title: 30 min post infection - donor C CRAM_OHU28K-235_2-18-05

description: 30 min post infection - donor C

source_name: L.(V.)panamensis infected human macrophage

source_name: human macrophage


title: Rat aorta Low WSS rep 2

status: Public on Dec 24 2012

type: RNA

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description: Rat aorta from region with Low WSS

hyb_protocol: RNA samples were hybridized at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.

scan_protocol: RNA samples were scanned at the Karolinska Institute microarray core facility. Affymetrix Rat Gene 1.1 ST Array Plate system and protocols were used.

data_processing: Raw data from cel-files was pre-processed using the RMA-algorithm. Gene annotation was downloaded from the Affymetrix web page (version RaGene-1_1-st-v1.na31.rn4). Probe sets without annotation and probe sets with mean expression level below 4 were omitted from analysis, resulting in the analysis of 13968 genes.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat aorta Low WSS

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

growth_protocol: Male Wistar rats under constant environmental temperature (21°C) and 12h:12h light/dark cycle, witg free access to standard rodent chow and water.

extract_protocol: With guidance from the CFD simulations, portions of the entire artery from high and low WSS regions, respectively, were cut out under RNase free conditions and directly put in pre-chilled Lysing Matrix D tubes (MP Biomedicals, Illkirch, France) containing Trizol (Invitrogen, Paisley, Scotland, UK). In order to yield significant amounts of RNA, tissue pieces from the specific high and low WSS regions from five animals were pooled for each sample (a total of 28 pools; 14 paired samples of high and low WSS regions). Samples were homogenized with FastPrep. Total RNA was isolated using RNeasy Mini kit (Qiagen, Maryland, USA), including DNase treatment for elimination of potential DNA contamination. RNA integrity was analyzed by the use of an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Paolo Alto, CA, USA) and quantified using NanoDrop (NanoDrop products, Wilmington, DE, USA).

treatment_protocol: No special treatment of rats - different regions of aorta were compared

tag: strain

value: Wistar

tag: stress

value: Low wall shear stress WSS

tag: replicate

tag: tissue

value: aorta from region with Low WSS


title: Rat aorta High WSS rep 13

description: Rat aorta from region with High WSS

source_name: Rat aorta High WSS

value: High wall shear stress WSS

value: aorta from region with High WSS


title: Rat aorta Low WSS rep 14

description: Rat aorta from region with Low WSS


title: Rat aorta Low WSS rep 13

description: Rat aorta from region with Low WSS


title: Rat aorta High WSS rep 14

description: Rat aorta from region with High WSS


title: Rat aorta High WSS rep 12

description: Rat aorta from region with High WSS


title: Rat aorta High WSS rep 11

description: Rat aorta from region with High WSS


title: Rat aorta High WSS rep 10

description: Rat aorta from region with High WSS


title: Rat aorta Low WSS rep 12

description: Rat aorta from region with Low WSS


title: 24 hrs post infection - donor B CRAM_OHU28K-234_2-10-05

status: Public on Dec 25 2012

city: New Haven

first: Diane

last: McMahon-Pratt

state: Ct

address: 60 College St

department: Epidemiology of Microbial Diseases

country: USA

institute: Yale School of Public Health

description: 24 hrs post infection - donor B

hyb_protocol: Labelled cDNA was hybridized to a 70-mer OHU28K Human oligo array, after addition of 1ug of Human Cot-1 DNA to the hybridization mixture in a 22x71 mm AdvaCard. Hybridization was done overnight at 55ºC, followed by washings with 2XSSC/0.2%SDS.

scan_protocol: Arrays were scanned  with Axon GenePix 4000A laser confocal scanner at 532 and 635 nm.

data_processing: Image files were analyzed with GenePix Pro Software and GeneSpring GX 7.2 software was used for gene expression data analysis. Lowess normalization was performed to eliminate dye-related artifacts.

organism: Homo sapiens

label_protocol: cDNA was ligated to the appropriate Cy5/Cy3 3DNA capture sequence

extract_protocol: RNA samples were extracted  with Trizol from adherent macrophages, and RNA recovery was done with Rneasy Micro Kit (Qiagen).

tag: cell type

value: monocyte differentiated macrophage

tag: infection

tag: individual

value: donor B

tag: time

value: 24 hrs post infection

value: control


title: Rat aorta Low WSS rep 9

description: Rat aorta from region with Low WSS


title: Rat aorta Low WSS rep 10

description: Rat aorta from region with Low WSS


title: bladder tumor procured UVA19

city: Charlottesville

first: Steven

middle: C

last: Smith

state: VA

department: Urology

institute: University of Virginia

description: snap-frozen bladder tumors procured intraoperatively and profiled for gene expression

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: RMA, using its standard settings as implemented in the Bioinformatics Suite commercially available as an add on for Matlab R2009B, (The Mathworks, Natick, MA).

source_name: snap-fozen bladder tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

growth_protocol: Human tumors, not applicable.

extract_protocol: Total RNA was extracted using an RNeasy kit, per manufacturer instructions (Qiagen, Valencia, CA, USA).

treatment_protocol: Snap-frozen, macrodissected tumor tissue

tag: tumor stage

value: pTa

tag: muscle invasion

value: non-muscle invasive

tag: histology

value: urothelial carcinoma


title: bladder tumor procured UVA18


title: Rat aorta High WSS rep 9

description: Rat aorta from region with High WSS


title: bladder tumor procured UVA17

value: muscle invasive


title: bladder tumor procured UVA15


title: Rat aorta High WSS rep 8

description: Rat aorta from region with High WSS


title: Rat aorta High WSS rep 5

description: Rat aorta from region with High WSS


title: Rat aorta Low WSS rep 6

description: Rat aorta from region with Low WSS


title: Rat aorta High WSS rep 7

description: Rat aorta from region with High WSS


title: bladder tumor procured UVA13


title: Rat aorta Low WSS rep 7

description: Rat aorta from region with Low WSS


title: TreatedK05/PoolControlWT Dye Swap

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Dye Swap 2/2

hyb_protocol: Microarray hybridization was carried on overnight at 48°C by submerging microarrays closed in a sealed chamber (HybChamber, GeneMachines, San Carlos, CA, USA) in a high-precision water bath (W28 Grant, Cambridge, UK). Post-hybridization washing was performed according to the protocol suggested in the Amino Allyl kit.

scan_protocol: Fluorescence signals were detected by analyzing the microarrays in a Perkin-Elmer LITE dual confocal laser scanner guided by ScanArray Microarray Analysis Software, and raw microarray images were analyzed with Scan Array Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: LOWESS normalized, background subtracted data

organism: Mus musculus

source_name: EDL KO5

label_protocol: Total RNA, 1 μg, was retro-transcribed and labelled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.

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

tag: genotype/variation

value: WT

tag: developmental stage

value: adult

value: Extensior Digitorum Longus (EDL) muscle

source_name: Pool EDL WT

value: calsequestrin 1 null


title: Hmt1-9myc ChIP-chip rep 2

type: genomic

city: AMHERST

first: Eric

last: Milliman

state: NY

address: 109 COOKE HALL

department: Biology

institute: SUNY AT BUFFALO

hyb_protocol: Labeled samples were then sent to Nimblegen for Hyb, scan and preprocessing

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Input DNA

label_protocol: ChIP and Input DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 dUTP  per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Yeast grown to OD600 0.4-0.6 were crosslinked with 1% formaldehyde for 20 min at 30 ˚C. Crosslinking was stopped via rapid centrifugation and washing 2x with ice-cold TBS.  Cells were lysed in 50 mM HEPES-KOH pH 7.5; 140 mM NaCl, 1 mM EDTA, 1% Triton X-100; 0.1 % NaDeoxycholate using fastprep maching (MP Biomedicals). Chromatin was sonicated with a Branson Digital Sonifer (20 sec pulse, 55 sec rest, 5 min total pulse time, amplitude 20%) to an average of 300bp. The lysate was then centrifuged to remove cell debris.  For IP, 1.2 mL of chromatin extract was incubated with 9E11 anti-myc antibody (ThermoFisher) pre-conjugated to Dynal Beads (pan-mouse IgG; Life Technologies) O/N at 4 ˚C. Immune complexes were collected and washed for 5 min at 4 ˚C with the following buffers; 2x Lysis Buffer (50 mM HEPES-KOH pH 7.5; 140 mM NaCl, 1 mM EDTA, 1% Triton X-100; 0.1 % NaDeoxycholate); 2x High Salt Lysis buffer (50 mM HEPES-KOH pH 7.5; 360 mM NaCl, 1 mM EDTA, 1% Triton X-100; 0.1 % Na Deoxycholate); 2x ChIP Wash (10 mM Tris pH 8.0; 250 mM LiCl; 0.5% NP-40; 0.5% Na-deoxycholate). Finally samples were eluted in 50 µL of 50 mM Tris pH 8.0; 1% SDS and 10 mM EDTA at 65 ˚C for 20 min and decrosslinked at 65 ˚C O/N. After reversal of the crosslinks,samples were treated wtih Proteinase K  at 37 ˚C for 2 hrs.  DNA (input and IP) was amplified linearly by LM-PCR.

tag: chip antibody

value: none Input DNA

source_name: Hmt1 ChIP DNA

value: anti-MYC (9E11)


title: bladder tumor procured UVA16


title: Rat aorta High WSS rep 4

description: Rat aorta from region with High WSS

value: Wistar


title: Hmt1-9myc ChIP-chip rep 3

description: Dye Swap expt.

