title: PTCs_GW4064_1

status: Public on Jun 26 2015

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026655 Whole Mouse Genome Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw intensity data were obtained using Agilent's Feature Extraction Software version 10.7 for array image analysis and the calculation of spot intensity measurements. Data analysis was carried out with R/Bioconductor. The processed intensities and normalized across samples were loaded by using quantile normalization. Differential expression was computed using the limma package. Additional details on the analysis methods can be found at: http://fgcz-bfabric.uzh.ch/wiki/tiki-index.php?page=app.two_groups

source_name: mouse proximal tubule cells, GW4064 (1uM), 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Kidney cortices from mice were dissected, sliced, minced and digested in 0.25% trypsin solution (Life Technologies BRL, Grand Island, NY) in a shaking incubator at 37°C for 1 hour. Trypsin was neutralized with growth medium (DMEM and 10% FBS containing 100 U/ml penicillin and 0.1 mg/ml streptomycin). The suspension was pipetted and was passed through a 100-μm cell strainer (Becton Dickinson Labware, Franklin Lakes, NJ). The samples were centrifuged (600 rpm for 5 minutes) to pellet the tubules, washed with 10 ml of medium, centrifuged, and washed twice more. The final pellet, consisting mostly of renal tubules, was resuspended in culture medium (REBM bullet kit, Clonetics), plated onto culture dishes (Nalge Nunc International, Naperville, IL) and incubated at 37°C in a carbon dioxide incubator with medium changes every 2 days until confluent.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen).

treatment_protocol: Experiments were carried out in serum-free DMEM. Cells were incubated by the addition of DMSO or 1μM GW4064 (Sigma-Aldrich (catalog #G5172), St. Louis, MO USA) for 24 hours.

tag: strain/background

value: 6 weeks

value: primary cultured kidney proximal tubule cells


title: PTCs_GW4064_3

type: RNA

molecule: total RNA

organism: Mus musculus

tag: gender

value: male

tag: age

tag: tissue

tag: treatment


title: PTCs_DMSO_3

source_name: mouse proximal tubule cells, DMSO, 24 hours

value: DMSO


title: Mesenchymal stromal cell, healthy donor, sample HB

status: Public on Jun 30 2015

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Microarray data were normalized using the Cubic Spline normalization method with the Illumina BeadStudio Gene Expression Module (Illumina). Statistical analysis of microarray was performed using Significance Analysis for Microarrays (SAM)

label: biotin

organism: Homo sapiens

source_name: Healthy donor MSC

label_protocol: As per manufacturer's instructions.

growth_protocol: Bone marrow derived mononuclear cells were obtained from 5 to 15 ml of heparinized bone marrow aspirate by density gradient centrifugation on Ficoll. Cells were plated on non-coated 75 cm2 polystyrene flasks at a cell density of 160000/cm2 in complete culture medium (LG-DMEM [Invitrogen, Paisley, United Kingdom] supplemented with penicillin and streptomycin [merk] and 10% fetal bovine serum [FBS; HyClone, Verviers, Belgium]). We used a characterized and defined FBS batch preselected for its potential to support MSC expansion and continued to use this specific batch throughout the culture period.

extract_protocol: RNA was isolated from frozen cell pellets of at least 1*10e6 undifferentiated mesenchymal stem cells at passage 2 to 5 using TRIzol reagent (Invitrogen). Cells were lysed in TRIzol, followed by phase separation in chloroform (merk), precipitation using 2-propanolol (merk) and washing in 75% ethanol. RNA clean-up was performed using the Qiagen Rneasy mini kit with on-column DNAse treatment. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000, respectively.

tag: cell type

value: Mesenchymal stromal cells


title: PTCs_GW4064_4


title: PTCs_DMSO_4


title: PTCs_DMSO_1


title: Mesenchymal stromal cell, osteosarcoma patient, sample 005

source_name: Osteosarcoma patient MSC


title: PTCs_GW4064_2


title: Water avoidance stress rep 3

status: Public on Jul 01 2015

city: Los Angeles

first: Sylvie

last: Bradesi

state: CA

address: 10833 Le Conte Avenue

department: Digestive Diseases

country: USA

institute: UCLA

hyb_protocol: miRCURY standard protocol

scan_protocol: miRCURY standard protocol

data_processing: miRCURY standard protocol

organism: Rattus norvegicus

source_name: spinal cord, control

label_protocol: miRCURY standard protocol

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN) following the manufacturer's recommendations.. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: spinal cord

value: control

value: 12 weeks old


title: PTCs_DMSO_2


title: E.coli gene expression data in deletion of chaperone DnaK

status: Public on Jun 18 2015

city: Beijing

first: Dongjie

last: Fan

address: Changbai Road NO 155,

country: China

institute: National institute for communicable disease control and prevention,Chinese center for disease control and prevention

description: The gene expression data were extracted from images using LuxScan 3.0 software (CapitalBio).

hyb_protocol: The 9300 E.coli genome oligo-arrays were manufactured by CapitalBio Corp.(Beijing,China) using the 5'-amino-modified operon 70-mer probe library(Operon, Huntsville,AL,USA).In addition to E.coli 4 house-keeping genes as internal controls,8 intergenic sequences from yeast were used as external controls. All nucleotides were dissolved in DNA spotting solution at 0.02 mM and printed on aminosilane-coated glass slides using SmartArray-136TM spotter(CapitalBio).After printing,the slides were baked for 1 h at 80 degrees and stored dry at room temperature unit use. Prior hybridization, the slides were rehydrated over 65 degrees water for 10s and UV cross-linked. The non-immoblized oligonucleotides were washed off with 0.5% SDS solution for 10 min at 42 degrees, and SDS was removed by dipping the slides in anhydrous ethanol for 30 s. Labeled control and experimental samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into hybridization solution [3¡Ásaline-sodium citrate(SSC),0.2% SDS,25% formamide and 5¡ÁDenhart's]. Microarrays were hybridized at 42 degrees overnight and washed with two consecutive washing solution (0.2% SDS,2¡ÁSSC at 42 degrees and 0.2% SSC) for 5 min at room temperature.

scan_protocol: After hybridization, slides were scanned with a confocal scanner LuxScanTM 10KA.

data_processing: The signal/noise ratio for each array was calculated, for each spot and each channel, as (foreground intensity minus background intensity)/(standard deviation of the background). The raw data were normalized  using a space and intensity-dependant LOWESS program. Faint spots were removed from the data if the intensities were lower than the average intensity plus 2 standard deviations of the negative controls. The significant genes differentiating wild-type and deleting dnaK were selected based on q<0.05 and greater than twofold as criteria.

organism: Escherichia coli

source_name: DnaK deletant_37C

label_protocol: Total RNA was reverse transcripted into cDNA using random primers.The cDNA were purified by PCR NucleoSpin Extract II kit(MN)and vacuum evaporated. The fluorescence labeling reactions contained Klenow enzyme,dNTP,Cy5-dCTP and Cy3-dCTP (GE Healthcare). The reaction was carried out at 37 ¡ãC for 90 min and stopped by addition of 25mM EDTA and 0.25% sodium dodecyl sulfate. Labeled DNA targets were purified by PCR NucleoSpin Extract II Kit(MN).

extract_protocol: Total RNA was isolated from strains using NucleoSpin RNAII kit (Macherey-Nagel Corporation) following the instruction. RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray.

tag: strain background

tag: genotype/variation

value: DnaK deletant

value: wild type


title: ESR1 Y537S vs. YFP, replicate 3

status: Public on Jun 12 2015

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: YFP vs Y537S-c

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was calculated

source_name: T47D YFP cRNA 0.85ug

growth_protocol: T47D stable cells expressing various transgenes were cultured in hormone-deprived media containing charcoal-stripped serum for seven days. YFP-expressing control cells were stimulated or not with 1nM beta-estradiol at day 6 for 24 hours.

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: see above for estradiol-treated cells

tag: cell line

value: YFP cRNA 0.85ug

source_name: T47D ESR1 Y537S cRNA 0.85ug

value: ESR1 Y537S cRNA 0.85ug


title: ESR1 Y537S vs. YFP, replicate 4

description: YFP vs Y537S-d

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: ESR1(412) truncation vs. YFP, replicate 3

description: YFP vs ESR1(412)-c


title: Estrogen treatment vs. YFP, replicate 2

description: YFP vs YFP+E2-2

source_name: T47D YFP+E2 cRNA 0.85ug

value: YFP+E2 cRNA 0.85ug


title: ESR1 Y537S vs. YFP, replicate 1

description: YFP vs Y537S-a


title: POLH vs. YFP, replicate 3

description: YFP vs POLH-c

source_name: T47D POLH cRNA 0.85ug

value: POLH cRNA 0.85ug


title: ESR1-PCDH11X fusion vs. YFP, replicate 1

description: YFP vs ESR1-PCDH11-1

source_name: T47D ESR1-PCDH11X cRNA 0.85ug

value: ESR1-PCDH11X cRNA 0.85ug


title: Estrogen treatment vs. YFP, replicate 6

description: YFP vs YFP+E2-c


title: Estrogen treatment vs. YFP, replicate 4

description: YFP vs YFP+E2-a


title: POLH vs. YFP, replicate 1

description: YFP vs POLH-a


title: Estrogen treatment vs. YFP, replicate 3

description: YFP vs YFP+E2-3


title: ESR1-PCDH11X fusion vs. YFP, replicate 3

description: YFP vs ESR1-PCDH11-3


title: ESR1(412) truncation vs. YFP, replicate 2

description: YFP vs ESR1(412)-b


title: ESR1-PCDH11X fusion vs. YFP, replicate 2

description: YFP vs ESR1-PCDH11-2


title: ESR1 Y537S vs. YFP, replicate 2

description: YFP vs Y537S-b


title: SHR_E16.0_kidney3 [gene-level]

