title: pleural_LTS_1hr_Z9_rep8

city: River Forest

first: Robert

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

description: US83800207_254938410005_S01_GE2_1105_Oct12_2_2.2

hyb_protocol: Samples were hybridized to the microarray slide at 65C and 10rpm for 17 hours.  All labeling and post-labeling processing was carried out in an ozone regulated environment, monitored at < 5ppb.

scan_protocol: Slides were scanned on an Agilent C scanner at 3um resolution.  Data was extracted using Agilent Feature Extraction software, v. 11.5.

data_processing: Microarray data was analyzed using limma  (G. Smyth, 2005) from the Bioconductor suite of tools (Gentleman et al., 2004) for R (Team, 2013).  Our processing script is posted on the Open Science Framework.   Median expression values were analyzed (Zahurak et al., 2007).  These were corrected for background using the normexp+offset algorithm recommended for Agilent microarrays by Ritchie et al. (2007).  An offset of 30 was selected based on inspection of MAPlots and based on maximizing correlations with qPCR measurements from the same material (a set of measurements for 10 transcripts).  Expression was normalized within each array using the loess function (G. K. Smyth & Speed, 2003).  Where multiple probes were used to measure the same EST or mRNA, these were then averaged.  Finally, trained and untrained expression were compared using an empirical Bayes-moderated t-test (G. K. Smyth, 2004).  Statistical significance was calculated using Benjamini-Hochberg correction for multiple comparisons to maintain a 5% overall false-discovery rate (Benjamini & Hochberg, 1995).  Rather than test for significant regulation and then use a fold-change threshold to evaluate practical significance, we used the treat function from limma (McCarthy & Smyth, 2009) to test not only against a null hypotheses of no change (Ho: |Mean Fold Change| > 1) but also changes of 1.1, 1.25, and 1.5 fold (e.g. Ho: |Mean Fold Change| > 1.5).

organism: Aplysia californica

source_name: untrained side pleural from two animals (1 left trained, 1 right trained)

label_protocol: A two-color approach was used with each array hybridized to a trained (Cy5) or untrained (Cy3) sample.  Sample integrity was determined by Bioanalyzer RNA 6000, Pico total RNA protocol.  300ng of total RNA was amplified and labeled with Cy3 or Cy5 using the Agilent Quick Amp Two-Color Labeling Kit. Dye incorporation and yield was determined by Nanodrop.

growth_protocol: Animals (75-125g) were obtained from the RSMAS National Resource for Aplysia (Miami, FL) and maintained at 16o C in one of two 90-gallon aquariums with continuously circulating artificial sea water (Instant Ocean, Aquarium Systems Inc.).  Animals were separately housed in rectangular colanders (11.5cm wide, 16.5cm long, 7.3cm deep), fed dried seaweed twice a week, and maintained on a 12 hr light-dark cycle.  2 days prior to any experimental testing, animals were fed to satiation and then food deprived for the remained of the experiment (Levenson, Byrne, & Eskin, 1999; Wainwright, Zhang, Byrne, & Cleary, 2002).  To control for batch/shipment effects, animals from at least 2 different shipments were used for each experiment.

extract_protocol: Animals were harvested 1 hour after training, the time point at which protein levels of the immediate-early gene C/EBP are most strongly up-regulated after training (Lyons, Collado, Khabour, Green, & Eskin, 2006).   To analyze transcription, pleural ganglia RNA was isolated.  These ganglia were selected because they contain the cell bodies of the VC nociceptors (Illich & Walters, 1997; Walters, Byrne, Carew, & Kandel, 1983) which are thought to serve as an important site for the neural plasticity underlying behavioral sensitization (Cleary et al., 1998) cit_af ref_bf(Noel, F. 1993 ref_num773)ref_af.  Briefly, animals were anesthetized with an injection of isotonic MgCl2 (50% of body weight), and an incision was then made along the ventral midline to expose the CNS.  As dissection can alter gene expression (Alberini et al., 1994) cit_af ref_bf(Alberini, C. M. 1994 ref_num764)ref_af, we extracted ganglia rapidly (< 5 minutes per animal) and transferred them immediately to RNAlater (Ambion, Austin, TX)on ice.  Tissue was homogenized and RNA extracted using Trizol (Invitrogen, Carlsbad CA) and Direct-Zol Mini RNA Kit (Zymo, Irvine, CA). Samples were homogenized using the Bullet Blender (NextAdvance, Averill Park, NY). Quantity and quality of RNA was assessed using the NanoDrop 1000 (Thermo Scientific, Wilmington, DE).  RNA was reverse transcribed using oligo(dT) primes and RevertAid First Strand cDNA Synthesis Kit (Fermentas, Glen Burnie MD).

treatment_protocol: A one-day long-term sensitization training protocol (Figure  1) was conducted similarly to Wainwright et al. (2002) but with a 90mA stimulus rather than a 60mA stimulus.   We have found that this higher stimulus amplitude produces stronger and more reliable elevations of both behavior and C/EBP expression (Bonnick et al., 2012). Training consisted of 4 rounds of noxious shock applied at 30 minute intervals to one side of the body with a hand-held electrode (WPI Constant-Current Stimulator, Sarasota, FL).  Each round consisted of 10 pulses of 500ms duration at a rate of 1hz and an amplitude of 90mA AC.  Side of training was counterbalanced within each experiment.

tag: tissue

value: pleural ganglia

value: untrained

value: trained


title: Young 1

status: Public on May 08 2014

type: RNA

city: Boston

first: Amy

middle: J

last: Wagers

state: MA

address: One Joslin place

department: Stem Cell and Regenerative Biology

country: USA

institute: Joslin diabetes center and Harvard University

description: Gene expression data from young mouse skeletal muscle precursor cells

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip® Mouse Genome 430 2.0 Array, washed and stained according to standard Affymetrix protocol (Affymetrix Hybridization, Wash and Stain kit).

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

data_processing:
Data were normalized using RMA (Robust Multi-array average).
Data were analyzed using GenePattern.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Skeletal muscle

label_protocol: Biotinylated cRNA was prepared from total RNA using 3'IVT ExpressKit from Affymetrix.

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

treatment_protocol: Myofiber-associated cells were isolated from mouse muscle by two-step enzymatic digestion and mechanical dissociation. Individual cell subsets were isolated by combinatorial cell surface marker staining and fluorescence-activated cell sorting.

tag: cell type

value: skeletal muscle precursor cells

tag: cell surface markers

tag: developmental stage

value: young (2 months)

tag: genetic background


title: pleural_LTS_1hr_Z4_rep4

description: US83800207_254938410005_S01_GE2_1105_Oct12_1_4

tag: treatment

source_name: trained side pleural from two animals (1 left trained, 1 right trained)


title: pleural_LTS_1hr_Z8_rep7

description: US83800207_254938410005_S01_GE2_1105_Oct12_2_2.1


title: pleural_LTS_1hr_Z5_rep5

description: US83800207_254938410005_S01_GE2_1105_Oct12_2_1


title: ΔNp53:WTp53, exp 0

city: Boulder

first: Shih-chieh

last: Lin

state: CO

address: 215 UCB

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

description:
Taatjes_23AG_0th
Gene expression data from transfected cell, 40hours after transfection

hyb_protocol: each sample was hybridized to Affymetrix GeneChip Human Gene 1.0 ST array

scan_protocol: examination with an Affymetrix GeneChip Scanner 3000

data_processing: Normalized RMA sketch were calculated by Expression Console (64bit, v1.1)

label: Biotin

organism: Homo sapiens

label_protocol: cDNA/cRNA/cDNA was generated with the Ambion WT Expression kit and biotin labelled with GeneChip WT Terminal Labeling Kit

growth_protocol: Null p53 cell lines NCI-H1299 was cultured with 10% FBS supplemented RPMI-1640 till 95% confluence

extract_protocol: Total RNA was extracted with RNAeasy kit from trypsinized cells 40 hours after transfection.

treatment_protocol: ΔNp53:WTp53 or WTp53 in GFP vectors with Lipofectamin 2000 were used for transient transfection.

tag: cell line

value: Null p53, non-small cell lung carcinoma cells

tag: transfected with

value: ΔNp53:WTp53 in GFP vector (pIRES-2EGFP)


title: pleural_LTS_1hr_Z6_rep6

description: US83800207_254938410005_S01_GE2_1105_Oct12_2_2


title: pleural_LTS_1hr_Z1_rep1

description: US83800207_254938410005_S01_GE2_1105_Oct12_1_1


title: pleural_LTS_1hr_Z2_rep2

description: US83800207_254938410005_S01_GE2_1105_Oct12_1_2


title: pleural_LTS_1hr_Z3_rep3

description: US83800207_254938410005_S01_GE2_1105_Oct12_1_3


title: AP-1B+/-_small intestinal epithelia_rep2

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

description: Small intestine epithelial cells from AP-1B+/- mice.

hyb_protocol: Hybridization, washing, and staining were performed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the provided manual.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: Raw MAS5 signals and the normalized values (per chip normalization) were determined using GeneSpring 7.3.1.

source_name: AP-1B+/- sIEC

label_protocol: One-Cycle Target Labeling and Control Reagents.

growth_protocol: Small intestine was dissected and soaked in Hank's Buffered Salt Solution (HBSS) (GIBCO) containing 30 mM EDTA. After incubation on ice for 20 min, IECs were isolated by manipulation with a fine needle under stereomicroscopic monitoring.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).

value: small intestine

value: epithelial cell

tag: source type

value: isolated cell

tag: strain

tag: genotype

value: adult

tag: age

value: 10 weeks

tag: microbial condition

value: specific pathogen-free (SPF)

tag: disease state

value: healthy


title: Escherichia coli_10mM H202_Rep2 (Dye swap)

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 2 of 2.

hyb_protocol: Standard Agilent procedures.