scan_protocol: Labeled samples were then sent to Nimblegen for Hyb, scan and preprocessing


title: Rat aorta Low WSS rep 8

description: Rat aorta from region with Low WSS

value: Low wall shear stress WSS

value: aorta from region with Low WSS


title: TreatedK05/PoolControlWT Replicated1

description: Dye Swap 1/2


title: bladder tumor procured UVA14


title: Resveratrol treatment exp 3T3-L1 cells, CT1

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

country: Canada

institute: Toronto General Hospital

description: All the chips were controlled for presence of any defect before scanning.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GCOS standard protocol

data_processing: GeneChip Operating Software was used for data processing

label: Biotin

source_name: untreated untrMurine 3T3-L1 cells

label_protocol:
Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children.
Affymetrix standard protocol

extract_protocol:
Trizol standard protocol
Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

tag: Murine 3T3-L1 progenitor adipocytes cell cultures, Control 1 (untreated with resveratrol)


title: Rat aorta High WSS rep 6

description: Rat aorta from region with High WSS

value: High wall shear stress WSS

value: aorta from region with High WSS


title: bladder tumor procured UVA12

value: squamous cell carcinoma


title: bladder tumor procured UVA11


title: TreatedK03/PoolControlWT Replicated1

description: Dye Swap 1/2

source_name: EDL KO3


title: Rat aorta Low WSS rep 11

description: Rat aorta from region with Low WSS


title: Hmt1-9myc ChIP-chip rep 1


title: bladder tumor procured UVA9


title: TreatedK02/PoolControlWT Dye Swap

description: Dye Swap 2/2

source_name: EDL KO2


title: Rat aorta High WSS rep 3

description: Rat aorta from region with High WSS


title: TreatedK03/PoolControlWT Dye Swap

description: Dye Swap 2/2


title: Rat aorta Low WSS rep 5

description: Rat aorta from region with Low WSS


title: bladder tumor procured UVA8


title: bladder tumor procured UVA5


title: bladder tumor procured UVA6


title: TreatedK01/PoolControlWT Dye Swap

description: Dye Swap 2/2

source_name: EDL KO1


title: bladder tumor procured UVA10


title: Rat aorta Low WSS rep 4

description: Rat aorta from region with Low WSS


title: bladder tumor procured UVA7


title: bladder tumor procured UVA3


title: bladder tumor procured UVA2


title: TreatedK01/PoolControlWT Replicated1

description: Dye Swap 1/2


title: TreatedK02/PoolControlWT Replicated1

description: Dye Swap 1/2


title: Rat aorta Low WSS rep 3

description: Rat aorta from region with Low WSS


title: bladder tumor procured UVA1


title: bladder tumor procured UVA4


title: Rat aorta High WSS rep 1

description: Rat aorta from region with High WSS


title: 24 hr MT+TBI Sample 1 Array b.txt

status: Public on Dec 23 2012

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Sample 24hr MT+TBI 1, Array Replicate 2

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Rat Whole Genome Microarrays in hybridization buffer. Arrays were hybridized at 37° C for 18 hrs. in a shaking incubator, and washed at 46° C for 1 hr.

scan_protocol: Rinsed and dried arrays were scanned with an Axon GenePix 4000B Microarray Scanner at 5 µm resolution.

data_processing: CodeLink software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Hippocampus LCM Neurons, traumatic brain injury, Metyrapone, 24hr

label_protocol: 2 rounds of amplification were performed using the Arcturus RiboAmp HS kit.  Biotinylated cRNA target was prepared from the DNA template purified after the  second round cDNA synthesis.  cRNA quality was verified on an Agilent Bioanalyzer  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

extract_protocol: Total RNA from laser captured hippocampal neurons was isolated and DNase treated prior to microarray analysis.

treatment_protocol: Sprague-Dawley rats were subjected to experimental fluid percussion traumatic brain injury or sham injury (control). The drug treatments, metyrapone (MT, 100mg/kg) or carbenoxolone (CB, 30mg/kg) and saline (TBI alone) were administered sub-cutaneously 90 min before TBI. Rats were sacrificed 4 and 24 hours after saline or drug treatments and brains were removed for frozen sectioning. CA3 hippoccampal neurons were obtained by laser capture microdissection.

value: Sprague-Dawley

value: Hippocampus LCM Neurons

tag: injury

value: traumatic brain injury

tag: treatment

value: Metyrapone


title: 24 hr MT+TBI Sample 2 Array a.txt

description: Sample 24hr MT+TBI 2, Array Replicate 1

tag: strain


title: Rat aorta High WSS rep 2

description: Rat aorta from region with High WSS

tag: stress


title: 24 hr MT+TBI Sample 1 Array a.txt

description: Sample 24hr MT+TBI 1, Array Replicate 1


title: 24 hr MT+TBI Sample 2 Array b.txt

description: Sample 24hr MT+TBI 2, Array Replicate 2


title: 24 hr CB+TBI Sample 2 Array a.txt

description: Sample 24hr CB+TBI 2, Array Replicate 1

source_name: Hippocampus LCM Neurons, traumatic brain injury, Carbenoxoione, 24hr

value: Carbenoxoione


title: Resveratrol treatment exp 3T3-L1 cells, T1

source_name: treated Murine 3T3-L1 cells

label_protocol: Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children. Affymetrix standard protocol

extract_protocol: Trizol standard protocol Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

tag: Murine 3T3-L1 progenitor adipocytes cell cultures, T1 (treated with resveratrol)


title: 24 hr Saline+TBI Sample 2 Array a.txt

description: Sample 24hrS+TBI 2, Array Replicate 1

source_name: Hippocampus LCM Neurons, traumatic brain injury, Saline, 24hr

value: Saline


title: 24 hr CB+TBI Sample 1 Array a.txt

description: Sample 24hr CB+TBI 1, Array Replicate 1


title: 24 hr CB+TBI Sample 1 Array b.txt

description: Sample 24hr CB+TBI 1, Array Replicate 2


title: 24 hr Saline+TBI Sample 1 Array b.txt

description: Sample 24hr S+TBI 1, Array Replicate 2


title: 24 hr CB+TBI Sample 2 Array b.txt

description: Sample 24hr CB+TBI 2, Array Replicate 2


title: 24 hr Saline+TBI Sample 1 Array a.txt

description: Sample 24hr S+TBI 1, Array Replicate 1


title: 24 hr Control Sample 1 Array b.txt

description: Sample 24hr C1, Array Replicate 2

source_name: Hippocampus LCM Neurons, sham injury, 24hr

value: sham injury


title: 4 hr MT+TBI Sample 1 Array b.txt

description: Sample 4hr MT+TBI 1, Array Replicate 2

source_name: Hippocampus LCM Neurons, traumatic brain injury, Metyrapone, 4hr

value: 4 h


title: 24 hr Saline+TBI Sample 2 Array b.txt

description: Sample 24hrS+TBI 2, Array Replicate 2


title: 4 hr MT+TBI Sample 1 Array a.txt

description: Sample 4hr MT+TBI 1, Array Replicate 1


title: 4 hr MT+TBI Sample 2 Array b.txt

description: Sample 4hr MT+TBI 2, Array Replicate 2


title: 24 hr Control Sample 2 Array a.txt

description: Sample 24hr C2, Array Replicate 1


title: 4 hr CB+TBI Sample 2 Array b.txt

description: Sample 4hr CB+TBI 2, Array Replicate 2

source_name: Hippocampus LCM Neurons, traumatic brain injury, Carbenoxoione, 4hr


title: 4 hr CB+TBI Sample 1 Array b.txt

description: Sample 4hr CB+TBI 1, Array Replicate 2


title: 24 hr Control Sample 2 Array b.txt

description: Sample 24hr C2, Array Replicate 2


title: 24 hr Control Sample 1 Array a.txt

description: Sample 24hr C1, Array Replicate 1


title: 4 hr MT+TBI Sample 2 Array a.txt

description: Sample 4hr MT+TBI 2, Array Replicate 1


title: 4 hr Saline+TBI Sample 2 Array b.txt

description: Sample 4hrS+TBI 2, Array Replicate 2

source_name: Hippocampus LCM Neurons, traumatic brain injury, Saline, 4hr


title: 4 hr Saline+TBI Sample 1 Array b.txt

description: Sample 4hr S+TBI 1, Array Replicate 2


title: 4 hr Saline+TBI Sample 2 Array a.txt

description: Sample 4hrS+TBI 2, Array Replicate 1


title: 4 hr Saline+TBI Sample 1 Array a.txt

description: Sample 4hr S+TBI 1, Array Replicate 1


title: 4 hr Control Sample 1 Array b.txt

description: Sample 4hr C1, Array Replicate 2

source_name: Hippocampus LCM Neurons, sham injury, 4hr

value: untreated


title: 4 hr CB+TBI Sample 2 Array a.txt

description: Sample 4hr CB+TBI 2, Array Replicate 1


title: 4 hr CB+TBI Sample 1 Array a.txt

description: Sample 4hr CB+TBI 1, Array Replicate 1


title: 4 hr Control Sample 2 Array b.txt

description: Sample 4hr C2, Array Replicate 2


title: Transgenic fly line Mut-101, female biological rep1

city: Chicago

first: Soo-Young

last: Park

address: 5841 S. Maryland Ave.

department: Medicine

institute: The University of Chicago

hyb_protocol: 3.75 µg of fragmented and biotin labeled targets was hybridized to array for 18 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640.

scan_protocol: GeneChip were scanned using  Affymetrix  GeneChip Scanner 3000 7G.

