title: NATURI_46_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_46
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

value: female


title: mid log, D-xylose minimal media, replicate 1

status: Public on Aug 02 2013

type: RNA

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

country: USA

institute: University of California San Diego

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.6.0.0 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Thermotoga maritima MSB8

source_name: Thermotoga maritima MSB8 (ATCC: 43589) wild type

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

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown anoxically at 80 °C in 500 mL serum bottles containing 200 mL of minimal media{Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85} supplemented with the carbon source associated with the condition listed above. This carbon source was the sole carbon source provided to the cells.

extract_protocol: RNA isolation was performed using the RNeasy mini kit (Qiagen) protocol with DNaseI treatment. Total RNA yields were measured by using a NanoDrop (Thermo) at wavelength of 260 nm and quality was checked on an agarose gel.  cDNA synthesis was conducted as described in {Qiu et al., 2010, Genome Res, 20, 1304-11}. In short, 10 μg of purified total RNA sample was reversed transcribed to cDNA with amino-allyl dUTP. The amino-allyl labeled cDNA samples were then coupled with Cy5 Monoreactive dyes (Amersham). Cy5 labeled cDNA samples were fragmented to 50-300 bp range with DNase I (Epicentre). High-density four-plex oligonucleotide tiling arrays consisting of 4 x 71,423 probes of variable length spaced across the whole Thermotoga maritima genome were used (Roche Nimblegen). Hybridization, wash and scan were performed according to the manufacturer’s instructions.

tag: genotype

value: Wild Type

tag: accession

tag: growth media

value: D-xylose minimal media


title: Leaf_CL_rep3

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

country: Spain

institute: Mision Biologica de Galicia (CSIC)

hyb_protocol: Fifteen µg of cRNA per sample were hybridized using Affymetrix standard procedures

scan_protocol: Fluorescence signaling was scanned using a GeneChip® 3000 scanner followinfg Affymetrix standard procedures

data_processing: Data analysis was performed using the Robust Multichip Average (RMA) tool included in the Affymetrix Expression Console software. Genes with an expression ratio (CL vs. CC) ≤ 0.5 or ≥ 2 were considered down and up-regulated respectively. To identify genes differentially expressed between treatments, a Benjamini-Hochberg multi-test adjusted FDR was calculated between log2-transformed expression ratios from CL and CC sections using the LIMMA software. Genes with a FDR ≤ 0.05 were considered as differentially expressed

label: Biotin

organism: Zea mays

source_name: Leaf tissue

label_protocol: Two hundred and fifty ng of total RNA were labeled with the GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA) following manufacturer’s instructions

growth_protocol: Maize seeds were grown on sterilized peat in phytotron under fluorescent light (228 µmol m-2 s-1) in a 14 h light/10 h dark light regime and watered as needed

extract_protocol: Sample tissues were ground in liquid nitrogen and the RNA was extracted using the RiboPureTM kit following manufacturer´s instructions

treatment_protocol: Plants were grown under cold conditions (15 ºC) for three weeks and then exposed to control temperatures (25 ºC) for one extra week. After this period the third leaf showed two well defined sections: distal (chlorophyll-less; CL) and proximal (chlorophyll-containing; CC) sections. Two centimeters of the distal (chlorophyll-less; CL) and proximal (chlorophyll-containing; CC) sections closest to the transition zone were collected from three biological replicates

tag: line

tag: leaf sections

value: Chlorophyll-Less (CL) section


title: Leaf_CL_rep1


title: Before laughing vs After laughing in control group 1

city: Tsurumi-ku, Yokohama

first: Miyo

last: Hori

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

country: Japan

institute: DNA Chip Research Inc.

hyb_protocol: Agilent two-color gene expression hybridization and wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution. Images were quantified using Agilent Feature Extraction software version 9.5.3.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

organism: Homo sapiens

source_name: Control subjects

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol.

extract_protocol: RNA was extracted from whole blood using the PAXgene™ Blood RNA System Kit following manufacturer's guidelines.

treatment_protocol: Training subjects were laughed according to "Effective laugh maker" instruction for one week. Control subjects spent one week without laughter instructed by "Effective laugh maker".

tag: cell type

value: peripheral leukocyte


title: Before laughing vs After laughing in control group 2

description: Control subjects spent one week without laughter instructed by "Effective laugh maker".


title: Before laughing in under-expression group vs Before laughing in over expression group prior to training

description: Training subjects were laughed according to "Effective laugh maker" instruction for one week.

source_name: Effective laugh maker training subjects

tag: training

value: Effective laugh maker training


title: NATURI_40_Nasal mucosa_AsmNoEx_baseline

city: Chicago

first: Peter

last: McErlean

state: Illinois

address: 240 E. Huron, McGaw M-530h

department: Allergy Immunology

institute: Northwestern University

description:
NATURI_40
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).

data_processing: Processed data are presented in one data matrix with the 36,866 Agilent Probe IDs (out of possible 41108 and 36926, respectively), which are represented in both platform records. This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al Bioinformatics. 2003 Jan 22;19(2):185-93. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

source_name: Nasal mucosa from asthmatic without exacerbation baseline after cold

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)

growth_protocol: In vivo sampling of nasal mucosa of the course of naturally occuring colds.

extract_protocol: Total RNA was extracted from nasal mucosa samples using RNeasy Mini Kit (QIAGEN) with the addition of a DNAse treatment (1U/mL fro 1hr at 37C; Promega) and re-purification phase. Extracted RNA was further purified using the RNA Clean and Concentrator (ZYMO Research) and quality assesed by Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Nasal mucosa was sampled using Rhinoprobe and stored in RLT lysis buffer (QIAGEN) at -80C

tag: group

value: Asthmatic_no exacerbation

tag: gender

tag: age

value: 30 yrs

tag: time point (visit)

value: Baseline (V3)

tag: tissue

value: Nasal mucosa


title: NATURI_39_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_39
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: male

value: 25 yrs


title: NATURI_41_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_41
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: 51 yrs


title: NATURI_44_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_44
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: 53 yrs


title: NATURI_45_Nasal mucosa_AsmNoEx_day 2

description:
NATURI_45
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms

source_name: Nasal mucosa from asthmatic without exacerbation at day 2 of cold symptoms

value: 28 yrs

value: Day 2 (V1)


title: Before laughing vs After laughing prior to training in under-expression group


title: mid log, L-rhamnose minimal media, replicate 2

value: L-rhamnose minimal media


title: mid log, trehalose minimal media, replicate 1

value: trehalose minimal media


title: Before laughing vs After laughing prior to training in over-expression group


title: mid log, D-ribose minimal media, replicate 2

value: Wild Type

value: D-ribose minimal media


title: mid log, pectin minimal media, replicate 1

value: pectin minimal media


title: Before laughing vs After laughing posterior to training in under-expression group

value: peripheral leukocyte


title: mid log, L-rhamnose minimal media, replicate 1


title: mid log, D-glucose minimal media, replicate 3

value: D-glucose minimal media


title: NATURI_38_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_38
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: Asthmatic_no exacerbation

value: 43 yrs


title: Before laughing vs After laughing posterior to training in over-expression group

value: Effective laugh maker training


title: mid log, D-ribose minimal media, replicate 1


title: mid log, trehalose minimal media, replicate 2


title: mid log, cellobiose minimal media, replicate 2

value: cellobiose minimal media


title: NATURI_31_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_31
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: female

value: 33 yrs

value: Baseline (V3)

value: Nasal mucosa


title: mid log, pectin minimal media, replicate 2


title: mid log, D-galactose minimal media, replicate 1

value: D-galactose minimal media


title: mid log, D-glucose minimal media, replicate 1


title: mid log, cellobiose minimal media, replicate 1


title: NATURI_30_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_30
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: male

value: 28 yrs


title: NATURI_28_Nasal mucosa_Allrg Rhin_day 6

description:
NATURI_28
Gene expression in the nasal mucosa of an individual with allergic rhinitis six days after the onset of cold symptoms

source_name: Nasal mucosa from allergic rhinitis at day 6 of cold symptoms

value: Allergic Rhinitis

value: 27 yrs

value: Day 6 (V2)


title: mid log, D-galactose minimal media, replicate 2

value: Wild Type


title: NATURI_26_Nasal mucosa_Allrg Rhin_day 6

description:
NATURI_26
Gene expression in the nasal mucosa of an individual with allergic rhinitis six days after the onset of cold symptoms

value: 20 yrs


title: mid log, D-glucose minimal media, replicate 2

value: D-glucose minimal media


title: NATURI_29_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_29
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: Asthmatic_no exacerbation

value: 25 yrs


title: NATURI_22_Nasal mucosa_Allrg Rhin_day 2

description:
NATURI_22
Gene expression in the nasal mucosa of an individual with allergic rhinitis two days after the onset of cold symptoms

source_name: Nasal mucosa from allergic rhinitis at day 2 of cold symptoms

value: Day 2 (V1)


title: NATURI_24_Nasal mucosa_Allrg Rhin_day 2

description:
NATURI_24
Gene expression in the nasal mucosa of an individual with allergic rhinitis two days after the onset of cold symptoms


title: mid log, L-arabinose minimal media, replicate 2

value: L-arabinose minimal media


title: maltose minimal media, c-limited, late exponential, replicate 2

source_name: T. maritima MSB8 (ATCC: 43589) wild type

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown in an 1 L bioreactors with pH control set to 6.5 +/- .1 and with continuous removal of evolved hydrogen using 80% Nitrogen and 20% Carbon Dioxide. Cells were cultivated in anoxic minimal media [Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85] with 5 mM maltose as the sole carbon source at 80C. RNA samples were collected upon the complete utilization of maltose.