city: Berlin

first: Reinhold

last: Kreutz

address: Charitéplatz 1

country: Germany

institute: Charité

description: LEO-MWF-19-Leo_302-220212-RatGe-St1-0.CEL

hyb_protocol: Arrays were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G using GeneChip® Operating Software (GCOS) for image processing

data_processing:
After normalization the arrays have been checked for outliers by principal component analysis (PCA), using a correlation dispersion matrix and normalized Eigenvector scaling. The analysis of differential expression of summarized gene level expression has been performed with Partek Genomic Suite version 6.5
RaGene-1_0-st-v1.r4.pgf
RaGene-1_0-st-v1.r4.mps

source_name: SHR-E16.0 kidney

label_protocol: Terminal labeling kits (Ambion, New-York, USA)

growth_protocol: Rat embryonic kidney dissected at day E15.5/E16.0 respectively

extract_protocol: embryonic kidneys were harvested, snap-frozen in liquid nitrogen and stored at -80°C. Total RNA preparations of male kidney tissues were performed for MWF rats at developmental stage E15.5 and SHRs at E16.0 (n=4) using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: not applicable

tag: strain

value: SHR

value: kidney


title: Estrogen treatment vs. YFP, replicate 5

description: YFP vs YFP+E2-b


title: Estrogen treatment vs. YFP, replicate 1

description: YFP vs YFP+E2-1


title: ESR1-PCDH11X fusion vs. YFP, replicate 4

description: YFP vs ESR1-PCDH11-4


title: POLH vs. YFP, replicate 2

description: YFP vs POLH-b


title: ESR1(365) truncation vs. YFP, replicate 4

description: YFP vs ESR1(365)-d


title: ESR1(412) truncation vs. YFP, replicate 1

description: YFP vs ESR1(412)-a


title: Balbc_p53null_T11_sorted_miR200_noDox4

status: Public on Jun 22 2015

description: Passaged Mammary Tumor

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Whole Mouse Reference RNA

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: reference

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

extract_protocol: Total RNA isolated using Qiagen miRNeasy Kit

value: Balbc

value: p53null mammary tumor


title: ESR1(365) truncation vs. YFP, replicate 3

description: YFP vs ESR1(365)-c


title: ESR1-YAP1 fusion vs. YFP, replicate 2

description: YFP vs ER-YAP1-2

source_name: T47D ESR1-YAP1 cRNA 0.85ug

value: ESR1-YAP1 cRNA 0.85ug


title: ESR1-CCDC170 fusion vs. YFP, replicate 2

description: YFP vs ESR1(253)->CCDC170-b

source_name: T47D ESR1-CCDC170 cRNA 0.85ug

value: ESR1-CCDC170 cRNA 0.85ug


title: ESR1(365) truncation vs. YFP, replicate 1

description: YFP vs ESR1(365)-a


title: Balbc_p53null_T11_sorted_miR200_plusDox2

description: Passaged Mammary Tumor

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: ESR1-CCDC170 fusion vs. YFP, replicate 3

description: YFP vs ESR1(253)->CCDC170-c


title: Rat_Liver_P3_4

status: Public on Jun 03 2015

city: Strasbourg

first: Fabrice

last: Bertile

address: 25 rue Becquerel

department: Analytical Sciences

country: France

institute: CNRS, IPHC

hyb_protocol: Samples were hybridized with GeneChip Rat Exon 1.0 ST Arrays (Affymetrix) and scanned within the IGBMC microarray and sequencing platform (Strasbourg, France).

scan_protocol: Array scanning using an Affymetrix GeneChip Scanner 3000 7G was performed according to the manufacturer's instructions (Affymetrix).

data_processing: Raw data were processed with the GeneChip Operating v1.4 (GCOS) and Expression Console v1.1 softwares (Affymetrix) for background correction, normalization and quantification. Data analysis and statistical evaluations were performed with customized R codes (version 2.8.1, http://www.r-project.org/). Analysis was performed on the extended set of probesets. Reference genes were eliminated. Levels of expression were considered differential on the basis of ANOVA and post-hoc Tukey tests results. Hierarchical clustering was performed using the Cluster v3.0 software. Dendrograms were generated and vizualized using the Treeview v1.1.3 program.

source_name: Male rat liver, fasted (P3)

label_protocol: cRNA were synthesized from total RNA depletd in rRNA. Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix). All assays were performed as per the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev. 2) (http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st).

growth_protocol: Male rats were nutritionally manipulated to create three different metabolic statuses, i.e., the fed and two fasted states (phase 2 and phase 3).

extract_protocol: RNA was isolated from homogenized liver samples with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Liver samples were quickly collected from freshly sacrificed rats, and pieces were immediately frozen in liquid nitrogen and stored at -80°C until analysis. Frozen liver samples homogenization was obtained using a laboratory ball mill.

value: Sprague Dawley

value: male

value: liver

tag: nutritional state

value: phase 3 of fasting


title: ESR1-CCDC170 fusion vs. YFP, replicate 1

description: YFP vs ESR1(253)->CCDC170-a


title: Rat_Liver_P3_3


title: Rat_Liver_P3R2_1

source_name: Male rat liver, re-fed after P3 (P3r2)

value: re-feeding after phase 3


title: Rat_Liver_P3R2_4


title: ESR1-NOP2 fusion vs. YFP, replicate 3

description: YFP vs ER-NOP2-3

value: YFP cRNA 0.85ug

source_name: T47D ESR1-NOP2 cRNA 0.85ug

value: ESR1-NOP2 cRNA 0.85ug


title: Rat_Liver_P3R2_2


title: Balbc_p53null_T11_sorted_miR200_plusDox1

description: Passaged Mammary Tumor


title: Rat_Liver_P3R2_3


title: ESR1-YAP1 fusion vs. YFP, replicate 1

description: YFP vs ER-YAP1-1


title: ESR1-NOP2 fusion vs. YFP, replicate 1

description: YFP vs ER-NOP2-1


title: Balbc_p53null_T11_sorted_miR200_noDox2

description: Passaged Mammary Tumor


title: Balbc_p53null_T11_sorted_miR200_noDox3

description: Passaged Mammary Tumor


title: ESR1(365) truncation vs. YFP, replicate 2

description: YFP vs ESR1(365)-b


title: ESR1-YAP1 fusion vs. YFP, replicate 3

description: YFP vs ER-YAP1-3


title: ESR1-NOP2 fusion vs. YFP, replicate 2

description: YFP vs ER-NOP2-2


title: ESR1-POLH fusion vs. YFP, replicate 2

description: YFP vs ER-POLH-2

source_name: T47D ESR1-POLH cRNA 0.85ug

value: ESR1-POLH cRNA 0.85ug


title: Rat_Liver_P3_2


title: ESR1-POLH fusion vs. YFP, replicate 1

description: YFP vs ER-POLH-1


title: ESR1-POLH fusion vs. YFP, replicate 3

description: YFP vs ER-POLH-3


title: Balbc_p53null_T11_sorted_miR200_noDox1

description: Passaged Mammary Tumor


title: Balbc_p53null_T11_sorted_miR200_plusDox3

description: Passaged Mammary Tumor


title: Rat_Liver_P2_4

source_name: Male rat liver, fasted (P2)

value: phase 2 of fasting


title: Rat_Liver_P2_3


title: Rat_Liver_Fed_4

source_name: Male rat liver, fed

value: feeding


title: Rat_Liver_Fed_3


title: Rat_Liver_P2_1


title: Rat_Liver_Fed_2


title: Wt mid-log Norepi with CDM 1

status: Public on May 12 2015

city: Louisville

first: Whitney

middle: Ann

last: Weigel

state: Kentucky

address: 501 S Preston St

department: OIID

institute: University of Louisville

description: Gene expression at mid-log

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 3x18k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

organism: Aggregatibacter actinomycetemcomitans

source_name: Wt Aggregatibacter actinomycetemcomitans mid-log

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Aa is inoculated from a glycerol stock into Brain Heart Infusion (BHI) until 0.3-0.4 OD600. From here it is inoculated into fresh BHI at a 1:30 dilution and grown until OD600 0.5-0.6. The culture is then diluted again 1:30 into a chemically defined media (CDM) supplemented with either ferrous chloride (100uM) or norepinephrine (50uM).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Aa is grown in CDM supplemented with either ferrous chloride (100uM) or norepinephrine (50uM) until mid-log phase (16 hours post inoculation). At this phase, the total RNA is extracted.