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1.

data_processing: Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

label_protocol: Approximately 10 µg of total RNA was processed to produce Cy5- or Cy3-labelled cDNA targets.

growth_protocol: In LB plus 0.8% glucose cells grew overnight, and then diluted to OD600=0.02, followed by culture until OD600 reaches 1.0. The culture was performed at 37 degree Celsius and 250rpm.

extract_protocol: Total RNA was isolated after 30 min incubation with hydrogen peroxide using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: Two conditions: 10mM hydrogen peroxide, 37 degree Celsius, 250rpm, 30min; 30mM hydrogen peroxide, 37 degree Celsius, 250rpm, 30min.

tag: substrain

value: luxS mutant

value: wild type


title: adult V-SVZ qNSCs, biological replicate 3

status: Public on May 07 2014

city: NYC

first: Fiona

last: Doetsch

state: NY

address: 630 West 168th St

institute: Columbia University

description: Gene expression data from quiescent adult neural stem cells of the ventricular-subventricular zone

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MOE430.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

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

source_name: GFAP::GFP+CD133+CD24- V-SVZ cells from adult brains

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

extract_protocol: Extraction of total RNA was performed using the miRNeasy kit according to the manufacturer's instructions and cDNA synthesized with Nugen Pico amplification kit.

value: ventricular-subventricular zone


title: AP-1B-/-_small intestinal epithelia_rep2

description: Small intestine epithelial cells from AP-1B KO mice.

source_name: AP-1B-/- sIEC


title: AP-1B+/-_small intestinal epithelia_rep1


title: adult V-SVZ aNSCs, biological replicate 3

description: Gene expression data from activated adult neural stem cells of the ventricular-subventricular zone

source_name: GFAP::GFP+CD133+EGFR+CD24- V-SVZ cells from adult brains


title: adult V-SVZ aNSCs, biological replicate 1

value: GFAP::GFP+CD133+EGFR+CD24- V-SVZ cells from adult brains


title: adult V-SVZ qNSCs, biological replicate 2

value: GFAP::GFP+CD133+CD24- V-SVZ cells from adult brains


title: adult V-SVZ aNSCs, biological replicate 2


title: female pupae replicate 1 [miRNA]

city: Falmer

middle: C

last: Ingleby

address: John Maynard Smith Building

department: School of Biology

country: United Kingdom

institute: University of Sussex

description: gene expression data from LHm outbred population

hyb_protocol: Affymetrix One-Cycle Target Labeling (Expression Analysis Technical Manual, 2001, Affymetrix).

data_processing: RMA standard

organism: Drosophila melanogaster

source_name: female Drosophila pupae

growth_protocol: LHm outbred population kept at 25oC

extract_protocol: ambion miRvana total RNA extraction kit used according to manufacturer's protocol

treatment_protocol: Flies laid in staggered vials and larvae, pupae and adults samples collected at the same time from vials at the right stage of development. 10 individuals included in each biological replicate collected.

tag: Sex

value: female

value: pupae


title: female adults replicate 1 [miRNA]

scan_protocol: Affymetrix One-Cycle Target Labeling (Expression Analysis Technical Manual, 2001, Affymetrix).

source_name: female Drosophila adults

value: adults


title: female adults replicate 2 [miRNA]

label_protocol: Affymetrix One-Cycle Target Labeling (Expression Analysis Technical Manual, 2001, Affymetrix).


title: male adults replicate 2 [miRNA]

source_name: male Drosophila adults

value: male


title: male adults replicate 1 [miRNA]


title: male pupae replicate 1 [miRNA]

source_name: male Drosophila pupae


title: male larvae replicate 2 [miRNA]

source_name: male third instar Drosophila larvae

value: larvae


title: female pupae replicate 2 [miRNA]


title: male pupae replicate 2 [miRNA]


title: male larvae replicate 1 [miRNA]


title: adult V-SVZ qNSCs biological replicate 1


title: Escherichia coli_30mM H202_Rep2

description: Biological replicate 2 of 2.


title: AP-1B-/-_small intestinal epithelia_rep1

value: small intestine


title: Escherichia coli_10mM H202_Rep1

description: Biological replicate 1 of 2.


title: female larvae replicate 1 [miRNA]

source_name: female third instar Drosophila larvae


title: Escherichia coli_30mM H202_Rep1

description: Biological replicate 1 of 2.


title: female larvae replicate 2 [miRNA]


title: 10887

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and normalised using MBCB algorithm

source_name: Human Bronchial Epithelial Cells

label_protocol: Biotinylated cRNA were prepared with Ambion TotalPrep RNA amplification kit with biotin UTP (Enzo) labeling

extract_protocol: Total RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bio-rad Experion system.

value: Human Bronchial Epithelial Cells

tag: radiation

value: x-ray

tag: dose (gray)

tag: post radiation time (hour)

tag: biological replicate

tag: technical replicate

value: A


title: 10904

tag: cell type


title: 10869


title: 10875


title: 10410

value: Si


title: 10910


title: 10392


title: 10381


title: 10375


title: 10851


title: 10898


title: 10263

value: Fe


title: 10857


title: 10246


title: 10357


title: 10881


title: 10863


title: 10398


title: 10415


title: 10363


title: 10345


title: 10252


title: 10845


title: 10387


title: 10369


title: 10915


title: 10404


title: 10258


title: 10351


title: 10235


title: 10229


title: 10211


title: 10193


title: 9294


title: 9276


title: 10217


title: 9240


title: 9300


title: 10199


title: 9282


title: 10240


title: 10223


title: 10205


title: 9306


title: 9264


title: 9246


title: 9270


title: 8136


title: 9252


title: 9234


title: 9288


title: 8076


title: 8100


title: 8118


title: ARDS lung Biological Replicate 4

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

description: Replicate 4 of 6 ARDS samples.

hyb_protocol: All of the small RNA samples were separately labeled with Cy3 or Cy5 capture sequence. After labeling and purification, equal amounts of small RNA from all the samples, labeled with the same dye, were pooled together as a common reference. To eliminate dye bias, dye-swap was performed. The tagged miRNAs were hybridized to a miRNA microarray slide at 52°C overnight. The array was washed in pre-warmed (52 °C) 2 × SSC, 0.2% SDS for 15 min, 2 × SSC for 12 min, and 0.2 × SSC for 12 min at room temperature. After washing, the Alexa Fluor 3 or 5 capture reagents were hybridized to the tagged miRNAs at 62°C for 4 h. The slides were then washed and dried.

scan_protocol: The hybridized slide was scanned with ScanArray Express (PerkinElmer Life and Analytical Sciences, Boston, MA)

data_processing: The images were analyzed with GenePix 5.0 pro (Axon Instruments, Inc. Union City, CA). The signal from each spot was normalized to the average signal of the whole block. The highest and lowest signals from the 6 identical probes in the same block were excluded from the data analysis. The geometric average of the remaining 4 signals was considered to be the signal of that particular miRNA.

organism: Rattus norvegicus

source_name: ARDS lung tissues

label_protocol: The labeling of miRNA was performed with the 3 DNA array 900 miRNA direct kit (Genisphere, Hatfield, PA)

extract_protocol: Small RNAs were isolated from  rat lungs (200 mg) using the mirVana microRNA isolation kit (Ambion, Austin, TX) exactly as per the instructions of the manufacturer

treatment_protocol: Rat model of ARDS was induced by saline lavage and mechanical ventilation

tag: tissue

value: Whole lung

source_name: Common reference from pooled all samples


title: ARDS lung Techincal Replicate 5

description: Replicate 5 of 6 ARDS samples.


title: 8082

tag: cell line


title: ARDS lung Techincal Replicate 6

description: Replicate 6 of 6 ARDS samples.


title: 8070


title: 8124


title: 9258


title: 8064


title: 8088


title: 7824


title: 7818


title: 8094


title: 8112


title: 10892


title: 8106


title: 7806


title: 8130


title: 7812


title: ARDS lung Biological Replicate 3

description: Replicate 3 of 6 ARDS samples.


title: ARDS lung Biological Replicate 1

description: Replicate 1 of 6 ARDS samples.


title: CON lung Techincal Replicate 6

description: Replicate 6 of 6 control samples.

source_name: Control lung tissues


title: ARDS lung Biological Replicate 2

description: Replicate 2 of 6 ARDS samples.


title: CON lung Techincal Replicate 5

description: Replicate 5 of 6 control samples.


title: CON lung Biological Replicate 3

description: Replicate 3 of 6 control samples.


title: CON lung Biological Replicate 1

description: Replicate 1 of 6 control samples.


title: CON lung Biological Replicate 4

description: Replicate 4 of 6 control samples.


title: CON lung Biological Replicate 2

description: Replicate 2 of 6 control samples.


title: 7794


title: 7776


title: 5516

value: B


title: 5480


title: 5462


title: 5498


title: 7758


title: Venus_3 (control)

city: Jiangsu

first: Yun

last: Zhao

address: No. 1, Shizi Street

country: China

institute: Cyrus Tang Hematology Center, Soochow University

description: Gene expression data of venus cells

hyb_protocol: 55ul of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).

scan_protocol: Slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies) and Agilent Feature Extraction Software.

data_processing: Removed control probes and the rest probes were Quantile-normalized using limma (R package) from Bioconductor.

source_name: Venus cell line

label_protocol: 4  μg of total RNA was labelled with Cy3 (DMSO treated cells).

growth_protocol: THP-1 cells were cultured with RPMI-1640 media supplemented with 10% FBS at 5% CO2. The The control (Venus) and TWIST2 lentiviral vectors were used to infect THP-1 cells and the fluorescent cells were purified with a cell sorter. The control and TWIST2 expressed THP-1 cells were cultured with same condition as their parental cells.

extract_protocol: PicoPure TM  RNA extraction kit (Arturus, Mountainview, CA, USA) was used to extract RNA,  during  the  procedure  DNaseI  (Life  Technologies)  treatment  was  applied  as  well according  to  the  manufacturer’s  protocol  to  minimize  the  contamination  with  genomic DNA. RNA was reverse transcribed with SuperScript III (Life Technologies) to generate first  strand  cDNA,  Q-RT-PCR  was  performed  using  SYBR  Green  PCR  MasterMix (Applied Biosystems, Foster City, CA, USA) with 7500 real time PCR system (Applied Biosystems).