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

organism: Drosophila melanogaster

source_name: Transgenic fly line Mut-101_female

label_protocol: Fragmentation and labeling process was carried out by FL-OvationTM cDNA Biotin Module V2 (NuGEN).

growth_protocol: We used the GMR-Gal4/UAS system to generate transgenic flies expressing wild-type (Wt) or mutant (Mut, C96Y) human proinsulin. Flies were hemizygous for the transgene and maintained at 25 degree.

extract_protocol: Extraction of total RNA by MELTTM Total Nucleic Acid Isolation System (Ambion) and amplification of total RNA by OvationTM RNA Amplification System V2 (NuGEN) were performed according to the manufacturer's instructions.

treatment_protocol: Eye imaginal disc was dissected from 3rd instar larval stage under the dissecting scope.

value: transgenic fly line Mut-101

tag: age

value: 3rd Instar larva

tag: gender

value: female

tag: tissue

value: Eye imaginal disc


title: 4 hr Control Sample 2 Array a.txt

description: Sample 4hr C2, Array Replicate 1

tag: cell type


title: Transgenic fly line Mut-1, male biological rep2

source_name: Transgenic fly line Mut-1_male

value: transgenic fly line Mut-1

value: male


title: Transgenic fly line Mut-1, male biological rep1


title: Transgenic fly line Mut-101, female biological rep2


title: Transgenic fly line Mut-1, female biological rep1

source_name: Transgenic fly line Mut-1_female


title: Transgenic fly line Mut-101, male biological rep1

source_name: Transgenic fly line Mut-101_male


title: Transgenic fly line WT-24, female biological rep2

source_name: Transgenic fly line WT-24_female

value: transgenic fly line WT-24


title: 4 hr Control Sample 1 Array a.txt

description: Sample 4hr C1, Array Replicate 1

tag: time


title: Transgenic fly line Mut-1, female biological rep2


title: Transgenic fly line WT-24, male biological rep1

source_name: Transgenic fly line WT-24_male


title: Sc cells vector ctrl  COS treatment 2

status: Public on Dec 22 2012

city: Bethesda

first: Maria

middle: de los Angeles

last: Jaime

state: Maryland

address: 50 South Drive, National Institutes of Health

department: NIDDK - LCDB

institute: NIH

description: This sample is the vector control (wild-type) strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Sample hybridization for NimbleGen 4X72k yeast microarrays (Roche NimbleGen, Inc.; Design ID A6186-00-01, TI4932 60mer expr X4) was performed as described in the manufacturer’s protocol.

scan_protocol: Microarrays were scanned with a Genepix 4000B scanner (Molecular Devices Inc. Sunnyvale, CA).

data_processing:
Raw images were obtained using GenePix Pro software (Version 5.0, Molecular Devices Inc. Sunnyvale, CA).  Raw probe intensities (x, y and signal reports) were obtained using NimbleScan software (v2.4, Roche NimbleGen, Inc). Data preprocessing of 60mer oligonucleotide arrays was performed using the BioConductor package Oligo. Genes with significant expression difference compared with the vector control (wild type, BY4743) were identified for each overexpressing strain using the BioConductor package Limma (Linear models for microarray analysis), taking P-value < 0.05 and log fold change > 1 as significant unless otherwise noted.
Data preprocessing of 60mer oligonucleotide arrays was performed using the BioConductor package Oligo (RMA-normalized, averaged gene-level signal intensity). Genes with significant expression difference compared with the vector control (wild type, BY4743) were identified for each overexpressing strain using the BioConductor package Limma (Linear models for microarray analysis), taking P-value < 0.05 and log fold change > 1 as significant unless otherwise noted.

source_name: Yeast cells, vector control  strain, 60 min, chitosan oligosaccharide treatment

label_protocol: cDNA synthesis and sample labeling for NimbleGen 4X72k yeast microarrays (Roche NimbleGen, Inc.; Design ID A6186-00-01, TI4932 60mer expr X4) was performed as described in the manufacturer’s protocol with minor modifications. cDNA synthesis was performed using 10 µg of total RNA. The sample labeling reactions were done using 1 µg of double stranded cDNA. Three cDNA biological replicates either with or without a 60 minutes exposure to COS-5.44 for each of the five overexpressing strains as well as an untransformed wild type BY4743 cells (vector control; for a total of 36 samples) were hybridized to NimbleGen 4X72k microarrays (Roche NimbleGen, Inc.).

growth_protocol: A confirmed colony of each overexpressing strain and the wild type with the empty vector was grown overnight at 30oC and shaking at 200 - 250 rpm. An overnight culture was used to inoculate 3 flasks each with 400 ml of 0.5X YPD pH 5. Cells were grown until the culture reached an OD600 of 0.8 and a 100 ml sample was collected (time zero).  Cells were collected by centrifugation (5 min, 4000 rpm) frozen with liquid nitrogen and stored at -80oC, for RNA extraction and labeling.

extract_protocol: Once all samples were collected a hot acid phenol-chloroform RNA extraction was performed.

treatment_protocol: The remaining 300 ml were treated with COS-5.44 (chitosan oligosaccharide, 112.5 μg/ml) and 100 ml samples were collected at 15, 30 and 60 minutes after treatment.

tag: growth stage

value: exponential

value: Chitosan oligosaccharide

tag: concetration

tag: time (min)

tag: overexpression

value: vector control


title: Sc cells vector ctrl  COS treatment 3

description: This sample is the vector control (wild-type) strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Transgenic fly line WT-6, male biological rep1

description: 6 Wt-M2

source_name: Transgenic fly line WT-6_male

tag: genotype/variation

value: transgenic fly line WT-6


title: Transgenic fly line WT-6, female biological rep2

description: 6 Wt-F3

source_name: Transgenic fly line WT-6_female


title: Non-transgenic fly, female biological rep1

source_name: Non-transgenic fly_female

value: Non-transgenic fly


title: Sc cells vector ctrl  control 2

description: This sample is the vector control (wild-type) strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, vector control  strain, untreated control


title: Sc cells vector ctrl  COS treatment 1

description: This sample is the vector control (wild-type) strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Transgenic fly line WT-24, female biological rep1


title: Transgenic fly line Mut-101, male biological rep2


title: Non-transgenic fly, female biological rep2


title: Transgenic fly line WT-6, male biological rep2

description: 6 Wt-M3


title: Transgenic fly line WT-24, male biological rep2


title: Sc cells RBA50 COS treatment 2

description: This sample is RBA50 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, RBA50 overexpressing strain, 60 min, chitosan oligosaccharide treatment


title: Sc cells RBA50 COS treatment 1

description: This sample is RBA50 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells RBA50 COS treatment 3

description: This sample is RBA50 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Transgenic fly line WT-6, female biological rep1

description: 6 Wt-F2


title: Sc cells vector ctrl  control 1

description: This sample is the vector control (wild-type) strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells RBA50 control 2

description: This sample is RBA50 overexpressing strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, RBA50 overexpressing strain, untreated control


title: Non-transgenic fly, male biological rep1

source_name: Non-transgenic fly_male


title: Sc cells RBA50 control 3

description: This sample is RBA50 overexpressing strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells MSG5 COS treatment 3

description: This sample is MSG5 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, MSG5 overexpressing strain, 60 min, chitosan oligosaccharide treatment


title: Sc cells RBA50 control 1

description: This sample is RBA50 overexpressing strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Non-transgenic fly, male biological rep2


title: Sc cells MSG5 control 2

description: This sample is MSG5 overexpressing strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, MSG5 overexpressing strain, untreated control


title: Sc cells MSG5 COS treatment 2

description: This sample is MSG5 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells MSG5 control 3

description: This sample is MSG5 overexpressing strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells MSG5 COS treatment 1

description: This sample is MSG5 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells MSG5 control 1

description: This sample is MSG5 overexpressing strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ERG24 COS treatment 3

description: This sample is ERG24 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, ERG24 overexpressing strain, 60 min, chitosan oligosaccharide treatment


title: Sc cells vector ctrl  control 3

description: This sample is the vector control (wild-type) strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ERG24 COS treatment 1

description: This sample is ERG24 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ERG24 control 3

description: This sample is ERG24 overexpressing strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, ERG24 overexpressing strain, untreated control


title: Sc cells ERG24 COS treatment 2

description: This sample is ERG24 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ERG24 control 2

description: This sample is ERG24 overexpressing strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells BCK2 COS treatment 3

description: This sample is BCK2 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, BCK2 overexpressing strain, 60 min, chitosan oligosaccharide treatment


title: Sc cells BCK2 COS treatment 2

description: This sample is BCK2 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ERG24 control 1

description: This sample is ERG24 overexpressing strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells BCK2 COS treatment 1

description: This sample is BCK2 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells BCK2 control 3

description: This sample is BCK2 overexpressing strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, BCK2 overexpressing strain, untreated control


title: Sc cells BCK2 control 2

description: This sample is BCK2 overexpressing strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ARL1 COS treatment 3

description: This sample is ARL1 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, ARL1 overexpressing strain, 60 min, chitosan oligosaccharide treatment


title: Sc cells ARL1 control 3

description: This sample is ARL1 overexpressing strain growth to OD 0.8. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Yeast cells, ARL1 overexpressing strain, untreated control


title: Sc cells ARL1 COS treatment 2

description: This sample is ARL1 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ARL1 COS treatment 1

description: This sample is ARL1 overexpressing strain growth to OD 0.8, then treated for 60 min with Chitosan oligosaccharide (5.44 kDa). It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ARL1 control 2

description: This sample is ARL1 overexpressing strain growth to OD 0.8. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells ARL1 control 1

description: This sample is ARL1 overexpressing strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Sc cells BCK2 control 1

description: This sample is BCK2 overexpressing strain growth to OD 0.8. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: MT_120

city: Gaithersburg

first: Peter

last: Johansson

address: 8717 Grovemont Circle

department: Pediatric Oncology Branch

institute: National Cancer Institute

description: Gene expression of NIH3T3 cells with mutant LPAR1

hyb_protocol: According to Affymetrix protocol

scan_protocol: Arrays were scanned with GeneChip Scanner 3000 following Affymetrix protocol

data_processing: Data were normalized with PLIER via apt-probeset-summarize 'plier-mm' (Affymetrix Power Tools v1.14.3.1) and further log-transformed to base 2

source_name: LPAR1 mutant, 120 mintues

label_protocol: According to Affymetrix protocol

extract_protocol: RNA was extracted as previously described by Wei et al in Cancer Res. 64: 6883-91, 2004.

tag: cell line

value: NIH3T3 Cells


title: MT_60

source_name: LPAR1 mutant, 60 mintues


title: DKK1

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description: Gene expression data from human DKK1 lentivirus transfected MOS-J cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C onMouse Genome 430 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner (Affymetrix)

data_processing: The data were analyzed with MAS5.0 algorithm

source_name: osteosarcoma cell

label_protocol: Biotinylated cRNA were prepared according to the 3' Express IVT protocol (Affymetrix) from 500 ng of total RNA.

