title: Neurosphere culture DMSO 48h Rep3

city: St. Louis

first: Liana

middle: Roberts

last: Stein

state: MO

address: Campus Box 8103, 660 South Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

description:
5467 - J6-C-D
Replicate 3

hyb_protocol: 750ug of each aRNA in water (5ul) was suspended in Illumina “HYB” buffer (10ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to Illumina Mouse Ref-8v2 Expression BeadChips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.  Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.

data_processing: Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Illumina GenomeStudio software.  On-array spot replicates were averaged by GenomeStudio and individual spot probe was reported.

source_name: Postnatal hippocampal neurospheres

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; Life Technologies).   200 ng of each total cellular RNA sample (11ul) was mixed with an oligo-dT T7 primer (1ul), 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and Arrayscript RT enzyme (1ul).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a column cleanup using Zymo DNA Clean and Concentrator 5s (Zymo Research) according to protocol, invitro-transcription was carried out by adding 10x T7 reaction buffer (2.5ul), T7 biotin-NTP mix (2.5ul), and T7 RNA polymerase enzyme mix (2.5ul) and incubation at 37C.    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (75ul), the amplified RNAs (aRNA) were cleaned with RNA columns provided in the MessageAmp TotalPrep kit.   The aRNAs were then quantitated on a spectrophotometer, and quality determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

growth_protocol: Postnatal day 0 or 1 hippocampi from C57Bl6 mice were dissected in HibernateA (Invitrogen A12475-01) and trypsinized at 37°C for 7 min. Cells were mechanically dissociated by pipetting and pelleted by centrifugation (1700 rpm, 7 min). Dissociation medium (0.1% sodium bicarbonate, 15 mM HEPES (Sigma), 0.5% glucose in HBSS) was used to wash the cells before resuspension in growth medium. Growth medium consisted of DMEM:F12 (1:1, Invitrogen 11966-025 and 21700-075, respectively), B27 (Invitrogen, 17504-044), N2 (Invitrogen, 17502-048), Pen/Strep (Invitrogen), epidermal growth factor (EGF, 20 ng/ml, Sigma, E4127), FGF (FGF, 10 ng/mL, R&D, 233-fb, and heparin (Sigma).  Cultures were maintained at 37°C with 5% CO2, and passaged twice before being used for experiments.

extract_protocol: Total RNA was extracted from neurospheres using the RNeasy kit (Qiagen). Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm.  Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

treatment_protocol: Dissociated passage 2 neurospheres were cultured with the Nampt-specific inhibitor FK866 (10 nM) or vehicle (DMSO, 1:1000) for 48 hours.

tag: age

value: Postnatal day 0 or 1

value: Hippocampus

tag: litter

tag: passage number


title: Neurosphere culture FK866 48h Rep4

status: Public on May 08 2014

type: RNA

country: USA

description:
5470 - J6-D-F
Replicate 4

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: genomic dna from breast_HCC1937_Mock_day7

type: genomic

city: Baltimore

first: Stephen

last: Baylin

state: Maryland

address: 1650 Orleans St CRB I RM 541

department: Oncology

institute: Johns Hopkins UniversityJohns Hopkins Medical Institutions

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing:
Data were extracted using Methylation Module of GenomeStudio v1.0 Software. The 'signal_intensities.txt' contains unmethylated and methylated signal intensities. Methylation status of each CpG site was presented as b (beta) value based on following definition:
b  value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Breast, colon, and ovarian cancer cell lines were maintained under ATCC recommended growth conditions.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Qiagen DNeasy Kit according to the manufacturer's instructions.

treatment_protocol: Cell lines were treated with 500 nM 5-azacitidine for 72 hours while in log-growth phase, changing the media and drug every 24 hours for AZA treatment. Cells were harvested at 1, 3, 7, 10, 14, or 21 days following initial application of drug.

tag: cell line

tag: cell type

value: breast cancer cell line

tag: sample group


title: genomic dna from breast_HCC1937_AZA_day3

label_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.


title: genomic dna from breast_HCC1937_Mock_day10


title: genomic dna from breast_HCC1937_Mock_day3


title: Neurosphere culture DMSO 48h Rep1

description:
5463 - J2-A-D
Replicate 1


title: Neurosphere culture FK866 48h Rep1

description:
5464 - J2-A-F
Replicate 1


title: KT2440(pCAR1DpmrDpnd)-biofilm

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
KT2440b520511FR-3.bpmap
KT2440b520511FF-3.bpmap

label: biotin

organism: Pseudomonas putida

source_name: cDNA prepared from LB culture of KT2440(pCAR1dpmrdpnd)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12  µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: Each strain was grown in 5 ml of LB at 300 strokes/min for 14-14.5 h (pre-culture) and then washed and transferred into 100-ml of NMM-4 buffer (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 0.1% succinate adjusting its turbidity (600 nm) at 0.05. The resultant culture was incubated on a rotary shaker at 120 rpm and cell growth was monitored in by measuring its turbidity (600 nm).