tag: lentviral vector

value: control (Venus)


title: 7770


title: Venus_2 (control)

description: Gene expression data of venus cells


title: 7800


title: 7788


title: 5510


title: 7752


title: 7782


title: Venus_1 (control)

description: Gene expression data of venus cells


title: 7764


title: TWIST2_4

description: Gene expression data of TWIST2 expressed THP-1 cells

source_name: TWIST2 cell line


title: 5048

value: D


title: Venus_4 (control)

description: Gene expression data of venus cells


title: TWIST2_2


title: 5492


title: TWIST2_3


title: 4886


title: 5504


title: 5450


title: 5487


title: 5469


title: 5522


title: 5456


title: 4868


title: 5474


title: 4880


title: 4898


title: 4874


title: 4856


title: 4892


title: TWIST2_1


title: 5000


title: 4850


title: 4838


title: SP treated stromal cell rep4

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

description: Affymetrix Human Gene 1.0 ST Array

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: GeneSpringGX 11, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples

source_name: stromal fibroblasts

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: Epithelial cells are grown on matrigel-coated plates in Defined KSFM.  Stromal cells are grown in 10% serum media on regular culture plastic plates.

extract_protocol: RNA is extracted using the Magery Nagel Nucleospin RNA II kit.

treatment_protocol: Cells are treated with 1% SP for 6h.

value: stromal fibroblasts

tag: treatment

value: seminal plasma

tag: tissue and passage

value: endometrium, P2


title: control stromal cell rep3

description: Affymetrix Human Gene 1.0 ST Array

value: control


title: 4832


title: control stromal cell rep2

description: Affymetrix Human Gene 1.0 ST Array


title: 4862


title: 4844


title: CYT2 Bio Rep1 Tech rep2 +NRG1

city: New Haven

first: James

middle: T.

last: Platt

state: CT

address: 333 Cedar ST

department: Medical Oncology

institute: Yale University

description: Tech Replicate2

data_processing: Illumina Beadchip Studio, log2 transformed

source_name: Mammary epithelial Cell Line

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

extract_protocol: RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: Control vector (VEC) and ERBB4 expression MCF10A cells(CYT1 or CYT2) were serum starved for 48 hours and incubated with or without ERBB4 ligand NRG1 for 2h.  RNA samples were collected and analyzed.

tag: expression

value: ERBB4 expression ICD CYT2

value: with ERBB4 ligand NRG1 for 2h


title: control epithelial cell rep4

description: Affymetrix Human Gene 1.0 ST Array

source_name: epithelial cells

value: endometrial epithelial cells

value: endometrium, P1


title: SP treated epithelial cell rep1

description: Affymetrix Human Gene 1.0 ST Array


title: CP2428

value: Human Bronchial Epithelial Cells

value: C


title: SP treated stromal cell rep3

description: Affymetrix Human Gene 1.0 ST Array


title: SP treated stromal cell rep2

description: Affymetrix Human Gene 1.0 ST Array


title: CP2422


title: control stromal cell rep1

description: Affymetrix Human Gene 1.0 ST Array


title: CP2416


title: SP treated epithelial cell rep2

description: Affymetrix Human Gene 1.0 ST Array


title: 4826


title: CYT2 Bio Rep2 Tech rep2 +NRG1

description: Tech Replicate2


title: CYT1 Bio Rep2 Tech rep2

description: Tech Replicate2

value: ERBB4 expression ICD CYT1

value: without ERBB4 ligand NRG1 for 2h


title: control stromal cell rep4

description: Affymetrix Human Gene 1.0 ST Array


title: control epithelial cell rep1

description: Affymetrix Human Gene 1.0 ST Array


title: SP treated stromal cell rep1

description: Affymetrix Human Gene 1.0 ST Array


title: control epithelial cell rep2

description: Affymetrix Human Gene 1.0 ST Array


title: CP2368

value: Fe


title: SP treated epithelial cell rep3

description: Affymetrix Human Gene 1.0 ST Array


title: SP treated epithelial cell rep4

description: Affymetrix Human Gene 1.0 ST Array


title: CYT2 Bio Rep1 Tech rep2

description: Tech Replicate2


title: control epithelial cell rep3

description: Affymetrix Human Gene 1.0 ST Array


title: CP2410


title: CYT1 Bio Rep1 Tech rep2

description: Tech Replicate2


title: CP2320

value: A


title: CP2356

value: B


title: VEC Bio Rep1 Tech rep2 +NRG1

description: Tech Replicate2

value: Control vector


title: CYT1 Bio Rep2 Tech rep2 +NRG1

description: Tech Replicate2


title: CYT1 Bio Rep1 Tech rep2 +NRG1

description: Tech Replicate2


title: VEC Bio Rep2 Tech rep2 +NRG1

description: Tech Replicate2


title: CP2314


title: CYT2 Bio Rep1 Tech rep1 +NRG1

description: Tech Replicate1


title: CP2392


title: CYT1 Bio Rep1 Tech rep1

description: Tech Replicate1


title: CP2302


title: CYT2 Bio Rep1 Tech rep1

description: Tech Replicate1


title: CP2404


title: VEC Bio Rep1 Tech rep2

description: Tech Replicate2


title: CYT2 Bio Rep2 Tech rep2

description: Tech Replicate2


title: CP2350


title: VEC Bio Rep2 Tech rep1 +NRG1

description: Tech Replicate1


title: CYT1 Bio Rep1 Tech rep1 +NRG1

description: Tech Replicate1


title: CYT2 Bio Rep2 Tech rep1 +NRG1

description: Tech Replicate1


title: CYT2 Bio Rep2 Tech rep1

description: Tech Replicate1


title: CYT1 Bio Rep2 Tech rep1

description: Tech Replicate1


title: CP2386


title: VEC Bio Rep2 Tech rep2

description: Tech Replicate2


title: CP2338


title: VEC Bio Rep2 Tech rep1

description: Tech Replicate1


title: VEC Bio Rep1 Tech rep1

description: Tech Replicate1


title: VEC Bio Rep1 Tech rep1 +NRG1

description: Tech Replicate1


title: CP2332


title: CP2296


title: CP2284


title: CP3148


title: CYT1 Bio Rep2 Tech rep1 +NRG1

description: Tech Replicate1


title: CYT1 BioRep1 Techrep2

description: Tech Replicate2

growth_protocol: Control vector (VEC) and ERBB4 expression MCF10A cells (ICD CYT1 or CYT2) maintained in regular medium containing 10% serum, were collected and RNA samples were extracted and analyzed.


title: CYT1 BioRep2 Techrep2

description: Tech Replicate2


title: CYT2 BioRep1 Techrep2

description: Tech Replicate2


title: CP2278


title: CP3154


title: CYT1 BioRep1 Techrep1

description: Tech Replicate1


title: CYT2 BioRep1 Techrep1

description: Tech Replicate1


title: CYT1 BioRep2 Techrep1

description: Tech Replicate1


title: VEC BioRep1 Techrep2

description: Tech Replicate2


title: CYT2 BioRep2 Techrep1

description: Tech Replicate1


title: VEC BioRep2 Techrep2

description: Tech Replicate2


title: VEC BioRep2 Techrep1

description: Tech Replicate1


title: 3098


title: CP3106


title: CP3124


title: CP3112


title: CP3136


title: VEC BioRep1 Techrep1

description: Tech Replicate1

treatment_protocol: Control vector (VEC) and ERBB4 expression MCF10A cells (ICD CYT1 or CYT2) maintained in regular medium containing 10% serum, were collected and RNA samples were extracted and analyzed.


title: 3068


title: mock

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

description:
Gene expression data from HeLa TO cells transfected with mock vector
_05_ExpRIC1_5

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

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

data_processing: The data were analyzed with the affy package (R) using RMA algorithm with default analysis settings with normalization.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HeLa TO cells were grown in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% foetal bovine serum (FBS) and antibiotics at 37°C in a humidified incubator with 5% CO2.

extract_protocol: To obtain RNA,  RNAiso plus was added and followed by RNA isolation in accordance with the manufacturer’sinstructions, using chloroform and 2-propanol.

treatment_protocol:
siRNAs were transfected into cells using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions. Briefly, siRNA duplexes (final concentration 10 nM) and cells were harvested 72 h post-transfection.
For poly I:C stimulation, cells were seeded into 12-well cell culture plates followed by transfection using the 20ng of poly I:C and Lipofectamine 2000

value: HeLa TO

tag: genotype/variation

value: mock vector transfection

tag: protocol

value: without poly I:C


title: naive WT P14_3

city: Zurich

first: Annette

last: Oxenius

address: Vladimir-Prelog-weg 1-5/10

department: Microbiology

country: Switzerland

institute: ETH Zurich

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. 600ug Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilents recommended hybridization chamber and oven. The microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene expression wash buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Flourescene signals of the hybridized Agilent Microarrays were detected using Agilent`s Microarray Scanner System.

data_processing: Agilent Feature Extraction Software was use to read out and process the microarray image files.

source_name: Day 3 post LCMV infection sorted P14 cells from the spleen of naïve mice

label_protocol: Cy3 labelling was achieved using the Agilent low input quick Amp labeling kit (Agilent Technologies)

extract_protocol: RNA was extracted using standard protocols (NucleoSpin RNA II)

treatment_protocol: naïve Bl6 mice were depleted of NK cells using the aNK1.1 depleting antibody or left untreated, followed by co-transfer of WT and Ifnar1-/- P14 cells. One day later the mice were infected with LCMV8.7 + Vaccinia Virus-G2. At day 3 post infection WT and Ifnar1-/- P14 cells were FACS sorted to purity, frozen and shipped to Miltenyi Biotec for microarray analysis

value: spleen

tag: nk depletion

value: no

tag: genetic background

tag: genotype

value: WT


title: CYT2 BioRep2 Techrep2

description: Tech Replicate2

value: ERBB4 expression ICD CYT2


title: CP3480

tag: radiation


title: CP3118

tag: dose (gray)


title: naive IFNAR P14_3

source_name: Day 3 post LCMV infection sorted IFNAR-/-  P14 cells from the spleen of naïve mice

value: ifnar1 -/-


title: DKO-R  -DOX 1

city: Cambridge

first: Antony

last: Jackson

state: Cambridgeshire

address: Tennis Court Road, Cambridge

department: Department of Biochemistry

institute: University of Cambridge

description: Biological replicate 1, Dye swap 1

hyb_protocol: Hybridisation was carried out overnight using the Genomic Solutions  GeneTAC automated hybridisation station in a buffer of 50% Ultrahyb containg BSA and sonicated salmon sperm DNA as non specific blocking agents.