growth_protocol: murine osteosarcoma cell line MOS-J (Joliat et al. 2002); The Jackson Laboratory at Bar Harbor) were expanded in medium consisting of αMEM, 10% FBS, 100 units ⋅ mL-1 penicillin G, and 100 µg ⋅ mL-1 streptomycin (Invitrogen).

extract_protocol: Total RNA was extracted from cell pellets using the HighPure RNA Isolation kit (Roche) following the manufacturer’s protocol. RNA quality was assessed by spectrophotometry and PCR for murine GAPDH after reverse transcription using the SuperScript III kit (Invitrogen).

treatment_protocol: In order to deliver the human Dkk1 gene into MOS-J cells, lentiviral particles were produced using the pLenti6/V5 Directional TOPO Cloning Kit and ViraPower Lentiviral Expression System (Invitrogen). Clones were selected for G418 resistance.   For non-viral transfection, human Dkk1 cDNA was cloned into the pLenti6.1 plasmid (Invitrogen) by standard methods. One million MOS-J cells were transfected with a NucleofectorII (Amaxa) using the manufacturer’s settings for Ewing sarcoma cells. Stable lines were generated by Blasticidin S selection. To follow tumor development in vivo, the transfected MOS-J cells were subsequently transduced with a lentiviral construct encoding dsRed-mito driven by the cytomegalovirus promoter (pDsRed2-Mito, BD Biosciences) to fluorescently label mitochondria. To achieve >99% purity, cells were enriched using a MoFlo XDP cell sorter (Beckman Coulter).

value: murine osteosarcoma cell line

value: MOS-J

tag: transfection

value: Human DKK1 lentivirus transfected


title: Control

description: Gene expression data from control lentivirus transfected MOS-J cells

value: Control lentivirus transfected


title: WT_0

description: Gene expression of NIH3T3 cells with wild-type LPAR1

source_name: LPAR1 wild-type, 0 minutes


title: S. aureus-oleic acid-rep3 [pdj812]

status: Public on Dec 21 2012

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St Jude Children's Research Hospital

description: Gene expression data for S. aureus treated with Oleic acid

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip S. aureus Genome  array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus subsp. aureus RN4220

source_name: S. aureus (RN4220) treated with Oleic acid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: S. aureus strain RN4220 was grown in tryptone broth or tryptone broth containing 500uM oleic acid to an OD600nm or 0.5

extract_protocol: Total RNA was isolated using Ambion RNAqueous purification kit according to the manufacturer's instructions and the purified RNA sample was treated with Turbo Dnase (Ambion).

treatment_protocol: DMSO or oleic acid

value: RN4220 is a derivative of  NCTC8325

tag: agent

value: Oleic acid


title: WT_120

source_name: LPAR1 wild-type, 120 mintues


title: MT_0

source_name: LPAR1 mutant, 0 minutes


title: S. aureus-oleic acid-rep1 [pdj810]


title: S. aureus-DMSO-rep2 [pdj808]

description: Gene expression data for S. aureus treated with DMSO only

source_name: S. aureus (RN4220) treated with DMSO

value: control


title: WT_60

source_name: LPAR1 wild-type, 60 mintues


title: S. aureus-DMSO-rep1 [pdj807]


title: S. aureus-DMSO-rep3 [pdj809]


title: breast_tissue_DNA [47273202]

city: Aarhus

first: Tomasz

middle: K

last: Wojdacz

address: Wilhelm Meyers Alle 230

department: Department of Biomedicine

institute: University of Aarhus

hyb_protocol: Performed using NimbleGen Hybridisation Sysyem accrding to manufactures protocol see:http://www.nimblegen.com/products/lit/06584098001_NG_Epigenetics_UGuide_v1p0.pdf

scan_protocol: MS 200 Microarray Scanner and the MS 200 Data Collection Software was used according to manufacturers protocol

data_processing:
Signal intensity data is extracted from the scanned images of each array using Roche NimbleGen's NimbleScan software.
Each feature on the array has a corresponding scaled log2 ratio (MeDIP/input), which is the ratio of the input signals for the experimental and test samples co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: tissue from breast reductions

label_protocol: MeDIP products were amplified using Sigma GenomePlex Complete WGA 2 Kit (Catalog No. WGA2-50RXN) to generate amount required by NimbleGen microarray service for this array type. Then purified samples using the Qiagen QIAquick PCR Purification Kit (Catalog No. 28106). Input and MeDIp fractions were directly labeled by random priming with Cy3 and Cy5 using exo-Klenow polimerase respectively  per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: DNA was extracted from tumors and breast tissue using DNeasy Blood & Tissue Kit (Qiagen, Germany). After extraction the methylated DNA fragments were enriched in each sample using the MeDIP protocol, as recommended by NimbleGen. The MeDip protcol used in this experiment was DNA_Methylation_Sample_Prep_v4p1 and it can be found at: www.nimblegen.com

value: female

tag: fraction

value: input

value: MeDIP


title: breast_cancer_DNA [47298802]

source_name: breast tumor tissue


title: breast_cancer_DNA [47287102]


title: S. aureus-oleic acid-rep2 [pdj811]

tag: strain


title: breast_cancer_DNA [47272302]


title: breast_cancer_DNA [47287702]


title: breast_cancer_DNA [47272602]


title: Rice-IR29-recovery-24h, biological rep2

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

country: China

institute: Chinese Acadamy of agricultural science

description: Indica, IR29

hyb_protocol: RNA from the three independent replicate samples of each treatment were used for hybridization to the Affymetrix Genechips® Rice Genome Array chips, which contain probes to query 51,279 transcripts from two rice cultivars, including 48,564 japonica transcripts and 1,260 indica transcripts from Affymetrix (Santa Clara, CA).Hybridization to the arrays and quality control checks were carried out at the Company of CapitalBio Corporation, Beijing. (Affymetrix GeneChip Expression Analysis g of this fragmented target cRNA wasmTechnical Manual).

scan_protocol: Genechip Scanner 3000 7G 4C

data_processing: The scanned images were visually examined and then processed to generate raw data saved as CEL files using GCOS1.4 default settings. Array normalization was performed using dChip software. The original microarray data set has been deposited in NCBI’s Gene Expression Omnibus (GSE No). Differentially expressed genes (DEGs) between the chilling stress sample and the control sample were identified by dChip software using a two-fold change threshold and in lower bound fold change method.

organism: Oryza sativa

source_name: Indica, IR29, leaf

label_protocol: Biotin labeled cRNA was produced with 5 ug of total RNA as starting material for each sample reaction.

growth_protocol: Mature non-dormant seeds were incubated at 30°C for 3 days prior to germination, and then sown in soil plates. LTH and IR29 were planted at the same spacing in the same plates; four plates each representing biological replicates were set up for both the chilling treatment and the control. Seedlings were allowed to grow to the S3 stage for 8 to 10 days at 29°C.

extract_protocol: For microarray hybridization experiments, total RNA was extracted using TRIzol reagent and then purified and concentrated using an RNeasy MinElute Cleanup Kit (Qiagen) for three replicates of each sample.

treatment_protocol: For the chilling stress treatments, S3-stage seedlings on soil plates were placed in a growth chamber (Beijing ZNYT, China) maintained at 4°C (± 1°C) with a 12 h light/12 h dark photoperiod. Control seedlings were grown under the same conditions except at 29°C. After 48 h of chilling treatment, seedlings on soil plates were moved to the control environment. Leaf samples from both chilled and control samples were collected with three biological replicates at 2, 8, 24, and 48 h time points during the course of the 48 h experiment, and then 24 h later, following recovery from chilling. All collected samples were snap-frozen in liquid nitrogen and stored at -70°C.

value: leaf

tag: genotype

value: Indica, IR29

tag: tolerance to chilling stress

value: chilling-sensitive

tag: stress

value: recovery from cold stress

tag: developmental stage

value: S3 stage


title: Rice-IR29-cold-48h, biological rep3

description: Indica, IR29

tag: tissue

value: cold stress


title: Rice-IR29-recovery-24h, biological rep3

description: Indica, IR29


title: Rice-IR29-recovery-24h, biological rep1

description: Indica, IR29


title: breast_cancer_DNA [47272902]

tag: gender


title: Rice-IR29-cold-48h, biological rep2

description: Indica, IR29

tag: time


title: breast_cancer_DNA [47268302]


title: breast_cancer_DNA [47273502]


title: Rice-IR29-cold-48h, biological rep1

description: Indica, IR29


title: Rice-IR29-cold-24h, biological rep3

description: Indica, IR29


title: breast_tissue_DNA [47268002]


title: breast_cancer_DNA [47295202]


title: breast_cancer_DNA [47268602]


title: breast_cancer_DNA [47287402]


title: Rice-IR29-cold-24h, biological rep2

description: Indica, IR29


title: Rice-IR29-cold-8h, biological rep3

description: Indica, IR29


title: Rice-IR29-cold-8h, biological rep1

description: Indica, IR29


title: breast_cancer_DNA [47260802]


title: breast_cancer_DNA [47266802]


title: Rice-IR29-cold-8h, biological rep2

description: Indica, IR29


title: Rice-IR29-cold-24h, biological rep1

description: Indica, IR29


title: breast_cancer_DNA [47267702]


title: Rice-IR29-cold-2h, biological rep2

description: Indica, IR29


title: breast_cancer_DNA [47272002]


title: breast_cancer_DNA [47267102]


title: breast_cancer_DNA [47296702]


title: breast_cancer_DNA [47267402]


title: Rice-IR29-cold-2h, biological rep1

description: Indica, IR29


title: Rice-IR29-control, biological rep3

description: Indica, IR29


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

source_name: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu, leaf

value: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: chilling-tolerant


title: Rice-IR29-control, biological rep1

description: Indica, IR29


title: Rice-IR29-cold-2h, biological rep3

description: Indica, IR29


title: breast_cancer_DNA [47268902]


