97

tag: human myeloma cell  P0*707_GPL97


title: P0*712_GPL97

source_name: human myeloma cell  P0*712_GPL97

tag: human myeloma cell  P0*712_GPL97


title: P0*480_GPL96

source_name: human myeloma cell  P0*480_GPL96

tag: human myeloma cell  P0*480_GPL96


title: P0*508_GPL96

source_name: human myeloma cell  P0*508_GPL96

tag: human myeloma cell  P0*508_GPL96


title: P0*724_GPL97

source_name: human myeloma cell  P0*724_GPL97

tag: human myeloma cell  P0*724_GPL97


title: P0*501_GPL96

source_name: human myeloma cell  P0*501_GPL96

tag: human myeloma cell  P0*501_GPL96


title: P0*495_GPL96

source_name: human myeloma cell  P0*495_GPL96

tag: human myeloma cell  P0*495_GPL96


title: P0*718_GPL97

source_name: human myeloma cell  P0*718_GPL97

tag: human myeloma cell  P0*718_GPL97


title: P0*474_GPL96

source_name: human myeloma cell  P0*474_GPL96

tag: human myeloma cell  P0*474_GPL96


title: P0*504_GPL96

source_name: human myeloma cell  P0*504_GPL96

tag: human myeloma cell  P0*504_GPL96


title: P0*698_GPL97

source_name: human myeloma cell  P0*698_GPL97

tag: human myeloma cell  P0*698_GPL97


title: P0*713_GPL97

source_name: human myeloma cell  P0*713_GPL97

tag: human myeloma cell  P0*713_GPL97


title: P0*481_GPL96

source_name: human myeloma cell  P0*481_GPL96

tag: human myeloma cell  P0*481_GPL96


title: P0*692_GPL97

source_name: human myeloma cell  P0*692_GPL97

tag: human myeloma cell  P0*692_GPL97


title: P0*689_GPL97

source_name: human myeloma cell  P0*689_GPL97

tag: human myeloma cell  P0*689_GPL97


title: P0*725_GPL97

source_name: human myeloma cell  P0*725_GPL97

tag: human myeloma cell  P0*725_GPL97


title: P0*492-2_GPL96

source_name: human myeloma cell  P0*492-2_GPL96

tag: human myeloma cell  P0*492-2_GPL96


title: P0*705_GPL97

source_name: human myeloma cell  P0*705_GPL97

tag: human myeloma cell  P0*705_GPL97


title: P0*702_GPL97

source_name: human myeloma cell  P0*702_GPL97

tag: human myeloma cell  P0*702_GPL97


title: P0*465_GPL96

source_name: human myeloma cell  P0*465_GPL96

tag: human myeloma cell  P0*465_GPL96


title: P0*482_GPL96

source_name: human myeloma cell  P0*482_GPL96

tag: human myeloma cell  P0*482_GPL96


title: P0*727_GPL97

source_name: human myeloma cell  P0*727_GPL97

tag: human myeloma cell  P0*727_GPL97


title: P0*691_GPL97

source_name: human myeloma cell  P0*691_GPL97

tag: human myeloma cell  P0*691_GPL97


title: P0*478_GPL96

source_name: human myeloma cell  P0*478_GPL96

tag: human myeloma cell  P0*478_GPL96


title: P0*502_GPL96

source_name: human myeloma cell  P0*502_GPL96

tag: human myeloma cell  P0*502_GPL96


title: P0*647_GPL97

source_name: human myeloma cell  P0*647_GPL97

tag: human myeloma cell  P0*647_GPL97


title: P0*655_GPL97

source_name: human myeloma cell  P0*655_GPL97

tag: human myeloma cell  P0*655_GPL97


title: P0*490_GPL96

source_name: human myeloma cell  P0*490_GPL96

tag: human myeloma cell  P0*490_GPL96


title: P0*447_GPL96

source_name: human myeloma cell  P0*447_GPL96

tag: human myeloma cell  P0*447_GPL96


title: P0*451_GPL96