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: genotype/variation


title: Neurosphere culture FK866 48h Rep2

description:
5466 - J2-B-F
Replicate 2


title: Neurosphere culture DMSO 48h Rep2

description:
5465 - J2-B-D
Replicate 2


title: Neurosphere culture DMSO 48h Rep4

description:
5469 - J6-D-D
Replicate 4


title: Neurosphere culture FK866 48h Rep3

description:
5468 - J6-C-F
Replicate 3


title: KT2440(pCAR1)-biofilm

source_name: cDNA prepared from LB culture of KT2440(pCAR1)


title: KT2440-biofilm

source_name: cDNA prepared from LB culture of KT2440


title: genomic dna from breast_HCC1937_Mock_day1


title: genomic dna from breast_ZR751_AZA_dye10


title: genomic dna from breast_ZR751_Mock_dye10


title: genomic dna from breast_ZR751_AZA_dye7


title: genomic dna from breast_HCC1937_AZA_day1


title: genomic dna from breast_ZR751_Mock_dye7


title: genomic dna from breast_ZR751_AZA_dye3


title: genomic dna from breast_ZR751_AZA_dye1


title: genomic dna from breast_MDA361_AZA_day10


title: genomic dna from breast_ZR751_Mock_dye1


title: TauTKO-Old 3

city: Kobe

first: Takashi

last: Ito

state: Hyogo

address: 1-3-6 Minatojima, Chuo-ku

department: Pharmacy

institute: Hyogo University of health Sciences

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Mouse GE microarray kit 8x60k (G4852A) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by nitrogen gas.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539B) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) (FE protocol: GE1-v1010-Sep10 and Grid: 028005-D-F-20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: tibial anterior muscle, TauT knockout, old

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the Sepasol®-RNA I Super G  (Nacalai Tesque, Japan) following the manufacturer's recommendations.  Then, RNA was purified by RNeasy Mini kit (Qiagen) following the manufacturer's protocol.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

value: skeletal muscle

value: 18 month olds


title: genomic dna from breast_MDA361_Mock_day10


title: genomic dna from breast_ZR751_Mock_dye3


title: genomic dna from breast_MDA361_Mock_day7


title: genomic dna from breast_MDA361_AZA_day7


title: _6_PU4T3 (3Plex)

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing:
Raw data: Probe-level .pair files.
Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm (Loess) within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

growth_protocol: Batch fermentations were conducted in approximately 5 L of MTC medium with switchgrass as carbon source as described previously (Yang et al., 2008).

extract_protocol: RNA was isolated essentially described previously (Yang et al. 2010. PNAS. 107:10395–10400). Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: time point

tag: array


title: _2_PU2T2 (3Plex)

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: _5_PU2T3 (3Plex)

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: _1_PU1T2 (3Plex)


title: WT-Old 2

source_name: tibial anterior muscle, wild-type, old


title: WT-Young 2

source_name: tibial anterior muscle, wild-type, young

value: 3 month olds


title: TauTKO-Young 1

source_name: tibial anterior muscle, TauT knockout, young


title: TauTKO-Young 3


title: WT-Old 1


title: TauTKO-Old 2


title: WT-Young 1


title: KT2440(pCAR1DpmrDphu)-biofilm

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444.1) at 9-bp density.  BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
pCAR1_8b520435FR-3.bpmap
pCAR1_8b520435FF-3.bpmap

source_name: cDNA prepared from LB culture of KT2440(pCAR1dpmrdphu)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: Total RNA extractions from Pseudomonas strains were performed as described previously (Yun et al., 2010). Briefly, an overnight LB culture of each strain was transferred into 1 ml of tilted LB media adjusting its OD600 to be 0.01 and then incubated under static culture conditions at 30°C. After 12 h of growth, we used the RNA Protect Bacterial Reagent (Qiagen, CA, USA) to stabilize the total RNA in the bacteria that formed biofilms at the liquid–air interface of the glass base dish, and RNA extraction was subsequently performed using Nucleospin RNA II (Macherey-Nagel GmbH and Co. KG, Düren, Germany) according to the manufacturers’ instructions.


title: KT2440(pCAR1DpmrDpnd)-biofilm


title: WT-Old 3


title: TauTKO-Young 2


title: WT-Young 3


title: genomic dna from breast_MDA361_Mock_day3


title: _3_PU4T2 (3Plex)


title: genomic dna from breast_MDA361_AZA_day1


title: genomic dna from breast_BT474_AZA_Day10


title: genomic dna from breast_MDA361_AZA_day3


title: TauTKO-Old 1


title: genomic dna from breast_BT474_Mock_Day10


title: genomic dna from breast_MDA361_Mock_day1


title: _4_PU1T3 (3Plex)


title: genomic dna from breast_BT474_Mock_Day7


title: genomic dna from breast_BT474_AZA_Day7


title: genomic dna from breast_BT474_AZA_Day3


title: genomic dna from breast_BT474_AZA_Day1


title: genomic dna from breast_BT474_Mock_Day3


title: genomic dna from breast_BT474_Mock_Day1


title: genomic dna from breast_CAMA1_AZA_Day10


title: genomic dna from breast_CAMA1_AZA_Day7


title: genomic dna from breast_CAMA1_Mock_Day10


title: genomic dna from breast_CAMA1_Mock_Day7


title: genomic dna from breast_CAMA1_AZA_Day3


title: genomic dna from breast_CAMA1_Mock_Day3


title: ovarian OVKATE Mock/AZA Day10

description: ovarian OVKATE d10-Mock/OVKATE d10-AZA

hyb_protocol: 825 ng labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Arrays were scanned by Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 Software.

data_processing: Data were extracted with Agilent Feature Extraction Software.

source_name: Control ovarian OVKATE Day10

label_protocol: 400 ng total RNA was amplified and labeled using Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