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: breast_cancer_DNA [47266502]


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-IR29-control, biological rep2

description: Indica, IR29


title: breast stroma specimen 12 UOQ

city: Windber

first: Rachel

last: Ellsworth

state: PA

address: 620 Seventh Street

department: Clinical Breast Care Project

institute: Windber Research Institute

description: Hybridized to 250K_Sty

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

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

data_processing:
SNP data was imported into Partek® Genomics Suite™ 6.5 (Partek, Inc, St Louis, MO) as CEL files using default Partek parameters.  The rest of the rows are individual markers from the microarray with the log2 normalized intensities associated with each marker (marker labels are the row headers).  See Partek Intensity data.txt, linked as a supplementary file on the Series record.
Copy number alterations were identified using Partek Genomics Suite.  Copy number was calculated as a paired analysis, using the genomic DNA from each patient as the referent sample.  Deletions and amplifications were detected using a Hidden Markov Model using a minimum of five consecutive altered markers.  See Partek copy number data.txt, linked as a supplementary file on the Series record.
Primary data description: The data provided is allele intensities from which copy number data was calculated.

source_name: OCT embedded breast stroma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Excess OCT was trimmed from each specimen before cutting 10-20 12 mm  sections on the CM3050 S Cryostat (Leica Microsystems, Wetzlar, Germany). The 200-400 mg of tissue was homogenized using the PRO250 laboratory homogenizer (PRO Scientific Inc., Oxford, CT) for 30-60 seconds and processed using the Gentra Puregene Tissue kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.  Genomic DNA, used as the referent, was isolated from blood clots using Clotspin and Puregene DNA purification kits (Qiagen, Valencia, CA) according to manufacturer’s protocols.

value: Breast stroma

tag: patient diagnosis

value: IDCA

tag: sample diagnosis

value: No abnormalities

tag: copy number status

value: No copy number changes


title: breast_tissue_DNA [46940202]


title: breast stroma specimen 12 UIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 11 UIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Apocrine metaplasia


title: breast stroma specimen 11 LIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 11 UOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts


title: genomic DNA patient 12

description: Hybridized to 250K_Sty

source_name: Periperal blood

value: Periperal blood


title: breast_tissue_DNA [47261102]

value: female

value: input


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: leaf


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: control


title: breast stroma specimen 10 UOQ

description: Hybridized to 250K_Sty

value: In situ

value: Fibrocystic changes, Stromal fibrosis, Cysts, Apocrine metaplasia, Columnar cell change


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-recovery-24h, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: recovery from cold stress

value: S3 stage


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: chilling-tolerant

value: cold stress


title: breast stroma specimen 10 UIQ

description: Hybridized to 250K_Sty

value: Breast stroma


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: breast stroma specimen 10 LOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell change


title: breast_tissue_DNA [46906902]

value: MeDIP


title: genomic DNA patient 11

description: Hybridized to 250K_Sty

value: IDCA


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep2

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-control, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-8h, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-24h, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-2h, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: breast stroma specimen 9 LIQ

description: Hybridized to 250K_Sty

value: Stromal fibrosis

value: No copy number changes


title: genomic DNA patient 9

description: Hybridized to 250K_Sty

value: Periperal blood


title: breast stroma specimen 9 LOQ

description: Hybridized to 250K_Sty


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep3

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu


title: breast stroma specimen 7 UOQ

description: Hybridized to 250K_Sty

value: Atypical hyperplasia

value: No abnormalities


title: genomic DNA patient 7

description: Hybridized to 250K_Sty


title: breast stroma specimen 7 central

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts


title: Rice-Li-Jiang-Xin-Tuan-Hei-Gu-cold-48h, biological rep1

description: Japonica,Li-Jiang-Xin-Tuan-Hei-Gu

value: leaf


title: me3_Wt_1

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: Affymetrix

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 200 bp bandwidth and perfect match only.
results file descriptions: The resulting CHP files are generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 200 bp bandwidth and perfect match only.

growth_protocol: Flies were cultivated in vials with potato mash-yeast-agar medium.

extract_protocol: We used 150 pairs of salivary glands for each biological replicate (75 for ChIP + 75 for input). The glands were dissected in PBS and directly transferred to 2% formaldehyde in PBS with 0.1% Triton X-100 for 1-2 minutes for fixation. The glands were then washed in PBS and glycine was added to a final concentration of 0.125 M. The glands were then washed once in PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by two washes in TBS, 1 mM PMSF, protease inhibitor cocktail. The samples were homogenized in 500 µl lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1). Approximately 120 µl glass beads were added prior to sonication for 2 × 10 sec at output level 1, 2 × 10 sec at output level 2, 2 × 10 sec at output level 3 and finally 2 × 10 sec at output level 4 (Misonix XL2020, microtip). The samples were cleared by centrifuging for 10 min at 16000 g. For chromatin immunoprecipitation, 150 μl of cell lysate was diluted by a factor of ten in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl), and protein inhibitors were added. The diluted lysate was precleared by incubation with 60 µl of Dynabeads conjugated to Protein A (Dynal), pre-blocked by equilibration in 150 µl ChIP buffer. The cleared lysates were then incubated with 3 µl anti-HP1a (PRB-291C, Covance), 3 µl anti-H3K9me2 (ab1220, abcam) or 6 µl anti-H3K9me3 (ab8898, abcam) antibodies overnight at 4 C. The antibody complexes were precipitated by incubation with DNA-blocked Protein A Dynabeads for 1 hour at 4 C. The beads were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate) and twice with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The protein/DNA complexes were eluted from the antibodies by incubating them for 2 × 15 minutes at room temperature in 250 µl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. NaCl was added to a final concentration of 200 mM and protein/DNA crosslinks were reversed by heating at 65 C for 4 hours. 10 µl of 0.5 M EDTA, 20 µl of 1M Tris-HCl pH 6.5 and 1 µl of 20 mg/ml proteinase K were added before an additional incubation at 45 C for 1 hour. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA was then dissolved in 20 µl water.

tag: age

value: third instar larvae

value: salivary glands

tag: antibody

tag: antibody vendor/catalog#

value: Wt


title: breast stroma specimen 4 LOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 4 LIQ

description: Hybridized to 250K_Sty


title: me3_Wt_2

label_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

tag: genotype/variation


title: genomic DNA patient 4

description: Hybridized to 250K_Sty


title: me3_Su(var)3-9_2


title: me3_Setdb1_2


title: breast stroma specimen 3 LOQ

description: Hybridized to 250K_Sty

value: focal DCIS, microcalcifications, Stromal fibrosis


title: me3_Su(var)3-9_1


title: breast stroma specimen 3 LIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Microcalcifications, Moderate Intraductal hyperplasia


title: breast stroma specimen 12 LIQ

description: Hybridized to 250K_Sty

value: DCIS (focal), Fibrocystic changes, Stromal fibrosis, Cysts, Apocrine metaplasia, Columnar cell hyperplasia with atypia


title: me3_G9a_2


title: me3_G9a_1


title: genomic DNA patient 3

description: Hybridized to 250K_Sty


title: breast stroma specimen 3 central

description: Hybridized to 250K_Sty

value: Breast stroma

value: Microcalcifications, Stromal fibrosis


title: breast stroma specimen 4 UIQ

description: Hybridized to 250K_Sty


title: me2_Wt_2


title: breast stroma specimen 25 mammoplasty

description: Hybridized to 250K_Sty

value: Reductive mammoplasty


title: me2_Wt_1


title: me2_Su(var)3-9_2


title: genomic DNA patient 25

description: Hybridized to 250K_Sty


title: me2_Su(var)3-9_1


title: breast stroma specimen 3 UOQ

description: Hybridized to 250K_Sty

value: IDCA

value: Fibrocystic changes, Stromal fibrosis, Cysts, Sclerosing adenosis, Microcalcifications


title: genomic DNA patient 21

description: Hybridized to 250K_Sty


title: breast stroma specimen 24 mammoplasty

description: Hybridized to 250K_Sty

value: No copy number changes


title: me3_Setdb1_1


title: me2_Setdb1_2


title: me2_Setdb1_1


title: me2_G9a_2


title: breast stroma specimen 5 RIGHT LIQ

description: Hybridized to 250K_Sty

value: Prophylactic mastectomy


title: breast stroma specimen 5 LEFT UIQ

description: Hybridized to 250K_Sty


title: me2_G9a_1


title: HP1_Wt_4


title: breast stroma specimen 5 LEFT LIQ

description: Hybridized to 250K_Sty


title: genomic DNA patient 24

description: Hybridized to 250K_Sty

value: Periperal blood


title: HP1_Wt_3


title: HP1_Su(var)3-9_3


title: breast stroma specimen 5 RIGHT LOQ

description: Hybridized to 250K_Sty

value: No abnormalities


title: breast stroma specimen 5 RIGHT UOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 5 LEFT UOQ

description: Hybridized to 250K_Sty


title: genomic DNA patient 5

description: Hybridized to 250K_Sty


title: breast stroma specimen 21 mammoplasty

description: Hybridized to 250K_Sty


title: HP1_Pof_3

value: Pof


title: HP1_Setdb1_1


title: HP1_Setdb1_2


title: genomic DNA patient 22

description: Hybridized to 250K_Sty


title: breast stroma specimen 22 mammoplasty

description: Hybridized to 250K_Sty


title: HP1_Pof_1


title: HP1_G9a_2


title: HP1_G9a_1


title: genomic DNA patient 23

description: Hybridized to 250K_Sty


title: breast stroma specimen 23 mammoplasty

description: Hybridized to 250K_Sty

value: Copy number gain 8q


title: genomic DNA patient 26

description: Hybridized to 250K_Sty


title: breast stroma specimen 26 mammoplasty

description: Hybridized to 250K_Sty


title: genomic DNA patient 20

description: Hybridized to 250K_Sty


title: HP1_Su(var)3-9_1

value: third instar larvae


title: breast stroma specimen 20 UOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 20 UIQ