source_name: human myeloma cell  P0*451_GPL96

tag: human myeloma cell  P0*451_GPL96


title: P0*434_GPL96

source_name: human myeloma cell  P0*434_GPL96

tag: human myeloma cell  P0*434_GPL96


title: P0*457_GPL96

source_name: human myeloma cell  P0*457_GPL96

tag: human myeloma cell  P0*457_GPL96


title: P0*418_GPL96

source_name: human myeloma cell  P0*418_GPL96

tag: human myeloma cell  P0*418_GPL96


title: P0*421_GPL96

source_name: human myeloma cell  P0*421_GPL96

tag: human myeloma cell  P0*421_GPL96


title: P0*438_GPL96

source_name: human myeloma cell  P0*438_GPL96

tag: human myeloma cell  P0*438_GPL96


title: P0*508_GPL97

source_name: human myeloma cell  P0*508_GPL97

tag: human myeloma cell  P0*508_GPL97


title: P0*678_GPL97

source_name: human myeloma cell  P0*678_GPL97

tag: human myeloma cell  P0*678_GPL97


title: P0*397_GPL96

source_name: human myeloma cell  P0*397_GPL96

tag: human myeloma cell  P0*397_GPL96


title: P0*511_GPL97

source_name: human myeloma cell  P0*511_GPL97

tag: human myeloma cell  P0*511_GPL97


title: P0*686_GPL97

source_name: human myeloma cell  P0*686_GPL97

tag: human myeloma cell  P0*686_GPL97


title: P0*681_GPL97

source_name: human myeloma cell  P0*681_GPL97

tag: human myeloma cell  P0*681_GPL97


title: P0*684_GPL97

source_name: human myeloma cell  P0*684_GPL97

tag: human myeloma cell  P0*684_GPL97


title: P0*433_GPL96

source_name: human myeloma cell  P0*433_GPL96

tag: human myeloma cell  P0*433_GPL96


title: P0*446_GPL96

source_name: human myeloma cell  P0*446_GPL96

tag: human myeloma cell  P0*446_GPL96


title: P0*510_GPL97

source_name: human myeloma cell  P0*510_GPL97

tag: human myeloma cell  P0*510_GPL97


title: P0*522_GPL97

source_name: human myeloma cell  P0*522_GPL97

tag: human myeloma cell  P0*522_GPL97


title: P0*440_GPL96

source_name: human myeloma cell  P0*440_GPL96

tag: human myeloma cell  P0*440_GPL96


title: P0*517_GPL97

source_name: human myeloma cell  P0*517_GPL97

tag: human myeloma cell  P0*517_GPL97


title: P0*503_GPL97

source_name: human myeloma cell  P0*503_GPL97

tag: human myeloma cell  P0*503_GPL97


title: P0*427_GPL96

source_name: human myeloma cell  P0*427_GPL96

tag: human myeloma cell  P0*427_GPL96


title: P0*502_GPL97

source_name: human myeloma cell  P0*502_GPL97

tag: human myeloma cell  P0*502_GPL97


title: P0*501_GPL97

source_name: human myeloma cell  P0*501_GPL97

tag: human myeloma cell  P0*501_GPL97


title: P0*504_GPL97

source_name: human myeloma cell  P0*504_GPL97

tag: human myeloma cell  P0*504_GPL97


title: P0*415_GPL96

source_name: human myeloma cell  P0*415_GPL96

tag: human myeloma cell  P0*415_GPL96


title: P0*408_GPL96

source_name: human myeloma cell  P0*408_GPL96

tag: human myeloma cell  P0*408_GPL96


title: P0*495_GPL97

source_name: human myeloma cell  P0*495_GPL97

tag: human myeloma cell  P0*495_GPL97


title: P0*401_GPL96

source_name: human myeloma cell  P0*401_GPL96

tag: human myeloma cell  P0*401_GPL96


title: P0*480_GPL97

source_name: human myeloma cell  P0*480_GPL97

tag: human myeloma cell  P0*480_GPL97


title: P0*490_GPL97