scan_protocol: Scaned on an Axon 2000A scanner

data_processing: Captured Images were processed using Bluefuse software. M v A plots [where M = log2 (Cy5/Cy3) and A = 1/2*(log2(Cy5) + log2(Cy3)] of the data for each slide were suitably linear to require only a simple global normalisation of the data.

organism: Gallus gallus

source_name: DKO-R A + DOX

label_protocol: 2 µg of total RNA was fluorescently labelled using the Stratagene FairPlay III  microarray labelling kit according to the manufacturers protocol.

growth_protocol: All cell lines were maintained in RPMI 1640 media, 0.2% (wt/vol) Na2HCO3, 1% (wt/vol) Lglutamine with 10% (vol/vol) heat-treated foetal calf serum (FCS)

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

value: DKO-R

value: Doxycyclin

source_name: DKO-R A - DOX


title: DKO-S  -DOX 4

description: Biological replicate 2, Dye swap 1

source_name: DKO-S B - DOX

value: DKO-S

source_name: DKO-S B + DOX


title: Neat1v2

description:
Gene expression data from HeLa TO cells transfected with Neat1v2 vector
_06_ExpRIC1_6

value: Neat1v2 vector transfection


title: DKO-S  -DOX 2

description: Biological replicate 2, Dye swap 1


title: DKO-S  -DOX 3

description: Biological replicate 1, Dye swap 1

source_name: DKO-S A - DOX

source_name: DKO-S A + DOX


title: DKO-R  -DOX 4

description: Biological replicate 2, Dye swap 1

source_name: DKO-R B - DOX

source_name: DKO-R B + DOX


title: siNEAT1 polyIC+

description:
Gene expression data from NEAT2 knockdown HeLa TO cells with poly I:C
_04_ExpRIC1_4

value: siNEAT1 knockdown (siNEAT1 transfection)

value: poly I:C stimulation


title: naive WT P14_2

source_name: Day 3 post LCMV infection sorted P14 cells from the spleen of naive mice


title: DKO-R  -DOX 2

description: Biological replicate 2, Dye swap 1


title: siNEAT1 polyIC-

description:
Gene expression data from NEAT1 knockdown HeLa TO cells without poly I:C
_03_ExpRIC1_3


title: DKO-S  -DOX 1

description: Biological replicate 1, Dye swap 1


title: naïve IFNAR P14_2


title: DKO-R  -DOX 3

description: Biological replicate 1, Dye swap 1


title: naive IFNAR P14_1


title: DKO-R v DKO-S

description: Biological replicate 1, Dye Swap 1


title: siCTRL polyIC+

description:
Gene expression data from Control HeLa TO cells with poly I:C
_02_ExpRIC1_2

source_name: Control HeLa TO cells with poly I:C

value: control (siCTRL transfection)


title: male adults replicate 1 [mRNA]

source_name: male Drosophila adults

tag: Sex

value: male

tag: developmental stage

value: adults


title: aNK IFNAR P14_3

source_name: Day 3 post LCMV infection sorted IFNAR-/-  P14 cells from the spleen of NK depleted mice

value: yes

value: NK depletion


title: aNK WT P14_3

source_name: Day 3 post LCMV infection sorted P14 cells from the spleen of NK depleted mice


title: male adults replicate 2 [mRNA]


title: DT40  -DOX 4

description: Biological replicate 2, Dye swap 1

source_name: DT40 B - DOX

source_name: DT40 B + DOX


title: DT40  -DOX 1

description: Biological replicate 1, Dye swap 1

source_name: DT40 A + DOX

source_name: DT40 A - DOX


title: naive WT P14_1

source_name: Day 3 post LCMV infection sorted P14 cells from the spleen of naïve mice


title: DKO-S v DKO-R

description: Biological replicate 1, Dye Swap 1

source_name: DKO-R A - DOX


title: DT40  -DOX 2

description: Biological replicate 2, Dye swap 1


title: siCTRL polyIC-

description:
Gene expression data from Control HeLa TO cells without poly I:C
_01_ExpRIC1_1

source_name: Control HeLa TO cells without poly I:C

value: HeLa TO

value: without poly I:C


title: male pupae replicate 2 [mRNA]

source_name: male Drosophila pupae

value: pupae


title: female adults replicate 2 [mRNA]

source_name: female Drosophila adults

value: female


title: aNK IFNAR P14_1

source_name: Day 3 post LCMV infection sorted IFNAR-/- P14 cells from the spleen of NK depleted mice

value: spleen


title: aNK WT P14_2

value: WT


title: aNK IFNAR P14_2

value: ifnar1 -/-


title: female adults replicate 1 [mRNA]


title: aNK WT P14_1


title: exosomes from NP69

city: Guangzhou

first: ping

last: lan

address: 651 Dongfend East Road

institute: Sun Yat-sen University Cancer Center

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: slides were scanned using the Agilent Microarray Scanner (part number G2505C).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
The corrected value is the signal of the probe after background correction =Foreground-Background Intensity. If the corrected value is a negative number ,then the final normalized value is defined as null.

source_name: exosomes from nasopharyngeal epithelial cells NP69

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: source


title: male pupae replicate 1 [mRNA]


title: exosomes from Tw03(EBV-)

source_name: exosomes from nasopharyngeal carcinoma cell line TW03（EBV-）


title: Bl6 IFNAR P14_3

source_name: Day 3 post LCMV infection sorted IFNAR-/-  P14 cells from the spleen

value: no


title: exosomes from Tw03(EBV+)

source_name: exosomes from nasopharyngeal carcinoma cell line TW03（EBV+）


title: Bl6 WT P14_1

source_name: Day 3 post LCMV infection sorted P14 cells from the spleen


title: female larvae replicate 1 [mRNA]

source_name: female third instar Drosophila larvae

value: larvae


title: female pupae replicate 2 [mRNA]

source_name: female Drosophila pupae


title: female larvae replicate 2 [mRNA]


title: Bl6 WT P14_2


title: Bl6 IFNAR P14_1

source_name: Day 3 post LCMV infection sorted IFNAR-/- P14 cells from the spleen


title: Bl6 IFNAR P14_2


title: Bl6 WT P14_3


title: male larvae replicate 2 [mRNA]

source_name: male third instar Drosophila larvae


title: male larvae replicate 1 [mRNA]


title: female pupae replicate 1 [mRNA]


title: Human_BTH_295-9538577T

status: Public on May 06 2014

type: genomic

city: Shanghai

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  scanner. Images were quantified using Agilent Feature Extraction Software (v 9.1)

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: gastric cancer frozen tumor tissues

label_protocol: 2 µg of genomic DNA were primed with 5µl random DNA primer at 96°C for 5 min

growth_protocol: Tumor tissues were collected after surgical resection and frozed for DNA extraction

extract_protocol: Genomic DNA was extracted using Gentra Puregene Cell Kit (Qiagen)  following manufacturer’s instructions. QC process was performed using 1% agarose gel at 120V for 45min and single clear band with its size ~4000bp was defined as QC pass.

