title: S463P/D538G CSS media rep2

city: New York

first: Sarat

last: Chandarlapaty

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

description:
Sample 35
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep 96 RNA kit for Illumina arrays

growth_protocol: MCF7 cells were grown in DMEM/F12 with 10% FBS and 1% L-glutamine and penicillin/streptomycin and maintained at 37°C and 5% CO2 in humidified atmosphere.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MCF7 cells were transfected with ER constructs (GFP vector control, WT, S463P, Y537S, D538G and S463P/D538G) in regular or phenol-red free, charcoal stripped FBS media and cells were collected 48 hours post-transfection.

tag: cell line

tag: transfected with er construct

tag: media

value: Charcoal stripped serum (CSS) media


title: D538G CSS media rep3

status: Public on Oct 25 2013

type: RNA

country: USA

description:
Sample 33
replicate 3

label: biotin

molecule: total RNA

organism: Homo sapiens


title: Mayo 54

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

description: FFPE samples from chemotherapy-naïve hormone-receptor-negative breast cancer annotated with distant recurrence information.

data_processing:
CT values for target genes are non-detected if there is a lack of gene amplification within 40 thermocycles.
ddCT values for target genes are generated by first normalizing to two reference genes (PPIG and NUP214), then to a universal human reference RNA (Stratagene) that was amplified with the same genes. Samples assayed in the same batch are normalized to a corresponding RNA reference; altogether, six RNA references were employed. CPMC samples are normalized to RP_1. Guy's Hospital samples: 5037-057, 5037-228, 5040-026, 5040-042, 5040-047, 5040-057, 5040-058, 5040-060, 5040-087, 5040-093, 5040-100, 5040-103, 5040-112, 5040-154, 5040-173, 5040-178, 5040-193, 5040-197, 5040-253, 5040-255 are normalized to RP_2, the remaining Guy's hospital samples are normalized to RP_3, Mayo clinic samples: Mayo 06, Mayo 15, Mayo 16, Mayo 18, Mayo 20, Mayo 27, Mayo 30, Mayo 31, Mayo 33, Mayo 36, Mayo 38, Mayo 40, Mayo 41, Mayo 44, Mayo 48, Mayo 54, Mayo 65, Mayo 66, Mayo 82, Mayo 88, Mayo 90, Mayo 93 are normalized to RP_4. Mayo clinic samples: Mayo 03, Mayo 08, Mayo 12, Mayo 14, Mayo 17, Mayo 21, Mayo 23, Mayo 24, Mayo 25, Mayo 26, Mayo 32, Mayo 35, Mayo 43, Mayo 45, Mayo 52, Mayo 55, Mayo 57, Mayo 62, Mayo 63, Mayo 64, Mayo 71, Mayo 73, Mayo 84, Mayo 86, Mayo 89, Mayo 92 are normalized to RP_5. All remaining Mayo clinic samples are normalized to RP_6.
ddCT values of target gene signatures are median-centered and scaled to standard deviation of 1 within each of the sample sources (California Pacific Medical Center, Guy's Hospital, Mayo Clinic).

label: Multiplexed - NED, VIC, Quasar 670, 6FAM

source_name: Primary breast cancer, hormone receptor negative, chemotherapy naive

label_protocol: The probe for each gene within a multiplex is labeled with a unique fluorophore with the exception of the two reference genes, which were both labeled with NED in the same mix. Amplifications were performed with AmpliTaq Gold in a buffer containing 15 mM Tris-HCl, 50 mM KCl, pH 8.0 , 2.5 mM MgCl2, 200 uM dAGC, 400 uM dUTP, and uracil-N-glycolysis.

extract_protocol: Total RNA was extracted from 10 micron FFPE sections using a modified commercially available isolation kit (Zymo Research). The FFPE sections were digested with proteinase K for 18-24 hours at 55°C, spun down and the supernatant treated with a mixture of 100% ethanol and a GuSCN-based extraction buffer. The extracted material was purified on Zymo-Spin II columns, eluted with TE buffer and the RNA reverse transcribed into cDNA using random hexamers and the High Capacity cDNA kit (Life Technologies).

tag: tissue

value: primary breast tumor

tag: sample source

value: Guy's Hospital

tag: er (0

tag: pr (0

tag: her2 (1

value: positive, 0:negative or equivocal):1

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: Mayo 52

value: positive, 0:negative or equivocal):NA


title: S463P/D538G CSS media rep1

description:
Sample 34
replicate 1


title: Mayo 55

value: positive, 0:negative or equivocal):0


title: Mayo 49


title: WT CSS media rep1

description:
Sample 22
replicate 1

value: WT


title: S463P CSS media rep2

description:
Sample 26
replicate 2


title: S463P CSS media rep1

description:
Sample 25
replicate 1


title: D538G CSS media rep1

description:
Sample 31
replicate 1


title: Y537S CSS media rep1

description:
Sample 28
replicate 1


title: Y537S CSS media rep3

description:
Sample 30
replicate 3


title: Y537S CSS media rep2

description:
Sample 29
replicate 2


title: GFP CSS media rep3

description:
Sample 21
replicate 3

value: GFP vector control


title: WT CSS media rep2

description:
Sample 23
replicate 2


title: S463P CSS media rep3

description:
Sample 27
replicate 3


title: WT CSS media rep3

description:
Sample 24
replicate 3


title: GFP CSS media rep2

description:
Sample 20
replicate 2


title: GFP CSS media rep1

description:
Sample 19
replicate 1


title: S463P/D538G CSS media rep3

description:
Sample 36
replicate 3


title: Mayo 48


title: Mayo 45


title: Mayo 40


title: Mayo 41


title: Mayo 37


title: Mayo 38


title: Mayo 44


title: Mayo 36


title: Mayo 35


title: Mayo 33


title: Mayo 43


title: Mayo 31


title: Mayo 32


title: Mayo 30


title: S463P/D538G Normal media rep2

description:
Sample 17
replicate 2

value: Normal media


title: S463P/D538G Normal media rep3

description:
Sample 18
replicate 3


title: D538G Normal media rep3

description:
Sample 15
replicate 3


title: Y537S Normal media rep2

description:
Sample 11
replicate 2


title: Mayo 27


title: Mayo 29


title: D538G Normal media rep1

description:
Sample 13
replicate 1


title: Y537S Normal media rep1

description:
Sample 10
replicate 1


title: S463P Normal media rep3

description:
Sample 9
replicate 3


title: Mayo 26


title: Mayo 24


title: Mayo 25


title: S463P/D538G Normal media rep1

description:
Sample 16
replicate 1


title: Mayo 23


title: WT Normal media rep2

description:
Sample 5
replicate 2


title: WT Normal media rep3

description:
Sample 6
replicate 3


title: D538G Normal media rep2

description:
Sample 14
replicate 2


title: S463P Normal media rep2

description:
Sample 8
replicate 2


title: Mayo 21


title: Y537S Normal media rep3

description:
Sample 12
replicate 3


title: Mayo 20


title: WT Normal media rep1

description:
Sample 4
replicate 1


title: Mayo 18


title: Mayo 17


title: Mayo 16


title: Mayo 15


title: GFP Normal media rep2

description:
Sample 2
replicate 2


title: GFP Normal media rep3

description:
Sample 3
replicate 3


title: GFP Normal media rep1

description:
Sample 1
replicate 1


title: AT.1

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: replicate 1

data_processing: The data were normalised using quantile normalisation with lumi in R using neqc() function.

organism: Mus musculus

source_name: brain

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

extract_protocol: Total cellular RNA was extracted with a standard Trizol protocol

tag: strain

value: mixed 129J x C57BL/6

tag: genotype

value: Atm-/-


title: WT.2

description: replicate 2

value: Atm+/+


title: Mayo 14


title: Mayo 13


title: Mayo 08


title: Mayo 07


title: Mayo 12


title: A2780 + temsirolimus 24-hr rep2

city: San Juan

first: Pablo

middle: E

last: Vivas-Mejia

state: PR

address: Medical Sciences Campus

department: Cancer Medicine

country: Puerto Rico

institute: University of Puerto Rico Cancer Center

hyb_protocol: After 16 hours of incubation at 45°C, the arrays were washed, stained and scanned

scan_protocol: Arrays were scanned (Affymetrix Model 3000 scanner) according to the manufacturer's instruction (Affymetrix)

data_processing: Data was analyzed using the Partek Genomics Suited (Partek, St. Louis, MO).  Experiments were done in duplicate. Two-way ANOVA was used to determine differences in gene expression (p<0.05 fold change 2). 1359 probes (4%) sets showed ±2-fold change between A2780CP20 and A2780 cells. Additional filtering (±3-fold change, and p<0.003) showed 321 probes (0.96%) changed between A2780CP20 and A2780 cells.

source_name: A2780 cells + temsirolimus 24-hr

label_protocol: One hundred nanograms of total RNA were used to cDNA synthesis. Complementary cDNA was synthesized, labeled, fragmented and hybridized to the Affymetrix GeneChip Gene 1.0 ST Human Array.

growth_protocol: Cells were growth in RPMI serum 10% fetal bovine serum.

extract_protocol: Total RNA was isolated from A2780 and A2780CP20 ovarian cancer cell lines with the “GenElute Mammalian Total RNA Purification Kit” (Sigma). The RNA concentration was read in a nanodrop. RNA quality was checked in a Bioanalyzer (Agilent).

treatment_protocol: A2780 were treated with temsirolimus (stock in DMSO). Cells were grown in RPMI (10% FBS) during the temsirolimus treatment

tag: cell type

value: ovarian carcinoma

tag: treatment

value: temsirolimus 24-hr


title: WT.1

description: replicate 1


title: A2780CP20 rep2

source_name: A2780CP20 cells

tag: cell line


title: A2780 + temsirolimus 48-hr rep2

source_name: A2780 cells + temsirolimus 48-hr

value: temsirolimus 48-hr


title: Mayo 03


title: Mayo 02


title: 5040-255


title: Mayo 06


title: A2780 + temsirolimus 48-hr rep1


title: A2780 rep1

source_name: A2780 cells


title: 5040-253


title: A2780 rep2


title: A2780CP20 rep1


title: 5040-246


title: A2780 + temsirolimus 24-hr rep1


title: Root_AlaAT-ox 1/7_2 mM N_Biological Rep3

city: Edmonton

first: Perrin

middle: Hudson

last: Beatty

state: Alberta

address: G425 Biological Sciences

department: Biological Sciences

country: Canada

institute: University of Alberta

hyb_protocol: All biologically replicated RNA samples were labelled and hybridized in parallel using the protocol suggested by the manufacturer (Syngenta Biotechnology).

scan_protocol: cDNA target synthesis quality was assessed by examination of the 3' and 5' probesets of the reference gene controls on the Affymetrix genechip and scanned using GCOS software.