source_name: human myeloma cell  P0*490_GPL97

tag: human myeloma cell  P0*490_GPL97


title: P0*392_GPL96

source_name: human myeloma cell  P0*392_GPL96

tag: human myeloma cell  P0*392_GPL96


title: P0*482_GPL97

source_name: human myeloma cell  P0*482_GPL97

tag: human myeloma cell  P0*482_GPL97


title: P0*474_GPL97

source_name: human myeloma cell  P0*474_GPL97

tag: human myeloma cell  P0*474_GPL97


title: P0*405_GPL96

source_name: human myeloma cell  P0*405_GPL96

tag: human myeloma cell  P0*405_GPL96


title: P0*381_GPL96

source_name: human myeloma cell  P0*381_GPL96

tag: human myeloma cell  P0*381_GPL96


title: P0*465_GPL97

source_name: human myeloma cell  P0*465_GPL97

tag: human myeloma cell  P0*465_GPL97


title: P0*420_GPL96

source_name: human myeloma cell  P0*420_GPL96

tag: human myeloma cell  P0*420_GPL96


title: P0*387_GPL96

source_name: human myeloma cell  P0*387_GPL96

tag: human myeloma cell  P0*387_GPL96


title: P0*391_GPL96

source_name: human myeloma cell  P0*391_GPL96

tag: human myeloma cell  P0*391_GPL96


title: P0*390_GPL96

source_name: human myeloma cell  P0*390_GPL96

tag: human myeloma cell  P0*390_GPL96


title: P0*478_GPL97

source_name: human myeloma cell  P0*478_GPL97

tag: human myeloma cell  P0*478_GPL97


title: P0*364_GPL96

source_name: human myeloma cell  P0*364_GPL96

tag: human myeloma cell  P0*364_GPL96


title: P0*365_GPL96

source_name: human myeloma cell  P0*365_GPL96

tag: human myeloma cell  P0*365_GPL96


title: P0*374_GPL96

source_name: human myeloma cell  P0*374_GPL96

tag: human myeloma cell  P0*374_GPL96


title: P0*492-2_GPL97

source_name: human myeloma cell  P0*492-2_GPL97

tag: human myeloma cell  P0*492-2_GPL97


title: P0*366_GPL96

source_name: human myeloma cell  P0*366_GPL96

tag: human myeloma cell  P0*366_GPL96


title: P0*368_GPL96

source_name: human myeloma cell  P0*368_GPL96

tag: human myeloma cell  P0*368_GPL96


title: P0*354_GPL96

source_name: human myeloma cell  P0*354_GPL96

tag: human myeloma cell  P0*354_GPL96


title: P0*457_GPL97

source_name: human myeloma cell  P0*457_GPL97

tag: human myeloma cell  P0*457_GPL97


title: P0*447_GPL97

source_name: human myeloma cell  P0*447_GPL97

tag: human myeloma cell  P0*447_GPL97


title: P0*434_GPL97

source_name: human myeloma cell  P0*434_GPL97

tag: human myeloma cell  P0*434_GPL97


title: P0*481_GPL97

source_name: human myeloma cell  P0*481_GPL97

tag: human myeloma cell  P0*481_GPL97


title: P0*440_GPL97

source_name: human myeloma cell  P0*440_GPL97

tag: human myeloma cell  P0*440_GPL97


title: P0*446_GPL97

source_name: human myeloma cell  P0*446_GPL97

tag: human myeloma cell  P0*446_GPL97


title: P0*427_GPL97

source_name: human myeloma cell  P0*427_GPL97

tag: human myeloma cell  P0*427_GPL97


title: P0*451_GPL97

source_name: human myeloma cell  P0*451_GPL97

tag: human myeloma cell  P0*451_GPL97


title: P0*418_GPL97

source_name: human myeloma cell  P0*418_GPL97

tag: human myeloma cell  P0*418_GPL97


title: P0*357_GPL96

source_name: human myeloma cell  P0*357_GPL96

tag: human myeloma cell  P0*357_GPL96