tag: gender

value: M

value: gastric

tag: phenotype

value: gastric cancer

source_name: standard reference genomic DNA


title: Human_BTH_329-9532578T

tag: tissue


title: Human_BTH_153-Z39-25765T


title: Human_BTH_585-9547182T


title: Human_BTH_3-A79-26973T


title: Human_BTH_293-9537867T

value: F


title: Human_BTH_593-9547050T


title: Human_BTH_587-9547147T


title: Human_BTH_215-A15-18920T


title: Human_BTH_423-9541535T


title: Human_BTH_15-A21-19605T


title: Human_BTH_251-9536376T


title: Human_BTH_453-9541959T


title: Human_BTH_291-9537600T


title: Human_BTH_209-Z65-26284T


title: Human_BTH_37-Z111-28681T


title: Human_BTH_191-Z9-24758T


title: Human_BTH_13-Z123-28886T


title: Human_BTH_575-9547496T


title: Human_BTH_573-9546266T


title: Human_BTH_501-9532666T


title: Human_BTH_535-9544115T


title: Human_BTH_525-9544427T


title: Human_BTH_223-N23-21184T


title: Human_BTH_589-9547138T


title: Human_BTH_579-9547022T


title: Human_BTH_503-9532669T


title: Human_BTH_203-N1-15388T


title: Human_BTH_511-9544004T


title: Human_BTH_515-9532963T


title: Human_BTH_559-9546067T


title: Human_BTH_125-A39-23912T


title: Human_BTH_165-Z17-24876T


title: Human_BTH_595-9547063T


title: Human_BTH_43-Z129-28993T


title: Human_BTH_111-Z77-26914T


title: Human_BTH_507-9532687T


title: Human_BTH_121-Z67-26306T


title: Human_BTH_167-A41-23993T


title: Human_BTH_513-9544112T


title: Human_BTH_327-9539112T


title: DT40  -DOX 3

description: Biological replicate 1, Dye swap 1

source_name: DT40 A - DOX

tag: cell line

source_name: DT40 A + DOX

value: Doxycyclin


title: Human_BTH_317-9538998T


title: Human_BTH_129-Z45-25880T


title: Human_BTH_57-Z85-28072T


title: Human_BTH_123-Z47-25943T


title: Human_BTH_69-N37-23830T


title: Human_BTH_47-Z95-28404T


title: Human_BTH_135-Z5-24668T


title: Human_BTH_363-9539657T


title: Human_BTH_357-9539681T


title: Human_BTH_355-9539603T


title: Human_BTH_131-Z59-26277T


title: Human_BTH_509-9532869T


title: Human_BTH_369-9539828T


title: Human_BTH_353-9539589T


title: Human_BTH_305-9532536T


title: Human_BTH_133-N13_18302T


title: Human_BTH_187-Z11-24811T


title: Human_BTH_171-N35-23553T


title: Human_BTH_307-9538826T


title: Human_BTH_469-9542538T


title: Human_BTH_51-Z159-33265T


title: Human_BTH_445-9541303T


title: Human_BTH_447-9541880T


title: Human_BTH_303-9538803T


title: Human_BTH_421-9541224T


title: Human_BTH_449-9541701T


title: Human_BTH_93-Z135-29520T


title: Human_BTH_455-9541997T


title: Human_BTH_87-N29_22640T


title: Human_BTH_425-9541358T


title: Human_BTH_163-Z37-25762T


title: Human_BTH_415-9541385T


title: Human_BTH_413-9541306T


title: Human_BTH_411-9540961T


title: Human_BTH_85-A69-26043T


title: Human_BTH_467-9542415T


title: Human_BTH_349-9539309T


title: Human_BTH_147-A51-25739T


title: Human_BTH_143-A35-23632T


title: Human_BTH_169-N33-22820T


title: Human_BTH_345-9532546T


title: Human_BTH_405-9540999T


title: Human_BTH_435-9541634T


title: Human_BTH_157-Z57-26261T


title: Human_BTH_333-9532579T


title: Human_BTH_341-9539270T


title: Human_BTH_119-Z71-26367T


title: Human_BTH_67-Z133-29445T


title: Human_BTH_431-9540474T


title: Human_BTH_117-Z21-24908T


title: Human_BTH_343-9539253T


title: Human_BTH_105-Z25-25564T


title: Human_BTH_517-9544005T


title: Human_BTH_101-N15_19601T


title: Human_BTH_289-9537671T


title: Human_BTH_75-Z119-28790T


title: Human_BTH_79-Z105-28485T


title: Human_BTH_483-9542765T


title: Human_BTH_473-9542834T


title: Human_BTH_569-9546090T


title: Human_BTH_481-9542761T


title: Human_BTH_109-Z69-26351T


title: Human_BTH_7-A17-19375T


title: Human_BTH_17-A25-20597T


title: Human_BTH_207-A45-24664T


title: Human_BTH_567-9546124T


title: Human_BTH_269-9537501T


title: Human_BTH_ 9-A03-15178T


title: Human_BTH_27-A27-21002T


title: Human_BTH_231-9534192T


title: Human_BTH_249-9536435T


title: Human_BTH_21-A23-19954T


title: Human_BTH_151-N9-18577T


title: Human_BTH_19-Z153-29967T


title: Human_BTH_25-A09-18495T


title: Human_BTH_265-9537441T


title: Human_BTH_255-9532010T


title: Human_BTH_1-Z131-29411T


title: Human_BTH_485-9542902T


title: Human_BTH_493-9540853T


title: Human_BTH_389-9540514T


title: Human_BTH_395-9540809T


title: Human_BTH_383-9540481T


title: Human_BTH_401-9540945T


title: Human_BTH_179-Z51-26028T


title: Human_BTH_379-9540283T


title: Human_BTH_229-9534948T


title: Copies per Cell, Frog G, TTNPB

city: Stanford

first: Stefan

last: Heller

address: 801 Welch Road

department: Otolaryngology

institute: Stanford University

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-G, TTN

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

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

data_processing:
The raw data were summarized by Affymetrix MAS5. The efficiency of in vitro transcription (IVT), and the dose-response linearity of the five GSC spikes was checked, and Percellome data, i.e. absolutized mRNA copy numbers of each ProbesSet were generated by the homemade software SCal4 (Spike Calculation version 4, by Ken-ichi Aisaki)
Percellome microarray data (copies per cell) were analyzed using CyberT statistical analysis, which corrects for low replicates and variability, allowing for less false negatives under two-fold change, and less false positives for large fold changes (Arima et al., 2005; Baldi and Long, 2001; Kayala and Baldi, 2012).

organism: Xenopus laevis

source_name: Xenopus embryos treated with TTNPB before gastrulation, collected at stage 18

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instructions from 5 ug total RNA by Enzo BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences) .

growth_protocol: Xenopus laevis eggs from three different females were fertilized in vitro and embryos were staged according to Nieuwkoop and Faber

extract_protocol: Each dish of embryos was harvested at stage 18 into 1.5 mL of RNAlater (Invitrogen) and kept overnight at 4C and until use. RNAlater was replaced in the 2 ml plastic tube with 1.0 ml of RLT buffer (Qiagen GmbH., Germany), and homogenized by adding a 5 mm diameter Zirconium bead (Funakoshi, Japan) and shaking with a MixerMill 300 (Qiagen GmbH., Germany) at a speed of 20Hz for 5 min (only the outermost row of the shaker box was used).  Three separate 10μl aliquots were taken from each sample homogenate to another tube and mixed thoroughly. A final 10 μl aliquot there from was treated with DNase-free RNase A (Nippon Gene Inc., Japan) for 30 min at 37C, followed by Proteinase K (Roche Diagnostics GmbH., Germany) for 3 h at 55C in 1.5 ml capped tubes. The aliquot was transferred to a 96-well black plate. PicoGreen fluorescent dye (Molecular Probes Inc., USA) was added to each well, shaken for 10 seconds four times and then incubated for 2 min at 30C. The DNA concentration was measured using a 96 well fluorescence plate reader with excitation at 485nm and emission at 538nm. λ phage DNA (PicoGreen Kit, Molecular Probes Inc., USA) was used as standard.   As reported previously, the grade-dosed spike cocktail (GSC) made of the following five Bacillus subtilis RNA sequences were selected from the gene list of Affymetrix GeneChip arrays (AFFX-ThrX-3_at, AFFX-LysX-3_at, AFFX-PheX-3_at, AFFX-DapX-3_at, and AFFX-TrpnX-3_at) present in the arrays was added to the sample homogenates in proportion to their DNA concentrations (BMC Genomics 7 64 2006).   Then, the sample homogenates spiked with GSC were processed by RNeasy Mini Kit (Qiagen GmbH., Germany).

treatment_protocol: Stage 7 embryos were treated in groups of 25 in 60-mm Petri dishes with 10 mL of 0.1x MBS containing 10-6M RAR agonist (TTNPB), 10-6M RAR inverse agonist (AGN193109), or vehicle control (0.1% EtOH).  Three dishes, per treatment, per female were collected (27 dishes total: 3 technical replicates, 3 biological replicates per treatment).

value: whole embryo

tag: Stage

value: Nieuwkoop & Faber St. 18

tag: agent

value: TTNPB


title: Copies per Cell, Frog F, TTNPB

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-F, TTN


title: Copies per Cell, Frog A, AGN193109

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-A, 109

source_name: Xenopus embryos treated with AGN193109 before gastrulation, collected at stage 18


title: Copies per Cell, Frog F, AGN193109

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-F, 109


title: Copies per Cell, Frog F, Vehicle

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-F, VEH

source_name: Xenopus embryos treated with Vehicle before gastrulation, collected at stage 18

value: Vehicle


title: Copies per Cell, Frog G, AGN193109

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-G, 109


title: Copies per Cell, Frog A, TTNPB

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-A, TTN


title: Copies per Cell, Frog A, Vehicle

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-A, VEH


title: Human_BTH_83-Z157-31406T


title: Human_BTH_211-A59-25914T


title: Copies per Cell, Frog G, Vehicle

description:
percellome normalization (absolutized mRNA copy numbers per cell, see BMC Genomics 7 64 2006)
CPC-G, VEH


title: MCF7_E2_16h_3

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

description: This sample is of MCF-7 cells treated with 10-8M E2 for 16h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems (Services, Reykjavic), following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Standard NimbleGen protocols (scanned at NimbleGen services, Reykjavic). See www.nimblegen.com.

data_processing:
Raw data (.pair) were subjected to the RMA algorithm (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) with quantile settings (Bolstad et al. Bioinformatics 19(2):185) for background correction and normalization, as implemented within the ArrayStar software package (DNAstar, Inc.).
RMA-normalized, averaged mRNA-level signal intensity. Expressed as log2 values.

source_name: MCF7 cells treated for 16h with 10-8M estradiol

label_protocol: Labeling was performed by NimbleGen Systems (Services, Reykjavic), following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were maintained in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS, BioWest) and antibiotics (Roche) at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) with homogenization facilitated by QIAShredders (Qiagen). Integrity and purity of the RNAs were controlled on an Agilent Bioanalyzer using the RNA 6000 Nano Assay (Agilent). Ten micrograms of selected samples exhibiting a RIN >9.8 were then subjected to cDNA synthesis using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and 50 pmol random hexamers. cDNAs were then treated for 10 min at 37°C with 5 μg RNaseA (Invitrogen), purified through a phenol:chloroform:isoamyl alcohol extraction on Phase Lock light gels (Fisher Scientific) and then precipitated.

treatment_protocol: MCF7 cells were plated in DMEM/10% FCS at a density of 7.5 x106 cells per 9cmØ dishes. Following two washes with PBS, cells were then cultivated for 3 days in DMEM/2.5% charcoal-stripped serum (BioWest). Confluent cells were then treated with Estradiol (E2, Sigma) at a final concentration of 10-8 M for 4h or 16h or with equivalent amounts of ethanol vehicle (0.1%).

tag: cell type

value: breast cancer cells

tag: er status

value: Positive

tag: integrated vector


title: MCF7_E2_16h_1

description: This sample is of MCF-7 cells treated with 10-8M E2 for 16h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

value: female


title: I602

city: St Lucia

first: Allan

middle: F

last: McRae

state: QLD

address: QBI Building (#79)