tag: protocol

value: Norepi with CDM


title: Wt mid-log Norepi with CDM 2

description: Gene expression at mid-log


title: Wt mid-log Norepi/FeCl2 with CDM1

description: Gene expression at mid-log

value: Norepi/FeCl2 with CDM


title: ESR1-CCDC170 fusion vs. YFP, replicate 4

description: YFP vs ESR1(253)->CCDC170-d


title: Wt mid-log Norepi/FeCl2 with CDM3

description: Gene expression at mid-log


title: Rat_Liver_P2_2


title: Wt mid-log Norepi/FeCl2 with CDM2

description: Gene expression at mid-log


title: Rat_Liver_P3_1


title: Rat_Liver_Fed_1


title: 2515102102107-2-4X44K

description: SUM149Luc 691 Brain Tumor Not-treated 01/12/12

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-504

growth_protocol: Total RNA isolated by stratagene

extract_protocol: Total RNA isolated by stratagene

value: Human Reference B

source_name: SUM149Luc Control Mouse 691

treatment_protocol: PBS Control

value: SUM149 Luc


title: Wt mid-log Norepi with CDM 3

description: Gene expression at mid-log


title: Wt mid-log CDM 3

description: Gene expression at mid-log

value: CDM


title: Wt mid-log CDM 2

description: Gene expression at mid-log


title: 2515102102107-3-4X44K

description: SUM149Luc 699 Brain Tumor Not-treated 01/12/12

source_name: SUM149Luc Control Mouse 699


title: Wt mid-log CDM 1

description: Gene expression at mid-log


title: Lrh-1_f/f_tunicamycin_rep3

city: Houston

first: Jennifer

middle: L

last: Mamrosh

state: TX

address: 1 Baylor Plaza N610

institute: Baylor College of Medicine

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Image data were converted into unnormalized Sample Probe Profiles using Illumina BeadStudio software. Chipster was used to convert Sample Probe Profiles to log2 values using standard settings for Illumina arrays (normalize.genes = quantile; produce.flags = no)
NON-NORMALIZED: Illumina BeadStudio Software-computer unnormalized values. NORMALIZED: Chipster quantile normalized log2 values

source_name: liver, tunicamycin treated (1mg/kg BW, 24h)

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: 8-12 week old male mice were used. Mice were of mixed background and maintained under standard conditions.

extract_protocol: TriZol reagent

value: 8-12 week old

value: Lrh-1 f/f


title: 251510210623-3-4X44K

description: 678 Brain Tumor Sum149 Luc ABT888 1.12.12

source_name: SUM149Luc ABT888 Mouse 678


title: 251510210623-1-4X44K

description: 690 Brain Tumor Sum149 Luc Carbo+ABT888 1.12.12

source_name: SUM149Luc Carboplatin+ABT888 Mouse 690


title: 251510210700-1-4X44K

description: 681 Brain Tumor Sum149 Luc Carbo+ABT888 1.12.12

source_name: SUM149Luc Carboplatin+ABT888 Mouse 681


title: Lrh-1_f/f_tunicamycin_rep1

description: SAMPLE 4


title: Lrh-1_f/f_tunicamycin_rep2

description: SAMPLE 5


title: Lrh-1_LKO_vehicle_rep2

description: SAMPLE 8

source_name: liver, vehicle treated (24h)

value: Lrh-1 LKO (Lrh-1 f/f; Alb-Cre/+)


title: Lrh-1_LKO_tunicamycin_rep2

description: SAMPLE 11

value: male


title: 2515102102107-4-4X44K

description: SUM149Luc 695 Brain Tumor ABT888 01/12/12

source_name: SUM149Luc ABT888 Mouse 695


title: Lrh-1_LKO_tunicamycin_rep1

description: SAMPLE 10


title: Lrh-1_LKO_vehicle_rep1

description: SAMPLE 7


title: Lrh-1_LKO_vehicle_rep3

description: SAMPLE 9


title: 251510210741-4-4X44K

description: 677 Brain Tumor Sum149 Luc Carbo 1.12.12

source_name: SUM149Luc Carboplatin Mouse 677

treatment_protocol: Carboplatin


title: 251510210700-3-4X44K

description: 694 Brain Tumor Sum149 Luc Carbo 1.12.12

source_name: SUM149Luc Carboplatin Mouse 694


title: Lrh-1_LKO_tunicamycin_rep3

description: SAMPLE 12


title: Lrh-1_f/f_vehicle_rep2

description: SAMPLE 2


title: Lrh-1_f/f_vehicle_rep1

description: SAMPLE 1


title: Lrh-1_f/f_vehicle_rep3

description: SAMPLE 3


title: 251510210741-1-4X44K

description: 687 Brain Tumor Sum149 Luc Carbo+ABT888 1.12.12 Repl1

source_name: SUM149Luc Carboplatin+ABT888 Mouse 687 Repeat


title: 251510210741-3-4X44K

description: 696 Brain Tumor Sum149 Luc ABT888 1.12.12

source_name: SUM149Luc ABT888 Mouse 696


title: 251510210701-1-4X44K

description: 684 Brain Tumor Sum149 Luc Carbo 1.12.12

source_name: SUM149Luc Carboplatin Mouse 684


title: 251510210741-2-4X44K

description: 694 Brain Tumor Sum149 Luc Carbo 1.12.12 Repl1

source_name: SUM149Luc Carboplatin Mouse 694 Repeat


title: 251510210700-2-4X44K

description: 687 Brain Tumor Sum149 Luc Carbo+ABT888 1.12.12

source_name: SUM149Luc Carboplatin+ABT888 Mouse 687


title: 251510210623-2-4X44K

description: 692 Brain Tumor Sum149 Luc Carbo+ABT888 1.12.12

source_name: SUM149Luc Carboplatin+ABT888 Mouse 692


title: Zf_devHypoxiaStudy_segmentation_HYPOXIA_rep2

status: Public on May 02 2015

city: La Jolla

first: Farhad

middle: Bryan

last: Imam

address: 9500 Gilman Drive #0734

department: Pediatrics

institute: University of California, San Diego

description: This sample is of wildtype, HYPOXIC embryos at the segmentation (8-somite, 12 hours) stage and is the second of two replicates.

hyb_protocol: Sample hybridization was performed as described in the NimbleChip Arrays user’s guide.

scan_protocol: Sample washing and scanning was performed as described in the NimbleChip Arrays user’s guide. Scans quality was assessed by comparison of the scan images and their pre-normalization global intensity boxplot and  histogram plots (R/BioConductor). Sample 8 was excluded from our downstream analysis due to a large artifact, but is left in the dataset should others wish to use partial data from that array.

data_processing: The raw data (from .xys files) was subjected to RMA and mean normalization (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) via R/BIoConductor.

organism: Danio rerio

source_name: Whole embryo

label_protocol: cDNA synthesis with incorpiration of Cy3 or Cy5-labeled nucleotides was performed as in Arbeitman et al., 2002.

growth_protocol: Wildtype embryos were grown at 28.5C until collection.

extract_protocol: Total RNA isolated using standard TRIzol protocol (Life Technologies)

treatment_protocol: For hypoxia treatment, a closed hypoxia chamber was used with a flow meter attached to a gas source (Billups-Rothenberg, Inc.). Hypoxia chambers were flushed for 4 minutes at 20 L/min, and repeated 30 minutes later with nitrogen gas. 50 mm Petri dishes containing 4ml of embryo water were pre-equilibrated in the hypoxia chamber prior for at least 4 hours prior to embryo transfer as this was determined to be the minimum time necessary to reach <1% oxygen as measured by a dissolved oxygen meter and gave similar viability results when compared with longer pre-equilibration times up to 24 hours (DO-5509; Alfa Electronics). A colorimetric resazurin indicator was used to monitor the hypoxic environment during pre-treatment of media and the duration of each experiment (<1% oxygen if colorless; Bio-Bag, Becton, Dickinson and Company)

tag: stress type

value: HYPOXIA

tag: developmental stage

value: 8 somite


title: MDA-MB-436 ABT Carbo Study 251510210863_4

description: MDA-MB-436 506 Control Mouse 251510210863_4

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: MDA-MB-436 Control Mouse 506


title: MDA-MB-436 ABT Carbo Study 251510210862_1

description: MDA-MB-436 504 Control Mouse 251510210862_1

source_name: MDA-MB-436 Control Mouse 504


title: MDA-MB-436 ABT Carbo Study 251510210864_3

description: MDA-MB-436 282 ABT 251510210864_3

source_name: MDA-MB-436 ABT888 Mouse 282 Repeat2


title: SDP8 + 24h DOX + heat shock_Exp_2

status: Public on Apr 30 2015

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 micro m. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing:
The Gene Expression Profile Analysis Suite, GEPAS v4.0 package (http://www.gepas.org/) was used to the processing of data: the Preprocessing tool was used to merge replicates and give the average value.
The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes. Spots with saturated values were excluded from the normalization process.

organism: Saccharomyces cerevisiae

source_name: SDP8 conditional mutant treated with doxycycline for 24 h + heat shock

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight hours later, when OD660: 0.609, a new culture was prepared at initial OD660: 0.01 from the proper amount of washed cells, that was also supplemented with fresh doxycycline and grown for 16 h. Fifty ml of the culture was then incubated at 40 ºC for 40 minutes and cells were collected by centrifugation, washed with cold water and the dried cell pellet was kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: Treated with doxycycline (100 microg/ml) in an ethanol:water mix (1:1) for 24 h and then incubated at 40 ºC for 40 minutes.