extract_protocol: RNA isolation was performed using the RNAeasy mini kit (Qiagen) protocol with DNaseI treatment. Total RNA yields were measured by using a NanoDrop (Thermo) at wavelength of 260 nm and quality was checked on an agarose gel.  cDNA synthesis was conducted as described in {Qiu et al., 2010, Genome Res, 20, 1304-11}. In short, 10 μg of purified total RNA sample was reversed transcribed to cDNA with amino-allyl dUTP. The amino-allyl labeled cDNA samples were then coupled with Cy5 Monoreactive dyes (Amersham). Cy5 labeled cDNA samples were fragmented to 50-300 bp range with DNase I (Epicentre). High-density four-plex oligonucleotide tiling arrays consisting of 4 x 71,423 probes of variable length spaced across the whole Thermotoga maritima genome were used (Roche Nimblegen). Hybridization, wash and scan were performed according to the manufacturer’s instructions.

tag: treatment

value: grown to late exponential + carbon limited


title: maltose minimal media, c-limited, late exponential, replicate 3


title: Control Wild type E.coli SE15 vs. LuxS mutant E.coli SE15

city: Suwon

first: Sang Rim

last: Kang

address: San 94-6,Iui-dong

department: Department of biological engineering

country: South Korea

institute: Kyonggi University

description: Compare with quorum sensing related to gene between E.coli SE15 and LuxS gene mutant E.coli SE15

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A 7.5)

data_processing: Genowiz 4.0.5.6 normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Escherichia coli SE15

source_name: E.coli SE15 isolated from indwelling catheter of patient

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: E.coli SE15 is cultured in LB broth and LuxS E.coli SE15 is cultured in LB broth with kanamycine at 37℃and in 150rpm shaking incubator

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

tag: strain

tag: genotype/variation

value: wild type

source_name: E.coli SE15 is isolated from indwelling catheter of patient and deleted LuxS gene (related to quorum sensing)

value: LuxS mutant


title: Patient genomic DNA BAB2806

type: genomic

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

molecule: genomic DNA

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: blood

value: Xq28 rearrangement

tag: sample type

value: Reference sample

tag: cell line


title: maltose minimal media, c-limited, late exponential, replicate 1

tag: genotype


title: NATURI_19_Nasal mucosa_Allrg Rhin_baseline

description:
NATURI_19
Gene expression in the nasal mucosa of an individual with allergic rhinitis following a cold.

source_name: Nasal mucosa from allergic rhinitis baseline after cold

value: male

value: Baseline (V3)

value: Nasal mucosa


title: mid log, L-arabinose minimal media, replicate 1

tag: accession


title: NATURI_35_Nasal mucosa_AsmNoEx_baseline

description:
NATURI_35
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, following a cold.

value: female

value: 36 yrs


title: Patient genomic DNA BAB2800


title: NATURI_20_Nasal mucosa_Allrg Rhin_baseline

description:
NATURI_20
Gene expression in the nasal mucosa of an individual with allergic rhinitis following a cold.

value: Allergic Rhinitis

value: 27 yrs


title: Patient genomic DNA BAB2799


title: Patient genomic DNA BAB2623


title: Patient genomic DNA BAB2771


title: maltose minimal media, hydrogen inhibited, stationary phase, replicate 4

growth_protocol: T. maritima MSB8 (ATCC: 43589) was grown in an 500 mL serum bottles containing 200 mL of anoxic minimal media{Rinker and Kelly, 1996, Appl Environ Microbiol, 62, 4478-85} with 10 mM maltose as the sole carbon source at 80˚ C.

value: Wild Type

value: grown to stationary phase + hydrogen inhibited


title: NATURI_16_Nasal mucosa_Healthy_day 6

description:
NATURI_16
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease six days after the onset of cold symptoms

source_name: Nasal mucosa from healthy at day 6 of cold symptoms

value: healthy (no underlying respiratory disease)

value: 32 yrs

value: Day 6 (V2)


title: maltose minimal media, hydrogen inhibited, stationary phase, replicate 3


title: maltose minimal media, heat shock, replicate 2

value: heat shock


title: maltose minimal media, hydrogen inhibited, stationary phase, replicate 1


title: maltose minimal media, heat shock, replicate 3


title: maltose minimal media, hydrogen inhibited, stationary phase, replicate 2


title: NATURI_10_Nasal mucosa_Healthy_day 2

description:
NATURI_10
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease two days after the onset of cold symptoms

source_name: Nasal mucosa from healthy at day 2 of cold symptoms

value: Day 2 (V1)


title: Patient genomic DNA BAB2618

value: blood


title: NATURI_04_Nasal mucosa_Healthy_baseline

description:
NATURI_04
Gene expression in the nasal mucosa of an individual with no underlying respiratory disease following a cold.

source_name: Nasal mucosa from healthy baseline after cold


title: Patient genomic DNA BAB2622

value: Xq28 rearrangement


title: arsenic trioxide resistant NB4 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression of ATO resistant NB4 cell line

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Whole Genome Human 4x44k (AMADID No: 014850). 1650ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and 75th percentile Normalization of the data was done in GeneSpring GX V 11.

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Cell lines cultured in RPMI media with 10% FBS

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

tag: phenotype

value: arsenic trioxide resistant


title: peripheral blood T-cells mRNA Patient9

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: gene expression data from T-cell

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix).The robust quantile method was applied to get normalized expression values using the Affymetrix software expression console.

source_name: peripheral blood T-cell

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

extract_protocol: Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))

treatment_protocol: Cells were snap frozen in -80 C

tag: disease state

value: multiple sclerosis

value: peripheral blood T-cells


title: Patient genomic DNA BAB2616

value: Reference sample


title: arsenic trioxide resistant NB4 1


title: maltose minimal media, heat shock, replicate 1


title: maltose minimal media, logphase, replicate 4

value: grown to midlog phase


title: maltose minimal media, logphase, replicate 3


title: peripheral blood T-cells mRNA Patient8

description: gene expression data from T-cell


title: maltose minimal media, logphase, replicate 2


title: naive NB4 1

description: Gene expression of naive NB4 cell line

source_name: NB4 CELL LINE

value: naive


title: naive NB4 2

description: Gene expression of naive NB4 cell line


title: maltose minimal media, logphase, replicate 1


title: Patient genomic DNA BAB3325


title: Patient genomic DNA BAB3274


title: Relapsed acute promyelocytic leukemia  APL 63

description: Gene expression at the time of relapse of acute promyelocytic leukemia

data_processing: Data extraction from Images was done using Feature Extraction software  and 75th percentile Normalization and baseline to median of all samples  was done in GeneSpring GX V 11.

source_name: Bone marrow, At relapse

growth_protocol: These are primary cell cultures of promyelocytes from APL patients collected at the time of diagnosis or at relapse, which are maintained in RPMI media with 10% FBS

tag: Sex

value: Male

tag: age (y)

value: Promyelocytes

value: Relapsed acute promyelocytic leukemia


title: peripheral blood T-cells mRNA Patient7

description: gene expression data from T-cell

tag: cell type


title: Relapsed acute promyelocytic leukemia  APL 31


title: Patient genomic DNA BAB3267


title: Patient genomic DNA BAB3273


title: Relapsed acute promyelocytic leukemia  APL 14


title: peripheral blood T-cells mRNA Patient5

description: gene expression data from T-cell


title: Patient genomic DNA BAB3261


title: Patient genomic DNA BAB3241


title: Patient genomic DNA BAB3247


title: Patient genomic DNA BAB3259


title: Patient genomic DNA BAB3255


title: peripheral blood T-cells mRNA Patient2

description: gene expression data from T-cell


title: Newly diagnosed acute promyelocytic leukemia  APL 38

description: Gene expression at the time of diagnosis of acute promyelocytic leukemia