title: P0*421_GPL97

source_name: human myeloma cell  P0*421_GPL97

tag: human myeloma cell  P0*421_GPL97


title: P0*371_GPL96

source_name: human myeloma cell  P0*371_GPL96

tag: human myeloma cell  P0*371_GPL96


title: P0*438_GPL97

source_name: human myeloma cell  P0*438_GPL97

tag: human myeloma cell  P0*438_GPL97


title: P0*343_GPL96

source_name: human myeloma cell  P0*343_GPL96

tag: human myeloma cell  P0*343_GPL96


title: P0*408_GPL97

source_name: human myeloma cell  P0*408_GPL97

tag: human myeloma cell  P0*408_GPL97


title: P0*397_GPL97

source_name: human myeloma cell  P0*397_GPL97

tag: human myeloma cell  P0*397_GPL97


title: P0*401_GPL97

source_name: human myeloma cell  P0*401_GPL97

tag: human myeloma cell  P0*401_GPL97


title: P0*405_GPL97

source_name: human myeloma cell  P0*405_GPL97

tag: human myeloma cell  P0*405_GPL97


title: P0*314_GPL96

source_name: human myeloma cell  P0*314_GPL96

tag: human myeloma cell  P0*314_GPL96


title: P0*175_GPL96

source_name: human myeloma cell  P0*175_GPL96

tag: human myeloma cell  P0*175_GPL96


title: P0*415_GPL97

source_name: human myeloma cell  P0*415_GPL97

tag: human myeloma cell  P0*415_GPL97


title: P0*399_GPL97

source_name: human myeloma cell  P0*399_GPL97

tag: human myeloma cell  P0*399_GPL97


title: P0*313_GPL96

source_name: human myeloma cell  P0*313_GPL96

tag: human myeloma cell  P0*313_GPL96


title: P0*387_GPL97

source_name: human myeloma cell  P0*387_GPL97

tag: human myeloma cell  P0*387_GPL97


title: P0*165_GPL96

source_name: human myeloma cell  P0*165_GPL96

tag: human myeloma cell  P0*165_GPL96


title: P0*226_GPL96

source_name: human myeloma cell  P0*226_GPL96

tag: human myeloma cell  P0*226_GPL96


title: P0*176_GPL96

source_name: human myeloma cell  P0*176_GPL96

tag: human myeloma cell  P0*176_GPL96


title: P0*157_GPL96

source_name: human myeloma cell  P0*157_GPL96

tag: human myeloma cell  P0*157_GPL96


title: P0*433_GPL97

source_name: human myeloma cell  P0*433_GPL97

tag: human myeloma cell  P0*433_GPL97


title: P0*392_GPL97

source_name: human myeloma cell  P0*392_GPL97

tag: human myeloma cell  P0*392_GPL97


title: P0*155_GPL96

source_name: human myeloma cell  P0*155_GPL96

tag: human myeloma cell  P0*155_GPL96


title: P0*107_GPL96

source_name: human myeloma cell  P0*107_GPL96

tag: human myeloma cell  P0*107_GPL96


title: P0*391_GPL97

source_name: human myeloma cell  P0*391_GPL97

tag: human myeloma cell  P0*391_GPL97


title: P0*399_GPL96

source_name: human myeloma cell  P0*399_GPL96

tag: human myeloma cell  P0*399_GPL96


title: P0*154_GPL96

source_name: human myeloma cell  P0*154_GPL96

tag: human myeloma cell  P0*154_GPL96


title: P0*98_GPL96

source_name: human myeloma cell  P0*98_GPL96

tag: human myeloma cell  P0*98_GPL96


title: P0*390_GPL97

source_name: human myeloma cell  P0*390_GPL97

tag: human myeloma cell  P0*390_GPL97


title: P0*85_GPL96

source_name: human myeloma cell  P0*85_GPL96

tag: human myeloma cell  P0*85_GPL96


title: P0*374_GPL97

source_name: human myeloma cell  P0*374_GPL97

tag: human myeloma cell  P0*374_GPL97