value: SDP8 (CML476 background)

tag: genotype

value: tetO7:PKH2 pkh1::HIS3 pkh3::NatMX4

value: with doxycycline for 24 h + heat shock

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight hours later, when OD660: 0.554, a new culture was prepared at initial OD660: 0.01 from the proper amount of washed cells, that was also supplemented with fresh doxycycline and grown for 16 h. Fifty ml of the culture was then incubated at 28ºC for 40 minutes and cells were collected by centrifugation, washed with cold water and the dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: Treated with doxycycline (100 microg/ml) in an ethanol:water mix (1:1) for 24 h.

value: with doxycycline for 24 h


title: Zf_devHypoxiaStudy_segmentation_HYPOXIA_rep1

description: This sample is of wildtype, HYPOXIC embryos at the segmentation (8-somite, 12 hours) stage and is the first of two replicates.


title: Zf_devHypoxiaStudy_gastrula_normoxia_rep2

description: This sample is of wildtype, normoxic embryos at the gastrula (shield, 6 hours) stage and is the second of two replicates.

value: shield


title: Zf_devHypoxiaStudy_gastrula_HYPOXIA_rep1

description: This sample is of wildtype, HYPOXIC embryos at the gastrula (shield, 6 hours) stage and is the first of two replicates.


title: 251510210760-1

description: 376 SUM149Luc BRTumor NT E050912

source_name: SUM149Luc Control Mouse 376


title: SDP8 + 24h DOX + heat shock_Exp_1

source_name: SDP8 conditional mutant strain treated with doxycycline for 24 h + heat shock


title: Zf_devHypoxiaStudy_segmentation_normoxia_rep2

description: This sample is of wildtype, normoxic embryos at the segmentation (8-somite, 12 hours) stage and is the second of two replicates"


title: MDA-MB-436 ABT Carbo Study 251510210862_4

description: MDA-MB-436 505 Control Mouse 251510210862_4

source_name: MDA-MB-436 Control Mouse 505


title: 251510210759-3

description: 386 SUM149Luc BRTumor Carboplatin+ABT888 E050912

source_name: SUM149Luc Carboplatin+ABT888 Mouse 386


title: MDA-MB-436 ABT Carbo Study 251510210865_3

description: MDA-MB-436 279 Carboplatin 251510210865_3

source_name: MDA-MB-436 Carboplatin Mouse 279


title: MDA-MB-436 ABT Carbo Study 251510210863_3

description: MDA-MB-436 288 ABT+Carboplatin 251510210863_3

source_name: MDA-MB-436 Carboplatin+ABT888 Mouse 288


title: Zf_devHypoxiaStudy_gastrula_normoxia_rep1

description: This sample is of wildtype, normoxic embryos at the gastrula (shield, 6 hours) stage and is the first of two replicates.


title: Zf_devHypoxiaStudy_gastrula_HYPOXIA_rep2

description: This sample is of wildtype, HYPOXIC embryos at the gastrula (shield, 6 hours) stage and is the second of two replicates.


title: MDA-MB-436 ABT Carbo Study 251510210865_1

description: MDA-MB-436 292 ABT + Carbo Mouse 251510210865_1

source_name: MDA-MB-436 Carboplatin+ABT888 Mouse 292


title: Zf_devHypoxiaStudy_segmentation_normoxia_rep1

description: This sample is of wildtype, normoxic embryos at the segmentation (8-somite, 12 hours) stage and is the first of two replicates.


title: WT + 24h DOX + heat shock_Exp_2

source_name: Wild type strain treated with doxycycline for 24 h + heat shock

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight hours later, when OD660: 0.554, a new culture was prepared at initial OD660: 0.01 from the proper amount of washed cells, that was also supplemented with fresh doxycycline and grown for 16 h. Fifty ml of the culture was then incubated at 40 ºC for 40 minutes and cells were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.

value: Wild type CML476 strain treatment:with doxycycline for 24 h at 28 ºC and then 40 minutes at 40 ºC

growth_protocol: Saturated culture grown in YPD medium was diluted at OD660 0.05 in YPD supplemented with doxycycline. Eight hours later, when OD660: 0.554, a new culture was prepared at initial OD660: 0.01 from the proper amount of washed cells, that was also supplemented with fresh doxycycline and grown for 16 h. Fifty ml of the culture was then incubated at 28ºC for 40 minutes and cells were collected by centrifugation and washed with cold water. The dried cell pellet was kept at -80 ºC until RNA purification.

value: Wild type CML476 strain treatment:with doxycycline for 24 h at 28 ºC and then 40 minutes at 28 ºC


title: 251510210760-4

description: 386 SUM149Luc BRTumor Carboplatin+ABT888 E050912 Repeat

source_name: SUM149Luc Carboplatin+ABT888 Mouse 386 Repeat


title: MDA-MB-436 ABT Carbo Study 251510210865_2

description: MDA-MB-436 282 ABT 251510210865_2

source_name: MDA-MB-436 ABT888 Mouse 282 Repeat3


title: 251510210758-4

description: 337 SUM149Luc BRTumor NT E050912

source_name: SUM149Luc Control Mouse 337


title: MDA-MB-436 ABT Carbo Study 251510210865_4

description: MDA-MB-436 287 Carboplatin 251510210865_4

source_name: MDA-MB-436 Carboplatin Mouse 287 Repeat


title: MDA-MB-436 ABT Carbo Study 251510210863_1

description: MDA-MB-436 282 ABT 251510210863_1

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: MDA-MB-436 ABT888 Mouse 282


title: MDA-MB-436 ABT Carbo Study 251510210862_3

description: MDA-MB-436 280 ABT + Carbo Mouse 251510210862_3

source_name: MDA-MB-436 Carboplatin+ABT888 Mouse 280


title: 251510210760-2

description: 378 SUM149Luc BRTumor Carboplatin E050912

source_name: SUM149Luc Carboplatin Mouse 378


title: 251510210758-2

description: 335 SUM149Luc BRTumor NT E050912

source_name: SUM149Luc Control Mouse 335


title: MDA-MB-436 ABT Carbo Study 251510210862_2

description: MDA-MB-436 287 Carboplatin Mouse 251510210862_2

source_name: MDA-MB-436 Carboplatin Mouse 287


title: 251510210760-3

description: 385 SUM149Luc BRTumor NT E050912

source_name: SUM149Luc Control Mouse 385


title: 251510210759-1

description: 340 SUM149Luc BRTumor Carboplatin E050912

source_name: SUM149Luc Carboplatin Mouse 340


title: NOMO1.H3K9ac

status: Public on Mar 30 2015

type: SRA

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Reads were filtered for quality and aligned to the human genome (hg18) using Helicos open source aligner IndexDP Genomic available at the open source HeliSphere.
To create density files, the reads were extended to 200 bp converted to tdf using igvtools (http://www.broadinstitute.org/igv/igvtools).
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: TDF files contain the read densities.

molecule: genomic DNA

source_name: human AML-derived cell line NOMO1, H3K9ac ChIP

growth_protocol: The MOLM13, MonoMac6, and NOMO1 cells were cultured in 10% RPMI plus 10% FBS.

extract_protocol:
ChIP was performed as previously described (Bernt et al. 2011 Cancer Cell). Briefly, cells samples were crosslinked by 1% formaldehyde for 10 minutes, and the reaction was stopped by addition of glycine to 125 mM final concentration. The fixed cells were lysed in SDS buffer, and the chromatin was fragmented by sonication. The sheared chromatin was incubated with the indicated antibodies, and recovered by binding to protein A/G agarose (Millipore).
Eluted DNA fragments were processed for the HeliScope according to the manufacturer's protocol.

value: MLL-AF9 human leukemia cell line

tag: chip antibody

value: anti-H3K9ac (Abcam; ab4441)


title: NOMO1.H3K79me2

source_name: human AML-derived cell line NOMO1, H3K79me2 ChIP

value: anti-H3K79me2 (Abcam; ab3594)


title: MonoMAC6.H3K9ac

source_name: human AML-derived cell line MonoMac6, H3K9ac ChIP


title: MOLM13.H3K79me2

source_name: human AML-derived cell line MOLM13, H3K79me2 ChIP


title: MOLM13.H3K9ac

source_name: human AML-derived cell line MOLM13, H3K9ac ChIP


title: ALS sample 3

status: Public on Apr 25 2015

city: São Paulo

first: Chrystian

middle: Junqueira

last: Alves

state: SP

address: Rua Dr Arnaldo 455

department: Neurology

country: Brazil

institute: School of Medicine of Sao Paulo University

hyb_protocol: Hybridation following manufacturer's instructions (Agilent)

scan_protocol: Scanned on an Agilent scanner

data_processing: Agilent Feature Extraction Software (version 11.0.1.1) was used for extract data and GeneSpring v.13 software was used for background correction and normalization.

source_name: hiPSC

label_protocol: RNA amplification and labeling following manufacturer's instructions (Agilent)

growth_protocol: hiPSC generation was performed based on the protocol described by Somers et al. (2010). Motor neuron differentiation was performed according to protocol described by Hu and Zhang (2009) and modified by our experience.

extract_protocol: Total RNA extracted using RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: The cells were collected at the differentiation day 20 for microarray experiments.

value: Fibroblasts from peripheral nerve

tag: disease state

value: ALS

source_name: HEK 293 cells

value: HEK 293


title: ALS sample 2


title: Control sample 1

value: control


title: ALS sample 1


title: Control sample 2


title: MonoMAC6.H3K79me2

source_name: human AML-derived cell line MonoMac6, H3K79me2 ChIP


title: PTC BRAF mut 4

status: Public on Feb 16 2015

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description:
Sample name: TM-187-11R
Gene expression data from PTC with a BRAF mutation