source_name: Bone marrow, At diagnosis


title: Relapsed acute promyelocytic leukemia  APL 24


title: peripheral blood T-cells mRNA Patient3

description: gene expression data from T-cell


title: Newly diagnosed acute promyelocytic leukemia  LA 506/06


title: peripheral blood T-cells mRNA Patient6

description: gene expression data from T-cell


title: Patient genomic DNA BAB3216


title: peripheral blood T-cells mRNA Patient1

description: gene expression data from T-cell


title: Newly diagnosed acute promyelocytic leukemia  APL 28

value: Female


title: peripheral blood T-cells mRNA Patient10

description: gene expression data from T-cell


title: peripheral blood T-cells mRNA Control9

description: gene expression data from T-cell

value: Control


title: peripheral blood T-cells mRNA Control8

description: gene expression data from T-cell


title: Patient genomic DNA BAB3204


title: Patient genomic DNA BAB3174


title: Newly diagnosed acute promyelocytic leukemia  APL-BLK-D9


title: Patient genomic DNA BAB3172


title: Relapsed acute promyelocytic leukemia  APL-MW-R2


title: Patient genomic DNA BAB3161


title: Relapsed acute promyelocytic leukemia  APL-Prd-R4


title: Relapsed acute promyelocytic leukemia  APL-AKP-R3


title: peripheral blood T-cells mRNA Control7

description: gene expression data from T-cell


title: peripheral blood T-cells mRNA Control4

description: gene expression data from T-cell


title: peripheral blood T-cells mRNA Control6

description: gene expression data from T-cell


title: Patient genomic DNA BAB3154


title: Patient genomic DNA BAB3147


title: Patient genomic DNA BAB2991


title: Patient genomic DNA BAB3027


title: peripheral blood T-cells mRNA Control10

description: gene expression data from T-cell


title: Relapsed acute promyelocytic leukemia  APL-R1-PS


title: peripheral blood T-cells mRNA Patient4

description: gene expression data from T-cell


title: Patient genomic DNA BAB3159


title: Newly diagnosed acute promyelocytic leukemia  APL-Myt-D8


title: peripheral blood T-cells mRNA Control2

description: gene expression data from T-cell


title: peripheral blood T-cells mRNA Control3

description: gene expression data from T-cell


title: Newly diagnosed acute promyelocytic leukemia  APL-D1-PS


title: peripheral blood T-cells mRNA Control5

description: gene expression data from T-cell


title: Patient genomic DNA BAB2624


title: Patient genomic DNA BAB2619


title: peripheral blood T-cells mRNA Control1

description: gene expression data from T-cell


title: Patient genomic DNA BAB3238


title: Patient genomic DNA BAB2626


title: Newly diagnosed acute promyelocytic leukemia  APL-D4


title: Newly diagnosed acute promyelocytic leukemia  APL-D5


title: HD mutant ST14A Cells_DMSO_Biological Replicate 2

status: Public on Aug 01 2013

city: Irvine

first: Leslie

last: Thompson

state: CA

address: Biological Sciences III

institute: University of California, Irvine

description: Gene expression data from differentiated HD mutant ST14A cells treated with DMSO

hyb_protocol: Fragmented cRNAs were hybridized to Affymetrix GeneChip Rat Genome 230 2.0 microarrays according to the manufacturer's instructions. GeneChips were washed and stained in the Gene Chip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Gene Chip Scanner 3000.

data_processing: Partek Genomics Suite Version 6.6 Beta (6.12.0207) was used for data processing. Only interrogating probes were imported. No probe filtering was done. RMA background correction was done. Quantile Normalization was applied. Log Probes using Base 2. Probeset summarization Median Polish was done.

organism: Rattus norvegicus

source_name: HD mutant ST14A Cells, Differentiated 24 hours, DMSO Treated.

label_protocol: Labeled cRNAs were prepared according to the manufacturer's instructions, according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ST14A cells were propagated at 33°C in presence of serum. To induce neuronal differentiation cells were serum deprived and cultured at 37°C in presence of N2 supplement (Invitrogen).

extract_protocol: RNA was extracted from HD mutant and wild type ST14A cells, differentiated for 24 hours and treated with vehicle (DMSO) or with 5µM MIND4, using the RNeasy kit (Qiagen).

treatment_protocol: Cells were treated with compounds (5µM MIND4 or DMSO) concurrent with induction of neuronal differentiation for 24 hours, as described  (Quinti et al., 2010).

value: rat striatal primordia

value: embryonic day 14


title: HD mutant ST14A Cells_5µM MIND4_Biological Replicate 2

description: Gene expression data from differentiated HD mutant ST14A cells treated with 5µM MIND4

source_name: HD mutant ST14A Cells, Differentiated 24 hours, 5µM MIND4 Treated.


title: Wildtype ST14A Cells_DMSO_Biological Replicate 1

description: Gene expression data from differentiated wildtype ST14A cells treated with DMSO

source_name: Wildtype ST14A Cells, Differentiated 24 hours, DMSO Treated.


title: HD mutant ST14A Cells_5µM MIND4_Biological Replicate 1


title: Wildtype ST14A Cells_DMSO_Biological Replicate 2


title: Wildtype ST14A Cells_5µM MIND4_Biological Replicate 1

description: Gene expression data from differentiated wildtype ST14A cells treated with 5µM MIND4

source_name: Wildtype ST14A Cells, Differentiated 24 hours, 5µM MIND4 Treated.


title: SAHA.24hr.pulse.rep4

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: Probes were hybridized onto Agilent 4x44k Whole Human Genome microarrays. Hybridization, washing and drying of the arrays were performed on Tecan HS 4800 Pro (Tecan, Research Triangle Park, NC), according to Agilent’s recommendations.

scan_protocol: Arrays were scanned using Agilent Scanner G2505C

data_processing: Image files were processed using Agilent’s Feature Extraction software, version 10.7.  Background correction of raw Agilent data was performed using the normexp function in the limma package using an offset of 50. Within array normalization was performed using the normalizeWithinArrays function with the loess method. Data for duplicate probes on the Agilent array were averaged using the avereps function and control probes were removed from subsequent analysis. Probes were filtered using the featureFilter function in limma with default parameters to ensure that each gene was represented by a single probe.

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740133

label_protocol: Cyanine 5-labeled probes were purified using the RNeasy Mini Kit (Qiagen, cat# 74104). Seven hundred and fifty nanograms of each Cy5 probe, along with the same amount of the Cy3-labeled Universal Human Reference (Stratagene, cat#740000).

growth_protocol: SH-SY5Y cells were plated in 6-well plates at 300K cells/well and treated in replicates of 5 with inhibitor or a DMSO vehicle control for the indicated durations.

extract_protocol: RNA was isolated using the Rneasy Mini Kit (Qiagen) with on-column DNase treatments. Starting total RNA quantity of each sample was assessed using Nanodrop-8000 (Thermo Fisher Scientific, Wilmington, DE). RNA quality was evaluated using Agilent Bioanalyzer 2100 Eukaryote Total RNA Pico assay (Agilent Technologies, Santa Clara, CA). One microgram of total RNA was processed for each sample using Agilent QuickAmp Labeling kit (Agilent, cat#5190-0447).

tag: reference

value: Universal Mouse Reference RNA

value: neuroblastoma


title: SAHA.24hr.pulse.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740132


title: HD mutant ST14A Cells_DMSO_Biological Replicate 1


title: Wildtype ST14A Cells_5µM MIND4_Biological Replicate 2


title: Control Rat-hypothalamus vs Tickled Rat-hypothalamus

first: Katsuyuki

last: Hayashi

institute: DNA Chip Research Inc

description: Tickled group received stimulation for 4weeks. Stimulation was conducted once per day consisting of two set of four succesive alternating cycles of 15 s of resting followed by 15 s of stimulation.

hyb_protocol: Equal volumes of Cy5 sample and Cy3 sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and hybridized to a Whole Rat Genome oligo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with

scan_protocol: Scanned on an Agilent G2505B scanner and images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Expression ratios were calculated using Feature Extraciton Software (version9.1). GE2-v5_91_0806 was used as a extraction protocol.

source_name: No stimulated rat

label_protocol: Second strand cDNAs were synthesized from 500ng of total RNA, and non-labeled aminoallyed cRNAs were generated by IVT reactions. cRNAs were labeled with Cy3/Cy5 monoreactive dyes.

extract_protocol: Total RNA was isolated from RNAlater-stabilized hypothalamus using a RNeasy Mini Kit (Qiagen)

tag: Hypothalamus of adolescent (60 days of age) Wistar male rat

source_name: Tickled rat


title: Light-touched Rat-hypothalamus vs Tickled Rat-hypothalamus

description: Both groups received stimulation for 4weeks. Stimulation was conducted once per day consisting of two set of four succesive alternating cycles of 15 s of resting followed by 15 s of stimulation.