description: Hybridized to 250K_Sty

value: Apocrine metaplasia


title: breast stroma specimen 20 LOQ

description: Hybridized to 250K_Sty

value: Columnar cell changes with atypia, Microcalcifications, Sclerosing adenosis


title: breast stroma specimen 20 LIQ

description: Hybridized to 250K_Sty

value: No abnormalites


title: breast stroma specimen 19 LIQ

description: Hybridized to 250K_Sty

value: Microcalcifications, Sclerosing adenosis, Columnar cell change, Radial scar


title: breast stroma specimen 19 central

description: Hybridized to 250K_Sty

value: Fibroadenoma, Multiple peripheral papillomas, Sclerosing adenosis, Radial scar


title: breast stroma specimen 27 mammoplasty

description: Hybridized to 250K_Sty

value: Breast stroma


title: genomic DNA patient 18

description: Hybridized to 250K_Sty

value: ILCA


title: breast stroma specimen genomic DNA patient 27

description: Hybridized to 250K_Sty

value: Reductive mammoplasty


title: breast stroma specimen 18 UOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 18 UIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Microcalcifications, Columnar cell change


title: Rattus_Liver_28-day_study_thioacetade-treated_rep1

city: Fuchu-shi

first: Atsunori

last: Yafune

state: Tokyo

address: 3-5-8 Saiwai-cho

country: Japan

institute: Tokyo University of Agriculture and Technology

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, 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 2.6 (Roche NimbleGen, Inc.).

source_name: thioacetamide-treated

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: A one-week acclimatization period before exposed to thioacetamide.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Animals were treated with thioacetamide for 28 days. Untreated control animals were maintained on the basal diet and tap water without any treatment during the experimental period.

tag: strain background

value: male

value: liver

tag: treated with

value: thioacetamide for 28 days

tag: treatment route

value: gavage


title: genomic DNA patient 19

description: Hybridized to 250K_Sty

value: Periperal blood

value: IDCA


title: breast stroma specimen 18 LOQ

description: Hybridized to 250K_Sty

value: No abnormalities

value: No copy number changes


title: Rattus_Liver_28-day_study_thioacetade-treated_rep3


title: Rattus_Liver_28-day_study_cont_rep2

source_name: non-treated control

value: tap water (control) for 28 days


title: Rattus_Liver_28-day_study_cont_rep4


title: breast stroma specimen 17 UOQ

description: Hybridized to 250K_Sty


title: genomic DNA patient 17

description: Hybridized to 250K_Sty


title: breast stroma specimen 17 UIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 8 UOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 18 LIQ

description: Hybridized to 250K_Sty


title: Rattus_Liver_28-day_study_thioacetade-treated_rep4


title: Rattus_Liver_28-day_study_cont_rep1


title: breast stroma specimen 17 LOQ

description: Hybridized to 250K_Sty


title: genomic DNA patient 10

description: Hybridized to 250K_Sty

value: In situ


title: genomic DNA patient 16

description: Hybridized to 250K_Sty


title: Taf15-3

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

description: GL3 Luc cells treated with siRNA-Taf15

hyb_protocol: The Cy3- and Cy5-labeled reverse transcription reactions were mixed together, and purified and concentrated using the Microcon YM-30 filter (Millipore; Molsheim, France) Cy3- and Cy5-labeled and purified probes were resuspended in 40µl of hybridization solution (50 % formamide, 4X SSC, 0.6 % SDS, 5X Denhardt solution, 0.25 mg/ml of mouse Cot-1 DNA, 1mg/ml salmon sperm DNA and 1mg/ml poly(dA) Before hybridization, this probe solution was incubated for at least 45 min at 46° C after a 2 min denaturation at 95° C (pre-annealing). The slides were immersed in a prehybridization solution (50 % formamide, 4X SSC, 0.1 % SDS, 0.1 % BSA fraction V) for 30 min at 46° C before probe hybridization in a humid chamber overnight at 46° C. Prior scanning, three posthybridization washes were performed (first in 2X SSC, 0.2 % SDS for 5 min at 65° C; second in 2X SSC for 3 min at room temperature and finally in 0.2X SSC for 3 min at room temperature).

scan_protocol: Arrays were scanned using a ScanArray 4000 (Perkin Elmer, Courtaboeuf, France). Scanning was performed using two levels of PMT (100% and reduced or SPE).

data_processing:
Raw numerical data were extracted from the TIF images of Cy3 and Cy5 using Imagene 4.0 (BioDiscovery, El Segundo, CA, USA). Mean values of the fluorescent signal obtained for each spot and each channel were used for data analysis
Intra-slide normalization was performed using a method based on Quantile using the Elea software (Tseng et al. 2001; http://www-microarrays.u-strasbg.fr/Elea/index.html) to generate files HsO1G-(**)-qtil.txt
For each scanning a ratio is calculated from the Cy3 and Cy5 fluorophore. The retained ratio is from the 100% PMT level for non saturated spots, while reduced PMT scanning ratio was taken into account for the saturated spots.

source_name: GL3 Luc cells treated with siRNA-Taf15

label_protocol:
Cy3- and Cy5- labeled cDNA probes were prepared by reverse transcription of 10 µg total RNA for 2 h at 42° C [400U SuperScript II from Gibco-BRL (Invitrogen Cell Culture, France), 1X reverse transcription buffer, 0.5mM DTT, 2µg anchored oligodT: T20VVN, 500µM dATP, 500µM dCTP, 500µM dGTP, 100µM dTTP and 0.1mM Cy3- or Cy5-dUTP in a 30µl reaction]
The reverse transcription was stopped by a 5 min heating at 70° C and RNA was degraded by RNAse A (4µg) for 45 min at 37° C. For quality control, a small fraction of the probes was tested by agarose gel electrophoresis.

growth_protocol: GL3 Hela cells were maintained in DMEM 5% fetal calf serum and antibiotics (GENTA), 5% CO2 at 37°C

extract_protocol: RNA extraction on QIAGEN columns

treatment_protocol:
HeLa GL3 stable cell line was generated by infecting HeLa cells with a lentivirus expressing the GL3 luciferase gene under the control of the phosphoglycerate kinase (PGK) promoter (MOI=10).
Immunostaining with antiluciferase antibodies confirmed a nearly 100% efficiency of transduction. Early passages post-infection were used for the microarray experiment. Cells were transfected with si-LUC and si-Taf15 siRNAs and RNA was extracted 48 hours after transfection.

tag: cell line

value: HeLa GL3

tag: treatment

source_name: GL3 Luc cells treated with siRNA-Luc

value: siRNA-Luc


title: breast stroma specimen 16 UOQ

description: Hybridized to 250K_Sty


title: Rattus_Liver_28-day_study_thioacetade-treated_rep2


title: breast stroma specimen 16 UIQ

description: Hybridized to 250K_Sty


title: Taf15-2

description: GL3 Luc cells treated with siRNA-Taf15


title: Taf15-4

description: GL3 Luc cells treated with siRNA-Taf15


title: breast stroma specimen 16 LOQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 17 LIQ

description: Hybridized to 250K_Sty


title: control Luc-4

description: GL3 Luc cells treated with siRNA-Luc


title: breast stroma specimen 16 LIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 15 UIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 15 LIQ

description: Hybridized to 250K_Sty


title: control Luc-3

description: GL3 Luc cells treated with siRNA-Luc


title: breast stroma specimen 15 LOQ

description: Hybridized to 250K_Sty


title: Rattus_Liver_28-day_study_cont_rep3


title: breast stroma specimen 15 CENTRAL

description: Hybridized to 250K_Sty


title: control Luc-2

description: GL3 Luc cells treated with siRNA-Luc


title: control Luc-1

description: GL3 Luc cells treated with siRNA-Luc


title: Taf15-1

description: GL3 Luc cells treated with siRNA-Taf15


title: breast stroma specimen 14 RIGHT UIQ

description: Hybridized to 250K_Sty

value: Stromal fibrosis


title: breast stroma specimen 14 RIGHT LIQ

description: Hybridized to 250K_Sty

value: Breast stroma

value: Sclerosing adenosis, Fibroadenoma, Intraductal hyperplasia moderate


title: breast stroma specimen 14 LEFT UOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell change


title: breast stroma specimen 14 LEFT LOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell hyperplasia with atypia


title: breast stroma specimen 14 RIGHT UOQ

description: Hybridized to 250K_Sty


title: genomic DNA patient 14

description: Hybridized to 250K_Sty


title: breast stroma specimen 13 RIGHT UOQ

description: Hybridized to 250K_Sty

value: ILCA

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell hyperplasia, moderate Intraductal hyperplasia


title: genomic DNA patient 15

description: Hybridized to 250K_Sty


title: breast stroma specimen 13 RIGHT LOQ

description: Hybridized to 250K_Sty

value: Stromal fibrosis, Columnar cell change, Columnar cell hyperplasia


title: breast stroma specimen 13 RIGHT LIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Apocrine metaplasia, Columnar cell change, Columnar cell hyperplasia


title: breast stroma specimen 13 RIGHT UIQ

description: Hybridized to 250K_Sty


title: breast stroma specimen 13 LEFT LIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts


title: genomic DNA patient 13

description: Hybridized to 250K_Sty

value: Periperal blood


title: breast stroma specimen 1 UOQ

description: Hybridized to 250K_Sty

value: IDCA

value: No abnormalities

value: Copy number gain 1q, 8p, 10q


title: breast stroma specimen 14 RIGHT LOQ

description: Hybridized to 250K_Sty

value: No copy number changes


title: genomic DNA patient 8

description: Hybridized to 250K_Sty


title: breast stroma specimen 8 LOQ

description: Hybridized to 250K_Sty

value: Sclerosing adenosis


title: breast stroma specimen 14 LEFT UIQ

description: Hybridized to 250K_Sty

value: Microcalcifications, Fibrocystic changes, Stromal fibrosis, Cysts, Sclerosing adenosis, Columnar cell hyperplasia with atypia, Columnar cell change with atypia