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

value: OVKATE

value: ovarian cancer cell line

value: Day 10

source_name: AZA-treatedovarian OVKATE Day10


title: genomic dna from breast_CAMA1_AZA_Day1


title: genomic dna from breast_CAMA1_Mock_Day1


title: ovarian EF027 Mock/AZA Day9

description: ovarian EF027 d9-Mock/EF027 d9-AZA

source_name: Control ovarian EF027 Day9

value: Day 9

source_name: AZA-treated ovarian EF027 Day9


title: genomic dna from breast_SKBR3_AZA_Day10


title: ovarian Tyk-mi Mock/AZA Day10

description: ovarian Tyk-mi d10-Mock/Tyk-mi d10-AZA

source_name: Control ovarian Tyk-mi Day10

value: Tyk-mi

source_name: AZA-treatedovarian Tyk-mi Day10


title: ovarian OVKATE Mock/AZA Day3

description: ovarian OVKATE d3-Mock/OVKATE d3-AZA

source_name: Control ovarian OVKATE Day3

value: Day 3

source_name: AZA-treatedovarian OVKATE Day3


title: ovarian OAW-28 Mock/AZA Day3

description: ovarian OAW-28 d3-Mock/OAW-28 d3-AZA

source_name: Control ovarian OAW-28 Day3

source_name: AZA-treatedovarian OAW-28 Day3


title: ovarian OVCAR5 Mock/AZA Day3

description: ovarian OVCAR5 d3-Mock/OVCAR5 d3-AZA

source_name: Control ovarian OVCAR5 Day3

source_name: AZA-treated ovarian OVCAR5 Day3


title: genomic dna from breast_SKBR3_AZA_Day7


title: ovarian OVCAR5 Mock/AZA Day10

description: ovarian OVCAR5 d10-Mock/OVCAR5 d10-AZA

source_name: Control ovarian OVCAR5 Day10

source_name: AZA-treated ovarian OVCAR5 Day10


title: genomic dna from breast_SKBR3_Mock_Day7


title: ovarian OV 2008 Mock/AZA Day10

description: ovarian OV 2008 d10-Mock/OV 2008 d10-AZA

source_name: Control ovarian OV 2008 Day10

source_name: AZA-treated ovarian OV 2008 Day10


title: ovarian ES-2 Mock/AZA Day3

description: ovarian ES-2 d3-Mock/ES-2 d3-AZA

source_name: Control ovarian ES-2 Day3

source_name: AZA-treated ovarian ES-2 Day3


title: ovarian OV 2008 Mock/AZA Day3

description: ovarian OV 2008 d3-Mock/OV 2008 d3-AZA

source_name: Control ovarian OV 2008 Day3

source_name: AZA-treated ovarian OV 2008 Day3


title: ovarian EF027 Mock/AZA Day3

description: ovarian EF027 d3-Mock/EF027 d3-AZA

source_name: Control ovarian EF027 Day3

source_name: AZA-treated ovarian EF027 Day3


title: ovarian OAW-28 Mock/AZA Day10

description: ovarian OAW-28 d10-Mock/OAW-28 d10-AZA

source_name: Control ovarian OAW-28 Day10

source_name: AZA-treatedovarian OAW-28 Day10


title: ovarian Kuramochi Mock/AZA Day10

description: ovarian Kuramochi d10-Mock/Kuramochi d10-AZA

source_name: Control ovarian Kuramochi Day10

value: Kuramochi

source_name: AZA-treatedovarian Kuramochi Day10


title: ovarian Kuramochi Mock/AZA Day3

description: ovarian Kuramochi d3-Mock/Kuramochi d3-AZA

source_name: Control ovarian Kuramochi Day3

source_name: AZA-treatedovarian Kuramochi Day3


title: ovarian ES-2 Mock/AZA Day10

description: ovarian ES-2 d10-Mock/ES-2 d10-AZA

source_name: Control ovarian ES-2 Day10

source_name: AZA-treated ovarian ES-2 Day10


title: ovarian OVMANA Mock/AZA Day10

description: ovarian OVMANA d10 MOCK/OVMANA d10 AZA

source_name: Control ovarian OVMANA Day10

value: OVMANA

source_name: AZA-treated ovarian OVMANA Day10


title: ovarian Tyk-mi Mock/AZA Day3

description: ovarian Tyk-mi d3-Mock/Tyk-mi d3-AZA

source_name: Control ovarian Tyk-mi Day3

source_name: AZA-treatedovarian Tyk-mi Day3


title: genomic dna from breast_SKBR3_Mock_Day10


title: genomic dna from breast_SKBR3_Mock_Day3


title: ovarian TOV-112D Mock/AZA Day10

description: ovarian TOV-112D d10 MOCK/TOV-112D d10 AZA

source_name: Control ovarian TOV-112D Day10

source_name: AZA-treated ovarian TOV-112D Day10


title: genomic dna from breast_SKBR3_AZA_Day1


title: genomic dna from breast_SKBR3_AZA_Day3


title: genomic dna from breast_HCC1187_AZA_Day10


title: genomic dna from breast_SKBR3_Mock_Day1


title: genomic dna from breast_HCC1187_Mock_Day10


title: genomic dna from breast_HCC1187_AZA_Day7


title: genomic dna from breast_HCC1187_Mock_Day7


title: genomic dna from breast_HCC1187_AZA_Day3


title: ovarian OVDA429 Mock/AZA Day10

description: ovarian OVDA429 d10 MOCK/OVDA429 d10 AZA

source_name: Control ovarian OVDA429 Day10

source_name: AZA-treated ovarian OVDA429 Day10


title: genomic dna from breast_HCC1187_Mock_Day3