data_processing: dCHIP was used to normalize and model the data. The raw microarray signals were normailized using the invarient set normailization method. The model-based expression values were calculated using the fifth percentile, perfect match only model with outlier detection.

organism: Oryza sativa

source_name: Root_AlaAT-ox 1/7_2 mM N

growth_protocol: Either 0.5, 2 or 5mM NH4+ as the nitrogen source, hydroponic growth, 28 degrees C, 70% relative humidity, 14 hr day length/10 hr night length, light intensity 750 uE.

extract_protocol: Total RNA was extracted using the TRI reagent protocol according to manufacturers instructions (Applied Biosystems). RNA samples were cleaned of phenol contamination using Rneasy plant mini kit

treatment_protocol: Tissue samples were taken, weighed and flash frozen in liquid nitrogen until groundwith liquid nitrogen in a mortar and pestle and the RNA extracted.

tag: cultivar

value: Nipponbare

value: Root

tag: genotype/variation

value: Transgenic_AlaAT-ox 1/7

tag: nitrogen source

value: 2 mM NH4+


title: Shoot_Wildtype_0.5 mM N Biological Rep3

source_name: Shoot_Wildtype_0.5 mM N

label_protocol: All biologically replicated RNA samples were labelled and hybridized in parallel using the protocol suggested by the manufacturer (Syngenta Biotechnology).

tag: tissue

value: Shoot

value: Wildtype


title: D538G CSS media rep2

description:
Sample 32
replicate 2

tag: transfected with er construct

tag: media

value: Charcoal stripped serum (CSS) media


title: 5037-228

value: primary breast tumor

tag: sample source

value: Guy's Hospital

tag: er (0

tag: pr (0

tag: her2 (1

value: positive, 0:negative or equivocal):0


title: 5037-057

value: positive, 0:negative or equivocal):1

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes


title: Root_AlaAT-ox 1/7_5 mM N_Biological Rep3

source_name: Root_AlaAT-ox 1/7_5 mM N

value: 5 mM NH4+


title: 5037-010

tag: tumor size (cm)


title: Shoot_AlaAT-ox 3/8_0.5 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 3/8_0.5 mM N

value: Transgenic_AlaAT-ox 3/8


title: 5040-225


title: 5040-215


title: Shoot_AlaAT-ox 3/8_5 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 3/8_5 mM N


title: 5040-243


title: 5040-198


title: 5040-206


title: 5040-207


title: 5040-197


title: Root_AlaAT-ox 3/8_2 mM N_Biological Rep3

source_name: Root_AlaAT-ox 3/8_2 mM N


title: 5040-194


title: Shoot_AlaAT-ox 3/8_2 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 3/8_2 mM N


title: Root_Wildtype_0.5 mM N Biological Rep3

source_name: Root_Wildtype_0.5 mM N


title: 5040-192


title: 5040-178


title: Shoot_AlaAT-ox 1/7_5 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 1/7_5 mM N

value: 5mM NH4+


title: Shoot_Wildtype_5 mM N Biological Rep3

source_name: Shoot_Wildtype_5 mM N


title: Shoot_Wildtype_0.5 mM N Biological Rep2


title: 5040-173


title: Root_AlaAT-ox 3/8_0.5 mM N_Biological Rep2

source_name: Root_AlaAT-ox 3/8_0.5 mM N


title: Shoot_Wildtype_2 mM N Biological Rep3

source_name: Shoot_Wildtype_2 mM N


title: Root_AlaAT-ox 1/7_2 mM N_Biological Rep2


title: Root_AlaAT-ox 3/8_5 mM N_Biological Rep3

source_name: Root_AlaAT-ox 3/8_5 mM N


title: Shoot_AlaAT-ox 1/7_2 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 1/7_2 mM N


title: Root_Wildtype_2 mM N Biological Rep3

source_name: Root_Wildtype_2 mM N


title: 5040-162

source_name: Primary breast cancer, hormone receptor negative, chemotherapy naive


title: 5040-193


title: Shoot_AlaAT-ox 3/8_0.5 mM N_Biological Rep2


title: 5040-155


title: 5040-169


title: Shoot_AlaAT-ox 1/7_5 mM N_Biological Rep2


title: Donor 3 blood, positively selected CD4+ T-cells 3P

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description:
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded onto OpenArray medium-throughput slides. Quantitative real-time PCR was performed for 758 features, including 754 human miRNAs.
RT and pre-amp protocol: Reverse-transcribed using human miRNA Megaplex primers, pools A and B (Applied Biosystems) was performed for 100 ng RNA per sample. cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, pools A and B (Applied Biosystems), then diluted per manufacturer's protocol.
qRT-PCR protocol: Diluted pre-amplified samples were provided to the Johns Hopkins DNA Analysis Facility of the Genetic Resources Core Facility, where samples were mixed with manufacturer's qPCR master mix and loaded onto OpenArray slides by robot. qRT-PCR was performed with the QuantStudio system per manufacturer's recommendations.
data collection protocol: Data collected by QuantStudio were downloaded from the Johns Hopkins Genetic Resources Core Facility GeneSifter server. Crt values of amplified wells with amplification score greater than 1.2 were determined by ExpressionSuite software (Life Technologies) and exported as a .txt file.

data_processing: Values for miRNAs detected in at least four of six samples were quantile normalized using R/Bioconductor preprocesscore.

label: FAM

label_protocol: TaqMan probe label: FAM

extract_protocol: Total RNA was extracted from isolated CD4+ T-cells by miRvana isolation kit (Ambion) per the manufacturer's protocol. RNA quantity and quality were determined by NanoDrop and Agilent BioAnalyzer.

tag: selection

value: positively selected CD4+ T-cells

tag: individual

value: donor 3

tag: cell type

value: CD4+ T-cells from peripheral blood


title: 5040-154


title: Root_Wildtype_5 mM N Biological Rep1

source_name: Root_Wildtype_5 mM N

tag: cultivar

value: Nipponbare

tag: genotype/variation


title: Root_AlaAT-ox 1/7_5 mM N_Biological Rep2

tag: tissue

value: Root

tag: nitrogen source


title: Donor 3 blood, negatively selected CD4+ T-cells 3N

value: negatively selected CD4+ T-cells


title: Donor 2 blood, negatively selected CD4+ T-cells 2N

value: donor 2


title: Root_Wildtype_0.5 mM N Biological Rep1


title: Shoot_Wildtype_5 mM N Biological Rep1

value: Shoot


title: Donor 1 blood, negatively selected CD4+ T-cells 1N

value: donor 1


title: S463P Normal media rep1

description:
Sample 7
replicate 1

tag: cell line

tag: transfected with er construct

tag: media

value: Normal media


title: Root_Wildtype_2 mM N Biological Rep1

value: Wildtype

value: 2 mM NH4+


title: Root_AlaAT-ox 3/8_5 mM N_Biological Rep2


title: Shoot_Wildtype_2 mM N Biological Rep1


title: 5040-112

value: primary breast tumor

tag: sample source

value: Guy's Hospital

tag: er (0

tag: pr (0

value: positive, 0:negative or equivocal):0


title: Root_AlaAT-ox 1/7_0.5 mM N_Biological Rep3

source_name: Root_AlaAT-ox 1/7_0.5 mM N

value: Transgenic_AlaAT-ox 1/7


title: 727I 04 A2_02

city: Barcelona

first: Aleix

last: Prat

address: Passeig Vall d´Hebron 119

department: Translational Genomics

country: Spain

institute: VHIO

description: 20130117_205611650814_727I 04 A2_02.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

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. 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: primary breast cancer

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

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

value: primary breast cancer

tag: treatfailureevent

tag: treatfailuretime


title: 5040-111

tag: her2 (1

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes


title: Donor 1 blood, positively selected CD4+ T-cells 1P

tag: selection

value: positively selected CD4+ T-cells

tag: individual

tag: cell type


title: Donor 2 blood, positively selected CD4+ T-cells 2P


title: 5040-124

tag: tissue

value: positive, 0:negative or equivocal):1

tag: tumor size (cm)


title: 6699B_03


title: AT.2

description: replicate 2

source_name: brain

tag: strain

value: mixed 129J x C57BL/6

tag: genotype

value: Atm-/-


title: Shoot_AlaAT-ox 1/7_0.5 mM N_Biological Rep3

source_name: Shoot_AlaAT-ox 1/7_0.5 mM N

tag: cultivar

value: Nipponbare

tag: genotype/variation

tag: nitrogen source


title: 4725 I A3_05

description: 20130117_205611650814_4725 I A3_05.RCC

tag: treatfailureevent


title: 4005 I 2010 A9_07

description: 20130117_205611650814_4005 I 2010 A9_07.RCC

tag: treatfailuretime


title: 5040-103

tag: sample source

tag: er (0

tag: pr (0

tag: her2 (1


title: 3424I 12 A1_01

description: 20130117_205611650814_3424I 12 A1_01.RCC


title: 3342 07 3_08

description: 20130117_205611650814_3342 07 3_08.RCC


title: 5040-093

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes


title: 5040-100

tag: tissue


title: 3109 I 05 A3_04

description: 20130117_205611650814_3109 I 05 A3_04.RCC

tag: cell type


title: 5040-091

tag: tumor size (cm)


title: 5040-087


title: Shoot_AlaAT-ox 3/8_2 mM N_Biological Rep2

value: Transgenic_AlaAT-ox 3/8


title: Shoot_Wildtype_5 mM N Biological Rep2

value: 5 mM NH4+


title: 5040-078


title: 5040-069


title: 478488_11


title: 5870I 2011 A1_12

description: 20130116_205612000814_5870I 2011 A1_12.RCC


title: 53811 A6_10

description: 20130116_205611990814_53811 A6_10.RCC


title: 62 A3 04_02

description: 20130116_205611990814_62 A3 04_02.RCC


title: 1390 06_06

description: 20130117_205611650814_1390 06_06.RCC


title: 9463 05_04

description: 20130116_205611990814_9463 05_04.RCC


title: 4724 I 04 A4_08

description: 20130116_205611990814_4724 I 04 A4_08.RCC


title: Shoot_AlaAT-ox 1/7_0.5 mM N_Biological Rep2

value: Shoot


title: 5040-067


title: 3110 I 05 A7_06

description: 20130116_205611990814_3110 I 05 A7_06.RCC


title: 3096 03 A3_03

description: 20130116_205611990814_3096 03 A3_03.RCC


title: Root_AlaAT-ox 1/7_0.5 mM N_Biological Rep1

value: Root


title: Shoot_AlaAT-ox 1/7_0.5 mM N_Biological Rep1


title: Root_Wildtype_5 mM N Biological Rep2


title: 5869I 2011 A6_01

description: 20130116_205611990814_5869I 2011 A6_01.RCC


title: Root_AlaAT-ox 1/7_0.5 mM N_Biological Rep2


title: Shoot_Wildtype_2 mM N Biological Rep2


title: 5040-058


title: 5040-254

value: positive, 0:negative or equivocal):NA


title: Shoot_AlaAT-ox 3/8_5 mM N_Biological Rep2

source_name: Shoot_AlaAT-ox 3/8_5 mM N


title: 1805 10 3_05

description: 20130116_205611990814_1805 10 3_05.RCC


title: 5040-042


title: 1568 I 03 B7_09

description: 20130116_205611990814_1568 I 03 B7_09.RCC


title: 2009 I3 4122-N2_07

description: 20130116_205611990814_2009 I3 4122-N2_07.RCC


title: 5040-057


title: 5040-060


title: Root_Wildtype_2 mM N Biological Rep2

value: Wildtype


title: 5040-034


title: Hemocytes_EcRDN_Larvae_bio rep3

city: Lisboa

first: Anna

last: Zaidman-Remy

address: Universidade Nova de Lisboa

country: Portugal

institute: CEDOC, Faculdade de Ciências Médicas, FCM, Universidade Nova de Lisboa