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using an Illumina bead array reader

data_processing:
GenomeStudio Methylation Module v1.8
Raw data file: raw_data_signal_intensities.txt contains Unmethylated and methylated signal intensities
Processed data file: average_beta.txt:  Normalised Average Beta (Normalised to internal controls, background subtraction) and the Detection P-value

label: Cy5 and Cy3

source_name: whole blood, healthy

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood lymphocytes by the salt precipitation method

value: peripheral blood lymphocytes

tag: twin

value: DZ

tag: age


title: I605

value: MZ


title: I604


title: I603


title: I607


title: I606


title: MCF7_EtOH_1

description: This sample is of MCF-7 cells treated with ethanol (vehicle control) for 4h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

source_name: MCF7 cells treated for 4h with 0.1% ethanol (vehicle control)


title: I613


title: I614


title: I609


title: I610


title: I611


title: I612


title: I608


title: MCF7_EtOH_3

description: This sample is of MCF-7 cells treated with ethanol (vehicle control) for 4h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: MCF7_E2_16h_2

description: This sample is of MCF-7 cells treated with 10-8M E2 for 16h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: MCF7_EtOH_2

description: This sample is of MCF-7 cells treated with ethanol (vehicle control) for 4h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I600


title: I597


title: I596


title: I598


title: I599


title: MDA::ER_E2_4h_1

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 4h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

source_name: MDA::ER cells treated for 4h with 10-8M estradiol

growth_protocol: Cells were maintained in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS, BioWest), antibiotics (Roche) at 37°C under 5% CO2 and complemented with 0.8 mg/ml Hygromycin (Calbiochem) for continuous selection.

treatment_protocol: MDA::ER cells were plated at 2x106 cells per 9cmØ dishes in DMEM/10% FCS complemented with 0.8 mg/ml hygromycin for 16h. Following two washes with PBS, cells were then cultivated for 3 days in DMEM/2.5% charcoal-stripped serum (BioWest) complemented with Hygromycin. Confluent cells were then treated with Estradiol (E2, Sigma) at a final concentration of 10-8 M for 4h or 16h or with equivalent amounts of ethanol vehicle (0.1%).


title: I594


title: I590


title: I588


title: I591


title: I593


title: I587


title: I589


title: I592


title: Human_BTH_193-A43-24647T


title: MDA::ER_E2_4h_2

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 4h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I601


title: I586


title: I585


title: I595


title: MCF7_E2_4h_3

description: This sample is of MCF-7 cells treated with 10-8M E2 for 4h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

source_name: MCF7 cells treated for 4h with 10-8M estradiol


title: I583


title: MDA::ER_E2_16h_2

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 16h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

source_name: MDA::ER cells treated for 16h with 10-8M estradiol


title: I581


title: I582


title: I584


title: I580


title: MCF7_E2_4h_2

description: This sample is of MCF-7 cells treated with 10-8M E2 for 4h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I579


title: I578


title: I573


title: I574


title: I571


title: I575


title: I572


title: I576


title: I577


title: I570


title: I569


title: I568


title: I566


title: I567


title: I565


title: I563


title: I564


title: I561


title: I559


title: MDA::ER_E2_16h_3

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 16h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I562


title: I558


title: I556


title: I555


title: I557


title: I554


title: I552


title: I551


title: I550


title: I549


title: I548


title: I547


title: I545


title: I544


title: I560


title: MDA::ER_EtOH_2

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with ethanol (vehicle control) for 4h. Second of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.

source_name: MDA::ER cells treated for 4h with 0.1% ethanol (vehicle control)


title: MCF7_E2_4h_1

description: This sample is of MCF-7 cells treated with 10-8M E2 for 4h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: MDA::ER_EtOH_3

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with ethanol (vehicle control) for 4h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: MDA::ER_EtOH_1

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with ethanol (vehicle control) for 4h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: MDA::ER_E2_4h_3

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 4h. Third of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I542


title: I541


title: I540


title: I537


title: I538


title: I553


title: I536


title: I535


title: I533


title: I531


title: I534


title: I530


title: MDA::ER_E2_16h_1

description: This sample is of MDA::ER cells (MDA-MB231 cells engineered to express the estrogen receptor) treated with 10-8M E2 for 16h. First of the three independent replicates used in this experiment, each constituted by a pool of three separate cultures.


title: I528


title: I527


title: I526


title: I532


title: I529


title: I546


title: I525


title: I524


title: I543


title: I539


title: I521


title: I522


title: I515


title: I518


title: I519


title: I514


title: I523


title: I520


title: I516


title: I517


title: I513


title: I511


title: I510


title: I505


title: I507


title: I504


title: I506


title: I509


title: I500


title: I502


title: I501


title: I497


title: I498


title: I496


title: I495


title: I494


title: I493


title: I490


title: I492


title: I489


title: I512


title: I487


title: I486


title: I484


title: I508


title: I488


title: I485


title: I482


title: I503


title: I483


title: I480


title: I477


title: I479


title: I476


title: I481


title: I473


title: I478


title: I499


title: I475


title: I474


title: I471


title: I470


title: I472


title: I469


title: I468


title: I491


title: I466


title: I464


title: I463


title: I458


title: I459


title: I465


title: I457


title: I453


title: I455


title: I456


title: I460


title: I449


title: I450


title: I451


title: I452


title: I447


title: I445


title: I444


title: I446


title: I442


title: I443


title: I441


title: I440


title: I438


title: I439


title: I467


title: I462


title: I461


title: I437


title: I436


title: I454


title: I435


title: I448


title: I433


title: I431


title: I428


title: I430


title: I429


title: I425


title: I421


title: I424


title: I417


title: I419


title: I418


title: I416


title: I423


title: I420


title: I422


title: I415


title: I412


title: I413


title: I410


title: I414


title: I411


title: I409


title: I434


title: I408


title: I407


title: I405


title: I406


title: I404


title: I426


title: I403


title: I427


title: I402


title: I400


title: I401


title: I398


title: I396


title: I394


title: I389


title: I393


title: I399


title: I388


title: I387


title: I390


title: I386


title: I381


title: I380


title: I382


title: I384


title: I385


title: I395


title: I379


title: I391


title: I378


title: I374


title: I377


title: I375


title: I376


title: I373


title: I397


title: I372


title: I392


title: I370


title: I369


title: I368


title: I367


title: I383


title: I361


title: I364


title: I362


title: I363


title: I360


title: I354


title: I356


title: I359


title: I358


title: I357


title: I353


title: I352


title: I355


title: I350


title: I351


title: I349


title: I347


title: I371


title: I346


title: I345


title: I343


title: I348


title: I341


title: I366


title: I365


title: I342


title: I340


title: I338


title: I339


title: I337


title: I334


title: I332


title: I333


title: I331


title: I329


title: I335


title: I327


title: I325


title: I323


title: I330


title: I321


title: I326


title: I324


title: I319


title: I320


title: I317


title: I322


title: I315


title: I314


title: I336


title: I313


title: I311


title: I312


title: I310


title: I344


title: I308


title: I309


title: I328


title: I306


title: I307


title: I304


title: I305


title: I303


title: I301


title: I299


title: I302


title: I296


title: I297


title: I318


title: I298


title: I295


title: I293


title: I292


title: I294


title: I316


title: I291


title: I290


title: I289


title: I288


title: I287


title: I286


title: I285


title: I284


title: I283


title: I281


title: I282


title: I280


title: I300


title: I279


title: I277


title: I275


title: I276


title: I278


title: I274


title: I269


title: I268


title: I266


title: I270


title: I271


title: I272


title: I267


title: I273


title: I265


title: I262


title: I264


title: I261


title: I259


title: I260


title: I257


title: I263


title: I258


title: I253


title: I256


title: I252


title: I254


title: I251


title: I249


title: I250


title: I248


title: I241


title: I245


title: I238


title: I247


title: I243


title: I240


title: I235


title: I246


title: I236


title: I234


title: I232


title: I233


title: I244


title: I255


title: I237


title: I230


title: I432


title: I227


title: I226


title: I225


title: I224


title: I223


title: I222


title: I242


title: I221


title: I229


title: I220


title: I239


title: I215


title: I219


title: I213


title: I217


title: I218


title: I214


title: I231


title: I209


title: I208


title: I207


title: I206


title: I204


title: I203


title: I228


title: I210


title: I211


title: I212


title: I202


title: I201


title: I200


title: I199


title: I205


title: I198


title: I197


title: I196


title: I194


title: I192


title: I195


title: I216


title: I185


title: I181


title: I182


title: I183


title: I187


title: I188


title: I178


title: I177


title: I179


title: I190


title: I189


title: I186


title: I180


title: I184


title: I193


title: I191


title: Whole Blood DNA 4762563077_A

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

description:
BS conversion C1 Grn 12.7385145324293
BS conversion C2 Grn 12.0282514281628

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

source_name: bi-sulphite converted genomic DNA

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from whole blood at Gen-Probe (www.gen-probe.com) using Qiagen QiAamp Blood Mini Kit (51106)

tag: brca1 mutation status

tag: subject group

value: BRCA1 mutants with breast cancer

tag: age (at draw)

value: whole blood


title: I176

value: M


title: I174


title: Whole Blood DNA 4762563077_F

description:
BS conversion C1 Grn 12.4519837772302
BS conversion C2 Grn 12.0549434165733


title: I173


title: Whole Blood DNA 4762563077_I

description:
BS conversion C1 Grn 12.9408641390496
BS conversion C2 Grn 12.0734721539765


title: I175


title: I170


title: Whole Blood DNA 4762563077_D

description:
BS conversion C1 Grn 12.5776648517648
BS conversion C2 Grn 11.9679467058127

value: BRCA1 wild-type and healthy


title: Whole Blood DNA 4762563077_K

description:
BS conversion C1 Grn 12.6573184495813
BS conversion C2 Grn 12.5868397879618


title: Whole Blood DNA 4762563077_C

description:
BS conversion C1 Grn 12.7435721889356
BS conversion C2 Grn 11.8344710499842


title: Whole Blood DNA 4762563077_H

description:
BS conversion C1 Grn 12.2775780024157
BS conversion C2 Grn 12.5478585060584


title: Whole Blood DNA 4762563077_J

description:
BS conversion C1 Grn 12.4424251933316
BS conversion C2 Grn 11.88378880326


title: I172


title: Whole Blood DNA 4762563077_E

description:
BS conversion C1 Grn 12.806549621986
BS conversion C2 Grn 11.843921051289


title: Whole Blood DNA 4762563069_L

description:
BS conversion C1 Grn 12.5894170757686
BS conversion C2 Grn 12.0576533399639