title: ovarian OVCA432 Mock/AZA Day3

description: ovarian OVCA432 d3 MOCK/OVCA432 d3 AZA

source_name: Control ovarian OVCA432 Day3

source_name: AZA-treated ovarian OVCA432 Day3


title: ovarian OVCA432 Mock/AZA Day10

description: ovarian OVCA432 d10 MOCK/OVCA432 d10 AZA

source_name: Control ovarian OVCA432 Day10

source_name: AZA-treated ovarian OVCA432 Day10


title: genomic dna from breast_HCC1187_AZA_Day1


title: ovarian PEO14 Mock/AZA Day3

description: ovarian PEO14 d3 MOCK/PEO14 d3 AZA

source_name: Control ovarian PEO14 Day3

source_name: AZA-treated ovarian PEO14 Day3


title: ovarian OVDA429 Mock/AZA Day3

description: ovarian OVDA429 d3 MOCK/OVDA429 d3 AZA

source_name: Control ovarian OVDA429 Day3

source_name: AZA-treated ovarian OVDA429 Day3


title: genomic dna from breast_HCC1187_Mock_Day1


title: ovarian PEO14 Mock/AZA Day10

description: ovarian PEO14 d10 MOCK/PEO14 d10 AZA

source_name: Control ovarian PEO14 Day10

source_name: AZA-treated ovarian PEO14 Day10


title: genomic dna from breast_HCC1954_Mock_Day10


title: genomic dna from breast_HCC1954_AZA_Day10


title: genomic dna from breast_HCC1954_AZA_Day7


title: genomic dna from breast_HCC1954_Mock_Day7


title: ovarian OVMANA Mock/AZA Day3

description: ovarian OVMANA d3 MOCK/OVMANA d3 AZA

source_name: Control ovarian OVMANA Day3

source_name: AZA-treated ovarian OVMANA Day3


title: ovarian HEYC2 Mock/AZA Day10

description: ovarian HEYC2 d10 MOCK/HEYC2 d10 AZA

source_name: Control ovarian HEYC2 Day10

source_name: AZA-treated ovarian HEYC2 Day10


title: ovarian CAOV3 Mock/AZA Day3

description: ovarian CAOV3 d3 Mock/CAOV3 d3 AZA 500nM

source_name: Control ovarian CAOV3 Day3

source_name: AZA-treated ovarian CAOV3 Day3


title: ovarian CAOV3 Mock/AZA Day8

description: ovarian CAOV3 d8 Mock/CAOV3 d8 AZA 500nM

source_name: Control ovarian CAOV3 Day8

value: Day 8

source_name: AZA-treated ovarian CAOV3 Day8


title: ovarian HEYC2 Mock/AZA Day3

description: ovarian HEYC2 d3 MOCK/HEYC2 d3 AZA

source_name: Control ovarian HEYC2 Day3

source_name: AZA-treated ovarian HEYC2 Day3


title: genomic dna from breast_HCC1954_AZA_Day3


title: ovarian OVAR3 Mock/AZA Day3

description: ovarian OVCAR3 d3 Mock/OVCAR3 d3 AZA 500nM

source_name: Control ovarian OVAR3 Day3

source_name: AZA-treated ovarian OVAR3 Day3


title: ovarian SKOV3 Mock/AZA Day3

description: ovarian SKOV3 d3 Mock/SKOV3 d3 AZA 500nM

source_name: Control ovarian SKOV3 Day3

source_name: AZA-treated ovarian SKOV3 Day3


title: ovarian OVAR3 Mock/AZA Day10

description: ovarian OVCAR3 d10 Mock/OVCAR3 d10 AZA 500nM

source_name: Control ovarian OVAR3 Day10

source_name: AZA-treated ovarian OVAR3 Day10


title: ovarian SKOV3 Mock/AZA Day10

description: ovarian SKOV3 d10 Mock/SKOV3 d10 AZA 500nM

source_name: Control ovarian SKOV3 Day10

source_name: AZA-treated ovarian SKOV3 Day10


title: ovarian Hey Mock/AZA Day10

description: ovarian Hey d10 Mock/Hey d10 AZA 500nM

source_name: Control ovarian Hey Day10

value: Hey

source_name: AZA-treated ovarian Hey Day10


title: ovarian Hey Mock/AZA Day3

description: ovarian Hey d3 Mock/Hey d3 AZA 500nM

source_name: Control ovarian Hey Day3

source_name: AZA-treated ovarian Hey Day3


title: ovarian TyK-nu Mock/AZA Day10

description: ovarian TyK-nu d10 Mock/TyK-nu d10 AZA 500nM

source_name: Control ovarian TyK-nu Day10

value: TyK-nu

source_name: AZA-treated ovarian TyK-nu Day10


title: genomic dna from breast_HCC1954_Mock_Day1


title: genomic dna from breast_MDA175_AZA_Day7


title: genomic dna from breast_HCC1954_Mock_Day3


title: genomic dna from breast_HCC1954_AZA_Day1


title: genomic dna from breast_MDA175_AZA_Day3


title: genomic dna from breast_MDA175_Mock_Day7


title: genomic dna from breast_MDA175_Mock_Day3


title: genomic dna from breast_MDA175_AZA_Day1


title: genomic dna from breast_MDA175_Mock_Day1


title: genomic dna from breast_HCC1419_AZA_Day10


title: genomic dna from breast_HCC1419_Mock_Day10


title: genomic dna from breast_HCC1419_AZA_Day7


title: genomic dna from breast_HCC1419_Mock_Day7


title: genomic dna from breast_HCC1419_Mock_Day3


title: genomic dna from breast_HCC1419_AZA_Day3


title: KT2440(pCAR1)-biofilm

source_name: cDNA prepared from LB culture of KT2440(pCAR1)