hyb_protocol: 3.5 µg of end-labeled, fragmented cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 ul were hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system

scan_protocol: Array strips were scanned on a GeneAtlas system using standard settings

data_processing:
12 scanned arrays were analyzed first with Affymetrix Expression Console software using RMA to obtain expression values and for quality control. Log2 expression values were then imported into Chipster 2.4 (Kallio et al., 2011) and differential expression was determined by empirical Bayes two-group test (Smyth, 2004) with Benjamini-Hochberg multiple testing correction and a p-value cut-off of 0.05.
DroGene-1_1-st-v1.Dmelanogaster.design-time.20121024.transcript.csv

organism: Drosophila melanogaster

source_name: Hemocytes, EcRDN Larvae

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) Drosophila Gene 1.1 ST Array Strips by using the Ambion WT Expression Kit (Life Technologies, CA, USA) and Affymetrix GeneChip WT Terminal Labeling Kit, according to the manufacturer’s protocols. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Ambion WT Expression Kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (Ambion WT Expression Kit). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (Ambion WT Expression Kit). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Flies were raised on standard corn medium. Adults were kept to lay eggs at 25C and off-spring was transferred at 29C for development.

extract_protocol: Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Staged larvae or prepupae were first cleaned and then bled in Schneider medium. Hemocytes were FACS-sorted based on their fluorescence. Sorted hemocytes were directly collected in lysis buffer.

tag: genotype

value: Hemocytes

tag: developmental stage

value: Late feeding 3rd instar larvae


title: Hemocytes_Control_Larvae_bio rep3

source_name: Hemocytes, Control Larvae

value: w;HmlDeltaGal4; UAS-GFP


title: Hemocytes_Control_Prepupae_bio rep2

source_name: Hemocytes,Control Prepupae

value: Prepupae 1h to 2h APF


title: Hemocytes_EcRDN_Larvae_bio rep1


title: Root_AlaAT-ox 1/7_2 mM N_Biological Rep1

source_name: Root_AlaAT-ox 1/7_2 mM N

tag: cultivar

tag: genotype/variation

value: Transgenic_AlaAT-ox 1/7

value: 2 mM NH4+


title: Hemocytes_Control_Prepupae_bio rep3


title: Hemocytes_EcRDN_Prepupae_bio rep3

source_name: Hemocytes, EcRDN Prepupae


title: Hemocytes_EcRDN_Prepupae_bio rep2


title: Root_AlaAT-ox 3/8_5 mM N_Biological Rep1

tag: nitrogen source


title: Root_AlaAT-ox 1/7_5 mM N_Biological Rep1

source_name: Root_AlaAT-ox 1/7_5 mM N


title: Hemocytes_EcRDN_Larvae_bio rep2


title: Shoot_AlaAT-ox 1/7_2 mM N_Biological Rep2


title: Shoot_AlaAT-ox 3/8_2 mM N_Biological Rep1

source_name: Shoot_AlaAT-ox 3/8_2 mM N


title: Shoot_AlaAT-ox 1/7_5 mM N_Biological Rep1

source_name: Shoot_AlaAT-ox 1/7_5 mM N


title: 5040-026

value: primary breast tumor

value: Guy's Hospital

value: positive, 0:negative or equivocal):0


title: Hemocytes_EcRDN_Prepupae_bio rep1


title: Hemocytes_Control_Larvae_bio rep2


title: Hemocytes_Control_Prepupae_bio rep1


title: 5040-019


title: 5040-014

value: positive, 0:negative or equivocal):1


title: 2838 10 3_12

description: 20130116_205611990814_2838 10 3_12.RCC

value: primary breast cancer

tag: treatfailureevent

tag: treatfailuretime


title: 5040-012

tag: sample source

tag: er (0


title: Hemocytes_Control_Larvae_bio rep1


title: Shoot_AlaAT-ox 1/7_2 mM N_Biological Rep1

source_name: Shoot_AlaAT-ox 1/7_2 mM N

value: Nipponbare


title: 5040-008

tag: pr (0

tag: her2 (1


title: callus_Lrp5-/-_3

city: Wuerzburg

first: Julia

last: Dotterweich

address: Friedrich-Bergius-Ring 15

department: Orthopedic Center for Musculoskeletal Research

country: Germany

institute: University of Wuerzburg

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized on Affymetrix Gene Chip MG 430 2.0 at 45°C for 16 h. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Hybridization signals were detected with Affymetrix GeneChip Scanner 3000.

data_processing: Global scaling was performed by Affymetrix Gene Chip Operating Software 1.4 using the MAS5 algorithm.

source_name: Lrp5-/-, callus tissue of femora, semi-rigidly fixated, 10 days after operation

label_protocol: RNA was amplified and labeled according to the GeneChip 3’IVT Express Kit (Affymetrix, High Wycombe, United Kingdom).

extract_protocol: Whole femur was dissected and immediately shock frozen in liquid nitrogen. Fracture callus was cut from frozen bone and crushed with manual pastel in 400 µl QIAzol Lysis Reagent (QIAgen GmbH, Hilden, Germany). For further homogenization we used a knife-rotor homogenizator (T 10 basic ULTRA-TURRAX®, IKA®-Werke GmbH & Co. KG, Staufen, Germany). Total RNA was isolated with RNeasy Lipid Tissue Mini Kit (QIAgen) according to manufacture’s instructions, including DNase digestion.

treatment_protocol: We generated Col1a1-Krm2 transgenic mice as previously described (Schulze et al., 2010), which express Krm2 under control of an osteoblast-specific Col1a1 promoter fragment. The Col1a1-Krm2 mice developed a severe osteoporosis due to disturbed bone formation and increased bone resorption. Lrp5 deficient mice (Lrp5-/-) were kindly provided by G. Karsenti (Columbio University, New York, USA). Deletion of Lrp5 resulted in low bone mass due to decreased bone formation, whereas bone resorption was unaffected (Kato et al., 2002). Osteotomy was set in femora of 26 weeks old female mice of each genotype and was stabilized by a semi-rigid fixator according to the previously described protocol (Röntgen et al., 2010). Animals were sacrificed 10 days after surgery.

tag: strain

value: fracture callus

tag: phenotype

value: low bone mass

tag: age

value: 26 weeks

tag: gender

value: female


title: Root_AlaAT-ox 3/8_0.5 mM N_Biological Rep1

source_name: Root_AlaAT-ox 3/8_0.5 mM N

tag: tissue

value: Root

value: Transgenic_AlaAT-ox 3/8


title: callus_Lrp5-/-_2


title: callus_Col1a1-Krm2_3

source_name: Col1a1-Krm2, callus tissue of femora, semi-rigidly fixated, 10 days after operation

value: severe osteoporosis


title: U904

source_name: Primary breast cancer, hormone receptor negative, chemotherapy naive

value: California Pacific Medical Center

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: callus_Col1a1-Krm2_1

tag: genotype/variation


title: Shoot_AlaAT-ox 3/8_5 mM N_Biological Rep1

tag: cultivar

value: Shoot

tag: nitrogen source

value: 5 mM NH4+


title: callus_WT_3

source_name: WT, callus tissue of femora, semi-rigidly fixated, 10 days after operation

value: wild-type


title: callus_WT_2


title: U860

value: primary breast tumor

tag: sample source


title: U877

tag: er (0


title: callus_WT_1


title: callus_Lrp5-/-_1


title: callus_Col1a1-Krm2_2


title: U857

tag: pr (0


title: U812

tag: her2 (1


title: U888


title: Y55_wild-type_rep2

city: Copenhagen V.

first: Richard

last: Baerends

state: Sealland

address: Gamle Carlsberg Vej 10

department: Yeast Biology

country: Denmark

institute: Carlsberg Laboratory

description: This sample is of wild-type Saccharomyces cerevisiae Y55. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: For gene expression profiling (single-color expression analysis), 4 µg dscDNA of each sample was labeled and hybridized in triplicate to Roche NimbleGen Saccharomyces cerevisiae 12x135K Array12 system following the manufacturer’s guidelines (NimbleGen Gene Expression Analysis v3.0 user’s guide). See www.nimblegen.com

scan_protocol: The arrays were scanned with a Molecular Devices scanner (GenePix 4000B with associated software) at a resolution of 5 microns and the images processed with NimbleGen NimbleScan v2.5 software, following their standard operating protocol. See www.nimblegen.com

data_processing: Data were analyzed with R (R Foundation: http://www.r-project.org/) and Bioconductor (Gentleman et al., 2004. Genome Biology 5:R80). The LIMMA package (Smyth, 2005; http://bioinf.wehi.edu.au/limma/) was used to perform a ‘normexp’ background correction and ‘quantiles’ normalization (Bolstad et al., 2003. Bioinformatics 19:185-193) on raw data. Univariate testing for differential expression was performed using the TREAT approach (McCarthy and Smyth, 2009. Bioinformatics 25:765-771).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae Y55, high-gravity maltose fermentation, day 2

growth_protocol: Saccharomyces cerevisiae Y55 wild-type and mutant strains were harvested at day 2 during fermentation on high-gravity maltose as described: Stirred semi-aerobic 200 mL fermentations were performed at 22 °C with rich complex medium, containing 1% yeast extract, 2% peptone and 20% maltose (YP 20% M) as described previously (Houghton-Larsen and Brandt, 2006, Appl. Environ. Microbiol. 72:7176-7182). The fermentations, containing 200 mL medium, were inoculated to an optical density at 600 nm (OD600) of 0.2 from a pre-culture grown aerobically for 72 h in YPD (1% yeast extract, 2% peptone and 2% glucose) at 30 °C.