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings. Data were RMA normalized and analyzed with Partek Genomics Suite 6.5.

source_name: PTC histology

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

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

tag: braf status

value: BRAFmutant

value: PTC with a BRAF mutation


title: PTC BRAF mut 12

description:
Sample name: TM-892-11R
Gene expression data from PTC with a BRAF mutation


title: WT + 24h DOX + heat shock_Exp_1

description: Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

source_name: Wild type strain treated with doxycycline for 24 h + heat shock

value: Wild type CML476 strain

value: with doxycycline for 24 h at 28 ºC and then 40 minutes at 40 ºC

value: with doxycycline for 24 h at 28 ºC and then 40 minutes at 28 ºC


title: ST486 EV Total Cy3

status: Public on Feb 20 2015

city: Groningen

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

description: Total RNA

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA were combined and hybridized following the Agilent's protocol

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol.

data_processing: Data were extracted using Feature Extraction software (v10.5.1.1, Agilent). Two-color microarrays were analyzed as one-color microarrays using GeneSpring GX, version 12.5 (Agilent). Data from TXT files were quantile normalized (threshold raw signal to 1.0) without baseline transformation. Probes detected in at least half of the samples (2 out of 4, Cy3 and Cy5 averaged), with consistent Cy3 and Cy5 signals in all samples were analyzed. Control probes were excluded.

source_name: ST486 cell line with empty MXW-PGK-IRES-GFP vector

label_protocol: ~ 100 ng of RNA was Cy3 or Cy5 labeled using two-color Quick Amp Labeling Kit  (Agilent) following the manufacturer's protocols. Dye incorporation and cRNA yield were checked with the NanoDrop 1000

growth_protocol: Cells were maintained in RPMI-1640 with 20%FCS, ultraglutamine (2mM), penicillin (100U/ml), streptomycin (0.1mg/ml) under standard culturing conditions.

extract_protocol: Total cellular RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions.

tag: malignancy

value: Burkitt lymphoma

value: Cells were transduced with empty MXW-PGK-IRES-GFP vector and GFP+ cells were sorted


title: FVPTC 4

description:
Sample name: TM-989-11R
Gene expression data from FVPTC

source_name: FVPTC histology

value: BRAF wild type

tag: tissue

value: FVPTC


title: Control sample 3


title: PTC BRAF mut 7

description:
Sample name: TM-602-11R
Gene expression data from PTC with a BRAF mutation


title: PTC BRAF mut 9

description:
Sample name: TM-824-12R
Gene expression data from PTC with a BRAF mutation


title: 504-46/129050

status: Public on Dec 31 2014

description:
20130326_31020548071_31020548071_12
raw data file: plate1-3-22-2013.xlsx

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized using 5 HK genes.  Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: breast

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol

extract_protocol: Total RNA was isolated from FFPE tissue using ROCHE High Pure FFPE Kit

value: Basal

tag: age

tag: bestresponse

value: Partial Response

tag: mrivolume

tag: clinicalbenefit


title: 110-36/129023

description:
20130326_31020548071_31020548071_09
raw data file: plate1-3-22-2013.xlsx


title: Seedlings -control rep.2

status: Public on Jan 01 2015

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

description:
Gene expression data from seedlings  of 11 day-old tomato - Wild type (cv. Micro-Tom)- control
EA09092_280569_Tomato_NL-2

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 11 day old ssedlings of wild type tomato

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf)

growth_protocol: Tomato seeds were germinated on MS medium (Magenta boxes) in light and harvested after 1 day and 11 days of cultivation.

extract_protocol: Seeds and seedlings were isolated and immediately frozen in liquid nitrogen. The harvested seeds and seedlings  were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special treatments before harvesting were carried out.

tag: cultivar

value: Micro-Tom

tag: genotype/variation

value: wild type

tag: growth protocol

value: seedlings of 11 day-old tomato


title: 1602/129030

description:
20130326_31020548071_31020548071_10
raw data file: plate1-3-22-2013.xlsx

value: Stable Disease


title: 102-02/129015

description:
20130326_31020548071_31020548071_08
raw data file: plate1-3-22-2013.xlsx


title: 1603-44/129032

description:
20130326_31020548071_31020548071_11
raw data file: plate1-3-22-2013.xlsx

source_name: cerebellum


title: Seedlings -control rep.1

description:
Gene expression data from seedlings  of 11 day-old tomato - Wild type (cv. Micro-Tom)- control
EA09092_280568_Tomato_NL-1


title: Seedlings -control rep.3

description:
Gene expression data from seedlings  of 11 day-old tomato - Wild type (cv. Micro-Tom)- control
EA09092_280570_Tomato_NL-3


title: 1402-28/129004

description:
20130326_31020548071_31020548071_06
raw data file: plate1-3-22-2013.xlsx

value: Progression


title: 702-22/119031

description:
20130326_31020548071_31020548071_05
raw data file: plate1-3-22-2013.xlsx


title: 105-07/119022

description:
20130326_31020548071_31020548071_04
raw data file: plate1-3-22-2013.xlsx

source_name: brain


title: PTC BRAF wt 10

description:
Sample name: TM-1039-11R
Gene expression data from PTC without a BRAF mutation

value: PTC without a BRAF mutation


title: 107-17/119018

description:
20130326_31020548071_31020548071_03
raw data file: plate1-3-22-2013.xlsx


title: 302-19/129009

description:
20130326_31020548071_31020548071_07
raw data file: plate1-3-22-2013.xlsx

value: Not Evaluable


title: 106-09/119004

description:
20130326_31020548071_31020548071_02
raw data file: plate1-3-22-2013.xlsx

source_name: lungs


title: T11 cell line treated with 8Gy 8hr time point vs 0hr

status: Public on Jan 21 2015

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141

scan_protocol: Agilent Technologies Scanner Using Feature Extraction Software

source_name: T11 cell line 0hr

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

tag: cell line

tag: cell type

value: p53 null breast cancer


title: 101-01/109017

description:
20130326_31020548071_31020548071_01
raw data file: plate1-3-22-2013.xlsx


title: Seeds -control rep.3

description:
Gene expression data from tomato seeds (1 day on MS medium) - Wild type (cv. Micro-Tom)- control
EA09092_278468_Tomato_NS-3

source_name: Seeds of wild type tomato (1 day on MS medium)

value: control

value: seeds


title: 106-09/119005

description:
20130423_31020567583_12
raw data file: plate2-4-22-2013.xlsx


title: 103-03/109018

description:
20130423_31020567583_11
raw data file: plate2-4-22-2013.xlsx

value: Normal


title: T11 cell line treated with 8Gy 48hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: 401-08/119008

description:
20130423_31020567583_10
raw data file: plate2-4-22-2013.xlsx


title: 303-29/129011

description:
20130423_31020567583_09
raw data file: plate2-4-22-2013.xlsx


title: Seeds -control rep.2

description:
Gene expression data from tomato seeds (1 day on MS medium) - Wild type (cv. Micro-Tom)- control
EA09092_278467_Tomato_NS-2


title: T11 cell line treated with 8Gy 24hr time point vs 0hr #2

description: T11 cell line treated with 8Gy 24hr time point #2 vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138


title: T11 cell line treated with 8Gy 4hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140


title: 1704-43/129040

description:
20130423_31020567583_07
raw data file: plate2-4-22-2013.xlsx


title: 1703-21/119019

description:
20130423_31020567583_06
raw data file: plate2-4-22-2013.xlsx


title: T11 cell line treated with 8Gy 12hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136


title: 1602-41/129013

description:
20130423_31020567583_04
raw data file: plate2-4-22-2013.xlsx


title: 1504-39/129039

description:
20130423_310205675833_03
raw data file: plate2-4-22-2013.xlsx


title: 801-06/119016

description:
20130423_31020567583_05
raw data file: plate2-4-22-2013.xlsx

source_name: lymph node


title: 301-16/129010

description:
20130423_31020567583_08
raw data file: plate2-4-22-2013.xlsx


title: 2250L cell line treated with 8Gy 24hr time point vs 0hr #2

description: 2250L cell line treated with 8Gy 24hr time point #2 vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: 2250L cell line 0hr


title: Seeds -control rep.1

description:
Gene expression data from tomato seeds (1 day on MS medium) - Wild type (cv. Micro-Tom)- control
EA09092_278466_Tomato_NS-1


title: T11 cell line treated with 8Gy 24hr time point vs 0hr

description: T11 cell line treated with 8Gy 24hr time point #1 vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: 2250L cell line treated with 8Gy 24hr time point vs 0hr #1

description: 2250L cell line treated with 8Gy 24hr time point #1 vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131


title: 2225L-H cell line treated with 8Gy 24hr time point vs 0hr #1

description: 2225L cell line treated with 8Gy 24hr time point #1 vs  0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: 2225L cell line 0hr