title: Whole Blood DNA 4762563077_G

description:
BS conversion C1 Grn 12.5318687751776
BS conversion C2 Grn 12.1771080417037

value: BRCA1 mutants and healthy


title: Whole Blood DNA 4762563069_K

description:
BS conversion C1 Grn 12.6836525973947
BS conversion C2 Grn 12.5823772356407


title: I169


title: Whole Blood DNA 4762563077_B

description:
BS conversion C1 Grn 12.6422773785039
BS conversion C2 Grn 11.7919768208987


title: I171


title: Whole Blood DNA 4762563077_L

description:
BS conversion C1 Grn 12.6454332751643
BS conversion C2 Grn 12.2449583931511


title: I168


title: I167


title: Whole Blood DNA 4762563069_J

description:
BS conversion C1 Grn 13.0140204703149
BS conversion C2 Grn 12.2437690319619


title: Whole Blood DNA 4762563069_H

description:
BS conversion C1 Grn 12.8548683832602
BS conversion C2 Grn 12.2128003344294


title: Whole Blood DNA 4762563069_F

description:
BS conversion C1 Grn 13.0301498249257
BS conversion C2 Grn 13.0311842621408


title: Whole Blood DNA 4762563069_E

description:
BS conversion C1 Grn 12.8770923750274
BS conversion C2 Grn 12.2015113445001


title: Whole Blood DNA 4762563069_G

description:
BS conversion C1 Grn 12.844117269588
BS conversion C2 Grn 12.1023038172126


title: I165

value: F


title: I164


title: Whole Blood DNA 4762563069_C

description:
BS conversion C1 Grn 13.0798180852124
BS conversion C2 Grn 12.513480875979


title: I163


title: Whole Blood DNA 4762563069_D

description:
BS conversion C1 Grn 13.1716459413471
BS conversion C2 Grn 12.7032547337481


title: Whole Blood DNA 4762563069_I

description:
BS conversion C1 Grn 13.1294440230319
BS conversion C2 Grn 13.1619191654272


title: I162


title: I161


title: Whole Blood DNA 4762563069_A

description:
BS conversion C1 Grn 13.0284241129485
BS conversion C2 Grn 12.9978851278291


title: Whole Blood DNA 4762563063_L

description:
BS conversion C1 Grn 12.7202442582876
BS conversion C2 Grn 12.0341111460966


title: I160


title: I159


title: I158


title: Whole Blood DNA 4762563063_G

description:
BS conversion C1 Grn 12.5154534553886
BS conversion C2 Grn 12.1250905393033


title: I166


title: I157


title: I155


title: I156


title: I154


title: I151


title: I152


title: I153


title: Whole Blood DNA 4762563063_E

description:
BS conversion C1 Grn 12.5755392468345
BS conversion C2 Grn 12.0704564159446


title: I150


title: Whole Blood DNA 4762563063_F

description:
BS conversion C1 Grn 12.3387363825739
BS conversion C2 Grn 11.9679467058127


title: Whole Blood DNA 4762563069_B

description:
BS conversion C1 Grn 12.8057438721516
BS conversion C2 Grn 12.1736771363034


title: I149


title: Whole Blood DNA 4762563063_D

description:
BS conversion C1 Grn 12.5901191741072
BS conversion C2 Grn 12.344850683943


title: Whole Blood DNA 4762563063_K

description:
BS conversion C1 Grn 12.815583433851
BS conversion C2 Grn 11.8653466448168


title: I148


title: Whole Blood DNA 4762563063_I

description:
BS conversion C1 Grn 12.7809497987497
BS conversion C2 Grn 12.1636496760158


title: I147


title: Whole Blood DNA 4762563063_J

description:
BS conversion C1 Grn 12.9867308981756
BS conversion C2 Grn 12.5612879451648


title: Whole Blood DNA 4762563042_L

description:
BS conversion C1 Grn 13.0284241129485
BS conversion C2 Grn 12.5112584955023


title: Whole Blood DNA 4762563042_K

description:
BS conversion C1 Grn 12.8538943132476
BS conversion C2 Grn 12.2949078809537


title: I145


title: I144


title: Whole Blood DNA 4762563042_H

description:
BS conversion C1 Grn 12.632995197143
BS conversion C2 Grn 12.1321783809155


title: I143


title: Whole Blood DNA 4762563063_A

description:
BS conversion C1 Grn 12.5043224482919
BS conversion C2 Grn 11.5788443915582


title: I142


title: Whole Blood DNA 4762563042_F

description:
BS conversion C1 Grn 12.9117664706596
BS conversion C2 Grn 12.4128344401193


title: I141


title: I146


title: Whole Blood DNA 4762563042_I

description:
BS conversion C1 Grn 12.8307132569519
BS conversion C2 Grn 12.3303567169579


title: CDM-LSRLUXS-30-A1a

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

institute: Drexel University College of Medicine

description:
422469A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

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

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

data_processing: Raw data (.pair file) was edited to remove subclusters (genes) that are not present in Haemophilus influenzae CZ4126/02 by merging it with a list of subclusters known to be present in CZ4126/02. In addition, to analyze data from two different gene expression platforms together the data were modified to match each other (averaging intensity values from sets of probes on the 144K array platform and removing certain control probes from the 72K array platform). These modified data (.pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae

source_name: Haemophilus influenzae CZ4126/02 ΔluxS::Specr,Δlsr::Cmr

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

growth_protocol: Haemophilus influenzae CZ4126/02ΔluxS::Specr and Haemophilus influenzae CZ4126/02ΔluxS::Specr,ΔLsr::Cmr were grown in CDM (Coleman et al. J Clin Microbiol. 41 (9), 4408-10.) with or without the addition of 3µM synthetic AI-2 to log phase and stationary phase using an inoculum from an overnight culture grown in BHI. 40 mL cultures incubated at 37°C and shaking at 200 rpm.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Plus kit with the standard protocol with gDNA eliminator columns. Eluted RNA (~85 µL) was DNased by adding 10 µL 10X TurboDNase buffer and 5 µL TurboDNase (2 units/µL) (Ambion) and incubating at 37 °C for 1.5 hours. 2 µL more TurboDNase was added and incubation continued for an additional 1.5 hours. DNased RNA samples were cleaned by passing the samples through the RNeasy protocol a second time (with gDNA eliminator steps). Samples were eluted in nuclease free (n.f.) water, quantitated on a Nanodrop 1000 spectrophotometer and stored at -80 °C. First and second-strand cDNA synthesis was performed using a SuperScript® One-Cycle cDNA Kit (Invitrogen) as outlined in the NimbleGen Microarray Experienced User’s Guide including RNaseA and cDNA precipitation steps.

treatment_protocol: 2 mL of culture was diluted in 4 mL RNAProtect (Qiagen) and stored at RT for 10 minutes, then 4 °C overnight. Samples were pelleted, the supernatant removed and the cell pellets resuspended in 100 µL of 1X Tris-EDTA (TE) + 1 mg/mL lysozyme (Worthington Biochemical) and 1 mg/mL proteinase K (Qiagen).

tag: genotype

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time

value: 30 minutes after ODA600 0.75

tag: biological replicate

tag: technical replicate

tag: probe set


title: CDM-LSRLUXS-30-A1b

description:
422469A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Whole Blood DNA 4762563063_B

description:
BS conversion C1 Grn 12.6593269974141
BS conversion C2 Grn 12.1541852092653

tag: tissue


title: Whole Blood DNA 4762563042_B

description:
BS conversion C1 Grn 12.782383991197
BS conversion C2 Grn 12.1019756709492


title: Whole Blood DNA 4762563042_E

description:
BS conversion C1 Grn 13.0292872269682
BS conversion C2 Grn 12.402479172215


title: Whole Blood DNA 4762563063_H

description:
BS conversion C1 Grn 12.8324944843361
BS conversion C2 Grn 12.8744050764095


title: Whole Blood DNA 4762563063_C

description:
BS conversion C1 Grn 12.5068034377956
BS conversion C2 Grn 12.3548003443506


title: Whole Blood DNA 4762563036_L

description:
BS conversion C1 Grn 13.1161814864312
BS conversion C2 Grn 12.6779398163901


title: Whole Blood DNA 4762563042_J

description:
BS conversion C1 Grn 12.3517674439599
BS conversion C2 Grn 11.919980595049


title: Whole Blood DNA 4762563042_C

description:
BS conversion C1 Grn 12.843921051289
BS conversion C2 Grn 12.2508905357233


title: Whole Blood DNA 4762563042_D

description:
BS conversion C1 Grn 12.714460188456
BS conversion C2 Grn 12.2570931444911


title: CDM-LUXS-30-A1b

description:
422469A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

source_name: Haemophilus influenzae CZ4126/02 ΔluxS::Specr


title: I140

tag: gender


title: Whole Blood DNA 4762563036_K

description:
BS conversion C1 Grn 12.2717548056465
BS conversion C2 Grn 11.3409627642517


title: Whole Blood DNA 4762563036_J

description:
BS conversion C1 Grn 12.8313072438021
BS conversion C2 Grn 12.4797802640291


title: Whole Blood DNA 4762563042_A

description:
BS conversion C1 Grn 12.9571020415623
BS conversion C2 Grn 12.3213644320394


title: Whole Blood DNA 4762563036_H

description:
BS conversion C1 Grn 13.2246046815385
BS conversion C2 Grn 12.7513348364013


title: Whole Blood DNA 4762563042_G

description:
BS conversion C1 Grn 13.1899789486325
BS conversion C2 Grn 12.728345714711


title: I139


title: Whole Blood DNA 4762563036_I

description:
BS conversion C1 Grn 12.5050671932319
BS conversion C2 Grn 12.0950673016071


title: CDM-LSRLUXS-A1b

description:
422169A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: I138


title: CDM-LUXS-30-A1a

description:
422469A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-LSRLUXS-A1a

description:
422169A03_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: I136


title: Whole Blood DNA 4762563036_F

description:
BS conversion C1 Grn 12.775404519504
BS conversion C2 Grn 12.2825093062408