extract_protocol: 40 mL samples of wild-type and mutant fhf1, 2 and 3 cells were collected at day two post inoculation of 200 mL stirred YP 20% maltose fermentation cultures at 22 °C. Total RNAs were extracted with RiboPure Yeast RNA isolation kit (Ambion, Applied Biosystems, Naerum, Denmark) following the manufacturer’s instruction (yielding 1.1 – 3.3 mg total RNA per sample). PolyA- mRNA (9.0 – 14.6 µg) was purified from 600 µg total RNA with Qiagen Oligotex mRNA midi kit (Qiagen, Copenhagen, Denmark). Double-stranded cDNA (dscDNA) was synthesized with Oligo(dT)20 primer from 2 µg mRNA using SuperScript double-stranded cDNA synthesis kit (Invitrogen A/S, Taastrup, Denmark). Two dscDNA synthesis reactions were needed for each sample to generate sufficient material for downstream analysis. The synthesized dscDNA was purified with Roche Microarray Target Purification Kit (Roche A/S, Hvidovre, Denmark) as described by the manufacturer. The purified dscDNAs (ranging 1.9 – 3.3 µg per sample) were checked by agarose gel electrophoresis.

tag: strain

value: Y55 (JT20150 [MAT-alpha MAL1 SUC1])

tag: genotype

value: Wild-type

tag: reference

value: McCusker and Haber, 1998, Genetics


title: U793

value: positive, 0:negative or equivocal):0


title: U797


title: Y55_maltose-fast-fermenting-mutant-fhf3_rep3

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf3. It is the third of three mutant fhf3 biological replicates used in this experiment, each from separate cultures.

label_protocol: For gene expression profiling (single-color expression analysis), 4 µg dscDNA of each sample was labeled and hybridized in triplicate to Roche NimbleGen Saccharomyces cerevisiae 12x135K Array12 system following the manufacturer’s guidelines (NimbleGen Gene Expression Analysis v3.0 user’s guide). See www.nimblegen.com

value: UV-induced mutant fhf3

tag: phenotype

value: fast-fermenting maltose


title: Root_AlaAT-ox 3/8_2 mM N_Biological Rep1

source_name: Root_AlaAT-ox 3/8_2 mM N

value: Nipponbare

tag: tissue

value: 2 mM NH4+


title: Y55_wild-type_rep3

description: This sample is of wild-type Saccharomyces cerevisiae Y55. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

scan_protocol: The arrays were scanned with a Molecular Devices scanner (GenePix 4000B with associated software) at a resolution of 5 microns and the images processed with NimbleGen NimbleScan v2.5 software, following their standard operating protocol. See www.nimblegen.com.


title: Shoot_AlaAT-ox 3/8_0.5 mM N_Biological Rep1

source_name: Shoot_AlaAT-ox 3/8_0.5 mM N


title: Y55_maltose-fast-fermenting-mutant-fhf3_rep2

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf3. It is the second of three mutant fhf3 biological replicates used in this experiment, each from separate cultures.


title: U780

tag: time to distant recurrence (years)


title: Y55_wild-type_rep1

description: This sample is of wild-type Saccharomyces cerevisiae Y55. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: U788

tag: distant recurrence indicator (1=yes, 0=no)


title: HF liver SNEB, biological rep6, animal L11

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

description: miRNA

hyb_protocol: Hybridisation on Affymetrix GeneChip miRNA 2.0 Array at 48°C for 16-18 hours (60rpm) in the Affymetrix hyb oven 640 according to the protocolFlashTag® Biotin HSR RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays (Feb 2011)

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix) and controlled by the Affymetrix software 'Command Console'.

data_processing: All microarray analyses including pre-processing, normalization and statistical analysis were carried out using R (Version 2.14 ) and Bioconductor . Data were quality assessed before  normalization using  the Bioconductor  package 'arrayQualityMetrics'. 4 samples from MNEB group and 5 from SNEB group were including in the analysis. Microarray data were pre-processed using the 'expresso' method of the Bioconductor package 'Affy'. Expression was normalized using  'quantile' normalization and differential expression was calculated using the 'samr' method both implemented in the Bioconductor package “samr”.

organism: Bos taurus

source_name: Bovine liver in post-partum period; severe negative energy balance

label_protocol: Direct labeling of 1µg total RNA with Biotin using Genisphere FlashTag Biotin HSR RNA Labeling Kit.

extract_protocol: Total RNA enriched for small RNA was prepared from 100 mg of fragmented frozen liver tissue using the TRIzol extraction method (Invitrogen, Stockholm, Sweden) in accordance with manufacturer’s guidelines supplied.

treatment_protocol: From day 2 after calving mild (MNEB) cows were fed ad lib grass silage with 8 kg/day of a 21% crude protein dairy concentrate and milked x1 daily; severe (SNEB) cows were fed 25 kg/day silage with 4 kg/day concentrate and milked x3 daily. Samples of uterine endometrium were collected from all cows following slaughter at 14 ± 0.4 days postpartum.

value: liver tissue

value: Holstein-Friesian

tag: age

value: 4.7 lactations


title: WT Lung 6 hrs post B16 F10 injection Replicate 1

city: Chapel Hill

first: Hendrik

middle: Wilhelm

last: van Deventer

state: NC

address: 170 Manning Drive

department: Medicine

institute: University of North Carolina Chapel Hill

hyb_protocol: The cRNA was then fragmented in fragmentation buffer (5X fragmentation buffer: 200mM Tris-acetate, pH8.1, 500mM KOAc, 150mM MgOAc) at 94oC for 35 minutes before the chip hybridization.  15 mg of fragmented cRNA was then added to a hybridization cocktail (0.05 mg/ml fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD,  and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20).  10 mg of cRNA was used for hybridization.  Arrays were hybridized for 16 hours at 45oC in the GeneChip Hybridization Oven 640.  The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 400

scan_protocol: The arrays were scanned with the Hewlett Packard GeneArray Scanner

data_processing:
Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis.  Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.
Affymetrix Expression Console Software was used generates RMA data.
Signal log ratio is an index, determined by the Affymetrix MICROARRAY SUITE program, to estimate the magnitude and direction of change of a gene transcript in pair comparison. If the signal log ratio is equal to or greater than 0, fold change is obtained with 2(Signal Log Ratio); otherwise, (-1)×2-(Signal Log Ratio) is used. In the Detection column, calls include P for Present, A for Absent, and M for Marginal.

molecule: polyA RNA

source_name: WT lung, B16-F10 tumor, 6 hours

label_protocol: 7 mg of total RNA was used to synthesize cDNA.  A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction.  Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit.

growth_protocol: After anesthesia, the liver was cut and 500 to 1000 mcl of cold PBS was perfused via the right ventricle.  The lungs were then excised en bloc before getting dissected free in a tissue culture hood.  The tissue was then placed in cryo vials and flash frozen in liquid nitrogen.  The vials were then transferrd to a -80 freezer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (Invitrogen) and cleaned over the RNEasy column (Qiagen).

treatment_protocol: B16 F10 cells were acquired from ATCC (CRL-6475), expanded by 3 passages, harvested, and stored in frozen aliquots.  From these aliquots, cells were thawed, expanded twice, and harvested in log phase growth.  100,000 cells were intravenously injected in 200 mcl PBS.  At conclusion of injection, cells were recounted to insure > 90% viability

tag: gender

value: Female

value: 8 to 10 weeks

value: Wild Type

value: Lung

tag: volume of injection

value: 200 mcl

tag: time point

value: 6 hr post B16 F10 injection


title: Y55_maltose-fast-fermenting-mutant-fhf2_rep3

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf2. It is the third of three mutant fhf2 biological replicates used in this experiment, each from separate cultures.

value: Y55 (JT20150 [MAT-alpha MAL1 SUC1])

value: UV-induced mutant fhf2


title: Y55_maltose-fast-fermenting-mutant-fhf3_rep1

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf3. It is the first of three mutant fhf3 biological replicates used in this experiment, each from separate cultures.

value: McCusker and Haber, 1998, Genetics


title: U769

description: FFPE samples from chemotherapy-naïve hormone-receptor-negative breast cancer annotated with distant recurrence information.

value: primary breast tumor

value: California Pacific Medical Center

value: positive, 0:negative or equivocal):0

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: WT Lung 24 hrs post B16 F10 injection Replicate 1

source_name: WT lung, B16-F10 tumor, 24 hours

tag: genotype/variation

value: 24 hr post B16 F10 injection


title: HF liver SNEB, biological rep4, animal L51

description: miRNA


title: Y55_maltose-fast-fermenting-mutant-fhf2_rep2

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf2. It is the second of three mutant fhf2 biological replicates used in this experiment, each from separate cultures.

value: fast-fermenting maltose


title: U745

tag: sample source

tag: er (0

tag: pr (0


title: U761

tag: her2 (1


title: Y55_maltose-fast-fermenting-mutant-fhf2_rep1

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf2. It is the first of three mutant fhf2 biological replicates used in this experiment, each from separate cultures.

tag: strain

tag: genotype

tag: reference


title: Y55_maltose-fast-fermenting-mutant-fhf1_rep3

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf1. It is the third of three mutant fhf1 biological replicates used in this experiment, each from separate cultures.

value: UV-induced mutant fhf1

tag: phenotype


title: WT Lung 48 hrs post B16 F10 injection Replicate 1

tag: tissue

value: 48 hr post B16 F10 injection


title: CCR5 Lung 24 hrs post B16 F10 injection Replicate 1

source_name: CCR5 KO lung, B16-F10 tumor, 24 hours

tag: age


title: U711

value: positive, 0:negative or equivocal):1

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)


title: CCR5 Lung 48 hrs post B16 F10 injection Replicate 1

tag: gender

value: Female

tag: volume of injection

tag: time point


title: Y55_maltose-fast-fermenting-mutant-fhf1_rep2

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf1. It is the second of three mutant fhf1 biological replicates used in this experiment, each from separate cultures.


title: U764

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: HF liver MNEB, biological rep5, animal L245

description: miRNA

source_name: Bovine liver in post-partum period; mild negative energy balance

value: liver tissue

value: Holstein-Friesian

value: 4.7 lactations


title: Oak_rep1

city: Gainesville

first: John

last: Davis

state: FL

address: 365 Newins-Ziegler Hall

department: School of Forest Resources and Conservation

institute: University of Florida

description: Gene expression during vegetative stage growth in oak leaves

hyb_protocol: hybridized with rotation at 65°C for 17 hours.  The arrays were washed according to the manufacturer’s protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7) and an Agilent G250B scanner.

data_processing: Agilent Feature Extraction Software (version 10.7) was used for local background subtraction and feature quality control. Background subtracted signal intensities were normalized by setting microarray means to zero with a standard deviation of 1.