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126


title: 109-33/129047

description:
20130423_31020567583_02
raw data file: plate2-4-22-2013.xlsx


title: 109-33/129046

description:
20130423_31020567583_01
raw data file: plate2-4-22-2013.xlsx


title: 2225L-H cell line treated with 8Gy 12hr time point vs 0hr

description: 2225L cell line treated with 8Gy 12hr time point vs 0 hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: 2250L cell line treated with 8Gy 8hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135


title: 2225L-H cell line treated with 8Gy 24hr time point vs 0hr #2

description: 2225L cell line treated with 8Gy 24hr time point #2 vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127


title: 2225L-H cell line treated with 8Gy 8hr time point vs 0hr

description: 2225L cell line treated with 8Gy 8hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: 2225L-H cell line treated with 8Gy 48hr time point vs 0hr

description: 2225L cell line treated with 8Gy 48hr time point vs 0 hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128


title: 2250L cell line treated with 8Gy 12hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130


title: 2250L cell line treated with 8Gy 4hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134


title: 2250L cell line treated with 8Gy 48hr time point vs 0hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133


title: 2225L-H cell line treated with 8Gy 4hr time point vs 0hr

description: 2225L cell line treated with 8Gy 4hr time point vs 0 hr

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129


title: 0805-10E_9819-071156B

type: genomic

description: Paired Normal Sample (Rref) came from Normal DNA from Normal Breast

hyb_protocol: The samples were loaded onto the Human610 array, and hybridized overnight for 16h at 48°C. Following hybridization, the beadchips were submerged in buffer, spun dry in a centrifuge, and assembled into a TeFlow hydro-chamber heated to 44°C

scan_protocol: Within three days, beadchips were imaged on the BeadArray reader using BeadScan software.

data_processing:
Illumina 660-Quad SNP arrays were used according to the manufacturer’s protocol. Quality control and data analysis were performed using GenomeStudio Genotyping Module v1.0 software (Illumina, Inc., San Diego, CA 92121 USA). A pool of 164 normal samples was used as Illumina’s standard clustering reference through GenomeStudio software, which estimates allele-specific intensity boundaries. SNP clustering and genotyping was performed on all samples. Replicates (having a genome-wide genotype correlation > 99%) and samples with call rates < 95% were removed. The B allele frequencies (proportion of minor (‘B’) alleles to total (‘A’ + ‘B’) alleles) were calculated and the LogR (A + B signal) were extracted.

Raw data not provided in order to protect the privacy of patients.

source_name: Breast Tumor

label_protocol: 250 ng of genomic DNA was used as template for WGA, using Illumina proprietary reagents. Following WGA, the amplified DNA was enzymatically fragmented, isopropanol precipitated and resuspended in Illumina resuspension buffer

extract_protocol: Peripheral blood was collected in EDTA and stored at -40°C. DNA was isolated using phenol/chloroform extraction and ethanol precipitation as described previously (Andersen et al., 1992). Tumor DNA from snap frozen tumors, stored at -80°C, was isolated following the same Phenol/Chloroform extraction procedure.

tag: tissue type

value: Breast Tumor

tag: subtype


title: 0805-10D_9819-070746B


title: 0805-02G_960096B

value: LumA


title: 0805-01G_950105B


title: 0634-01A_9830-020018B

value: Claudin-low


title: 0501-10D_UNC06-0694B


title: 0805-01E_950061B

value: LumB


title: 0501-08C_LCCC-9006-Bx0


title: 0501-08A_LCCC-6005-BxComb


title: 0501-11C_UNC03-0311B


title: 0501-11F_UNC05-0046C5

value: Basal


title: 0501-11G_UNC05-0375C5


title: 0501-10E_UNC06-1067B


title: 0634-03C_06-0756B


title: 0501-10F_UNC07-0342B


title: 0501-11D_UNC03-0521C5


title: 0502-04E_BC00054


title: 0501-07B_LCCC-6005-Bx0


title: 0501-07D_LCCC-9002-Bx0


title: 0501-08D_LCCC-9009-Bx0


title: 0805-01A_940182B


title: 0501-11B_UNC01-0098C5


title: 0501-07C_LCCC-9001-BxComb


title: 0501-07F_LCCC-9003-Bx0


title: 0501-07E_LCCC-9002-BxComb


title: 0501-07H_LCCC-9003-BxSingle


title: 0501-07G_LCCC-9003-BxComb


title: 0501-11E_UNC04-0490C5


title: 0501-07A_LCCC-4012-BxSingle


title: 0501-06G_LCCC-4005-BxComb


title: 0501-06C_LCCC-4003-BxComb


title: 0501-06B_LCCC-3006-BxComb


title: 0501-06F_LCCC-4005-Bx0


title: 0501-06E_LCCC-4004-BxComb


title: 0501-05H_LCCC-2002-BxComb


title: 0501-06D_LCCC-4004-Bx0


title: 0501-04B_UNC030459B


title: 0501-05G_LCCC-2002-Bx0


title: 0501-05B_LCCC-1010-BxComb


title: 0501-05D_LCCC-12001-BxSingle


title: 0501-03E_UNC020155B


title: 0501-06A_LCCC-3006-Bx0


title: 0501-05C_LCCC-12001-Bx0


title: 0501-02G_UNC000161B


title: 0501-05A_LCCC-1010-Bx0


title: 0501-04E_UNC040227B


title: 0501-04D_UNC040211B


title: 0501-02E_UNC030183B


title: 0501-02B_UNC020320B


title: 0501-02F_UNC030528B


title: 0501-03G_UNC020242B


title: 0501-03A_UNC010208B


title: 0501-03B_UNC010224B


title: 0501-02H_UNC000279B


title: 0501-01G_BR-000365B


title: 0501-03F_UNC020157B


title: 0501-03D_UNC010348B


title: 0501-04A_UNC030429B


title: 0501-03C_UNC010235B


title: 0501-01F_BR-990348B


title: 0500-12G_9830-030597B


title: 0501-02C_UNC020510B


title: 0501-02A_BR-980261B


title: 0501-02D_UNC030065B


title: 0501-01H_BR-010125B


title: 0500-12F_9830-030562B


title: 0500-12D_9830-010384B


title: 0501-01C_9830-030446B


title: 0500-11A_UNC99-0216B


title: 0501-01B_9830-020039B


title: 0500-12C_9830-010214B


title: 0500-11D_UNC99-0339B


title: 0500-12A_9830-000248B


title: 0500-11E_UNC99-0363B


title: 0500-11B_UNC99-0281B


title: 0500-11F_UNC99-0364B


title: 0500-11H_UNC99-0543B


title: 0501-01E_BR-990207B


title: 0500-11G_UNC99-0456B


title: 0501-01D_BR-940187B


title: 0500-12B_9830-000471B


title: 0500-10G_UNC99-0158B


title: 0500-10H_UNC99-0182B


title: 0500-11C_UNC99-0306B


title: 0500-10F_UNC99-0141B


title: 0500-09H_UNC04-0297B


title: 0500-10A_UNC04-0547B


title: 0500-10C_UNC98-0107B


title: 0500-10E_UNC98-2049B


title: 0500-09E_UNC02-0575B


title: 0500-09C_UNC00-0164B


title: 0500-10D_UNC98-2048B


title: 0500-09A_UNC040182B


title: 0500-09B_UNC040191B


title: 0500-09D_UNC00-0552B


title: 0500-09G_UNC04-0115B


title: 0500-09F_UNC03-0447B


title: 0500-08H_UNC040134B


title: 0500-08F_UNC030408B


title: 0500-08C_UNC020439B


title: 0500-08E_UNC020578B


title: 0500-08B_030521-Bmet


title: 0500-07E_UNC010355B


title: Liu-206 MDA-MB231 (15)

description: Liu-206 MDA-MB231 (15):Breast Cell Line

source_name: Human Reference B

tag: reference

value: Reference:Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

extract_protocol: Qiagen Rneasy Kit

tag: sample

value: Breast Cell Line


title: 0500-07H_UNC020297B


title: 0500-07G_UNC010532B


title: 0500-08D_UNC020464B


title: 0500-07F_UNC010456B


title: 0500-08A_UNC020306B


title: Liu-Sample_5(9885 LungMet)

description: Liu-Sample_5(9885 LungMet):Breast Cell Line

source_name: Liu-Sample_5(9885 LungMet)


title: 0500-07A_BR-950184T


title: Liu-206 MDA-MB231 (5)

description: Liu-206 MDA-MB231 (5):Breast Cell Line


title: 0500-07B_BR970137B


title: 0500-06G_BR-010349T


title: Liu-206 MDA-MB231 (10)

description: Liu-206 MDA-MB231 (10):Breast Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: 0500-06E_BR-000587T


title: Liu-Sample_4(9898 LungMet)

description: Liu-Sample_4(9898 LungMet):Breast Cell Line

source_name: Liu-Sample_4(9898 LungMet)


title: 0500-07D_UNC010353B


title: 0500-06F_BR-010123T


title: 0500-06H_BR-950017T


title: 0500-07C_UNC010318B


title: 0500-08G_UNC040114B


title: 0500-06B_BR-000387T


title: 0500-05F_BC00094T


title: 0500-05H_BR-000284T


title: Liu-mimic MDA-MB231 (7)

description: Liu-mimic MDA-MB231 (7):Breast Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: Liu-mimic MDA-MB231 (7)


title: 0500-06A_BR-000344B


title: Liu-Sample_2(5044 CD66+)

description: Liu-Sample_2(5044 CD66+):Breast Cell Line


title: Liu-Sample_0(5451 MIP4)

description: Liu-Sample_0(5451 MIP4):Breast Cell Line

source_name: Liu-Sample_0(5451 MIP4)


title: 0500-06C_BR-000504T


title: Liu-mimic MDA-MB231 (2)