title: I135


title: Whole Blood DNA 4762563036_E

description:
BS conversion C1 Grn 12.6821167649501
BS conversion C2 Grn 12.3401282737006


title: I134


title: I133


title: Whole Blood DNA 4762563036_D

description:
BS conversion C1 Grn 12.6535168794214
BS conversion C2 Grn 12.3655022681931


title: CDM-LUXS-A1b

description:
422169A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-LUXS-A1a

description:
422169A04_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media without AI-2 added and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: AI2+CDM-LUXS-30-A1b

description:
422469A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

value: chemically-defined media (CDM) with 3uM AI-2 added


title: I137


title: I132


title: Whole Blood DNA 4762563035_K

description:
BS conversion C1 Grn 12.7198166030181
BS conversion C2 Grn 12.5950243186136


title: Whole Blood DNA 4762563035_L

description:
BS conversion C1 Grn 13.2114320582988
BS conversion C2 Grn 12.8630247102369


title: AI2+CDM-LSRLUXS-30-A1a

description:
422469A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: AI2+CDM-LSRLUXS-30-A1b

description:
422469A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Whole Blood DNA 4762563035_F

description:
BS conversion C1 Grn 13.2398968224459
BS conversion C2 Grn 12.9885071789232


title: Whole Blood DNA 4762563036_C

description:
BS conversion C1 Grn 12.1385917946375
BS conversion C2 Grn 11.654636028528


title: AI2+CDM-LUXS-30-A1a

description:
422469A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled 30 minutes after AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: I131


title: Whole Blood DNA 4762563035_J

description:
BS conversion C1 Grn 13.1101570189541
BS conversion C2 Grn 12.5318687751776


title: AI2+CDM-LSRLUXS-A1b

description:
422169A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Whole Blood DNA 4762563035_G

description:
BS conversion C1 Grn 13.2162911557571
BS conversion C2 Grn 12.9459924243968


title: Whole Blood DNA 4762563035_E

description:
BS conversion C1 Grn 13.1124395067816
BS conversion C2 Grn 12.704984324893


title: AI2+CDM-LSRLUXS-A1a

description:
422169A02_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr,Δlsr::Cmr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is a double mutant that contains an isogenic deletion of the luxS gene  as well as a full locus deletion mutant in which the 9 genes of the Lsr locus (lsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: I130


title: I129


title: Whole Blood DNA 4762563035_B

description:
BS conversion C1 Grn 12.914571997649
BS conversion C2 Grn 12.1153688378202


title: I128


title: Whole Blood DNA 4762563035_A

description:
BS conversion C1 Grn 12.7136013135738
BS conversion C2 Grn 12.5543490220634


title: AI2+CDM-LUXS-A1a

description:
422169A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Whole Blood DNA 4762563035_H

description:
BS conversion C1 Grn 12.3920490393642
BS conversion C2 Grn 11.579787329527


title: I126


title: Whole Blood DNA 4762563036_A

description:
BS conversion C1 Grn 12.7901448269498
BS conversion C2 Grn 12.0406322005623


title: Whole Blood DNA 4762563036_G

description:
BS conversion C1 Grn 12.8694010597781
BS conversion C2 Grn 12.0529076283133


title: Whole Blood DNA 4762563036_B

description:
BS conversion C1 Grn 12.5485811181651
BS conversion C2 Grn 11.9574648468052


title: Whole Blood DNA 4762563034_I

description:
BS conversion C1 Grn 12.5612879451648
BS conversion C2 Grn 12.0973737689902


title: AI2+CDM-LUXS-A1b

description:
422169A01_42020_532.pair
This sample is of Haemophilus influenzae CZ4126/02ΔluxS::Specr grown in chemically defined media with 3uM AI-2 added exogenously and sampled before AI-2 uptake. This strain is an isogenic deletion mutant in which the luxS gene is deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Whole Blood DNA 4762563035_C

description:
BS conversion C1 Grn 13.2039597032395
BS conversion C2 Grn 13.0280787227049


title: I125


title: Whole Blood DNA 4762563035_I

description:
BS conversion C1 Grn 12.450953464713
BS conversion C2 Grn 11.729620743553


title: Whole Blood DNA 4762563034_J

description:
BS conversion C1 Grn 12.6960981709559
BS conversion C2 Grn 12.7982692749497


title: Whole Blood DNA 4762563034_K

description:
BS conversion C1 Grn 13.0036935827378
BS conversion C2 Grn 12.4022126727146


title: Whole Blood DNA 4762563034_E

description:
BS conversion C1 Grn 13.0630579636235
BS conversion C2 Grn 12.8484273340239


title: I127


title: Whole Blood DNA 4762563034_F

description:
BS conversion C1 Grn 12.6735299244011
BS conversion C2 Grn 12.6204489520133


title: Cf_LM0

city: Agripolis - Legnaro (PD)

first: Mery

last: Giantin

state: Padova

address: Viale Università, 16

department: Dip. Biomedicina Comparata e Alimentazione

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software

organism: Canis lupus familiaris

source_name: mast cell tumour sample

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol:
Aliquot from the central part of the mast cell tumor mass aseptically collected during surgical intervention, submerged in RNAlater solution and stored at –20°C until extraction
Mast cell tumor total RNA was extracted using Trizol reagent according to manufacturer instruction and purified according to Qiagen RNeasy Mini Kit protocol for tissue samples

tag: breed

value: Shar-pei

value: male

value: 5 yr old

tag: tumor case id

value: mast cell tumor case LM0

value: mast cell tumor (MCT)


title: Whole Blood DNA 4762563034_B

description:
BS conversion C1 Grn 12.6302671250268
BS conversion C2 Grn 12.8991680761343


title: Whole Blood DNA 4762563034_L

description:
BS conversion C1 Grn 12.8037275265531
BS conversion C2 Grn 12.4752267777423


title: Whole Blood DNA 4762563034_C

description:
BS conversion C1 Grn 12.7321674256634
BS conversion C2 Grn 12.5425482623352


title: Whole Blood DNA 4762563034_A

description:
BS conversion C1 Grn 12.8953859398985
BS conversion C2 Grn 12.5943246039248


title: Cf_T134.3

value: Dachshund

value: female

value: 9 yr old

value: mast cell tumor case T134


title: I124

value: peripheral blood lymphocytes

value: DZ


title: Whole Blood DNA 4762563034_G

description:
BS conversion C1 Grn 12.6199906626064
BS conversion C2 Grn 12.3976746329483

value: BRCA1 wild-type and healthy

value: whole blood


title: I123

value: M


title: Whole Blood DNA 4762563035_D

description:
BS conversion C1 Grn 12.6512759733466
BS conversion C2 Grn 12.075479149488


title: I122

value: F


title: I121


title: Cf_T135

value: American Staffordshire

value: 9.5 yr old

value: mast cell tumor case T135


title: I119


title: Whole Blood DNA 4762563034_H

description:
BS conversion C1 Grn 12.5018371849023
BS conversion C2 Grn 12.2726297849764


title: Human_BTH_229-9534948T

first: Hua

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Hu133Plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Expression Console. RMA algorithm provided by software ExpressionConsole was used to call gene level expression values from raw signals.

source_name: gastric cancer frozen tumor tissues

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

growth_protocol: Tumor tissues were collected after surgical resection and frozed for total RNA extraction

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

value: gastric

tag: phenotype

value: gastric cancer


title: I118


title: Human_BTH_179-Z51-26028T


title: I120


title: Cf_T130

value: Boxer

value: male

value: 6 yr old

value: mast cell tumor case T130


title: Whole Blood DNA 4762563034_D

description:
BS conversion C1 Grn 13.1233131245687
BS conversion C2 Grn 12.8540891798706


title: Human_BTH_395-9540809T


title: I117


title: Human_BTH_1-Z131-29411T


title: Human_BTH_101-N15_19601T


title: Human_BTH_231-9534192T


title: Human_BTH_401-9540945T


title: Cf_T115

value: mast cell tumor case T115

value: mast cell tumor (MCT)


title: Human_BTH_485-9542902T


title: Human_BTH_211-A59-25914T


title: Human_BTH_269-9537501T


title: Cf_T122

value: Dachshund

value: 8 yr old

value: mast cell tumor case T122


title: Human_BTH_133-N13_18302T


title: Human_BTH_19-Z153-29967T


title: Cf_T132

value: mast cell tumor case T132


title: Cf_T131

value: Crossbred

value: 13 yr old

value: mast cell tumor case T131


title: Cf_T121

value: 10 yr old

value: mast cell tumor case T121


title: Human_BTH_255-9532010T

value: gastric


title: I116

value: peripheral blood lymphocytes

value: F

value: DZ


title: Human_BTH_7-A17-19375T

value: gastric cancer


title: Human_BTH_289-9537671T


title: Cf_T114.1

value: Boxer

value: male

value: mast cell tumor case T114


title: Cf_T117.2

value: female

value: mast cell tumor case T117

value: mast cell tumor (MCT)


title: I115

value: M


title: Human_BTH_17-A25-20597T


title: Human_BTH_481-9542761T


title: I114


title: I113


title: I112


title: I111


title: I110


title: I108


title: Cf_T113

value: Crossbred

value: 8 yr old

value: mast cell tumor case T113


title: Human_BTH_79-Z105-28485T


title: Human_BTH_119-Z71-26367T


title: Human_BTH_157-Z57-26261T


title: Human_BTH_413-9541306T


title: Cf_T102

value: Labrador Retriever

value: mast cell tumor case T102


title: Cf_T107

value: 7 yr old

value: mast cell tumor case T107


title: Human_BTH_447-9541880T

value: gastric


title: Human_BTH_431-9540474T


title: Human_BTH_143-A35-23632T


title: I109

value: peripheral blood lymphocytes


title: Human_BTH_67-Z133-29445T

value: gastric cancer


title: Human_BTH_151-N9-18577T


title: Human_BTH_109-Z69-26351T


title: Cf_T104

value: English Setter

value: 11 yr old

value: mast cell tumor case T104


title: Cf_T106

value: female

value: mast cell tumor case T106


title: Human_BTH_207-A45-24664T


title: Human_BTH_435-9541634T