organism: Cronartium quercuum

source_name: infected northern red oak leaves

label_protocol: Agilent’s Low Input Quick Amp Labeling Kit was used to label 200ng total RNA

growth_protocol: Northern red oak seedlings were grown in greenhouse conditions at the USDA Forest Service Resistance Screening Center, Asheville, NC using standard operating procedures.

extract_protocol: Frozen harvested oak leaf samples (3 leaves pooled from an individual plant) were ground in liquid nitrogen to a fine powder. Total RNA was extracted from approximately 200mg of ground oak sample using a cetyltrimethylammonium bromide (CTAB) buffer method (Chang et al., 1993).

treatment_protocol: Northern red oak seedlings were inoculated on the underside of the juvenile leaves using the single aeciospore isolate, SC20-21, at the USDA Forest Service Resistance Screening Center, Asheville, NC using standard operating procedures.

tag: inoculum genotype

tag: days post inoculation


title: HF liver SNEB, biological rep5, animal L214

description: miRNA


title: HF liver MNEB, biological rep4, animal L330

description: miRNA


title: U696

tag: sample source

tag: er (0

tag: pr (0

tag: her2 (1


title: Y55_maltose-fast-fermenting-mutant-fhf1_rep1

description: This sample is of Saccharomyces cerevisiae Y55 mutant fhf1. It is the first of three mutant fhf1 biological replicates used in this experiment, each from separate cultures.

tag: strain

tag: genotype

tag: phenotype

tag: reference


title: Pine_rep8

description: Gene expression during vegetative growth stage in a pine gall

source_name: slash pine stem gall

growth_protocol: Open pollinated slash pine seedlings were grown in greenhouse conditions at the USDA Forest Service Resistance Screening Center, Asheville, NC using standard operating procedures.

extract_protocol: Pine stem gall samples were freeze dried for 4 days before extraction. They were broken into small pieces using a coffee grinder. The small pieces were further ground to a fine powder using three 5/32-inch stainless steel balls in microcentrifuge tubes processed in a Geno/Grinder 2000 homogenizer. Total RNA was extracted from approximately 200mg of ground pine sample using a cetyltrimethylammonium bromide (CTAB) buffer method (Chang et al., 1993).

treatment_protocol: 6 to 8 week old slash pine seedlings were spray inoculated (20,000 spores/ml) using basidiospores shed from the oak seedlings (inoculated with single aeciospore isolate SC20-21) in this experiment, in an inoculation chamber at the USDA Forest Service Resistance Screening Center, Asheville, NC using standard operating procedures.


title: U691

tag: tissue

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)


title: Oak_rep8


title: U690


title: HF liver MNEB, biological rep3, animal L1106

description: miRNA

tag: age


title: Pine_rep7


title: U675

tag: sbr grade


title: U672

tag: number positive nodes


title: Oak_rep7


title: Oak_rep6


title: HF liver SNEB, biological rep3, animal L231R

description: miRNA


title: Oak_rep5


title: U575

tag: tumor size (cm)


title: Pine_rep5

tag: inoculum genotype


title: U567


title: U557

value: positive, 0:negative or equivocal):NA


title: U373


title: U255


title: HF liver MNEB, biological rep2, animal L1098

description: miRNA


title: U176


title: metastatic hepatocellular carcinoma (M) of case 3

city: Tokyo

first: Ken

last: Okano

address: Toyo Ekimae bldg. 2-20, Toyo 2-Chome, Koto-Ku

country: Japan

institute: Cosmo Bio Co., LTD.

description: Universal Reference means that the sample was mixed with a equal volumes of all samples.

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees C and washed with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

scan_protocol: Hybridization signals were detected by DNA microarray scanner G2505B (Agilent Technologies) with resolution of 10 micrometres . The scanned images were analyzed using Agilent Feature Extraction ver. 9.1.3.1.

data_processing: At first Hy3 (samples) signal was normalized with division used Hy5 (Universal reference) signal. Then each signal value of unique probe ID was calculated from average of Hy3/Hy5 normalized signal intensities of replicated probes.

source_name: liver biopsy

label_protocol: 400 ug of total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

extract_protocol: Total RNA containing miRNA was isolated from the frozen liver tissues using mirVana miRNA isolation kit (Ambion, Austin, TX) in accordance with the manufacturer’s protocol.

value: metastatic hepatocellular carcinoma

tag: subject

value: case 3

tag: gender

value: male

tag: disease state

value: hepatocellular carcinoma with lung recurrences and hepatitis C virus

source_name: Universal Reference

tag: sample type

value: equal mixture of all samples


title: U175

value: primary breast tumor

tag: sample source

value: California Pacific Medical Center

tag: er (0

tag: pr (0

tag: her2 (1


title: U166

value: positive, 0:negative or equivocal):0


title: Pine_rep4

tag: days post inoculation


title: Pine_rep3


title: Oak_rep4


title: Oak_rep3


title: non-cancerous liver (N) of case 3

tag: tissue

value: non-cancerous liver


title: U147

tag: time to distant recurrence (years)


title: Pine_rep2

extract_protocol: Pine stem gall samples were freeze dried for 4 days before extraction. They were broken into small pieces using a coffee grinder. The small pieces were further ground to a fine powder using three 5/32-inch stainless steel balls in microcentrifuge tubes processed in a Geno/Grinder 2000 homogenizer. Frozen harvested oak leaf samples (3 leaves pooled from an individual plant) were ground in liquid nitrogen to a fine powder. Total RNA was extracted from approximately 200mg of ground oak or pine sample using a previously described cetyltrimethylammonium bromide (CTAB) buffer method (Chang et al., 1993).


title: Oak_rep2


title: primary hepatocellular carcinoma (T) of case 3

value: primary hepatocellular carcinoma


title: Pine_rep1


title: primary hepatocellular carcinoma (T) of case 2

value: case 2

value: female

value: hepatocellular carcinoma


title: non-cancerous liver (N) of case 2


title: U139

value: positive, 0:negative or equivocal):1

tag: distant recurrence indicator (1=yes, 0=no)


title: U107


title: U060


title: non-cancerous liver (N) of case 1

value: case 1

tag: age

value: hepatocellular carcinoma with peritoneal recurrence and infected by hepatitis B virus


title: metastatic hepatocellular carcinoma (M) of case 1


title: U102

tag: sbr grade


title: U169

tag: number positive nodes


title: U057

tag: tumor size (cm)


title: primary hepatocellular carcinoma (T) of case 1


title: metastatic hepatocellular carcinoma (M) of case 2


title: BreastTumor_1377

status: Public on Oct 24 2013

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5

scan_protocol: Scanning on Agilent scanner G2565A and Feature Extraction (FE) v9.5.3.1 was used to extract signals

data_processing: signals were extracted using Feature Extraction v9.5 and the subsequent data processing was performed using the GeneSpring software v12.0 (Agilent Technologies). In brief, the miRNA signal intensities were log2-transformed and normalized to the 90th percentile, and miRNAs that were detected in less than 10% of the samples were excluded. This resulted in 448 unique mature miRNAs.

source_name: Breast primary tumor

growth_protocol: Human primary tumors

extract_protocol: TRIzol, following manufactors protocol

treatment_protocol: Fresh frozen in liquid nitrogen

value: breast tumor

tag: sample no

tag: tumor size grade

tag: anaplasi grade

tag: er status

tag: her2 status


title: BreastTumor_1411

label_protocol: Agilent miRNA Labeling Reagent and Hybridization Kit, Protocol v.1.5


title: BreastTumor_4192


title: BreastTumor_4059


title: histological normal livers (NL) from three living donors

value: histological normal livers

tag: subject

value: 3 donors

tag: sample type


title: BreastTumor_960


title: BreastTumor_3169


title: BreastTumor_3866


title: BreastTumor_3317


title: BreastTumor_3888


title: PBMC, patient. Mtx+Et rep13

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix Human U133 Plus 2.0 GeneChips following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner.

data_processing: CHP files were generated by Affymetrix expression console software using  the 3' exp array -RMA program.

source_name: PBMC RNA from a patient who achieved remission on MTX+Et

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated from granulocytes and red blood cells by density-gradient centrifugation.  Red cells were removed from granulocytes by hypotonic lysis, and PBMC and granulocytes were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

tag: cell type

value: PBMC

tag: group

value: Patient

tag: patient treatment

value: Mtx+Et


title: PBMC, patient. Mtx+Et rep14


title: BreastTumor_99

tag: tissue


title: BreastTumor_1034


title: BreastTumor_3676


title: PBMC, patient. Mtx+Et rep10


title: BreastTumor_365


title: BreastTumor_905


title: BreastTumor_162


title: BreastTumor_265


title: PBMC, patient. Mtx+Et rep7


title: HF liver SNEB, biological rep1, animal L3156

description: miRNA

value: liver tissue

tag: genotype

value: Holstein-Friesian

value: 4.7 lactations


title: PBMC, patient. Mtx+Et rep2


title: PBMC, patient. Mtx+Et rep1


title: BreastTumor_3696


title: BreastTumor_1348


title: PBMC, patient. Mtx+Et rep5


title: PBMC, patient. Mtx+Et rep9


title: PBMC, patient. Mtx+Et rep6


title: PBMC, patient. Mtx+Et rep12


title: PBMC, patient. Mtx+Et rep4


title: PBMC, patient. Mtx+Et rep8


title: PBMC, patient. Mtx+Et rep3


title: PBMC, patient. Mtx rep13

source_name: PBMC RNA from a patient who achieved remission on MTX

value: Mtx


title: BreastTumor_3166


title: BreastTumor_4099


title: BreastTumor_949


title: BreastTumor_596


title: PBMC, patient. Mtx rep10


title: PBMC, patient. Mtx rep11


title: 5040-047

source_name: Primary breast cancer, hormone receptor negative, chemotherapy naive

extract_protocol: Total RNA was extracted from 10 micron FFPE sections using a modified commercially available isolation kit (Zymo Research). The FFPE sections were digested with proteinase K for 18-24 hours at 55°C, spun down and the supernatant treated with a mixture of 100% ethanol and a GuSCN-based extraction buffer. The extracted material was purified on Zymo-Spin II columns, eluted with TE buffer and the RNA reverse transcribed into cDNA using random hexamers and the High Capacity cDNA kit (Life Technologies).