title: P0*381_GPL97

source_name: human myeloma cell  P0*381_GPL97

tag: human myeloma cell  P0*381_GPL97


title: P0*103_GPL96

source_name: human myeloma cell  P0*103_GPL96

tag: human myeloma cell  P0*103_GPL96


title: P0*365_GPL97

source_name: human myeloma cell  P0*365_GPL97

tag: human myeloma cell  P0*365_GPL97


title: P0*364_GPL97

source_name: human myeloma cell  P0*364_GPL97

tag: human myeloma cell  P0*364_GPL97


title: P0*92_GPL96

source_name: human myeloma cell  P0*92_GPL96

tag: human myeloma cell  P0*92_GPL96


title: P0*91_GPL96

source_name: human myeloma cell  P0*91_GPL96

tag: human myeloma cell  P0*91_GPL96


title: P0*57_GPL96

source_name: human myeloma cell  P0*57_GPL96

tag: human myeloma cell  P0*57_GPL96


title: P0*420_GPL97

source_name: human myeloma cell  P0*420_GPL97

tag: human myeloma cell  P0*420_GPL97


title: P0*56_GPL96

source_name: human myeloma cell  P0*56_GPL96

tag: human myeloma cell  P0*56_GPL96


title: P0*65_GPL96

source_name: human myeloma cell  P0*65_GPL96

tag: human myeloma cell  P0*65_GPL96


title: P0*368_GPL97

source_name: human myeloma cell  P0*368_GPL97

tag: human myeloma cell  P0*368_GPL97


title: P0*53_GPL96

source_name: human myeloma cell  P0*53_GPL96

tag: human myeloma cell  P0*53_GPL96


title: P0*371_GPL97

source_name: human myeloma cell  P0*371_GPL97

tag: human myeloma cell  P0*371_GPL97


title: P0*54_GPL96

source_name: human myeloma cell  P0*54_GPL96

tag: human myeloma cell  P0*54_GPL96


title: P0*343_GPL97

source_name: human myeloma cell  P0*343_GPL97

tag: human myeloma cell  P0*343_GPL97


title: P0*366_GPL97

source_name: human myeloma cell  P0*366_GPL97

tag: human myeloma cell  P0*366_GPL97


title: P0*67_GPL96

source_name: human myeloma cell  P0*67_GPL96

tag: human myeloma cell  P0*67_GPL96


title: P0*354_GPL97

source_name: human myeloma cell  P0*354_GPL97

tag: human myeloma cell  P0*354_GPL97


title: P0*124_GPL96

source_name: human myeloma cell  P0*124_GPL96

tag: human myeloma cell  P0*124_GPL96


title: P0*357_GPL97

source_name: human myeloma cell  P0*357_GPL97

tag: human myeloma cell  P0*357_GPL97


title: P0*52_GPL96

source_name: human myeloma cell  P0*52_GPL96

tag: human myeloma cell  P0*52_GPL96


title: P0*51_GPL96

source_name: human myeloma cell  P0*51_GPL96

tag: human myeloma cell  P0*51_GPL96


title: P0*48_GPL96

source_name: human myeloma cell  P0*48_GPL96

tag: human myeloma cell  P0*48_GPL96


title: P0*313_GPL97

source_name: human myeloma cell  P0*313_GPL97

tag: human myeloma cell  P0*313_GPL97


title: P0*314_GPL97

source_name: human myeloma cell  P0*314_GPL97

tag: human myeloma cell  P0*314_GPL97


title: P0*43_GPL96

source_name: human myeloma cell  P0*43_GPL96

tag: human myeloma cell  P0*43_GPL96


title: P0*29_GPL96

source_name: human myeloma cell  P0*29_GPL96

tag: human myeloma cell  P0*29_GPL96


title: P0*19_GPL96

source_name: human myeloma cell  P0*19_GPL96

tag: human myeloma cell  P0*19_GPL96


title: P0*165_GPL97

source_name: human myeloma cell  P0*165_GPL97

tag: human myeloma cell  P0*165_GPL97