title: genomic dna from breast_HCC1419_AZA_Day1


title: genomic dna from breast_HCC1419_Mock_Day1


title: ovarian TOV-112D Mock/AZA Day3

description: ovarian TOV-112D d3 MOCK/TOV-112D d3 AZA

source_name: Control ovarian TOV-112D Day3

source_name: AZA-treated ovarian TOV-112D Day3


title: genomic dna from breast_EFM192A_AZA_Day10


title: ovarian A2780 Mock/AZA Day3

description: ovarian A2780 d3 Mock/A2780 d3 AZA 500nM

source_name: Control ovarian A2780 Day3

source_name: AZA-treated ovarian A2780 Day3


title: ovarian TyK-nu Mock/AZA Day3

description: ovarian TyK-nu d3 Mock/TyK-nu d3 AZA 500nM

source_name: Control ovarian TyK-nu Day3

source_name: AZA-treated ovarian TyK-nu Day3


title: colon SNU-C1 Mock/AZA Day14

description: colon SNU-C1_Mock_D14/SNU-C1_Aza_D14

source_name: Control colon SNU-C1 Day14

value: colon cancer cell line

value: Day 14

source_name: AZA-treated colon SNU-C1 Day14


title: ovarian DOV-13 Mock/AZA Day10

description: ovarian DOV-13 d10 Mock/DOV-13 d10 AZA

source_name: Control ovarian DOV-13 Day10

source_name: AZA-treated ovarian DOV-13 Day10


title: colon SNU-C1 Mock/AZA Day28

description: colon SNU-C1_Mock_D28/SNU-C1_Aza_D28

source_name: Control colon SNU-C1 Day28

value: Day 28

source_name: AZA-treated colon SNU-C1 Day28


title: genomic dna from breast_EFM192A_Mock_Day10

value: breast cancer cell line


title: ovarian OAW-42 Mock/AZA Day10

description: ovarian OAW-42 d10 Mock/OAW-42 d10 AZA

source_name: Control ovarian OAW-42 Day10

source_name: AZA-treated ovarian OAW-42 Day10


title: ovarian OV-90 Mock/AZA Day10

description: ovarian OV-90 d10 Mock/OV-90 d10 AZA

source_name: Control ovarian OV-90 Day10

source_name: AZA-treated ovarian OV-90 Day10


title: genomic dna from breast_EFM192A_AZA_Day7


title: ovarian OV-90 Mock/AZA Day3

description: ovarian OV-90 d3 Mock/OV-90 d3 AZA

source_name: Control ovarian OV-90 Day3

source_name: AZA-treated ovarian OV-90 Day3


title: colon SNU-C1 Mock/AZA Day7

description: colon SNU-C1_Mock_D7/SNU-C1_Aza_D7

source_name: Control colon SNU-C1 Day7

value: Day 7

source_name: AZA-treated colon SNU-C1 Day7


title: ovarian OV-167 Mock/AZA Day10

description: ovarian OV167 d10 Mock/OV167 d10 AZA

source_name: Control ovarian OV-167 Day10

source_name: AZA-treated ovarian OV-167 Day10


title: ovarian DOV-13 Mock/AZA Day3

description: ovarian DOV-13 d3 Mock/DOV-13 d3 AZA

source_name: Control ovarian DOV-13 Day3

source_name: AZA-treated ovarian DOV-13 Day3


title: ovarian OAW-42 Mock/AZA Day3

description: ovarian OAW-42 d3 Mock/OAW-42 d3 AZA

source_name: Control ovarian OAW-42 Day3

source_name: AZA-treated ovarian OAW-42 Day3


title: ovarian A2780 Mock/AZA Day10

description: ovarian A2780 d10 Mock/A2780 d10 AZA 500nM

source_name: Control ovarian A2780 Day10

source_name: AZA-treated ovarian A2780 Day10


title: ovarian OV-167 Mock/AZA Day3

description: ovarian OV167 d3 Mock/OV167 d3 AZA

source_name: Control ovarian OV-167 Day3

source_name: AZA-treated ovarian OV-167 Day3


title: colon COLO320 Mock/AZA Day21

description: colon COLO320_Mock_D21/COLO320_Aza_D21

source_name: Control colon COLO320 Day21

value: Day 21

source_name: AZA-treated colon COLO320 Day21


title: colon SNU-C1 Mock/AZA Day3

description: colon SNU-C1_Mock_D3/SNU-C1_Aza_D3

source_name: Control colon SNU-C1 Day3

source_name: AZA-treated colon SNU-C1 Day3


title: colon COLO320 Mock/AZA Day28

description: colon COLO320_Mock_D28/COLO320_Aza_D28

source_name: Control colon COLO320 Day28

source_name: AZA-treated colon COLO320 Day28


title: colon SNU-C1 Mock/AZA Day21

description: colon SNU-C1_Mock_D21/SNU-C1_Aza_D21

source_name: Control colon SNU-C1 Day21

source_name: AZA-treated colon SNU-C1 Day21


title: colon SNU-C1 Mock/AZA Day10

description: colon SNU-C1_Mock_D10/SNU-C1_Aza_D10

source_name: Control colon SNU-C1 Day10

source_name: AZA-treated colon SNU-C1 Day10


title: genomic dna from breast_EFM192A_AZA_Day3


title: genomic dna from breast_EFM192A_Mock_Day3


title: colon COLO320 Mock/AZA Day7

description: colon COLO320_Mock_D7/COLO320_Aza_D7

source_name: Control colon COLO320 Day7

source_name: AZA-treated colon COLO320 Day7


title: genomic dna from breast_EFM192A_AZA_Day1


title: genomic dna from breast_EFM192A_Mock_Day1


title: colon COLO320 Mock/AZA Day10

description: colon COLO320_Mock_D10/COLO320_Aza_D10

source_name: Control colon COLO320 Day10

source_name: AZA-treated colon COLO320 Day10