title: breast stroma specimen 1 UIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Microcalcifications, Columnar cell change


title: breast stroma specimen 2 LIQ

description: Hybridized to 250K_Sty

value: Breast stroma

value: Mucinous carcnioma

value: Post-surgical changes


title: breast stroma specimen 1 LIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Apocrine metaplasia, microcalcifications, moderate intraductal hyperplasia, Columnar cell change

value: Copy number gain 1q, 9q, 10q, 11p


title: breast stroma specimen 2 UIQ

description: Hybridized to 250K_Sty

value: Copy number gain 10q, 11p, 14q


title: breast stroma specimen 1 LOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell change


title: genomic DNA patient 1

description: Hybridized to 250K_Sty


title: breast stroma specimen 2 LOQ

description: Hybridized to 250K_Sty

value: Stromal fibrosis, Microcalcifications


title: breast stroma specimen 13 LEFT UIQ

description: Hybridized to 250K_Sty

value: ILCA

value: Fibrocystic changes, Stromal fibrosis, Cysts


title: breast stroma specimen 13 LEFT LOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell hyperplasia, moderate Intraductal hyperplasia


title: genomic DNA patient 2

description: Hybridized to 250K_Sty

value: Periperal blood


title: breast stroma specimen 6 RIGHT UOQ

description: Hybridized to 250K_Sty

value: IDCA

value: Fibrocystic changes, Stromal fibrosis, Cysts, Sclerosing adenosis


title: breast stroma specimen 9 UOQ

description: Hybridized to 250K_Sty

value: In situ

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell change, Mild intraductal hyperplasia

value: No copy number changes


title: breast stroma specimen 6 RIGHT UIQ

description: Hybridized to 250K_Sty

value: Breast stroma

value: Fibrocystic changes, Stromal fibrosis, Cysts, Fibroadenomatoid nodule


title: breast stroma specimen 6 RIGHT LOQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cyst


title: breast stroma specimen 6 RIGHT LIQ

description: Hybridized to 250K_Sty

value: Fibrocystic changes, Stromal fibrosis, Cysts, Columnar cell change, Sclerosing adenosis


title: breast stroma specimen 6 LEFT UOQ

description: Hybridized to 250K_Sty

value: No abnormalities


title: breast stroma specimen 6 LEFT UIQ

description: Hybridized to 250K_Sty

value: Columnar cell change with atypia


title: genomic DNA patient 6

description: Hybridized to 250K_Sty


title: breast stroma specimen 6 LEFT LIQ

description: Hybridized to 250K_Sty


title: Array 2 - Cy3 B vs Cy5 A

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: RNA extracted from Caco-2 cells grown in conventional conditions or with an anaerobic apical compartment

hyb_protocol: The labelled samples were hybridized onto Agilent Technologies 44k whole human genome oligonucleotide arrays (G4112A) according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies).

scan_protocol: The microarray slides were scanned using a DNA Microarray Scanner G2565CA (Agilent Technologies) according to the manufacturer’s instructions.

data_processing: Microarrays scanned using Agilent Microarray Scanner G2565CA. Data processed using limma package in R 2.14.2.  No background correction, Loess within array normalisation and Aquantile between array normalisation.

source_name: B_rep6:Caco-2-Apical anaerobic

label_protocol: The RNA samples were amplified and labeled with either cyanine-3 or cyanine-5 labeled CTP dye using the Agilent Quick-Amp Labeling Kit (5190-0424) as per the manufacturer's instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies).

growth_protocol: Caco-2 cells were cultured in Transwell inserts in Medium 199 (M199; Invitrogen) containing 10% (v/v) fetal bovine serum (GIBCO), 1% (v/v) nonessential amino acids (MEM nonessential amino acids 100x solution; Sigma-Aldrich) and 1% Penicillin-Streptomycin (10,000 U penicillin G sodium salt and 10,000 mg streptomycin sulphate in 0.85% (v/v) saline; GIBCO) at 37°C in 5% CO₂.

extract_protocol: RNAprotect Cell Reagent (Qiagen) was added at a volume of approximately nine times the volume of the apical media to lyse the Caco-2 cells and stabilize the RNA. Total RNA was extracted from the Caco-2 cells using an RNeasy mini kit (Qiagen) as per the manufacturer’s protocol.

treatment_protocol: After 14 days the inserts were transfered to one of two custom built co-culture chambers either placed in a 5 % CO₂ incubator (control, conventional conditions) or an anaerobic workstation for 12 hours. Caco-2 cell in the anaerobic workstation were exposed to an anaerobic environement (10% CO₂, 10% H₂ in N₂) on the apical side, while recieving oxygen from the basal side (apical anaerobic conditions).

tag: culture condition

value: Apical anaerobic

source_name: A_rep5:Conventional -Total RNA

value: Conventional


title: Array 3 - Cy3 A vs Cy5 B

source_name: B_rep2:Apical anaerobic -Total RNA


title: cell line L-428, knock-down of PRAME

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Hodgkin's lymphoma cell line after knock-down of PRAME

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133Plus2.0 Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed using the MAS5.0 algorithm and Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. We used Expression Console version 1.1 (Affymetrix) for the scaling of the data.

source_name: Hodgkin’s lymphoma cell line L-428, transfected with vector pcDNA6.2-GW/EmGFP-miR-PRAME

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Established Hodgkin's lymphoma cells were grown under standard conditions.

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

treatment_protocol: Cells were transfected with empty control vector pcDNA6.2-GW/EmGFP-miR-neg or with vector pcDNA6.2-GW/EmGFP-miR-PRAME

tag: cell type

value: Hodgkin’s lymphoma cell line


title: Array 6 - Cy3 A vs Cy5 B

source_name: B_rep1:Apical anaerobic -Total RNA


title: SW480 APC, biological replicate C

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

description: Gene expression data from  SW480 cells reconstituted with wild-type APC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing:
RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human colorectal cancer cell line SW480, stably transfected with wild-type APC-expressing vector, transfected with Control siRNA

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: SW480 cells were cultured in RPMI 1640 with 10% FBS, glutamine and antibiotics, freshly supplemented with insulin, hydrocortisone, 1-thyoglicerol

treatment_protocol: Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions


title: Array 1 - Cy3 A vs Cy5 B

source_name: B_rep3:Apical anaerobic -Total RNA


title: SW480 APC, biological replicate A

value: transfected with wild-type APC-expressing vector, transfected with Control siRNA


title: SW480 APC, biological replicate D


title: kidney

city: Tokushima

first: Masato

last: Komatsu

address: Kuramoto-cho 3-18-15

institute: Genome Medicine

hyb_protocol: 2 μg of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent Whole Human Genome Microarray 4 × 44K slide (Agilent-014850, G4110F), with rotating incubation at 65˚C for 18 h.

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent Microarray scanner system (G2505B) in an ozone protection fume hood.

data_processing: Features of scanned image files containing the Cy3-fluorescence signals of the hybridized Agilent Microarrays were extracted using the Agilent Feature Extraction (ver. 9.5).  The data files were subjected to the GeneSpring (ver. 11.5) for analysis.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: kidney

label_protocol: For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit according to the manufacture’s guidance.  100 ng of total RNA of each sample and normal organs including heart, lung, liver, and kidney (Takara) was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

extract_protocol: We purified 30 TNBC, 13 normal ductal cells using lasermicrobeam microdissection system (PALM MicroBeam, Carl Zeiss MicroImaging Co., Ltd) in accordance with the manufacturer’s guidance.  Dissected cancer and normal ductal cells were dissolved in RLT lysis buffer (QIAGEN, Maryland, CA) containing 1% β-mercaptoethanol.  The extracted total RNAs were purified with RNeasy Mini Kit (QIAGEN, Velanica, CA) according to the manufacture’s protocol.  For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit according to the manufacture’s guidance.  Briefly, 100 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

tag: disease state

value: normal

tag: tissue

value: whole kidney tissue

tag: sample type

value: commercially available (Clonetech)


title: Array 5 - Cy3 B vs Cy5 A

source_name: B_rep5:Caco-2-Apical anaerobic

source_name: A_rep4:Conventional -Total RNA


title: liver

source_name: liver

value: whole liver tissue


title: cell line L-428, vector control

description: Gene expression data from established Hodgkin's lymphoma cell line

source_name: Hodgkin’s lymphoma cell line L-428, transfected with control vector pcDNA6.2-GW/EmGFP-miR-neg


title: SW480 APC, biological replicate B

institute: University of Padova


title: ID_Array-18

city: Greenwood

first: Chin-Fu

last: Chen

state: South Carolina

address: 113 Gregor Mendel Circle

department: Center for Molecuar Studies

institute: Greenwood Genetic Center

description: Contrast pair 34

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1 & version A.9.1.1 ).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Normalized log10 (Cy5/Cy3) ratios are available in the supplementary files.

source_name: Lymphoblastoid cell line, ID4

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

growth_protocol: Lymphoblastoid cells were grown with a complete medium in standard tissue culture conditions.

extract_protocol: Total RNA was extracted using the Qiagen RNA kit following manufacturer's instructions.

value: lymphoblastoid cells

tag: condition

value: intellectual disability

source_name: Lymphoblastoid cell line, control9

value: control


title: ID_Array-17

description: Contrast pair 33

source_name: Lymphoblastoid cell line, ID3

source_name: Lymphoblastoid cell line, control7


title: Array 4 - Cy3 B vs Cy5 A

source_name: B_rep4:Caco-2-Apical anaerobic

source_name: A_rep6:Conventional -Total RNA


title: SW480 sibcat, biological replicate C

description: Gene expression data from  SW480 cells depleted of b-catenin

source_name: human colorectal cancer cell line SW480, stably transfected with empty vector, transfected with beta-catenin siRNA


title: SW480 sibcat, biological replicate D

value: stably transfected with empty vector, transfected with beta-catenin siRNA


title: ID_Array-16

description: Contrast pair 32

source_name: Lymphoblastoid cell line, ID9


title: lung

source_name: lung

value: whole lung tissue


title: ID_Array-15

description: Contrast pair 31

source_name: Lymphoblastoid cell line, control10


title: SW480 siTAZ, biological replicate D

description: Gene expression data from  SW480 cells depleted of TAZ

source_name: human colorectal cancer cell line SW480, stably transfected with empty vector, transfected with TAZ siRNA


title: evolved clone B11_1 vs wt DNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: evolved clone B11_1 vs wt DNA