source_name: Light-touched rat


title: SAHA.24hr.pulse.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740134


title: C1.24hr.pulse.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740128


title: C1.24hr.pulse.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740126


title: C1.24hr.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740124


title: C1.24hr.pulse.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740127


title: C1.24hr.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740121


title: SAHA.24hr.pulse.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740130


title: SAHA.24hr.pulse.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740131


title: C1.24hr.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740122


title: SAHA.24hr.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740117


title: SAHA.24hr.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740118


title: C1.24hr.pulse.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740125


title: SAHA.24hr.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740119


title: SAHA.24hr.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740116


title: C1.24hr.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740123


title: C1.24hr.pulse.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740129


title: C1.24hr.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740120


title: C1.6hr.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740110


title: SAHA.24hr.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740115


title: C1.6hr.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740111


title: DMSO.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740104

source_name: DMSO


title: C1.6hr.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740113


title: SAHA.6hr.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740109


title: SAHA.6hr.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740107


title: SAHA.6hr.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740105


title: C1.6hr.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740112


title: C1.6hr.rep5

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740114


title: SAHA.6hr.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740106


title: DMSO.rep1

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740100


title: SAHA.6hr.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740108


title: DMSO.rep2

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740101


title: N28

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary data were extracted using BeadArray. Data werte further processed and quantile normalised using BeadStudio software

label: biotin

label_protocol: Standard Illumina labelling protocol

extract_protocol: Archival FFPE SNB blocks were sectioned to a thickness of 7 uM by using sterile blades. RNA was extracted using a protocol based on the Recover All Total nucleic acid isolation kit (Ambion) modified to include a deparaffinization step in 15 ml xylene repeated twice and overnight digestion with protease at 50°C. RNA 260/280 nm ratios values ranged between 1.9-2.2 and yields between 1 to 6 ug RNA/mm3 tissue.

value: Cutaneous melanoma

value: SNB biopsy

tag: snb status

value: neg

tag: snb number and status

tag: nsln status at clnd 1

tag: number of positive nsln

tag: patient status at 5 yrs fu 2

value: NP

tag: snb tumor burden at hystopathology 3

tag: rotterdam classification 4

tag: primary tm classification

tag: primary tm localization 5

value: F

tag: stage after surgery 6

value: IB

tag: gender

tag: age at diagnosis


title: DMSO.rep4

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740103

tag: cell line


title: DMSO.rep3

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740102


title: N31

tag: disease state

tag: tissue

value: L

value: M


title: N25

value: T


title: PP32

value: pos

value: P

value: IIIC


title: PP12

value: 4, M, ip


title: N21


title: PP36

value: 1, M, ip


title: PN8

value: IIIB


title: N5


title: PP27

value: 2, m, sc


title: PP41


title: N19

value: IIA


title: PP39

value: Cutaneous melanoma


title: PP40

value: SNB biopsy

value: 2, M, ip


title: HCT116 Combination

city: Los Angeles

first: Xiaojing

last: Yang

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

description: colorectal carcinoma cell line

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified by phenol chloroform extractions

value: Male

tag: treatment

value: 5-Aza-CdR and Clorgyline


title: N18

value: neg

value: NP

value: IIB

value: F


title: PN30

value: pos

value: 1, m, sc

value: IIIA


title: PN33

value: L

value: M


title: PN15

value: 1, m, ip


title: PN11

value: 3, m, sc+ip

value: T


title: HCT116 Clorgyline

description: colorectal carcinoma cell line

value: Clorgyline


title: T24 Combination

description: Human bladder carcinoma cell line

source_name: bladder

value: Female


title: N20

value: Cutaneous melanoma

value: SNB biopsy

value: IB


title: PP42

value: P

value: IIIC


title: 5MC_SNP_S093T_T

city: Pittsburgh

first: Yan P.

last: Yu

state: PA

address: 3550 Terrace st.

department: Pathology

institute: University of Pittsburgh

description:
S093T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

hyb_protocol: DNA was restriction digested, methylated genomic DNA  was immunoprecipitated and purified with 5-hmc antibody,  PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number analysis on CEL files were performed using Partek genomics suite. The values in the data matrix ( copy_number.txt available on Series records) represent copy number of each locus for methylation enrich DNA. The matched plain DNA is the baseline for the calculation: autosomal chromosome=2 and sex chromosome=1. The general rule in the assay is that when the value is significantly less than 2 in autosomal chromosomes, the DNA is not methylated, while higher than 2, hypermethylated.
Amplification called in methylated Genomic DNA (5mc_data) were obtained using matched genomic DNA as baseline.

source_name: prostate specimens_5MC_SNP_T

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from microdissected prostate tissues using Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Prostate tissues were microdissected to obtain T or N samples.

tag: tissue type

value: prostate specimens

tag: tissue subtype

value: tumor (T)

tag: sample type

value: Methylation enriched genome


title: PN4

tag: snb status

value: pos

tag: snb number and status

tag: nsln status at clnd 1

value: neg

value: NP

value: single cells, ip

value: F


title: PN2

tag: number of positive nsln

tag: patient status at 5 yrs fu 2

tag: snb tumor burden at hystopathology 3

value: IIIA


title: T24 5-Aza-CdR

description: Human bladder carcinoma cell line


title: PN13

value: 2, m, ip

tag: rotterdam classification 4

tag: primary tm classification

tag: primary tm localization 5

value: L


title: SNP_TB10-S093T_T

description:
S093T
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_T

value: Genome baseline


title: T24 Clorgyline

description: Human bladder carcinoma cell line

tag: gender

value: Female

value: Clorgyline


title: SNP_TP09-S0408T_T

description:
S0408T
Hybridized to Affymetrix SNP 6.0


title: HCT116 5-Aza-CdR

description: colorectal carcinoma cell line

value: Male

tag: cell line


title: si-RMST

city: Cambridge

first: Shi Yan

last: Ng

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: RMST siRNA

data_processing: Data was quantile normalized using GeneSpring

source_name: Differentiating neural progenitors

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

growth_protocol: N2B27 media

extract_protocol: Total RNA was extracted using Trizol and purified using Rneasy mini columns

treatment_protocol: non-targeting siRNA (si-NT), RMST siRNA (si-RMST) or SOX2 si-RNA (si-SOX2)

value: ReN-VM

tag: transfection

value: RMST siRNA


title: 5MC_SNP_S0408T_T

description:
S0408T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

value: prostate specimens


title: HCT116 Ctrl

description: colorectal carcinoma cell line


title: si-SOX2

description: SOX2 siRNA

value: SOX2 siRNA


title: T24 Ctrl

description: Human bladder carcinoma cell line


title: PFKFB3 & NICD overexpression rep2

city: Leuven

first: Bert

last: Cruys

address: Herestraat 49

country: Belgium

institute: Vesalius Research Center

description:
Replicate 2
8099164084_K

data_processing: Background correction was performed in the GenomeStudio software. Using the lumi package in R, the data was normalized by applying variance stabilizing transformation and quantile normalization (followed by probe filtering).

source_name: PFKFB3 & NICD overexpression

label_protocol: Biotynilated cRNA was prepared with the Ambion Total Prep Kit, according to the manufacturer's protocol.

extract_protocol: Invitrogen standard RLT buffer

tag: sample barcode

tag: passage

value: passage 2

tag: cell type

value: Umbilical vein endothelial cells


title: si-NT

description: non-targeting siRNA

value: non-targeting siRNA


title: NICD overexpression rep3

description:
Replicate 3
8099164084_I

source_name: NICD overexpression


title: PFKFB3 & NICD overexpression rep3

description:
Replicate 3
8099164084_L


title: PFKFB3 & NICD overexpression rep1

description:
Replicate 1
8099164084_J


title: SNP_Lncap_Cell line

description:
Lncap
Hybridized to Affymetrix SNP 6.0

source_name: SNP_Cell line

tag: tissue type

tag: tissue

value: cell line


title: 5MC_SNP_KB170T_T

description:
KB170T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

tag: tissue subtype

value: tumor (T)

tag: sample type

value: Methylation enriched genome


title: 5MC_SNP_PC3_Cell line

description:
PC3
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

source_name: 5MC_SNP_Cell line


title: 5MC_SNP_PR310T_T

description:
PR310T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_KB170T_T

description:
KB170T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_JB770T_T

description:
JB770T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_PC3_Cell line

description:
PC3
Hybridized to Affymetrix SNP 6.0


title: NICD overexpression rep1

description:
Replicate 1
8099164084_G


title: PFKFB3 overexpression rep2

description:
Replicate 2
8099164084_E

source_name: PFKFB3 overexpression


title: 5MC_SNP_LNcap_Cell line

description:
Lncap
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Control overexpression vector rep2

description:
Replicate 2
8099164084_B

source_name: Control overexpression vector


title: Control overexpression vector rep3

description:
Replicate 3
8099164084_C


title: 5MC_SNP_IB684T_T

description:
IB684T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_JB426T_T

description:
JB426T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_PR310T_T

description:
PR310T
Hybridized to Affymetrix SNP 6.0


title: SNP_JB426T_T

description:
JB426T
Hybridized to Affymetrix SNP 6.0


title: Control overexpression vector rep1

description:
Replicate 1
8099164084_A


title: PFKFB3 overexpression rep1

description:
Replicate 1
8099164084_D


title: SNP_IB362T_T

description:
IB362T
Hybridized to Affymetrix SNP 6.0


title: shPFKFB3-DAPT rep3

description:
Replicate 3
8099164070_L


title: shPFKFB3-DAPT rep2

description:
Replicate 2
8099164070_K


title: 5MC_SNP_IB362T_T

description:
IB362T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: NICD overexpression rep2