title: genomic dna from breast_MDA436_Mock_Day10


title: colon COLO320 Mock/AZA Day14

description: colon COLO320_Mock_D14/COLO320_Aza_D14

source_name: Control colon COLO320 Day14

source_name: AZA-treated colon COLO320 Day14


title: genomic dna from breast_EFM192A_Mock_Day7


title: colon COLO320 Mock/AZA Day3

description: colon COLO320_Mock_D3/COLO320_Aza_D3

source_name: Control colon COLO320 Day3

source_name: AZA-treated colon COLO320 Day3


title: genomic dna from breast_MDA436_Mock_Day7


title: genomic dna from breast_MDA436_Mock_Day3


title: genomic dna from breast_MDA436_AZA_Day7


title: genomic dna from breast_MDA436_AZA_Day3


title: genomic dna from breast_MDA436_AZA_Day10


title: genomic dna from breast_MDA436_Mock_Day1


title: genomic dna from breast_MDA175_Mock_Day10


title: genomic dna from breast_MDA175_AZA_Day10


title: genomic dna from breast_MDA415_Mock_Day10


title: colon COLO201 Mock/AZA Day14

description: colon COLO201_Mock_D14/COLO201_Aza_D14

source_name: Control colon COLO201 Day14

source_name: AZA-treated colon COLO201 Day14


title: colon COLO201 Mock/AZA Day10

description: colon COLO201_Mock_D10/COLO201_Aza_D10

source_name: Control colon COLO201 Day10

source_name: AZA-treated colon COLO201 Day10


title: colon SW48 Mock/AZA Day7

description: colon SW48_Mock_D7/SW48_Aza_D7

source_name: Control colon SW48 Day7

source_name: AZA-treated colon SW48 Day7


title: colon COLO201 Mock/AZA Day28

description: colon COLO201_Mock_D28/COLO201_Aza_D28

source_name: Control colon COLO201 Day28

source_name: AZA-treated colon COLO201 Day28


title: colon SW48 Mock/AZA Day10

description: colon SW48_Mock_D10/SW48_Aza_D10

source_name: Control colon SW48 Day10

source_name: AZA-treated colon SW48 Day10


title: genomic dna from breast_MDA415_AZA_Day7


title: colon SW48 Mock/AZA Day28

description: colon SW48_Mock_D28/SW48_Aza_D28

source_name: Control colon SW48 Day28

source_name: AZA-treated colon SW48 Day28


title: colon SW48 Mock/AZA Day3

description: colon SW48_Mock_D3/SW48_Aza_D3

source_name: Control colon SW48 Day3

source_name: AZA-treated colon SW48 Day3


title: colon SW48 Mock/AZA Day21

description: colon SW48_Mock_D21/SW48_Aza_D21

source_name: Control colon SW48 Day21

source_name: AZA-treated colon SW48 Day21


title: colon COLO201 Mock/AZA Day7

description: colon COLO201_Mock_D7/COLO201_Aza_D7

source_name: Control colon COLO201 Day7

source_name: AZA-treated colon COLO201 Day7


title: genomic dna from breast_MDA436_AZA_Day1


title: colon RKO Mock/AZA Day28

description: colon RKO_Mock_D28/RKO_Aza_D28

source_name: Control colon RKO Day28

value: RKO

source_name: AZA-treated colon RKO Day28


title: colon SW48 Mock/AZA Day14

description: colon SW48_Mock_D14/SW48_Aza_D14

source_name: Control colon SW48 Day14

source_name: AZA-treated colon SW48 Day14


title: genomic dna from breast_MDA415_Mock_Day3


title: genomic dna from breast_MDA415_Mock_Day7


title: colon COLO201 Mock/AZA Day3

description: colon COLO201_Mock_D3/COLO201_Aza_D3

source_name: Control colon COLO201 Day3

source_name: AZA-treated colon COLO201 Day3


title: genomic dna from breast_MDA415_AZA_Day1


title: genomic dna from breast_MDA415_AZA_Day10


title: colon RKO Mock/AZA Day14

description: colon RKO_Mock_D14/RKO_Aza_D14

source_name: Control colon RKO Day14

source_name: AZA-treated colon RKO Day14


title: genomic dna from breast_MDA415_Mock_Day1


title: genomic dna from breast_MDA415_AZA_Day3


title: colon RKO Mock/AZA Day21

description: colon RKO_Mock_D21/RKO_Aza_D21

source_name: Control colon RKO Day21

source_name: AZA-treated colon RKO Day21


title: genomic dna from breast_HCC1500_AZA_Day10


title: genomic dna from breast_HCC1500_Mock_Day10


title: genomic dna from breast_HCC1500_Mock_Day7


title: genomic dna from breast_HCC1500_AZA_Day7


title: colon HCT116 Mock/AZA Day21

description: colon HCT116_Mock_D21/HCT116_Aza_D21

source_name: Control colon HCT116 Day21

source_name: AZA-treated colon HCT116 Day21


title: colon COLO201 Mock/AZA Day21

description: colon COLO201_Mock_D21/COLO201_Aza_D21

source_name: Control colon COLO201 Day21

source_name: AZA-treated colon COLO201 Day21


title: colon RKO Mock/AZA Day7

description: colon RKO_Mock_D7/RKO_Aza_D7

source_name: Control colon RKO Day7

source_name: AZA-treated colon RKO Day7


title: genomic dna from breast_HCC1500_AZA_Day3


title: genomic dna from breast_HCC1500_Mock_Day3