title: P0*226_GPL97

source_name: human myeloma cell  P0*226_GPL97

tag: human myeloma cell  P0*226_GPL97


title: P0*890_GPL96

source_name: human myeloma cell  P0*890_GPL96

tag: human myeloma cell  P0*890_GPL96


title: P0*157_GPL97

source_name: human myeloma cell  P0*157_GPL97

tag: human myeloma cell  P0*157_GPL97


title: P0*175_GPL97

source_name: human myeloma cell  P0*175_GPL97

tag: human myeloma cell  P0*175_GPL97


title: RNA extracted from liver of mice IV injected with PBS-Rep3

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

description: PBS replicate 3

hyb_protocol: ILLUMINA WG-6 V2 mouse bead-chips (#BD 201-0202) were used. Hybridization conditions employed Illumina HYB buffer, 18 hours @ 58○C

scan_protocol: Illumina BeadArray Reader, PMT setting 100%, 532nm for Cy3.

data_processing: Standard Illumina BeadStudio processing of images plus cubic_spline normalization

source_name: Liver

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA from murine livers was extracted using mirVana miRNA isolation kit (Ambion)

treatment_protocol: IV injected with PBS

tag: treatment

value: PBS

tag: strain

value: Nu/Nu mice

tag: gender

tag: age

value: 12 weeks old

tag: tissue

value: Liver


title: P0*154_GPL97

source_name: human myeloma cell  P0*154_GPL97

tag: human myeloma cell  P0*154_GPL97


title: P0*103_GPL97

source_name: human myeloma cell  P0*103_GPL97

tag: human myeloma cell  P0*103_GPL97


title: P0*176_GPL97

source_name: human myeloma cell  P0*176_GPL97

tag: human myeloma cell  P0*176_GPL97


title: P0*107_GPL97

source_name: human myeloma cell  P0*107_GPL97

tag: human myeloma cell  P0*107_GPL97


title: P0*98_GPL97

source_name: human myeloma cell  P0*98_GPL97

tag: human myeloma cell  P0*98_GPL97


title: P0*155_GPL97

source_name: human myeloma cell  P0*155_GPL97

tag: human myeloma cell  P0*155_GPL97


title: P0*92_GPL97

source_name: human myeloma cell  P0*92_GPL97

tag: human myeloma cell  P0*92_GPL97


title: P0*85_GPL97

source_name: human myeloma cell  P0*85_GPL97

tag: human myeloma cell  P0*85_GPL97


title: P0*36_GPL96

source_name: human myeloma cell  P0*36_GPL96

tag: human myeloma cell  P0*36_GPL96


title: RNA extracted from liver of mice IV injected with PBS-Rep2

description: PBS replicate 2


title: P0*124_GPL97

source_name: human myeloma cell  P0*124_GPL97

tag: human myeloma cell  P0*124_GPL97


title: Liver harvested 48hrs post injection with non-replicating Ad5 virus Rep2

description: Luc replicate 2

treatment_protocol: 5 0000000000 non-replicating Ad5 viral particles/mouse IV injected,

value: non-replicating Ad5 virus


title: RNA extracted from liver of mice IV injected with PBS-Rep1

description: PBS replicate 1


title: Liver harvested 48hrs post injection with non-replicating Ad5 virus Rep3

description: Luc replicate 3


title: Liver harvested 48hrs post injection with non-replicating Ad5 virus Rep1

description: Luc replicate 1

source_name: liver

treatment_protocol: 5 0000000000 wild type Ad5 viral particles/mouse IV injected, these Ad5 virus bearing miR122-binding sites in the 3'UTR of E1A