description:
Replicate 2
8099164084_H


title: shPFKFB3-DMSO rep3

description:
Replicate 3
8099164070_I


title: SNP_IB134T_T

description:
IB134T
Hybridized to Affymetrix SNP 6.0


title: shPFKFB3-DMSO rep1

description:
Replicate 1
8099164070_G


title: shPFKFB3-DAPT rep1

description:
Replicate 1
8099164070_J


title: PFKFB3 overexpression rep3

description:
Replicate 3
8099164084_F


title: shPFKFB3-DMSO rep2

description:
Replicate 2
8099164070_H


title: 5MC_SNP_IB113T_T

description:
IB113T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Control DAPT rep1

description:
Replicate 1
8099164070_D

source_name: Control DAPT


title: Control DAPT rep3

description:
Replicate 3
8099164070_F


title: SNP_IB113T_T

description:
IB113T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_IB071T_T

description:
IB071T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Control DMSO rep2

description:
Replicate 2
8099164070_B

source_name: Control DMSO


title: Control DMSO rep3

description:
Replicate 3
8099164070_C


title: 5MC_SNP_IB134T_T

description:
IB134T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Control DAPT rep2

description:
Replicate 2
8099164070_E


title: SNP_HB504T_T

description:
HB504T
Hybridized to Affymetrix SNP 6.0


title: Ctr MCF10A.B2 2

city: Turin

first: antonio

last: lembo

state: Turin

address: Via Nizza, 52

department: Dept. of Genetics, Biology and Biochemistry

institute: University of Turin

description:
M- 3.4 III Hyb.AVG_Signal
replicate 2

hyb_protocol: Illumina Ref-8v2 BeadChips

scan_protocol: GenomeStudio software (Illumina)

data_processing: The data were normalised using quantile normalisation in R

source_name: Modified MCF10A Cells

label_protocol: Illumina Ref-8v2 BeadChips

extract_protocol: trizol extraction

value: mammary epithelial cells

value: MCF10A Cells

tag: genotype/variation

value: Ctr MCF10A.B2


title: 5MC_SNP_IB071N_AT

description:
IB071N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

source_name: prostate specimens_5MC_SNP_AT

value: benign tissue adjacent to cancer (AT)


title: SNP_JB770T_T

description:
JB770T
Hybridized to Affymetrix SNP 6.0

value: Genome baseline


title: Ctr MCF10A.B2 1

description:
M- 1.2 III Hyb.AVG_Signal
replicate 1


title: Ctr MCF10A.B2 3

description:
M- 5.6 II Hyb.AVG_Signal
replicate 3


title: SNP_IB071N_AT

description:
IB071N
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_AT


title: SNP_HB526N_AT

description:
HB526N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_HB526N_AT

description:
HB526N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_HB46T_T

description:
HB46T
Hybridized to Affymetrix SNP 6.0


title: Cas/ErbB2 1

description:
C+ 1.2.AVG_Signal
replicate 1


title: SNP_IB071T_T

description:
IB071T
Hybridized to Affymetrix SNP 6.0


title: Cas/ErbB2 2

description:
C+ 3.4.AVG_Signal
replicate 2


title: 5MC_SNP_HB504T_T

description:
HB504T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_HB305T_T

description:
HB305T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: ovarian cancer cell line RMG-1

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

description: hybridized to Affymetrix SNP 6.0

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.  The array image was acquired using Affymetrix GeneChip® Command Console.

data_processing:
Copy number values for individual SNP and CNV probes were extracted and converted from CEL files into signal intensities using Partek Genomics Suite (v6.6) software.
Copy number data was estimated from signal intensity on Affmetrix SNP 6.0 arrays. Copy number ratio values (ratio of the intensity readings from the raw data file to a control) were generated in Partek Genomics Suite (v 6.6) using a Partek corporation distributed baseline (control) file of normal (2N) genomic DNA and default parameters. Post import values were corrected for localized GC content using the inbuilt Partek feature based on methods described in Diskin et al. (Nucleic Acids Research. 2008. 36:19).

source_name: human ovarian cancer cell line: RMG-1

extract_protocol: Genomic DNA was extracted using the Gentra Pure Gene DNA extraction Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Q-Bit fluoremtric assay.

tag: originating repository

value: HSRRB

tag: literature reported histotype

value: clear cell carcinoma

tag: predicted histology

value: unclassifiable


title: Cas 2

description:
C- 3.4.AVG_Signal
replicate 2

value: Cas


title: Cas 3

description:
C- 5.6.AVG_Signal
replicate 3


title: Cas/ErbB2 3

description:
C+ 5.6.AVG_Signal
replicate 3


title: ovarian cancer cell line TOV21G

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: TOV21G

value: ATCC


title: 5MC_SNP_HB46T_T

description:
HB46T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

value: prostate specimens


title: SNP_IB684T_T

description:
IB684T
Hybridized to Affymetrix SNP 6.0


title: SNP_HB305T_T

description:
HB305T
Hybridized to Affymetrix SNP 6.0


title: ovarian cancer cell line RMG-2

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: RMG-2


title: ovarian cancer cell line OVTOKO

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: OVTOKO

value: OVTOKO

value: JCRB


title: ovarian cancer cell line OVMANA

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: OVMANA

value: OVMANA


title: ovarian cancer cell line ES-2

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: ES-2

value: Atypical non-serous carcinoma


title: SNP_HB261T_T

description:
HB261T
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_T

value: tumor (T)


title: 5MC_SNP_HB261T_T

description:
HB261T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

source_name: prostate specimens_5MC_SNP_T

value: Methylation enriched genome


title: ErbB2 1

description:
M+ 1.2.AVG_Signal
replicate 1

value: mammary epithelial cells


title: SNP_HB235T_T

description:
HB235T
Hybridized to Affymetrix SNP 6.0


title: SNP_FB238T_T

description:
FB238T
Hybridized to Affymetrix SNP 6.0


title: ovarian cancer cell line OVISE

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: OVISE

value: OVISE


title: 5MC_SNP_HB235T_T

description:
HB235T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: ovarian cancer cell line JHOC-9

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: JHOC-9

value: RIKEN


title: ErbB2  3

description:
M+ 5.6.AVG_Signal
replicate 3

value: MCF10A Cells


title: Cas 1

description:
C- 1.2.AVG_Signal
replicate 1


title: ErbB2 2

description:
M+ 3.4.AVG_Signal
replicate 2


title: HCT116 Combination_1

description: colorectal carcinoma cell line

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

label_protocol: Standard as recommended by Illumina

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment and Quality control experiment performed

tag: treatment

value: AZA and Clorgyline


title: 5MC_SNP_FB120T_T

description:
FB120T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_FB421T2_T

description:
FB421T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_FB421T2_T

description:
FB421T2
Hybridized to Affymetrix SNP 6.0

value: Genome baseline


title: 5MC_SNP_DU145_Cell line

description:
Du145
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

source_name: 5MC_SNP_Cell line

value: cell line


title: 5MC_SNP_FB238T_T

description:
FB238T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_FB120T_T

description:
FB120T
Hybridized to Affymetrix SNP 6.0


title: ovarian cancer cell line JHOC-5

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: JHOC-5

value: clear cell carcinoma


title: 5MC_SNP_D025_D

description:
D025
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_5MC_SNP_D

value: organ donor prostate (D)


title: SNP_D022_D

description:
D022
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_D


title: SNP_D025_D

description:
D025
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_Du145_Cell line

description:
Du145
Hybridized to Affymetrix SNP 6.0

source_name: SNP_Cell line


title: HCT116 AZA_1

description: colorectal carcinoma cell line

value: AZA


title: Control DMSO rep1

description:
Replicate 1
8099164070_A

source_name: Control DMSO

value: passage 2

value: Umbilical vein endothelial cells


title: HCT116 Clorgyline_1

description: colorectal carcinoma cell line

value: Clorgyline


title: HL-60 Clorgyline_2

description: Human promyelocytic leukemia cells

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.8.0). It was vst transformed and quantile normalized.