value: primary breast tumor

tag: sample source

value: Guy's Hospital

tag: er (0

tag: pr (0

tag: her2 (1

value: positive, 0:negative or equivocal):0

tag: time to distant recurrence (years)

tag: distant recurrence indicator (1=yes, 0=no)


title: BreastTumor_1056

tag: sample no

tag: tumor size grade


title: PBMC, patient. Mtx+Et rep11


title: BreastTumor_1255

tag: anaplasi grade

tag: er status


title: BreastTumor_1277

tag: her2 status


title: BreastTumor_3055


title: BreastTumor_3604


title: BreastTumor_4342


title: PBMC, patient. Mtx rep14


title: BreastTumor_1419


title: PBMC, patient. Mtx rep12


title: U707

value: California Pacific Medical Center

tag: sbr grade

tag: number positive nodes

tag: tumor size (cm)


title: BreastTumor_3363


title: BreastTumor_843


title: PBMC, patient. Mtx rep7

tag: cell type

tag: group

tag: patient treatment


title: PBMC, patient. Mtx rep6


title: PBMC, patient. Mtx rep5


title: PBMC, patient. Mtx rep4


title: BreastTumor_3213

tag: tissue


title: PBMC, patient. Mtx rep8


title: PBMC, patient. Mtx rep2


title: PBMC, patient. Mtx rep9


title: CCR5 Lung 6 hrs post B16 F10 injection Replicate 1

source_name: CCR5 KO lung, B16-F10 tumor, 6 hours

tag: gender

value: Female

tag: age

value: 8 to 10 weeks

tag: genotype/variation

tag: strain

value: Lung

tag: volume of injection

value: 200 mcl

tag: time point

value: 6 hr post B16 F10 injection


title: BreastTumor_22

value: breast tumor

tag: sample no

tag: tumor size grade


title: BreastTumor_3623

tag: anaplasi grade

tag: er status


title: PBMC, patient. Mtx rep3

value: PBMC


title: BreastTumor_3886

tag: her2 status


title: BreastTumor_1254


title: BreastTumor_243


title: BreastTumor_3640


title: BreastTumor_3448


title: BreastTumor_1075


title: BreastTumor_57


title: PBMC, healthy control, biological rep14

source_name: PBMC RNA from a healthy control

value: Healthy control

value: not applicable


title: Pine_rep6

tag: inoculum genotype

tag: days post inoculation


title: PBMC, patient. Mtx rep1

tag: cell type

value: Patient


title: PBMC, healthy control, biological rep13

tag: group


title: PBMC, healthy control, biological rep8

tag: patient treatment


title: BreastTumor_3497

tag: tissue


title: BreastTumor_206


title: PBMC, healthy control, biological rep15


title: BreastTumor_1238


title: PBMC, healthy control, biological rep9


title: PBMC, healthy control, biological rep12


title: PBMC, healthy control, biological rep10


title: PBMC, healthy control, biological rep6


title: BreastTumor_1437


title: BreastTumor_415


title: BreastTumor_1630


title: PBMC, healthy control, biological rep5


title: PBMC, healthy control, biological rep11


title: PBMC, healthy control, biological rep7


title: PBMC, healthy control, biological rep3


title: BreastTumor_327


title: PBMC, healthy control, biological rep4


title: BreastTumor_4077


title: BreastTumor_3398


title: PBMC, healthy control, biological rep2


title: PBMC, healthy control, biological rep1


title: granulocyte, patient. Mtx+Et rep12

source_name: granulocyte RNA from patient achieved remission on MTX+Et

value: granulocytes

value: Mtx+Et


title: granulocyte, patient. Mtx+Et rep10


title: BreastTumor_3797


title: BreastTumor_1292


title: BreastTumor_4337


title: BreastTumor_533


title: BreastTumor_127


title: granulocyte, patient. Mtx+Et rep11


title: BreastTumor_579


title: granulocyte, patient. Mtx+Et rep9


title: BreastTumor_699


title: BreastTumor_3223


title: BreastTumor_3168


title: BreastTumor_702


title: BreastTumor_1559


title: BreastTumor_278


title: granulocyte, patient. Mtx+Et rep8


title: granulocyte, patient. Mtx+Et rep5


title: granulocyte, patient. Mtx+Et rep7


title: BreastTumor_1541


title: granulocyte, patient. Mtx+Et rep4


title: BreastTumor_478


title: granulocyte, patient. Mtx+Et rep6


title: BreastTumor_1688


title: granulocyte, patient. Mtx rep10

source_name: granulocyte RNA from patient achieved remission on MTX

value: Mtx


title: granulocyte, patient. Mtx rep9


title: granulocyte, patient. Mtx+Et rep3


title: granulocyte, patient. Mtx rep7


title: granulocyte, patient. Mtx+Et rep2


title: BreastTumor_1589


title: granulocyte, patient. Mtx rep8


title: BreastTumor_262


title: granulocyte, patient. Mtx rep2


title: BreastTumor_3214


title: granulocyte, patient. Mtx rep6


title: BreastTumor_945


title: granulocyte, patient. Mtx rep1


title: BreastTumor_3046


title: granulocyte, patient. Mtx rep5


title: BreastTumor_1374


title: granulocyte, patient. Mtx+Et rep1


title: granulocyte, patient. Mtx rep4


title: BreastTumor_147


title: BreastTumor_4350


title: BreastTumor_95


title: BreastTumor_1517


title: BreastTumor_4050


title: granulocyte, healthy control, biological rep10

source_name: granulocyte RNA from healthy control


title: granulocyte, healthy control, biological rep13


title: BreastTumor_1077


title: granulocyte, patient. Mtx rep3


title: granulocyte, healthy control, biological rep9


title: granulocyte, healthy control, biological rep12


title: granulocyte, healthy control, biological rep3


title: BreastTumor_1297


title: granulocyte, healthy control, biological rep11


title: BreastTumor_348


title: granulocyte, healthy control, biological rep8


title: BreastTumor_1198


title: granulocyte, healthy control, biological rep7


title: granulocyte, healthy control, biological rep5


title: BreastTumor_4117


title: BreastTumor_753


title: BreastTumor_3801


title: BreastTumor_3599


title: BreastTumor_235


title: BreastTumor_3967


title: BreastTumor_3119


title: BreastTumor_3053


title: BreastTumor_1352


title: granulocyte, healthy control, biological rep1


title: BreastTumor_544


title: 100µM zebularine, LNCaP, biological rep 3

city: Berlin

first: Hans

last: Krause

address: Charitéplatz 1

department: Klinik für Urologie

institute: Charité - Universitätsmedizin Berlin

description:
HK_32_LNCaP_treat_3
ATCC No.: HTB-1740

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on the GeneChip Scanner 3000 G7.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LNCaP cells, 100µM zebularine, 216hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monolayer cell culture (RPMI-1640 + 10%FCS) in the presence (100µM) or absence of Zebularine (SIGMA, cat. no. Z4775).

extract_protocol: miRNeasy Mini Kit Qiagen (Cat. No.217004) total RNA extraction was done according to manufacturer's instructions, QC by AGILENT Bioanalyzer (only RIN >8.0 used).

treatment_protocol: Cell seeding (day0), treatment start (24 hours later, day1), medium change and splitting of cells on day3 and day6.

tag: cell line

value: LNCaP

value: prostate cancer cell line

tag: treatment

value: 100µM zebularine

tag: time

value: 216 hrs


title: 100µM zebularine, LNCaP, biological rep 2

description:
HK_30_LNCaP_treat_2
ATCC No.: HTB-1740


title: Untreated control, LNCaP, biological rep 3

description:
HK_31_LNCaP_mock_3
ATCC No.: HTB-1740

source_name: LNCaP cells, 0µM zebularine, 216hours


title: Untreated control, LNCaP, biological rep 2

description:
HK_29_LNCaP_mock_2
ATCC No.: HTB-1740


title: granulocyte, healthy control, biological rep2


title: BreastTumor_4028


title: BreastTumor_115


title: granulocyte, healthy control, biological rep4


title: BreastTumor_320


title: 100µM zebularine, LNCaP, biological rep 1

description:
HK_28_LNCaP_treat_1
ATCC No.: HTB-1740


title: BreastTumor_457


title: 100µM zebularine, DU-145, biological rep 3

description:
HK_26_DU_145_treat_3
ATCC No.: HTB-81

source_name: DU-145 cells, 100µM zebularine, 216hours


title: BreastTumor_258


title: Untreated control, LNCaP, biological rep 1

description:
HK_27_LNCaP_mock_1
ATCC No.: HTB-1740


title: BreastTumor_1443


title: OA-MT-18

city: Durham

first: Ching-Heng

last: Chou

address: 904 S LaSalle street

department: pathology

institute: Duke university

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-18

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.

data_processing: The array signal intensities were further analyzed by the Agilent GeneSpring GX software (version 11.5) (Agilent Technologies, Santa Clara, CA, USA). Gene expression values of all data sets were normalized using quantile normalization; probes with low signal intensities were excluded by setting the filter above 32. The normalized values were log transformed. Significant differentially expressed genes between lateral and medial samples in OA patients were identified using an adjusted Student’s t-test (P < 0.05) corrected for multiple comparisons with the Benjamini-Hochberg test.

label_protocol: 400 ng of total RNA per sample was used for one round of cRNA synthesis and amplification. Cyanine 3-labeled cRNA was then purified and hybridized to Agilent whole human genome 44k microarray chips (Agilent Technologies, Santa Clara, CA, USA). All procedures were carried out according to the manufacturer's instructions (Agilent Technologies, Taipei, Taiwan).

extract_protocol: Approximately 100 mg of powdered subchondral bone from the tibial plateau was obtained for RNA extraction. 5 mls of Trizol (Invitrogen, CA) were added to 100 mg (dry weight) of the ground tissue powder and mixed by vortexing until homogeneous. A total of 1 ml chloroform was added to the homogenized sample and centrifuged at 12,000 x g for 15 minutes at 4℃ to achieve a phase separation. The clear aqueous phase was transferred to a fresh tube for a second phase separation with Phenol/Chloroform/Isoamyl Alcohol (25:24:1) (Sigma-Aldrich, Mo), followed by RNA precipitation with pure isopropanol. After washing with 70% ethanol, the air-dried pellet was dissolved in RNase free water and genomic DNA was removed by DNase digestion (Qiagen, Germany) according to the manufacturer’s instructions. To further improve RNA quality, one half volume of 7.5M LiCl (Invitrogen, CA) was added and incubated at -20℃ for at least 30 minutes followed by RNA precipitation by centrifugation at 12,000g for 15 minutes. After 70% ethanol washing, the RNA was resuspended in RNase-free water.

treatment_protocol: The tissues were manipulated at all times under liquid nitrogen to prevent RNA degradation.

tag: disease state

value: OA

tag: gender

value: Female

tag: age


title: 100µM zebularine, DU-145, biological rep 2

description:
HK_24_DU_145_treat_2
ATCC No.: HTB-81


title: Untreated control, DU-145, biological rep 3

description:
HK_25_DU_145_mock_3
ATCC No.: HTB-81

source_name: DU-145 cells, 0µM zebularine, 216hours


title: Untreated control, DU-145, biological rep 2

description:
HK_23_DU_145_mock_2
ATCC No.: HTB-81


title: BreastTumor_356

tag: sample no


title: BreastTumor_246

tag: tumor size grade


title: OA-MT-16

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-16

scan_protocol: All procedures were carried out according to the manufacturer's instructions (Agilent Technologies, Taipei, Taiwan).