description: Liu-mimic MDA-MB231 (2):Breast Cell Line

source_name: Liu-mimic MDA-MB231 (2)


title: 0500-05D_BC00063T


title: Liu-mimic MDA-MB231 (12)

description: Liu-mimic MDA-MB231 (12):Breast Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: Liu-mimic MDA-MB231 (12)


title: 0500-06D_BR000572B


title: 0500-05E_BC00086T


title: Liu-dharma-blank MDA-MB231 (1)

description: Liu-dharma-blank MDA-MB231 (1):Breast Cell Line

source_name: Liu-dharma-blank MDA-MB231 (1)


title: Liu-dharma-blank MDA-MB231 (6)

description: Liu-dharma-blank MDA-MB231 (6):Breast Cell Line

source_name: Liu-dharma-blank MDA-MB231 (6)


title: Liu-Sample_1(5044 CD66-)

description: Liu-Sample_1(5044 CD66-):Breast Cell Line


title: 0500-05G_BC00097T


title: Liu-Sample_3(9983 LungMet)

description: Liu-Sample_3(9983 LungMet):Breast Cell Line

source_name: Liu-Sample_3(9983 LungMet)


title: Liu-138 MDA-MB231 (8)

description: Liu-138 MDA-MB231 (8):Breast Cell Line


title: 0500-05B_BC00041T


title: Liu-138 MDA-MB231 (3)

description: Liu-138 MDA-MB231 (3):Breast Cell Line


title: 0500-05C_BC00043T


title: Liu-dharma-blank MDA-MB231 (11)

description: Liu-dharma-blank MDA-MB231 (11):Breast Cell Line

source_name: Liu-dharma-blank MDA-MB231 (11)


title: 0500-04F_A15-LivMet


title: Liu-138 MDA-MB231 (13)

description: Liu-138 MDA-MB231 (13):Breast Cell Line


title: 0500-04A_A7LiverMet


title: 0500-04H_BC00017T


title: 0500-04G_BC00016T


title: 0500-05A_BC00033T


title: 0500-04B_A8-SpiCordmet


title: 0500-04C_A9-1LivMet


title: 0500-04D_A12-LivMet


title: 0500-03G_A5-SkinMet


title: 0500-03F_A4-LLLmet


title: 0500-03E_A1-17primary/A1-13Li


title: 0500-03B_9830-030619B


title: 0500-02F_9830-020461B


title: Melanoma cell line Ma-Mel-105

status: Public on Oct 25 2014

city: Heidelberg

first: Rajiv

last: Kumar

address: Im Neuenheimer Feld 580

department: Division of Molecular Genetic Epidemiology

institute: German Cancer Research Center

hyb_protocol: RNA was converted into double stranded cDNA and cRNA and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Image analysis was performed with the Affymetrix GeneChip Operating Software (GCOS) and for pair-wise comparisons of expression profiles. SAM (significance analysis of micro-arrays) was used for statistically significant changes in expression. Marker analysis was performed using GeneCluster 2.0.

label: Biotin

source_name: Melanoma cell line Ma-Mel-08b, derived from metastatic tumor

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen). Concentrations of  RNA were measured by UV spectrophotometry and the integrity of total RNA isolated from cell lines was determined on the Bioanalyzer 2100 System


title: 0500-03A_9830-030584B


status: Public on Oct 16 2014

city: Pomona

first: Maria

middle: P

last: Lambros

address: 309 E Second Street

department: Pharmaceutical Sciences

institute: Western Univ of Health Sci

description:
Sample name: NAC-QYD
Pretreated with NAC-QYD and irradiated (12Gy)

hyb_protocol: Fragmented aRNA was hybridized at 42°c overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Devices™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing:
3 replicate samples were averaged.  The F532 channel data in each raw data file should be ignored. Only Cy5 dye was used for the experiment.  The data from all microarrays in each experimental set was then passed to Rosetta resolver (v.7.2.2.0.0) for analysis. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques. Normalization algorithm -> Median scaling.
averaged normalized data, signals not significantly above background have been deleted

source_name: Human primary oral 3D keratinocytes pretreated with NAC-QYD and irradiated with 12 Gy

label_protocol: High-quality RNA (RIN>9.5) was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The product ws conjugated with Cy5 NHS ester.

growth_protocol: The primary 3-D cell culture of human oral keratinocytes and supplemented with MatTek serum free media.

extract_protocol: Six hours after the irradiation total RNA was extracted using Rneasy Plus kit, Qiagen

treatment_protocol: The tissues were irradiated with 12 Gy.  Group 1: Human Prirmary 3-D Cultures of Human Keratinocytes were irradiated with 12 Gy (Control Group); Group 2: Human Prirmary 3-D Cultures of Human Keratinocytes were pretreated with NAC and then irradiated with 12 Gy; Human Prirmary 3-D Cultures of Human Keratinocytes were pretreated with QYD and then irradiated with 12 Gy; Human Prirmary 3-D Cultures of Human Keratinocytes were pretreated with NAC-QYD (50:50 w/w mixture of NAC:QYD) and then irradiated with 12 Gy.                                                                                Each sample was done in triplicate.

value: Primary oral keratinocytes

tag: growth

value: grown in 3D culture

tag: pre-treatment

value: NAC-QYD

tag: treatment

value: radiation


title: Melanoma cell line Ma-Mel-61h

source_name: Melanoma cell line Ma-Mel-28, derived from metastatic tumor


description:
Sample name: QYD
Pretreated with QYD and Irradiated  (12Gy)

source_name: Human primary oral 3D keratinocytes pretreated with QYD and irradiated with 12 Gy

value: QYD


title: Melanoma cell line Ma-Mel-62

source_name: Melanoma cell line Ma-Mel-40, derived from metastatic tumor


title: Melanoma cell line Ma-Mel-113

source_name: Melanoma cell line Ma-Mel-08a, derived from metastatic tumor


title: Sox4 vilCre KO Ms 241

description: US80903207_252800517801_S01_GE2_107_Sep09_2_1

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.

source_name: wild-type whole proximal jejunum

tag: tissue

value: whole proximan jejunum

value: wild-type

source_name: Sox4 knockout whole proximal jejunum

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: Sox4 knockout


title: 0500-02B_9830-020185B

source_name: Breast Tumor


title: Melanoma cell line Ma-Mel-67

source_name: Melanoma cell line Ma-Mel-02, derived from metastatic tumor


title: 0500-02D_9830-020340B


description:
Sample name: NAC
Pretreated with NAC and Irradiated (12Gy)

source_name: Human primary oral 3D keratinocytes pretreated with NAC and irradiated with 12 Gy

value: NAC


title: 0500-01C_9830-000424B

description: Paired Normal Sample (Rref) came from Normal DNA from Normal Breast


title: Sox4 vilCre KO Ms 242

description: US80903207_252800517801_S01_GE2_107_Sep09_2_2


title: 0500-01D_9830-000517B


title: 0500-02A_9830-020025B


title: 0500-02G_9830-030118B


title: 0500-01G_9830-010255B


description:
Sample name: NTNR
Control (non-pretreated and non-irradiated)

source_name: Human primary oral keratinocytes grown in 3D culture

value: non-pretreated

value: untreated


title: 0500-02C_9830-020310B

value: Breast Tumor


title: 0500-03C_9830-040072B


title: Sox4 vilCre KO Ms 243

description: US80903207_252800517801_S01_GE2_107_Sep09_2_3


title: 0500-01E_9830-010118B


title: 0500-02E_9830-020416B


title: 0500-01B_9830-000094B

value: LumA


title: 0500-01A_9830-000060B


title: 0500-01F_9830-010130B


title: 0500-03D_A11-1BR.T/A11-2LivMe


title: 0500-02H_9830-030399B

value: LumB


title: H2N-28-1-NT

status: Public on Aug 22 2014

source_name: Human Reference

value: whole human total RNA

value: Cell Line H2N-28-1-NT


title: Non-pretreated and Irradiated  (12Gy)

description:
Sample name: NTR
Non-pretreated and Irradiated  (12Gy)

source_name: Human primary oral keratinocytes grown in 3D culture were irradiated with 12 Gy


title: H2N+19-1-NT

value: Cell Line +19-1-NT


title: H2N+13-1-NT

value: Cell Line H2N+13-1-NT


title: H2N-23-1-NT

value: Cell Line H2N-23-1-NT


title: H2N-22-1-NT

value: Cell Line H2N-22-1-NT


title: DT23-Tumor


title: 0500-01H_9830-010461B


title: DT21-Tumor


title: DT13-Tumor


title: DT21p11


title: DT22-Tumor


title: DT19-Tumor


title: 982049B-244K

status: Public on Aug 20 2014

description:
Age:72;ER:1;PR:1;Node_status:0;Grade:3;Size:4;RFS_event:1;RFS_months:2;Overall_survival_event:1;Overall_survival_months:60
H244Kv5-251976013525-982049B