title: SNP_D019_D

description:
D019
Hybridized to Affymetrix SNP 6.0

value: prostate specimens


title: HCT116 AZA_2

description: colorectal carcinoma cell line


title: HCT116 Ctrl_2

description: colorectal carcinoma cell line


title: HCT116 Clorgyline_2

description: colorectal carcinoma cell line


title: HL-60 Combination_2

description: Human promyelocytic leukemia cells


title: 5MC_SNP_D019_D

description:
D019
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: HCT116 Ctrl_1

description: colorectal carcinoma cell line


title: SNP_D015_D

description:
D015
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_D022_D

description:
D022
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_D013_D

description:
D013
Hybridized to Affymetrix SNP 6.0


title: HL-60 Aza_2

description: Human promyelocytic leukemia cells


title: HL-60 Combination_1

description: Human promyelocytic leukemia cells


title: 5MC_SNP_D013_D

description:
D013
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: HL-60 Aza_1

description: Human promyelocytic leukemia cells


title: HL-60 Clorgyline_1

description: Human promyelocytic leukemia cells


title: SNP_D011_D

description:
D011
Hybridized to Affymetrix SNP 6.0


title: HL-60 Ctrl_2

description: Human promyelocytic leukemia cells


title: HL-60 Ctrl_1

description: Human promyelocytic leukemia cells


title: 5MC_SNP_D015_D

description:
D015
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_D010_D

description:
D010
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_D011_D

description:
D011
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: ovarian cancer cell line JHOC-7

description: hybridized to Affymetrix SNP 6.0

source_name: human ovarian cancer cell line: JHOC-7


title: 5MC_SNP_D010_D

description:
D010
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_D008_D

description:
D008
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: T24 Combination_1

description: established from a highly malignant grade III human urinary bladder carcinoma

source_name: Human bladder carcinoma cell line


title: T24 Clorgyline_2


title: 5MC_SNP_D007_D

description:
D007
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_D005_D

description:
D005
Hybridized to Affymetrix SNP 6.0


title: SNP_D004_D

description:
D004
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_D004_D

description:
D004
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: T24 Clorgyline_1


title: 5MC_SNP_D003_D

description:
D003
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: T24 AZA_2


title: SNP_D002_D

description:
D002
Hybridized to Affymetrix SNP 6.0


title: HCT116 Combination_2

description: colorectal carcinoma cell line


title: SNP_D008_D

description:
D008
Hybridized to Affymetrix SNP 6.0


title: T24 Ctrl_2


title: T24 AZA_1


title: SNP_D001_D

description:
D001
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_D002_D

description:
D002
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_D007_D

description:
D007
Hybridized to Affymetrix SNP 6.0


title: SNP_29671N_AT

description:
29671N
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_AT

value: benign tissue adjacent to cancer (AT)


title: 5MC_SNP_28925N_AT

description:
28925N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

source_name: prostate specimens_5MC_SNP_AT


title: 5MC_SNP_D005_D

description:
D005
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_28925T_T

description:
28925T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

value: tumor (T)


title: 5MC_SNP_28685T_T

description:
28685T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine

value: Methylation enriched genome


title: 5MC_SNP_29671N_AT

description:
29671N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_29671T_T

description:
29671T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_28685N_AT

description:
28685N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_29671T_T

description:
29671T
Hybridized to Affymetrix SNP 6.0


title: SNP_28925T_T

description:
28925T
Hybridized to Affymetrix SNP 6.0


title: SNP_28925N_AT

description:
28925N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_D001_D

description:
D001
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_28685T2_T

description:
28685T2
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_28278T2_T

description:
28278T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_28278T2_T

description:
28278T2
Hybridized to Affymetrix SNP 6.0


title: SNP_27086T_T

description:
27086T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_28278N_AT

description:
28278N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: T24 Ctrl_1

description: established from a highly malignant grade III human urinary bladder carcinoma


title: 5MC_SNP_27086T_T

description:
27086T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_27086N_AT

description:
27086N
Hybridized to Affymetrix SNP 6.0


title: T24 Combination_2


title: 5MC_SNP_27086N_AT

description:
27086N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_25313T_T

description:
25313T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_25313N_AT

description:
25313N
Hybridized to Affymetrix SNP 6.0


title: SNP_25265T_T

description:
25265T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_25313N_AT

description:
25313N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_25313T_T

description:
25313T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_25265T_T

description:
25265T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_20968T_T

description:
20968T
Hybridized to Affymetrix SNP 6.0


title: SNP_28685N_AT

description:
28685N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_25265N2_AT

description:
25265N2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_20968T_T

description:
20968T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_20968N_AT

description:
20968N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_19381N_AT

description:
19381N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_19381T_T

description:
19381T
Hybridized to Affymetrix SNP 6.0


title: SNP_16947T_T

description:
16947T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_16947T_T

description:
16947T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_25265N2_AT

description:
25265N2
Hybridized to Affymetrix SNP 6.0


title: SNP_19381N_AT

description:
19381N
Hybridized to Affymetrix SNP 6.0


title: SNP_28278N_AT

description:
28278N
Hybridized to Affymetrix SNP 6.0


title: SNP_16947N_AT

description:
16947N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_16947N_AT

description:
16947N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_15922T2_T

description:
15922T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_15922N_AT

description:
15922N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_15922N_AT

description:
15922N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_15463T_T

description:
15463T
Hybridized to Affymetrix SNP 6.0


title: SNP_20968N2_AT

description:
20968N2
Hybridized to Affymetrix SNP 6.0


title: SNP_15922T2_T

description:
15922T2
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_15463T_T

description:
15463T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_15463N2_AT

description:
15463N2
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_19381T_T

description:
19381T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_14878T2_T

description:
14878T2
Hybridized to Affymetrix SNP 6.0


title: SNP_11462T2_T

description:
11462T2
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_14878T2_T

description:
14878T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_11462T2_T

description:
11462T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_11462N_AT

description:
11462N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_11462N_AT

description:
11462N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_11423T_T

description:
11423T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_11423T_T

description:
11423T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_11423N2_AT

description:
11423N2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_11423N2_AT

description:
11423N2
Hybridized to Affymetrix SNP 6.0


title: SNP_9122N_AT

description:
9122N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_9122T2_T

description:
9122T2
Hybridized to Affymetrix SNP 6.0


title: SNP_8741T_T

description:
8741T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_8741T_T

description:
8741T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_9122N_AT

description:
9122N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_8741N (2)_AT

description:
8741N
Hybridized to Affymetrix SNP 6.0


title: SNP_8432T_T

description:
8432T
Hybridized to Affymetrix SNP 6.0


title: SNP_8432N_AT

description:
8432N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_8432T_T

description:
8432T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_15463N2_AT

description:
15463N2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_8378T_T

description:
8378T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_8432N_AT

description:
8432N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_14878N_AT

description:
14878N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_14878N_AT

description:
14878N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_8378N_AT

description:
8378N
Hybridized to Affymetrix SNP 6.0


title: SNP_7943T2_T

description:
7943T2
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_8378N_AT

description:
8378N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_98-9122T_T

description:
9122T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_7943T2_T

description:
7943T2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_7504T_T

description:
7504T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_7943N_AT

description:
7943N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_7943N_AT

description:
7943N
Hybridized to Affymetrix SNP 6.0


title: SNP_7504T_T

description:
7504T
Hybridized to Affymetrix SNP 6.0


title: SNP_7504N_AT

description:
7504N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_7504N_AT

description:
7504N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_6647T_T

description:
6647T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_6647T_T

description:
6647T
Hybridized to Affymetrix SNP 6.0


title: SNP_6647N_AT

description:
6647N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_6647N_AT

description:
6647N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_6634T_T

description:
6634T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_6634T_T

description:
6634T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_8741N_AT

description:
8741N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_6634N_AT

description:
6634N
Hybridized to Affymetrix SNP 6.0


title: SNP_4336T_T

description:
4336T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_6634N_AT

description:
6634N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_4336T_T

description:
4336T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_4336N_AT

description:
4336N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_8378T_T

description:
8378T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_4336N_AT

description:
4336N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_4308T_T

description:
4308T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_4308T_T

description:
4308T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_4308N_AT

description:
4308N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_2644N_AT

description:
2644N
Hybridized to Affymetrix SNP 6.0


title: SNP_2644T_T

description:
2644T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_2644N_AT

description:
2644N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_1199T_T

description:
1199T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_1199T_T

description:
1199T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_1199N_AT

description:
1199N
Hybridized to Affymetrix SNP 6.0


title: SNP_4308N_AT

description:
4308N
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_1199N_AT

description:
1199N
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: SNP_678T_T

description:
678T
Hybridized to Affymetrix SNP 6.0


title: 5MC_SNP_2644T_T

description:
2644T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: 5MC_SNP_678T_T

description:
678T
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Wild-type epididymis, biological rep 1

city: Cincinnati

first: Steve

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: A hybridization cocktail is created for each sample. The samples are hybridized to a standard Probe Array Cartridge (GeneChip Mouse Gene 1.0 ST Array-Affymetrix) in the GeneChip Hybridization Oven 640 (Affymetrix). Probe arrays are washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays are scanned with the Affymetrix GeneChip Scanner 3000 7G following manufacturer's instructions. Raw data files are created by Command Console, the Affymetrix operating software program.

data_processing: Data were analyzed using GeneSpring GX software with the RMA16 summarization algorithm without baseline transformation. Probe sets were filtered on expression keeping only those with >150 raw expression in 1 genotype per comparison. Each Hox mutant (n=3/tissue/genotype) was compared to WT (n=3), and probe sets changed >2 fold with p<0.05 were counted as significant changes.