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2012-03-06 Scan Time : 12:28:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

extract_protocol:
Extracted molecule : DNA
Extraction method : Zymo genomic DNA kit

tag: strain name

source_name: Clone B11_1

value: clone B11_1


title: SW480 sibcat, biological replicate A


title: ID_Array-13

description: Contrast pair 29

source_name: Lymphoblastoid cell line, ID11

source_name: Lymphoblastoid cell line, ID7


title: evolved clone B13_1 vs wt DNA

description: evolved clone B13_1 vs wt DNA

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentDNA.pdf

source_name: Clone B13_1

value: clone B13_1


title: ID_Array-12

description: Contrast pair 28

source_name: Lymphoblastoid cell line, ID2


title: evolved clone B9_1 vs wt DNA

description: evolved clone B9_1 vs wt DNA

source_name: Clone B9_1

value: clone B9_1


title: ID_Array-14

description: Contrast pair 30


title: heart

source_name: heart

value: whole heart tissue


title: SW480 sibcat, biological replicate B


title: normal mammary gland ductal cells N10

source_name: normal mammary gland ductal cells

value: mammary gland ductal cells

tag: gender

value: female

tag: age (y)


title: ID_Array-10

description: Contrast pair 26

source_name: Lymphoblastoid cell line, ID5

source_name: Lymphoblastoid cell line, control8


title: normal mammary gland ductal cells N36


title: ID_Array-9

description: Contrast pair 25

source_name: Lymphoblastoid cell line, ID10

source_name: Lymphoblastoid cell line, ID6


title: evolved clone B10_1 vs wt DNA

description: evolved clone B10_1 vs wt DNA

source_name: Clone B10_1

value: clone B10_1


title: normal mammary gland ductal cells N53


title: SW480 siTAZ, biological replicate A

value: stably transfected with empty vector, transfected with TAZ siRNA


title: ID_Array-11

description: Contrast pair 27


title: ID_Array-7

description: Contrast pair 23

source_name: Lymphoblastoid cell line, control9

source_name: Lymphoblastoid cell line, ID1


title: ID_Array-8

description: Contrast pair 24


title: SW480 siGFP, biological replicate D

description: Gene expression data from control SW480 cells

source_name: human colorectal cancer cell line SW480, stably transfected with empty vector, transfected with Control siRNA


title: ASD_Array-16

description: Contrast pair 16

source_name: Lymphoblastoid cell line, control6

source_name: Lymphoblastoid cell line, autism7

value: autism


title: ASD_Array-14

description: Contrast pair 14

source_name: Lymphoblastoid cell line, control5

source_name: Lymphoblastoid cell line, autism10


title: ASD_Array-13

description: Contrast pair 13

source_name: Lymphoblastoid cell line, autism9


title: ASD_Array-15

description: Contrast pair 15


title: ASD_Array-12

description: Contrast pair 12

source_name: Lymphoblastoid cell line, control4


title: ASD_Array-11

description: Contrast pair 11

source_name: Lymphoblastoid cell line, autism8


title: ASD_Array-10

description: Contrast pair 10

source_name: Lymphoblastoid cell line, control3


title: SW480 siTAZ, biological replicate C

source_name: human colorectal cancer cell line SW480, stably transfected with empty vector, transfected with TAZ siRNA


title: normal mammary gland ductal cells N56

source_name: normal mammary gland ductal cells

value: normal


title: ASD_Array-8

description: Contrast pair 8

source_name: Lymphoblastoid cell line, autism4

source_name: Lymphoblastoid cell line, autism2


title: ASD_Array-9

description: Contrast pair 9


title: normal mammary gland ductal cells N8


title: SW480 siTAZ, biological replicate B


title: ASD_Array-7

description: Contrast pair 7

source_name: Lymphoblastoid cell line, control2

source_name: Lymphoblastoid cell line, autism6


title: normal mammary gland ductal cells N43


title: SW480 siGFP, biological replicate C

value: stably transfected with empty vector, transfected with Control siRNA


title: normal mammary gland ductal cells N51


title: SW480 siGFP, biological replicate B


title: normal mammary gland ductal cells N50


title: SW480 siGFP, biological replicate A


title: ASD_Array-6

description: Contrast pair 6

source_name: Lymphoblastoid cell line, autism5


title: ASD_Array-4

description: Contrast pair 4

source_name: Lymphoblastoid cell line, control1

source_name: Lymphoblastoid cell line, autism1


title: ASD_Array-5

description: Contrast pair 5


title: ASD_Array-3

description: Contrast pair 3

source_name: Lymphoblastoid cell line, autism3


title: normal mammary gland ductal cells N45


title: MII sibcat/siTAZ, biological replicate D

description: Gene expression data from  MII cells depleted of b-catenin and TAZ

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA and TAZ siRNA

growth_protocol: MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.

value: MCF10-T1k (MII)


title: normal mammary gland ductal cells N46


title: ASD_Array-2

description: Contrast pair 2

value: lymphoblastoid cells


title: ASD_Array-1

description: Contrast pair 1


title: normal mammary gland ductal cells N21


title: MII sibcat/siTAZ, biological replicate B

value: transfected with beta-catenin siRNA and TAZ siRNA


title: triple negative breast cancer cells T78

source_name: triple negative breast cancer cells

value: triple negative breast cancer

value: triple negative breast cancer cells


title: normal mammary gland ductal cells N19


title: triple negative breast cancer cells T453


title: triple negative breast cancer cells T392


title: MII sibcat, biological replicate C

description: Gene expression data from  MII cells depleted of b-catenin

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA

value: transfected with beta-catenin siRNA


title: MII sibcat/siTAZ, biological replicate C


title: normal mammary gland ductal cells N42


title: triple negative breast cancer cells T438


title: MII sibcat/siTAZ, biological replicate A


title: MII sibcat, biological replicate B


title: MII sibcat, biological replicate A


title: MII sibcat, biological replicate D


title: MII siAPC/siTAZ, biological replicate C

description: Gene expression data from  MII cells depleted of APC and TAZ

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA and TAZ siRNA


title: MII siAPC/siTAZ, biological replicate D

value: transfected with APC siRNA and TAZ siRNA


title: triple negative breast cancer cells T445


title: triple negative breast cancer cells T337


title: MII siAPC/siTAZ, biological replicate B


title: MII siAPC/siTAZ, biological replicate A


title: triple negative breast cancer cells T566


title: triple negative breast cancer cells T562


title: MII siAPC, biological replicate D

description: Gene expression data from  MII cells depleted of APC

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA

value: transfected with APC siRNA


title: triple negative breast cancer cells T651


title: triple negative breast cancer cells T423


title: MII siAPC, biological replicate B


title: SK-N-MC control

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

description:
S1318_SK_N_MC_nsiRNA
knock-down control SK-N-MC cells treated with control siRNA

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: Expression Console, RMA normalization.

source_name: Ewing tumor cell line SK-N-MC

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Cells were grown in plastic cell culture flasks in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 20% heat-inactivated fetal bovine serum, 1% glutamine, 100 µg/mL gentamycin and 200 mg/dl D-glucose .

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions.

value: Ewing tumor cell line SK-N-MC

tag: sirna treatment group

value: control


title: SK-N-MC siDKK2_1

description:
S1319_SK_N_MC_DKK_1
DKK2 knock-down SK-N-MC cells treated with DKK2 siRNA


title: SK-N-MC siITM2A_1

description:
S1320_SK_N_MC_ITM2A_1
ITM2A knock-down SK-N-MC cells treated with ITM2A siRNA


title: MII siAPC, biological replicate A


title: triple negative breast cancer cells T27


title: Mouse#43

city: Koeln

first: Bernhard

last: Schermer

address: Kerpener Str. 62

department: Dept. II for Internal Medicine

institute: Universitaet zu Koeln

description: SAMPLE 20

hyb_protocol: Manufacturer's protocol (Affymetrix GeneChip)

scan_protocol: Affymetrix GeneChip 3000 6G scanner

data_processing: Robust Multiarray Average (RMA), Affymetrix Power Tools, v1.12.0

source_name: Ercc1 mouse at 14 wks

label_protocol: Encore Biotin Module, NuGen Technologies, San Carlos, CA, USA

extract_protocol: Frozen glomeruli were thawn and total RNA was extracted and purified using commercial homogenization (Bio 101 FastPrep FP120-120V, Savant, Midland, MI, USA) and the RNeasy kit (Qiagen, Hilden, Germany).

value: genetically uniform hybrid C57BL/6-FVB [PMID 22953029]

tag: age

value: 14 weeks


title: MII siGFP, biological replicate A

description: Gene expression data from control MII cells

source_name: human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA

value: transfected with Control siRNA


title: Mouse#34

description: SAMPLE 15

source_name: Ercc1 mouse at 4 wks

tag: genotype/variation

value: 4 weeks


title: MII siGFP, biological replicate D


title: Mouse#42

description: SAMPLE 19

tag: strain background


title: A673 siDKK2_1

description:
S1316_a673_dkk2_1
DKK2 knock-down A673 cells treated with DKK2 siRNA

source_name: Ewing tumor cell line A673

value: Ewing tumor cell line A673


title: Mouse#41

description: SAMPLE 18


title: Mouse#36

description: SAMPLE 17


title: A673 siITM2A_7

description:
S1317_a673_itm2a_7
ITM2A knock-down A673 cells treated with ITM2A siRNA