title: genomic dna from breast_HCC1500_AZA_Day1


title: genomic dna from breast_HCC1500_Mock_Day1


title: colon HCT116 Mock/AZA Day14

description: colon HCT116_Mock_D14/HCT116_Aza_D14

source_name: Control colon HCT116 Day14

source_name: AZA-treated colon HCT116 Day14


title: colon RKO Mock/AZA Day3

description: colon RKO_Mock_D3/RKO_Aza_D3

source_name: Control colon RKO Day3

source_name: AZA-treated colon RKO Day3


title: colon RKO Mock/AZA Day10

description: colon RKO_Mock_D10/RKO_Aza_D10

source_name: Control colon RKO Day10

source_name: AZA-treated colon RKO Day10


title: colon HCT116 Mock/AZA Day10

description: colon HCT116_Mock_D10/HCT116_Aza_D10

source_name: Control colon HCT116 Day10

source_name: AZA-treated colon HCT116 Day10


title: colon HCT116 Mock/AZA Day3

description: colon HCT116_Mock_D3/HCT116_Aza_D3

source_name: Control colon HCT116 Day3

source_name: AZA-treated colon HCT116 Day3


title: colon HCT116 Mock/AZA Day7

description: colon HCT116_Mock_D7/HCT116_Aza_D7

source_name: Control colon HCT116 Day7

source_name: AZA-treated colon HCT116 Day7


title: colon HCT116 Mock/AZA Day28

description: colon HCT116_Mock_D28/HCT116_Aza_D28

source_name: Control colon HCT116 Day28

source_name: AZA-treated colon HCT116 Day28


title: colon DLD1 Mock/AZA Day28

description: colon DLD1_Mock_Day 28/DLD1_AZA_Day 28

source_name: Control colon DLD1 Day28

source_name: AZA-treated colon DLD1 Day28


title: colon Lovo Mock/AZA Day3

description: colon Lovo_Mock_Day 3/Lovo_AZA_Day 3

source_name: Control colon Lovo Day3

value: Lovo

source_name: AZA-treated colon Lovo Day3


title: colon Lovo Mock/AZA Day7

description: colon Lovo_Mock_Day 7/Lovo_AZA_Day 7

source_name: Control colon Lovo Day7

source_name: AZA-treated colon Lovo Day7


title: colon Lovo Mock/AZA Day14

description: colon Lovo_Mock_Day 14/Lovo_AZA_Day 14

source_name: Control colon Lovo Day14

source_name: AZA-treated colon Lovo Day14


title: colon Lovo Mock/AZA Day10

description: colon Lovo_Mock_Day 10/Lovo_AZA_Day 10

source_name: Control colon Lovo Day10

value: Day 10

source_name: AZA-treated colon Lovo Day10


title: genomic dna from breast_ZR7530_Mock_Day7


title: colon Lovo Mock/AZA Day28

description: colon Lovo_Mock_Day 28/Lovo_AZA_Day 28

source_name: Control colon Lovo Day28

source_name: AZA-treated colon Lovo Day28


title: genomic dna from breast_ZR7530_AZA_Day3


title: genomic dna from breast_ZR7530_Mock_Day3


title: colon Lovo Mock/AZA Day21

description: colon Lovo_Mock_Day 21/Lovo_AZA_Day 21

source_name: Control colon Lovo Day21

source_name: AZA-treated colon Lovo Day21


title: genomic dna from breast_ZR7530_AZA_Day10


title: genomic dna from breast_ZR7530_Mock_Day10


title: genomic dna from breast_ZR7530_AZA_Day7


title: colon DLD1 Mock/AZA Day21

description: colon DLD1_Mock_Day 21/DLD1_AZA_Day 21

source_name: Control colon DLD1 Day21

source_name: AZA-treated colon DLD1 Day21


title: colon SW480 Mock/AZA Day7

description: colon SW480 mock D7/SW480 AZA D7

source_name: Control colon SW480 Day7

source_name: AZA-treated colon SW480 Day7


title: colon SW480 Mock/AZA Day28

description: colon SW480 mock D28/SW480 AZA D28

source_name: Control colon SW480 Day28

source_name: AZA-treated colon SW480 Day28


title: genomic dna from breast_ZR7530_Mock_Day1


title: colon DLD1 Mock/AZA Day7

description: colon DLD1_Mock_Day 7/DLD1_AZA_Day 7

source_name: Control colon DLD1 Day7

source_name: AZA-treated colon DLD1 Day7


title: colon SW480 Mock/AZA Day10

description: colon SW480 mock D10/SW480 AZA D10

source_name: Control colon SW480 Day10

source_name: AZA-treated colon SW480 Day10


title: colon SW480 Mock/AZA Day14

description: colon SW480 mock D14/SW480 AZA D14

source_name: Control colon SW480 Day14

source_name: AZA-treated colon SW480 Day14


title: colon DLD1 Mock/AZA Day14

description: colon DLD1_Mock_Day 14/DLD1_AZA_Day 14

source_name: Control colon DLD1 Day14

source_name: AZA-treated colon DLD1 Day14


title: colon SW480 Mock/AZA Day21

description: colon SW480 mock D21/SW480 AZA D21

source_name: Control colon SW480 Day21

source_name: AZA-treated colon SW480 Day21


title: colon DLD1 Mock/AZA Day10

description: colon DLD1_Mock_Day 10/DLD1_AZA_Day 10

source_name: Control colon DLD1 Day10

source_name: AZA-treated colon DLD1 Day10


title: genomic dna from breast_SUM159_AZA_Day10


title: genomic dna from breast_SUM159_Mock_Day10