organism: Mus musculus

source_name: caudal epididymis, adult 3-7 months, WT

label_protocol: For each sample, the Ambion® WT Expression Kit (Life Technologies) synthesizes cDNA target from 300 nanograms of total RNA. Then the GeneChip® WT Terminal Labeling Kit (Affymetrix) is used to both chemically fragment and biotin-label the cDNA target.

extract_protocol: Total RNA was extracted from fresh tissue using the Qiagen RNeasy Mini kit.

tag: strain/background

value: WT

tag: developmental stage

value: adult

value: caudal epididymis

value: male


title: Wild-type epididymis, biological rep 2

tag: gender


title: Hoxa9,10,11-/- epididymis, biological rep 3

source_name: caudal epididymis, adult 3-7 months, Hoxa9,10,11-/-


title: Lgi1 knock-out NPC cells, biological rep1

city: Augusta

first: Mingqiang

last: Ren

state: GA

address: 1120 15th Street

department: Cancer Center

institute: Georgia Regents University

description: Gene expression data from Lgi1 knock-out neural precursor-like cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MoGene 1.0 ST array chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

source_name: immortalized Lgi1 knock-out neural precursor-like cells

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: NPC cells grew in neurobasal medium (Invitrogen) supplemented with B-27 on poly-D-lysine coated dishes.  Immortalized NPC cells grew in RPMI supplemented with 1% FBS.

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

tag: strain

value: embryo brain

tag: genotype

value: Lgi1 knock-out

tag: age

value: embryos at day 13.5


title: Hoxa9,10,11-/-d9,10,11+/- vas deferens, biological rep 3

source_name: vas deferens, adult 3-7 months, Hoxa9,10,11-/-d9,10,11+/-

value: vas deferens


title: Hoxa9,10,11-/- epididymis, biological rep 2


title: Lgi1 wild type NPC cells, biological rep2

description: Gene expression data from Lgi1 wild type neural precursor-like cells

source_name: immortalized Lgi1 wild type neural precursor-like cells

value: Lgi1 wild type


title: Hoxa9,10,11-/- epididymis, biological rep 1


title: Lgi1 knock-out NPC cells, biological rep2


title: Hoxa9,10,11+/-d9,10,11-/- vas deferens, biological rep 3

source_name: vas deferens, adult 3-7 months, Hoxa9,10,11+/-d9,10,11-/-


title: Lgi1 wild type NPC cells, biological rep3


title: Hoxa9,10,11+/-d9,10,11-/- vas deferens, biological rep 2


title: Wild-type epididymis, biological rep 3


title: Hoxa9,10,11+/-d9,10,11-/- vas deferens, biological rep 1


title: Lgi1 knock-out NPC cells, biological rep3


title: Lgi1 wild type NPC cells, biological rep1


title: Hoxa9,10,11-/-d9,10,11+/- vas deferens, biological rep 2


title: Hoxa9,10,11-/-d9,10,11+/- vas deferens, biological rep 1


title: 5MC_SNP_678N2_AT

description:
678N2
Hybridized to Affymetrix SNP 6.0 after IP with Ab for methyl-cytosine


title: Hoxd9,10,11-/- vas deferens, biological rep 3

source_name: vas deferens, adult 3-7 months, Hoxd9,10,11-/-


title: Hoxd9,10,11-/- vas deferens, biological rep 2


title: SNP_678N2_AT

description:
678N2
Hybridized to Affymetrix SNP 6.0

value: Genome baseline


title: WM35_DMSO_6h

city: Boston

first: Rhoda

last: Alani

address: 609 Albany Street, Suite 6J

department: Dermatology

institute: Boston University School of Medicine

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cDNA. The staining was further amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner.

data_processing:
Image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings.
HuEx-1_0-st-v2.na30.hg19.probeset.csv

source_name: WM35 radial phase melanoma, DMSO treated, 6h

label_protocol: RNA was labeled using the Ambion WT Express kit and Affymetrix cDNA Terminal labeling kit following the manufacturer’s recommended procedure. Briefly, 100 nanograms of total RNA from each sample was used to synthesize first strand cDNA with T7 primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, cRNA was generated through in vitro transcription and purified using magnetic beads.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  Sense strand cDNA was then purified using cDNA clean-up column, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: DMEM with 10% FBS, L-glutamine, and penicillin/streptomycin, cultured in 5% CO2

extract_protocol: Cells were trypsinized and collected via centrifugation; RNA was extracted with Qiagen RNeasy kit and eluted in nuclease-free water.

treatment_protocol: Direct addition of compound C646 (20uM f.c.) or DMSO (0.2% f.c.) to culture media, followed by 6h or 24h incubation under regular growth condition

tag: cell line

value: DMSO

tag: time


title: Hoxd9,10,11-/- vas deferens, biological rep 1


title: WM35_DMSO_24h

source_name: WM35 radial phase melanoma, DMSO treated, 24h


title: Hoxa9,10,11-/- vas deferens, biological rep 3

source_name: vas deferens, adult 3-7 months, Hoxa9,10,11-/-


title: SNP_D003_D

description:
D003
Hybridized to Affymetrix SNP 6.0

source_name: prostate specimens_SNP_D

tag: tissue type

value: organ donor prostate (D)


title: WM35_C646_24h

source_name: WM35 radial phase melanoma, C646 treated, 24h


title: WM35_C646_6h

source_name: WM35 radial phase melanoma, C646 treated, 6h


title: Hoxa9,10,11-/- vas deferens, biological rep 2

tag: tissue


title: Naive none C

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
Naive CD8+ T cells
6197801051_B

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Mouse Chips at 58 °C  for 20 h.

scan_protocol: The arrays were scanned using an Illumina BeadStation 500GX scanner and Illumina BeadStudio v3 software. Illumina probe data were exported from BeadStudio as raw data and screened for quality. Samples failing chip visual inspection and control examination were removed.

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Technical replicates were averaged.

source_name: CD8+ T cells from mouse spleen

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct Hybridization protocol

extract_protocol: Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad Laboratories). Total RNA was then amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol. This protocol involves a first cDNA synthesis step followed by in vitro transcription for cRNA synthesis.

value: spleen

tag: cell type

value: CD8+ T cells

tag: subset

value: Naive

tag: vaccine


title: Naive none D

description:
Naive CD8+ T cells
6197801051_D


title: ZNF708

city: Baltimore

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.

data_processing:
Analysis was performed in R with the oligo package, RMA was used for normalization at both exon and gene levels.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.transcript.csv

source_name: GIST-T1 Cell Line

label_protocol: RNA from control and experimental samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Ambion and Affymetrix. Briefly, 100ng of total RNA was used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the double strand cDNA was purified using magnetic beads, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  The resulting sense strand cDNA was then purified, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: GIST-T1 cell line was grown in DMEM +10%FBS

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

treatment_protocol: for drug treatment, drugs were added directly to the cell medium; for siRNA treatment Transfection conditions were determined for GIST T1 cells using siRNA smart pools against KIT and GL-2 (Dharmacon) controls to achieve Z’ factor of 0.5 or greater.  We used a reverse transfection protocol in which the final concentration of siRNA was 50 nM.

tag: transfection

value: siRNA knockdown of ZNF708


title: RASSF8

value: siRNA knockdown of RASSF8


title: Naive none B

description:
Naive CD8+ T cells
6197801051_C


title: ZNF431

value: siRNA knockdown of ZNF431


title: Wild-type vas deferens, biological rep 2

source_name: vas deferens, adult 3-7 months, WT

tag: genotype/variation

value: WT

value: adult


title: ZNF254

value: siRNA knockdown of ZNF254


title: Wild-type vas deferens, biological rep 1

value: male


title: Hoxa9,10,11-/- vas deferens, biological rep 1


title: IGF2R

value: siRNA knockdown of IGF2R


title: ZNF85

value: siRNA knockdown of ZNF85


title: ZNF528

value: siRNA knockdown of ZNF528


title: ZNF43

value: siRNA knockdown of ZNF43


title: EM DNA_rAd 101

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990123_E

value: EM


title: ZNF665

value: siRNA knockdown of ZNF665


title: Wild-type vas deferens, biological rep 3

value: vas deferens


title: ZNF429

value: siRNA knockdown of ZNF429


title: Naive none A

description:
Naive CD8+ T cells
6197801051_A

value: spleen

value: CD8+ T cells


title: EM rAd_rAd 100

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990123_D


title: IGFBP2

value: siRNA knockdown of IGFBP2


title: ZNF91

value: siRNA knockdown of ZNF91


title: ZNF100

value: siRNA knockdown of ZNF100


title: Hoxa9,10,11-/- oviduct, biological rep 3

source_name: oviduct, diestrus, adult 3-7 months, Hoxa9,10,11-/-

value: oviduct (diestrus)

value: female


title: CM rAd_LCMV 97

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990123_A

value: CM


title: Hoxa9,10,11-/- oviduct, biological rep 2

value: adult


title: EM rAd_LCMV 23

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990110_G


title: Wild-type oviduct, biological rep 1

source_name: oviduct, diestrus, adult 3-7 months, WT

value: WT


title: Hoxa9,10,11-/- oviduct, biological rep 1


title: Healthy control 21

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: array version 12

hyb_protocol: Hybridization on miRCURY LNA™ Arrays, using MAUI® hybridization system.