value: Male


title: OA-MT-17

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-17


title: BreastTumor_1408

tag: anaplasi grade


title: BreastTumor_3251

tag: er status


title: OA-MT-2

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-2


title: Untreated control, DU-145, biological rep 1

description:
HK_21_DU_145_mock_1
ATCC No.: HTB-81


title: OA-MT-19

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-19


title: 100µM zebularine, DU-145, biological rep 1

description:
HK_22_DU_145_treat_1
ATCC No.: HTB-81


title: hNP_non_non_wildtype

city: Guangzhou

first: Qingjian

last: Zou

state: Guangdong

address: 190 Kaiyuan Street, Guangzhou Science district

country: China

institute: Guangzhou Institutes of Biomedicine and Health, CAS

description: This sample is neural progenitors which differentiated from human iPS cells.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20 h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, Slides were scanned using an Agilent Scanner G2505C.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis. Differentially expressed genes between two samples were identified through Fold Change filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 12.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: hNPs: human iPS cells

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix was incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: HFF were cultured in DMEM supplemented with 10% FBS, Glutamax(2mM). hiNRP and hNP cells were cultured in medium containing KnockOut™ DMEM/F-12 supplemented with StemPro® NSC SFM Supplement, Glutamax (2 mM), human bFGF (10 ng/ml) and EGF (10 ng/ml).

extract_protocol: Fibroblasts, hNPs and hiNRPs were collected in TRIzol (Invitrogen), followed by total RNA extraction as manual.

value: male

tag: developemental stage

value: Eight-week fetus

value: neural progenitors


title: OA-MT-3

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-3


title: BreastTumor_3959

value: breast tumor

tag: her2 status


title: BreastTumor_1247


title: OA-MT-1

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-1


title: granulocyte, healthy control, biological rep6

value: Healthy control


title: hiNRP_MSB4_11days_reprogram

description: This sample is the cells in neuronal restricted progenitor stage when human fibroblasts been reprogrammed by Sox2, c-myc, Brn4.

source_name: MSB4-hiNRPs: fibroblasts infected with MSB4 and cultured in NP medium

value: induced neuronal progenitors


title: BreastTumor_650


title: hiNRP_MSB2_11days_reprogram

description: This sample is the cells in neuronal restricted progenitor stage when human fibroblasts been reprogrammed by Sox2, c-myc, Brn2.

source_name: MSB2-hiNRPs: fibroblasts infected with MSB2 and cultured in NP medium


title: BreastTumor_3328


title: OA-MT-4

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-4


title: OA-MT-6

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-6


title: BreastTumor_3516


title: OA-MT-8

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-8


title: hiNRP_MSB2B4_11days_intermediate

description: This sample is the cells in intermediate  differentiated stage when human fibroblasts been reprogrammed by Sox2, c-myc, Brn2 and Brn4.

source_name: Diff-hiNRPs: fibroblasts infected with MSB2B4 and cultured in NP medium


title: OA-MT-9

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-9


title: OA-MT-7

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-7


title: OA-MT-5

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-5


title: OA-MT-11

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-11


title: HFF_non_non_wildtype

description: This sample is wildtype control of fibroblasts

source_name: fibroblasts in fibroblast medium

value: embryonic fibroblasts


title: OA-MT-20

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-20


title: BreastTumor_3998

source_name: Breast primary tumor


title: OA-MT-10

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-10


title: OA-MT-12

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-12


title: OA-MT-13

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-13


title: BreastTumor_3397


title: BreastTumor_3164


title: BreastTumor_4152


title: BreastTumor_3861


title: BreastTumor_4150


title: BreastTumor_185


title: OA-MT-15

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-15


title: OA-LT-14

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-14


title: BreastTumor_3969


title: BreastTumor_3232


title: BreastTumor_4167


title: OA-LT-16

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-16


title: OA-LT-15

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-15


title: BreastTumor_3720


title: OA-MT-14

description: Gene expression profiles of OA-Subchondral bone from medial tibial plateau-14


title: BreastTumor_3973


title: OA-LT-17

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-17


title: BreastTumor_3095


title: BreastTumor_3814


title: BreastTumor_3111


title: OA-LT-2

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-2


title: BreastTumor_3195


title: OA-LT-3

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-3


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.6 / hr

city: Pittsburgh

first: Zoltan

last: Oltvai

state: PA

address: Rm. S701 Scaife Hall, 3550 Terrace St.

department: Department of Pathology

institute: University of Pittsburgh

description: Gene expression profiles from cells grown at the specific growth rate

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip E. Coli Genome 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: MAS 5

organism: Escherichia coli

source_name: E.coli MG1655 cells grown at 0.6/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)

label_protocol: Biotin labeling was performed as described in Chapter 5 (Prokaryotic Target Preparation) of the Gene Chip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: E. coli MG1655 cells were grown in LB o/n. The o/n culture was inoculated into a fresh M9 media supplemented with  glucose, galactose, glycerol, lactate and maltose (0.04% w/v) in a 1.5 L bioreactor. Cells were cultured with 400rpm stiring with air agitation while being diluted with the same media at different rates. Cells grew back to compensate the culture volume loss within 24 hrs and achieved a stable growth rate.

extract_protocol: Cells were lysised and RNA were extracted with Epicenter’s Masterpure RNA isolation kit (using the manufacturer’s product manual). Purified 100ng RNA of each sample was sent for Microarray.

treatment_protocol: Cell culture were diluted at different rates to achieve different stable growth rates 24 hrs after the dilution rates were adjusted.

tag: strain

value: E. coli K12 MG1655


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.7 / hr

source_name: E.coli MG1655 cells grown at 0.7/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)


title: OA-LT-5

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-5


title: OA-LT-6

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-6


title: OA-LT-4

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-4


title: OA-LT-1

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-1


title: BreastTumor_4324


title: BreastTumor_1251


title: BreastTumor_4002


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.3 / hr

source_name: E.coli MG1655 cells grown at 0.3/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)


title: 4239166175

type: genomic

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.

scan_protocol: After allele-specific staining BeadChip arrays were scanned on a BeadArray Reader

data_processing: Data processing was carried out with BeadStudio software v3.1.0 provided by Illumina

molecule: genomic DNA

source_name: Urinary bladder carcinoma

label_protocol: 400ng of genomic DNA was whole-genome amplified, fragmented , precipitated and resuspended in hybridization buffer

extract_protocol: Extraction of genomic DNA from fresh frozen tissue using the DNAeasy blood and tissue kit (Qiagen)

value: M

value: bladder

value: carcinoma


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.4 / hr

source_name: E.coli MG1655 cells grown at 0.5/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.2 / hr

source_name: E.coli MG1655 cells grown at 0.2/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)


title: BreastTumor_3345


title: OA-LT-18

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-18


title: 4239166219


title: OA-LT-19

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-19


title: 4239166116


title: metabolism network gene expression profile of mixed substrate culture at growth rate of 0.1 / hr

source_name: E.coli MG1655 cells grown at 0.1/hr growth rate in Minimum media supplemented with glucose, galactose, glycerol, lactate and maltose (0.04% w/v)


title: 4239166100


title: 4239166062


title: BreastTumor_3867


title: BreastTumor_3348


title: OA-LT-8

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-8


title: 1000µM zebularine, A-498, biological rep 3

description:
A07_1zeb
ATCC No.: HTB-44

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hr at 45C on GeneChip Human 133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: A-498 cells, 1000µM zebularine, 120hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monolayer cell culture (RPMI-1640 + 10%FCS) in the presence (1000µM) or absence of Zebularine (SIGMA, cat. no. Z4775).

extract_protocol: RNAzolB total RNA extraction according to manufacturer's instructions, QC by AGILENT Bioanalyzer (only RIN >9.0 used).

treatment_protocol: Treatment start (day1) after cell seeding (day0), medium changed and splitting of cells on day3 and day5.

tag: cell type

value: renal cell carcinoma cell line

value: 1000µM zebularine

value: 120 hrs


title: BreastTumor_3279


title: 4239166109


title: Untreated control, A-498, biological rep 3

description:
A07_0zeb
ATCC No.: HTB-44

source_name: A-498 cells, 0µM zebularine, 120hours


title: 4239166023


title: OA-LT-20

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-20

value: OA


title: 4235966295


title: 4235966013


title: 1000µM zebularine, A-498, biological rep 2

description:
A06_1zeb
ATCC No.: HTB-44


title: BreastTumor_3071


title: 4235966298


title: BreastTumor_3718


title: OA-LT-7

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-7

value: Female


title: 1000µM zebularine, A-498, biological rep 1

description:
A05_1zeb
ATCC No.: HTB-44


title: BreastTumor_4305


title: 4235966296


title: OA-LT-12

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-12

value: Male


title: 4235966234


title: 4235966250


title: 4235966253


title: OA-LT-10

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-10


title: BreastTumor_4005


title: Untreated control, A-498, biological rep 1

description:
A05_0zeb
ATCC No.: HTB-44


title: 4235966256

value: F


title: 4235966189


title: BreastTumor_4370


title: 4239166047


title: Sodium arsenite 12h, biological rep3

city: Mexico

first: Angelica

last: Martinez

state: DF

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Tlalpan

department: Investigación

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description: Cell line treated with arsenite for 12 hours, biological rep 3

scan_protocol: The GeneChip Scanner 3000 7G collected fluorescent signals, and the Expression Console software subsequently amassed intensity and quality data on the scanned arrays (Affymetrix, Santa Clara, CA).

data_processing: Expression Console-generated rma-gene from the 9 arrays in .CEL format

source_name: lymphoblastoid cell line (CL-1)

label_protocol: Target cDNA was prepared according to the Whole-Transcript (WT) Sense Target Labeling Protocol and hybridized to the Human Gene 1.0 ST microarray (Affymetrix, Santa Clara CA).

growth_protocol: We used human lymphoblastoid primary cultures and two human lymphoblastoid cell lines, independently immortalized with Epstein-Barr virus (catalog No. VR-1492; ATCC, Manassas, VA). All cell cultures were propagated in RPMI media supplemented with 10% fetal bovine serum (FBS), L-glutammine 2 mM and antiobiotics (10 000 U/ml penicillin and 10 mg/ml streptomycin) (Invitrogen Calrsbad, CA) at 37ºC in an atmosphere of 5% CO2. In the case of primary cultures, 1% phytohemaglutinine were added

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

treatment_protocol: Cell cultures (1x106) were treated with 5µM sodium arsenite (Sigma, St. Louis, MO) for 2 and 12 hrs while control cultures were incubated with PBS. Nine biological replicates for each condition were used for microarray analysis.