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Human Reference B

extract_protocol: Total RNA isolated using Qiagen Rneasy Kit

tag: tumor

value: primary breast tumor

tag: age

tag: er

tag: pr

tag: grade

tag: size


title: UACC812

status: Public on Jul 29 2014

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-155

value: Whole human total RNA

value: Cell Line


title: T47D cell line

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-154


title: ZR75-1 p8

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156


title: 990141B-244K

description:
Age:42;ER:NA;PR:NA;Node_status:1;Grade:NA;Size:3;RFS_event:1;RFS_months:69;Overall_survival_event:1;Overall_survival_months:70
H244Kv5-251976013524-990141B


title: 040182B-244K

description:
Age:88;ER:1;PR:1;Node_status:1;Grade:3;Size:2;RFS_event:0;RFS_months:16;Overall_survival_event:0;Overall_survival_months:16
H244Kv5-251976013526-040182B


title: 020578B-244Kb

description:
Age:76;ER:0;PR:0;Node_status:0;Grade:3;Size:4;RFS_event:1;RFS_months:3;Overall_survival_event:1;Overall_survival_months:5
H244Kv5-251976013527-020578B


title: MDA-MB-453 cell line

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-145


title: SUM190PT

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-153


title: MDA-IBC3

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-157


title: DU4775 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-158


title: MDAMB435

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: SUM149 pp8

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-151


title: SUM1315

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-150


title: MDAMB415

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-142


title: MDAMB468

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-146


title: Hs578T-244Kv5

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138


title: SUM159 cell line

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-152


title: 9830-000030B-244Kv5

description:
Age:64;ER:1;PR:1;Node_status:1;Grade:1;Size:3;RFS_event:0;RFS_months:56;Overall_survival_event:0;Overall_survival_months:56
251976010527-244K-V5

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125


title: ME16C p6

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-147


title: Sum102p25

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-149

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: SKBR3 p9

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148


title: MCF10A-shSlugpool vs MCF10AControlpool2

status: Public on Jun 23 2014

description: MCF10A-shSlugpool vs MCF10AControlpool2


title: HCC38 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-137


title: HCC1954 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136


title: MDA-MB231 cell line -1

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-140


title: MCF10A-shSlugpool vs MCF10AControlpoola

description: MCF10A-shSlugpool vs MCF10AControlpoola


title: HCC1500 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-134

source_name: 9830-000060B NEW PROTOCOL V98


title: MDAMB436 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-144


title: MDA-MB-361 cell line

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-141


title: MCF10A-shLSD1pool vs MCF10AControlpoola

description: MCF10A-shLSD1pool vs MCF10AControlpoola


title: MCF10A-shLSD1pool vs MCF10AControlpool

description: MCF10A-shLSD1pool vs MCF10AControlpool


title: HME636-shLSD1pool vs 636-Controlpool

description: HME636-shLSD1pool vs 636-Controlpool

value: HMEC (Patient2)


title: MCF10A Basal

description: 20130618_205635370814_MCF10A Basal_03.RCC

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized using 5 HK genes. Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system

source_name: MCF10A Basal

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol

tag: cell subpopulation

value: basal


title: MCF10A Luminal

description: 20130618_205635370814_MCF10A Luminal_01.RCC

source_name: MCF10A Luminal

tag: cell line

value: luminal


title: MCF10A Stem

description: 20130618_205635370814_MCF10A Stem_02.RCC

source_name: MCF10A Stem

value: stem


title: HME636-shLSD1pool vs 636-Controlpoola

description: HME636-shLSD1pool vs 636-Controlpoola


title: HME636-shSlugpool vs 636-Controlpool

description: HME636-shSlugpool vs 636-Controlpool


title: HCC1395 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-132

source_name: 9830-000060B NEW PROTOCOL V96


title: MCF10A-shSlugpool vs MCF10AControlpool

description: MCF10A-shSlugpool vs MCF10AControlpool


title: HCC1187 cellline

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

source_name: 9830-000060B NEW PROTOCOL V95


title: HME630-shLSD1pool vs 630-Controlpool2

description: HME630-shLSD1pool vs 630-Controlpool2

value: HMEC (Patient1)


title: HME636-shSlugpool vs 636-Controlpool2

description: HME636-shSlugpool vs 636-Controlpool2


title: HME630-shLSD1pool vs 630-Controlpoola

description: HME630-shLSD1pool vs 630-Controlpoola


title: HME630-shSlugpool vs 630-Controlpool2

description: HME630-shSlugpool vs 630-Controlpool2


title: HCC1143

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-130

source_name: 9830-000060B NEW PROTOCOL V94


title: MCF10A-shLSD1pool vs MCF10AControlpool2

description: MCF10A-shLSD1pool vs MCF10AControlpool2


title: HME636-shSlugpool vs 636-Controlpoola

description: HME636-shSlugpool vs 636-Controlpoola


title: CAMA-1 cell line

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-129

source_name: 9830-000060B NEW PROTOCOL V93


title: HME630-shSlugpool vs 630-Controlpool

description: HME630-shSlugpool vs 630-Controlpool


title: 101777-146

status: Public on May 21 2014

city: Amsterdam

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

institute: AMC

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H70

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using neqc background correction and quantile normalisation with the beadarray package in R (2.15.3).

source_name: heart, left ventricle

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

extract_protocol: RNA was extracted with mirVana miRNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser and spectrophotometry. The Illumina TotalPrep-96 RNA Amplification Kit was used to generate cRNA starting from 200 ng total RNA.

tag: gender

value: female

value: left ventricular myocardium

tag: center


title: HME630-shSlugpool vs 630-Controlpoola

description: HME630-shSlugpool vs 630-Controlpoola


title: HME636-shLSD1pool vs 636-Controlpool2

description: HME636-shLSD1pool vs 636-Controlpool2


title: HME630-shLSD1pool vs 630-Controlpool

description: HME630-shLSD1pool vs 630-Controlpool


title: MCF7 p13

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-139


title: 101777-95

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H38

value: male


title: 101777-92

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N1877


title: 101777-22

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H43


title: BT483

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: 9830-000060B NEW PROTOCOL V91


title: BT549 p3

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

source_name: 9830-000060B NEW PROTOCOL V92


title: 101777-154

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
5126


title: 101777-108

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H17


title: 101777-158

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H48


title: 101777-14

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
4184


title: 101777-71

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H19


title: 101777-67

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
711M


title: BT474 p7

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-126

source_name: 9830-000060B NEW PROTOCOL V90

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: 101777-85

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H64


title: 101777-119

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H13


title: 101777-01

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
573M


title: BABE p7

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

source_name: 9830-000060B NEW PROTOCOL V89


title: HCC1428 p12

description: Cell Line

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

source_name: 9830-000060B NEW PROTOCOL V97


title: 101777-96

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H42


title: 101777-188

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H3


title: 101777-113

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N5288


title: 101777-150

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
6008


title: 101777-190

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3145


title: HCC1937 cellline

description: Cell Line

source_name: Human Reference

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-135

source_name: 9830-000060B NEW PROTOCOL V99


title: 101777-151

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H79


title: 101777-129

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N8073


title: 101777-36

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N5713


title: 101777-147

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3683


title: 101777-89

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N1754


title: 101777-109

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
7054


title: 101777-63

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
5033


title: 101777-185

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H86


title: 101777-13

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N9511


title: 101777-40

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H22


title: 101777-179

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
5138


title: 101777-182

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H40


title: 101777-101

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
713M


title: 101777-171

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H35


title: 101777-39

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
6092


title: 101777-159

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
455M


title: 101777-18

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H23


title: 101777-116

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
259M


title: 101777-187

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
14


title: 101777-09

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H76


title: 101777-174

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
3091


title: 101777-56

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
4049


title: 101777-91

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H29


title: 101777-38

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N0762


title: 101777-142

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
3112


title: 101777-24

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
608M


title: 101777-162

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
3083


title: 101777-176

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H15


title: 101777-43

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N9303


title: 101777-135

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3736


title: 101777-172

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
29


title: 101777-60

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
461M


title: 101777-149

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H26


title: 101777-117

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
039M


title: 101777-84

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H49


title: 101777-183

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H24


title: 101777-193

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H28


title: 101777-178

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3878


title: 101777-11

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N7990


title: 101777-52

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H68


title: 101777-115

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H20


title: 101777-32

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
5140


title: 101777-170

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H2


title: 101777-137

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
429M


title: 101777-54

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H8


title: 101777-04

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H30


title: 101777-31

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N9365


title: 101777-59

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H54


title: 101777-100

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H82


title: 101777-29

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
4062


title: 101777-64

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
7024


title: 101777-21

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H6


title: 101777-77

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3060


title: 101777-127

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H50


title: 101777-44

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
7040


title: 101777-34

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H37


title: 101777-66

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H71


title: 101777-61

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H46


title: 101777-51

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
7060


title: 101777-83

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H9


title: 101777-186

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
6028


title: 101777-62

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
238M


title: 101777-133

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H31


title: 101777-06

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H27


title: 101777-144

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H69


title: 101777-88

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H65


title: 101777-73

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H44


title: 101777-163

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H73


title: 101777-49

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
843M


title: 101777-111

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N3077


title: 101777-90

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H5


title: 101777-33

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
10


title: 101777-120

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H4


title: 101777-105

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
3108


title: 101777-161

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H25


title: 101777-26

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
N2765


title: 101777-42

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H12


title: 101777-78

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H77


title: 101777-153

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
827M


title: 101777-30

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H39


title: 101777-143

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
23


title: 101777-103

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H59


title: 101777-107

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H78


title: 101777-97

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H66


title: 101777-47

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
H33


title: 101777-141

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
475M


title: 101777-138

description:
Total RNA of left ventricular myocardium was hybridized to Human HT12 Version 4 BeadChips (Illumina).
16