scan_protocol: Hybridization images were scanned and digitized using InnoScan 700 microarray scanner (Innopsys, France).

data_processing: miRNA microarray data were analyzed by subtracting the background signal (B532nm) from the test signal (F532nm).

source_name: Blood samples

label_protocol: LNA-modified oligonucleotide (Exiqon, Denmark) probes for human, mouse and rat miRNAs annotated in miRBase version 16.0 were used in the microarray. Total RNA (1 µg) was 3′-end –labeled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark).

growth_protocol: Primary cultures of cortical neurons were established from E15 Swiss albino mouse brains. The cortices were dissected from E15 mouse embryos and washed with Hanks’ balanced salt solution (HBSS, 14025-092, Gibco, Invitrogen, USA). The cortical slices was dissociated with 0.05% (w/v) trypsin in HBSS without Ca2+/Mg2+ (14175-095, Gibco, Invitrogen, USA) for 30 min at 37 °C and neutralized with 1mg/ml trypsin inhibitor (T6522, Sigma, USA). Single cells were obtained by gentle trituration in Neurobasal medium (21103-049, Gibco, Invitrogen, USA) supplemented with B27 (17504-044, Invitrogen, USA), L-glutamine and Penicillin-streptomycin (Gibco, Invitrogen, USA). The cells were counted by trypan blue exclusion and seeded on to poly-d-lysine coated 24 well plates at a density of 120, 000 cells/cm2. Cultures were maintained at 37 °C with 5% CO2 in a tissue culture incubator. Cells were harvested on Days 2, 4, 6, 8.

extract_protocol: Total RNA (+ microRNA) was extracted from cells by Ribopure Kit (Ambion, USA) according to the manufacturers’ protocol. The concentration and integrity of the RNA were determined using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del) and denaturing polyacrylamide gel electrophoresis, respectively.

value: blood

tag: infection status

value: Healthy controls


title: Healthy control 20

description: array version 12


title: BV-0-12h

city: Houston

first: wei

last: Qi

state: TX

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

description: control 12h

data_processing: BeadStudio normalization = rank invariant

source_name: 253JB-V, control 12h

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

value: bladder cancer


title: Hoxa9,10,11+/-d9,10,11-/- uterus, biological rep 2

source_name: uterus, diestrus, adult 3-7 months, Hoxa9,10,11+/-d9,10,11-/-

value: uterus (diestrus)


title: GTF21

value: siRNA knockdown of GTF21


title: Wild-type oviduct, biological rep 3


title: Hoxa9,10,11+/-d9,10,11-/- uterus, biological rep 1


title: UC13-0-12h

description: control 12h

source_name: UM-UC13, control 12h


title: EM rAd_rAd 18

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990110_B

value: EM


title: Healthy control 23

description: array version 12


title: Healthy control 22

description: array version 12


title: Hoxa9,10,11+/-d9,10,11-/- uterus, biological rep 3


title: Wild-type oviduct, biological rep 2


title: Ctrl72hr

value: negative control siRNA (nonsilencing) for 72 hr


title: EM rAd_LCMV 22

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990110_F

value: spleen


title: Healthy control 19

description: array version 12


title: EM rAd_LCMV 21

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990110_E

value: CD8+ T cells


title: BV-Vel-12h

description: vel treatment 12h

source_name: 253JB-V, vel treatment 12h


title: EM rAd_LCMV 19

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990110_C


title: EM rAd_rAd 16

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990102_H


title: EM rAd_rAd 17

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990110_A


title: Ctrl24hr

value: negative control siRNA (nonsilencing) for 24 hr


title: BV-Vel-6h

description: vel treatment 6h

source_name: 253JB-V, vel treatment 6h


title: EM rAd_LCMV 20

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990110_D


title: Hoxa9,10,11-/-d9,10,11+/- uterus, biological rep 3

source_name: uterus, diestrus, adult 3-7 months, Hoxa9,10,11-/-d9,10,11+/-


title: BV-0-6h

description: control 6h

source_name: 253JB-V, control 6h


title: UC13-Vel-6h

description: vel treatment 6h

source_name: UM-UC13, vel treatment 6h


title: UC13-0-6h

description: control 6h

source_name: UM-UC13, control 6h


title: Hoxa9,10,11-/-d9,10,11+/- uterus, biological rep 2


title: Healthy control 17

description: array version 12


title: Healthy control 16

description: array version 12


title: UC13-Vel-12h

description: vel treatment 12h

source_name: UM-UC13, vel treatment 12h


title: EM rAd_rAd 15

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990102_G


title: Healthy control 15

description: array version 12


title: Healthy control 14

description: array version 12


title: Healthy control 18

description: array version 12


title: EM rAd_rAd 14

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990102_F


title: Hoxd9,10,11-/- uterus, biological rep 2

source_name: uterus, diestrus, adult 3-7 months, Hoxd9,10,11-/-


title: Hoxd9,10,11-/- uterus, biological rep 3


title: Hoxa9,10,11-/-d9,10,11+/- uterus, biological rep 1


title: Hoxd9,10,11-/- uterus, biological rep 1


title: Healthy control 13

description: array version 12


title: Healthy control 12

description: array version 12


title: EM DNA_rAd 11

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990102_C

source_name: CD8+ T cells from mouse spleen


title: Healthy control 11

description: array version 12


title: Hoxa9,10,11-/- uterus, biological rep 3

source_name: uterus, diestrus, adult 3-7 months, Hoxa9,10,11-/-


title: Healthy control 10

description: array version 12


title: EM DNA_rAd 12

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990102_D


title: Healthy control 9

description: array version 12


title: EM DNA_rAd 10

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990102_B


title: EM rAd_LCMV 8

description:
EM CD8+ T cells arising from rAd_LCMV vaccination
4514990087_H


title: Healthy control 8

description: array version 12


title: EM DNA_rAd 9

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990102_A


title: EM DNA_rAd 13

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990102_E


title: Healthy control 6

description: array version 12


title: Healthy control 5

description: array version 12


title: Hoxa9,10,11-/- uterus, biological rep 2


title: EM DNA_rAd 5

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990087_E


title: EM rAd_rAd 6

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990087_F


title: Healthy control 4

description: array version 12


title: Wild-type uterus, biological rep 3

source_name: uterus, diestrus, adult 3-7 months, WT


title: Wild-type uterus, biological rep 1


title: EM DNA_rAd 4

description:
EM CD8+ T cells arising from DNA_rAd vaccination
4514990087_D


title: Wild-type uterus, biological rep 2


title: CM rAd_LCMV 96

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990071_H


title: Healthy control 7

description: array version 12


title: CM rAd_LCMV 95

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990071_G


title: EM rAd_rAd 7

description:
EM CD8+ T cells arising from rAd_rAd vaccination
4514990087_G


title: Hoxa9,10,11-/- uterus, biological rep 1


title: Healthy control 2

description: array version 12


title: Healthy control 3

description: array version 12


title: Healthy control 1

description: array version 12


title: p53-, Rb-, Myc+, rep3

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed at 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using GeneChip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000, using Command Console Software.

data_processing: Raw intensity files from the Affymetrix Mouse Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.  Gene-level expression measurements were computed using the iterPLIER algorithm on the core probesets and exported with annotation release 32, dated June 23rd, 2011.

source_name: mammary epithelial cells, p53- Rb- Myc+

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: Mammary epithelial cells were isolated from 8-week-old female mice and sub-cultured in DMEM/F12 media supplemented with 5% horse serum, 20ng/mL EGF, 10μg/ml insulin, 1ng/ml cholera toxin, 100μg/ml hydrocortisone, 100 U/ml penicillin/streptomycin and 2mM L-glutamine at 37oC in 5% CO2.

extract_protocol: RNA was harvested from proliferating cell populations using the RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Adenoviral expression of Cre-recombinase was used to delete the RB and/or p53 genes, and retrovirus was used to achieve MYC overexpression.

value: mammary epithelial cells

value: 8 weeks

tag: myc

value: OE

value: KO

tag: rb


title: p53-, Rb-, Myc+, rep2

value: female


title: H1N1 infected patient 43

description: array version 16

value: Influenza A H1N1 infection


title: CM rAd_rAd 92

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990071_D

value: CM


title: p53-, Myc+, rep3

source_name: mammary epithelial cells, p53- Myc+

value: WT


title: CM rAd_LCMV 94

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990071_F


title: p53-, Rb-, Myc+, rep1


title: CM rAd_LCMV 93

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990071_E


title: CM rAd_rAd 90

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990071_B