title: Liver harvested 48hrs post injection with wild type Ad5 virus bearing miR122-binding sites in the 3'UTR of E1A Rep1

description: miR replicate 1


title: Liver harvested 48hrs post injection with wild type Ad5 virus bearing miR122-binding sites in the 3'UTR of E1A Rep2

description: miR replicate 2


title: Liver harvested 48hrs post injection with wild type Ad5 virus bearing miR122-binding sites in the 3'UTR of E1A Rep3

description: miR replicate 3


title: P0*91_GPL97

source_name: human myeloma cell  P0*91_GPL97

tag: human myeloma cell  P0*91_GPL97


title: P0*67_GPL97

source_name: human myeloma cell  P0*67_GPL97

tag: human myeloma cell  P0*67_GPL97


title: 14178551 - 1093 -2 vs Col0 -2

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

institute: INRA

description: Genes regulated by MPK4 pathway.

hyb_protocol: Col0 -2 Cy5 / 1093 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

source_name: Col0 -2

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: whole plant - Media: MS-Agar 0.5X with MES - 1% sucrose  Hygrometry: 75% Temperature: 26°C 16h light/8h dark

extract_protocol: Col0 -2:36ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

tag: genotype/variation

value: wildtype

value: 14 days

tag: developmental stage

value: boyes 1.02 (Boyes et al. Plant Cell 2001, PMID:11449047)

extract_protocol: 1093 -2:27ug. (Qiagen_RNeasy.pdf)

value: mpk4/MPK4 GOF


title: P0*65_GPL97

source_name: human myeloma cell  P0*65_GPL97

tag: human myeloma cell  P0*65_GPL97


title: Shewanella Onidensis MR-1 -MEC-Control- Carbon- anode-rep2

city: corvallis

first: Shoutao

last: Xu

state: OR

address: 116 gilmore hall, OSU

department: Department of biological and ecological engineering

institute: oregon State University

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on graphite disk anode. It is the second of three  biological replicates used in this experiment, each from separate cultures at the same batch.

hyb_protocol: Hybridization was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Shewanella oneidensis MR-1

source_name: S. onidensis MR-1 -MEC-Control- Carbon- anode

label_protocol: Labeling was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University following their standard operating protocol. See www.nimblegen.com.

growth_protocol: S. oneidensis MR-1 was grown aerobically using a medium containing 30 g/L Trypticase Soy Broth at 30°C. Cells in early stationary growth phase (optical density of 1.5-1.6 at 600nm) were washed two times then injected into the chamber of the MEC for current production. Trypticase Soy Broth medium with 30 mM sodium lactate as electron donor was used in MECS. Phosphate buffer (100mM) was used to maintain the solution pH 7 and solution conductivity at 15 mS/cm

extract_protocol: Total RNA was extracted using Trizol (Ambion inc., Austin,TX) following the manufacturer’s instructions.DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.MessageAmpTM II-Bacteria Prokaryotic RNA Amplification kit was used to amplify RNA.

tag: growth condition

value: biofilm on graphite disk anode  control


title: Shewanella Onidensis MR-1 -MEC-Control- Carbon- anode-rep3

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on graphite disk anode. It is the third of three  biological replicates used in this experiment, each from separate cultures at the same batch.

value: biofilm on graphite disk anode control


title: P0*56_GPL97

source_name: human myeloma cell  P0*56_GPL97

tag: human myeloma cell  P0*56_GPL97


title: 14178550 - Col0 -2 vs 1093 -2

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -2 Cy5 / Col0 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age


title: Liver haversted 48hrs post injection with wild type Ad5 virus rep3

description: WT replicate 3

source_name: Liver

treatment_protocol: 5 0000000000 wild type Ad5 viral particles/mouse IV injected

tag: treatment

value: wild type Ad5 virus

tag: strain

tag: gender

value: female

tag: tissue


title: 14178548 - 1067 -2 vs 1093 -2

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -2 Cy5 / 1067 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1067 -2:27ug. (Qiagen_RNeasy.pdf)