title: Untreated control, A-498, biological rep 2

description:
A06_0zeb
ATCC No.: HTB-44


title: Normal-LT-2

description: Gene expression profiles of Normal-Subchondral bone from lateral tibial plateau-2

value: Normal


title: BreastTumor_3388


title: BreastTumor_3027


title: OA-LT-13

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-13


title: Normal-MT-1

description: Gene expression profiles of Normal-Subchondral bone from medial tibial plateau-1


title: Sodium arsenite 12h, biological rep2

description: Cell line treated with arsenite for 12 hours, biological rep 2

hyb_protocol: hybridized to the Human Gene 1.0 ST microarray (Affymetrix, Santa Clara CA)


title: OA-LT-9

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-9


title: 4235966233


title: Sodium arsenite 12h, biological rep1

description: Cell line treated with arsenite for 12 hours, biological rep 1


title: 4235966149


title: 4235966118


title: BreastTumor_4103


title: Sodium arsenite 2h, biological rep3

description: Cell line treated with arsenite for 2 hours, biological rep3


title: OA-LT-11

description: Gene expression profiles of OA-Subchondral bone from lateral tibial plateau-11


title: Sodium arsenite 2h, biological rep2

description: Cell line treated with arsenite for 2 hours, biological rep 2


title: Normal-MT-4

description: Gene expression profiles of Normal-Subchondral bone from medial tibial plateau-4


title: BreastTumor_4275


title: 4235966056

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).


title: Normal-MT-3

description: Gene expression profiles of Normal-Subchondral bone from medial tibial plateau-3


title: BreastTumor_3134


title: Normal-LT-1

description: Gene expression profiles of Normal-Subchondral bone from lateral tibial plateau-1


title: 4235966055


title: BreastTumor_4049


title: Normal-MT-5

description: Gene expression profiles of Normal-Subchondral bone from medial tibial plateau-5


title: CL, biological rep3

description: untreated control, rep3


title: Sodium arsenite 2h, biological rep1

description: Cell line treated with arsenite for 2 hours, biological rep1


title: Normal-MT-2

description: Gene expression profiles of Normal-Subchondral bone from medial tibial plateau-2


title: BreastTumor_3184


title: CL, biological rep2

description: untreated control, rep2


title: 4235966148


title: BreastTumor_3151


title: 4235966045


title: BreastTumor_4134


title: BreastTumor_3891


title: BreastTumor_4367


title: Normal-LT-3

description: Gene expression profiles of Normal-Subchondral bone from lateral tibial plateau-3


title: 4235966076


title: 4235966030


title: BreastTumor_522


title: 4235966050


title: Normal-LT-4

description: Gene expression profiles of Normal-Subchondral bone from lateral tibial plateau-4


title: BreastTumor_31


title: CL, biological rep1

description: untreated control, rep1


title: BreastTumor_609


title: BreastTumor_4345


title: BreastTumor_3087


title: 4235966029


title: Normal-LT-5

description: Gene expression profiles of Normal-Subchondral bone from lateral tibial plateau-5


title: 4235966024


title: Ebf2- rep3

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Cells sorted as CD45-TER119-CD31-EBF2-

hyb_protocol: cRNA fragments hybridized against MOE430 2.0 Affymetrix gene expression arrays chip according to manufacturer instructions

scan_protocol: Chips were scanned using a GeneChip TM Scanner 3000

data_processing: Expression values were acquired using RMA and Mouse430_2.cdf file

source_name: mouse bone marrow

label_protocol: RNA was labelled and amplified according to Affymetrix TM GeneChip Expression Analysis Technical Manual 2011

growth_protocol: Cells obtained fresh from the bone marrow of mice.

extract_protocol: RNeasy Micro kit (Qiagen) has been used to extract RNA according to manufacturer instruction

treatment_protocol: No treatment has been used.

tag: genotype

value: wild-type

value: bone marrow CD45-TER119-CD31-EBF2-

tag: genetic background


title: Ebf2- rep1

description: Cells sorted as CD45-TER119-CD31-EBF2-


title: Ebf2- rep2

description: Cells sorted as CD45-TER119-CD31-EBF2-


title: 4239166013

tag: tissue


title: ATF2_2

city: Chicago

first: Subhradip

last: Karmakar

state: IL

address: 900 E 57th Street

department: Genetics

institute: U of Chicago

description: replicare 2

hyb_protocol: standard hyb protocol following Ilumina recommendations

scan_protocol: standard Illumina scannign protocol

data_processing: standard Quantile normaliztion

source_name: ATF2 siRNA

label_protocol: standard labelling procedure

growth_protocol: cells were grown and maintaned in RPM1 1640 media supplemented with L Glutamine, 10% heat inactvated fetal bovine serum and 1% Antimycotic antibiotics

extract_protocol: standard as recommened by Qiagen following RNAeasy kit . RNA was extracted using RLT buffer and subjected to purification after in-coloumn digestion with DNAse

treatment_protocol: cells were treated with 50nM siRNA for 48 hrs

tag: cell line

value: K562 cells


title: ATF2_1

description: replicate 1


title: Ebf2+ rep2

description: Cells sorted as CD45-TER119-CD31-EBF2+

value: bone marrow CD45-TER119-CD31-EBF2+


title: NT2

description: replicate 2

source_name: Scrambled siRNA


title: 4118698560


title: Ebf2+ rep1

description: Cells sorted as CD45-TER119-CD31-EBF2+


title: 4118698575


title: mandible_at_E14.5_M_embryo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

institute: The Nippon Dental University

description:
Mus_E14.5_MA_M
Gene expression data from 40 embryos

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Microarray (Mouse expression 430 2.0, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The expression value and detection calls were computed from the raw data with Affymetrix® Expression Console  1.1 software (v.1.1).

source_name: Medial region Mandibular arch from E14.5 mouse embryos

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Timed-pregnant ICR mice were kept under a 12-h light-dark cycle and were given standard laboratory fodder and water ad libitum.

extract_protocol: Total RNA was extracted from the sample using RNeasy Micro Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: Dams were sacrificed by cervical dislocation and the uteri dissected out were placed in Hanks’ balanced salt solution (HBSS) at 4C. Embryos were rinsed with fresh HBSS to remove amniotic fluid and blood. Mandibular arches were collected from the embryos.

value: ICR

tag: developmental stage

value: Mandibular arches (tongue)

tag: region

value: Medial/anterior 2/3


title: Ebf2+ rep3

description: Cells sorted as CD45-TER119-CD31-EBF2+


title: NT1

description: replicate 1


title: H24010-HYP

status: Public on Oct 23 2013

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

description: Hypertrophic chondrocytes, replicate 7

data_processing: The non-normalized_data.txt file contains the CT values exported from the OpenArray ® Real-Time qPCR Analysis . Data were analyzed with the Applied Biosystems DataAssist ™ Software.CT values normalized to RNU44 using the Applied Biosystems DataAssist ™ Software. Series supplementary file GSE49152_non-normalized.txt reports raw CT values. Series supplementary file GSE49152_fold-change_data.txt reports test/control ratios.

label: FAMTP

source_name: human embryonic limb tissue

label_protocol: Megaplex ™ RT Primers were used to label the cDNA. Protocol specified  in TaqMan(R) OpenArray(R) MicroRNA Panels User Guide June 2011.

growth_protocol: Frozen blocks of human embryonic limb tissue were sectioned (20um) onto RNAse-free polyethylene naphthalate (PEN)-coated glass slides (Leica Microsystems) that are specifically designed for laser capture microdissection (LCM).Frozen sections were stored at minus 80oC for up to 48 h before being processed for LCM.

extract_protocol: Total RNA including small RNAs was isolated using either the Total RNA Purification Micro Kit (Norgen Biotek Corp.) or the mirVanaTM miRNA Isollation kit in accordance with the manufacturer’s protocol.

treatment_protocol: Upon removal from cold storage, the tissue sections were exposed to 30 s incubations in cold 75% ethanol followed by 50% ethanol, 20% ethanol, dH2O, 0.02% Toluidine Blue (prepared in RNAse free H2O), two dH20 washes, 75% ethanol, 95% ethanol and 100% ethanol. Finally, sections were transferred to xylene for 3 min and air-dried.LCM was immediately carried out using the LMD7000 system (Leica Microsystems). The three cartilage regions of interest in each tissue section were selected using the system software resulting in a contact and contamination-free collection of tissue directly into one of the three sterile 0.5 mL Eppendorf caps containing 60 ul of lysis buffer from the RNA isolation kit of choice.

value: Hypertrophic chondrocytes


title: 4118698524

value: M

value: bladder

tag: disease state

value: carcinoma


title: 4118698451

tag: gender


title: H23814-DC

description: Differentiated chondrocytes, replicate 6

value: Differentiated chondrocytes


title: H23387-HYP

description: Hypertrophic chondrocytes, replicate 2


title: H23689-HYP

description: Hypertrophic chondrocytes, replicate 3


title: H23374-HYP

description: Hypertrophic chondrocytes, replicate 1


title: H24010-DC

description: Differentiated chondrocytes, replicate 7


title: H23804-HYP

description: Hypertrophic chondrocytes, replicate 5


title: H24051-DC

description: Differentiated chondrocytes, replicate 8


title: H24243-HYP

description: Hypertrophic chondrocytes, replicate 9


title: H24051-HYP

description: Hypertrophic chondrocytes, replicate 8


title: 4118698511


title: 4118698441


title: 4118698434


title: H23814-HYP

description: Hypertrophic chondrocytes, replicate 6


title: 4235966022


title: H23804-DC

description: Differentiated chondrocytes, replicate 5


title: H23689-DC

description: Differentiated chondrocytes, replicate 3


title: H23387-DC

description: Differentiated chondrocytes, replicate 2


title: H24243-PC

description: Precursor chondrocytes, replicate8

value: Precursor chondrocytes


title: 4118698432


title: H23731-HYP

description: Hypertrophic chondrocytes, replicate 4


title: H24051-PC

description: Precursor chondrocytes, replicate7


title: H23374-PC

description: Precursor chondrocytes, replicate1


title: H23387-PC

description: Precursor chondrocytes, replicate2


title: H23804-PC

description: Precursor chondrocytes, replicate5


title: H23689-PC

description: Precursor chondrocytes, replicate3


title: H23731-PC

description: Precursor chondrocytes, replicate4


title: H23374-DC

description: Differentiated chondrocytes, replicate 1


title: H24010-PC

description: Precursor chondrocytes, replicate6


title: 4118698427

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Genotyping BeadChips (Illumina).


title: H23731-DC

description: Differentiated chondrocytes, replicate 4


title: SB380225_replicate

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium Human 1M Duo Genotyping BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays (Human 1M Genotyping BeadChips (Illumina)). After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.