title: 14178549 - 1093 -2 vs 1067 -2

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1067 -2 Cy5 / 1093 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: P0*57_GPL97

source_name: human myeloma cell  P0*57_GPL97

tag: human myeloma cell  P0*57_GPL97


title: 14178544 - Col0 -1 vs 1093 -1

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -1 Cy5 / Col0 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1093 -1:14.2ug. (Qiagen_RNeasy.pdf)

value: 13 days

source_name: Col0 -1

extract_protocol: Col0 -1:30ug. (Qiagen_RNeasy.pdf)


title: 14178545 - 1093 -1 vs Col0 -1

description: Genes regulated by MPK4 pathway.

hyb_protocol: Col0 -1 Cy5 / 1093 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Shewanella Onidensis MR-1 -MEC- Fe Nano-Decorared-Carbon-rep3

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on Fe nano decraded anode. It is the third of three  biological replicates used in this experiment, each from separate cultures at the same batch.

source_name: S. onidensis MR-1 -MEC-Fe Nano-Decorared-Carbon

value: biofilm on Fe nano decreted graphite disk anode


title: Liver harvested 48hrs post injection with wild type Ad5 virus rep1

description: WT replicate 1


title: Shewanella Onidensis MR-1 -MEC-Control- Carbon- anode-rep1

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on graphite disk anode . It is the first of three  biological replicates used in this experiment, each from separate cultures at the same batch.


title: P0*53_GPL97

source_name: human myeloma cell  P0*53_GPL97

tag: human myeloma cell  P0*53_GPL97


title: HL-60-L359V_rep2

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Raw CEL files were normalised with RMA method using aroma.affymetrix and the batch effect was removed using ComBat analysis.

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 L359V

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

growth_protocol: HL-60 cell lines were grown in RPMI containing 10%FBS (Sigma-Aldrich), 500 µg/ml hygromycin, 3 µg/ml puromycin, 10 µg/ml gentamicin at density of 1-5x106/ml. 24 hours prior to 4HT addition, the cells were changed into fresh RPMI medium containing 5% FBS with 10 µg/ml gentamicin and without hygromycin and puromycin.

extract_protocol: Total RNA was purified using the RNeasy protocol (Qiagen)

treatment_protocol: 24 hours prior to 4HT addition, the cells were changed into fresh RPMI medium containing 5% FBS with 10 µg/ml gentamicin and without hygromycin and puromycin. HL-60 cell lines were then treated with 100nM 4HT for 24 hours and, after this time, cells were harvested and RNA purified.

tag: cell line

tag: cell type

value: Promyelocytic Leukaemia


title: 14178543 - 1093 -1 vs 1067 -1

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1067 -1 Cy5 / 1093 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1067 -1:11.7ug. (Qiagen_RNeasy.pdf)


title: 14178546 - 1065 -2 vs 1093 -2

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -2 Cy5 / 1065 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1065 -2:31.7ug. (Qiagen_RNeasy.pdf)


title: Shewanella Onidensis MR-1 -MEC- Fe Nano-Decorared-Carbon-rep2

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on Fe nano decraded anode. It is the second of three  biological replicates used in this experiment, each from separate cultures at the same batch.


title: 14178541 - 1093 -1 vs 1065 -1

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1065 -1 Cy5 / 1093 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1065 -1:15.3ug. (Qiagen_RNeasy.pdf)


title: Liver haversted 48hrs post injection with wild type Ad5 virus rep2

description: WT replicate 2

treatment_protocol: 5 0000000000 viral particles/mouse injected


title: P0*51_GPL97

source_name: human myeloma cell  P0*51_GPL97

tag: human myeloma cell  P0*51_GPL97


title: 14178542 - 1067 -1 vs 1093 -1

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -1 Cy5 / 1067 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HL-60-355delT_rep2

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 355delT


title: HL-60-355delT_rep3

value: constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 355delT