title: genomic dna from breast_SUM159_AZA_Day7


title: genomic dna from breast_SUM159_Mock_Day7


title: colon DLD1 Mock/AZA Day3

description: colon DLD1_Mock_Day 3/DLD1_AZA_Day 3

source_name: Control colon DLD1 Day3

source_name: AZA-treated colon DLD1 Day3


title: genomic dna from breast_SUM159_AZA_Day3


title: colon HT29 Mock/AZA Day21

description: colon HT29 mock D21/HT29 AZA D21

source_name: Control colon HT29 Day21

source_name: AZA-treated colon HT29 Day21


title: colon HT29 Mock/AZA Day10

description: colon HT29 mock D10/HT29 AZA D10

source_name: Control colon HT29 Day10

source_name: AZA-treated colon HT29 Day10


title: colon COLO205 Mock/AZA Day10

description: colon COLO205_Mock_D10/COLO205_Aza_D10

source_name: Control colon COLO205 Day10

source_name: AZA-treated colon COLO205 Day10


title: colon HT29 Mock/AZA Day28

description: colon HT29 mock D28/HT29 AZA D28

source_name: Control colon HT29 Day28

source_name: AZA-treated colon HT29 Day28


title: genomic dna from breast_SUM159_Mock_Day1


title: genomic dna from breast_SUM159_Mock_Day3


title: genomic dna from breast_SUM159_AZA_Day1


title: colon COLO205 Mock/AZA Day21

description: colon COLO205_Mock_D21/COLO205_Aza_D21

source_name: Control colon COLO205 Day21

source_name: AZA-treated colon COLO205 Day21


title: genomic dna from breast_SUM149_AZA_Day10


title: colon HT29 Mock/AZA Day3

description: colon HT29 mock D3/HT29 AZA D3

source_name: Control colon HT29 Day3

source_name: AZA-treated colon HT29 Day3


title: colon SK-CO-1 Mock/AZA Day21

description: colon SK-CO-1_Mock_D21/SK-CO-1_Aza_D21

source_name: Control colon SK-CO-1 Day21

source_name: AZA-treated colon SK-CO-1 Day21


title: colon SK-CO-1 Mock/AZA Day7

description: colon SK-CO-1_Mock_D7/SK-CO-1_Aza_D7

source_name: Control colon SK-CO-1 Day7

source_name: AZA-treated colon SK-CO-1 Day7


title: colon SW620 Mock/AZA Day14

description: colon SW620_Mock_D14/SW620_Aza_D14

source_name: Control colon SW620 Day14

source_name: AZA-treated colon SW620 Day14


title: colon COLO205 Mock/AZA Day28

description: colon COLO205_Mock_D28/COLO205_Aza_D28

source_name: Control colon COLO205 Day28

source_name: AZA-treated colon COLO205 Day28


title: colon SW480 Mock/AZA Day3

description: colon SW480 mock D3/SW480 AZA D3

source_name: Control colon SW480 Day3

source_name: AZA-treated colon SW480 Day3


title: colon SK-CO-1 Mock/AZA Day28

description: colon SK-CO-1_Mock_D28/SK-CO-1_Aza_D28

source_name: Control colon SK-CO-1 Day28

source_name: AZA-treated colon SK-CO-1 Day28


title: colon SK-CO-1 Mock/AZA Day14

description: colon SK-CO-1_Mock_D14/SK-CO-1_Aza_D14

source_name: Control colon SK-CO-1 Day14

source_name: AZA-treated colon SK-CO-1 Day14


title: colon SK-CO-1 Mock/AZA Day3

description: colon SK-CO-1_Mock_D3/SK-CO-1_Aza_D3

source_name: Control colon SK-CO-1 Day3

source_name: AZA-treated colon SK-CO-1 Day3


title: colon COLO205 Mock/AZA Day3

description: colon COLO205_Mock_D3/COLO205_Aza_D3

source_name: Control colon COLO205 Day3

source_name: AZA-treated colon COLO205 Day3


title: colon COLO205 Mock/AZA Day14

description: colon COLO205_Mock_D14/COLO205_Aza_D14

source_name: Control colon COLO205 Day14

source_name: AZA-treated colon COLO205 Day14


title: colon COLO205 Mock/AZA Day7

description: colon COLO205_Mock_D7/COLO205_Aza_D7

source_name: Control colon COLO205 Day7

source_name: AZA-treated colon COLO205 Day7


title: colon SK-CO-1 Mock/AZA Day10

description: colon SK-CO-1_Mock_D10/SK-CO-1_Aza_D10

source_name: Control colon SK-CO-1 Day10

source_name: AZA-treated colon SK-CO-1 Day10


title: genomic dna from breast_SUM149_AZA_Day7


title: colon HT29 Mock/AZA Day14

description: colon HT29 mock D14/HT29 AZA D14

source_name: Control colon HT29 Day14

source_name: AZA-treated colon HT29 Day14


title: genomic dna from breast_SUM149_Mock_Day7


title: genomic dna from breast_SUM149_AZA_Day3


title: colon SW620 Mock/AZA Day21

description: colon SW620_Mock_D21/SW620_Aza_D21

source_name: Control colon SW620 Day21

source_name: AZA-treated colon SW620 Day21


title: genomic dna from breast_SUM149_Mock_Day10


title: genomic dna from breast_SUM149_Mock_Day3


title: genomic dna from breast_SUM149_AZA_Day1


title: colon CACO2 Mock/AZA Day28

description: colon CACO2_Mock_D28/CACO2_Aza_D28

source_name: Control colon CACO2 Day28

source_name: AZA-treated colon CACO2 Day28


title: colon CACO2 Mock/AZA Day21

description: colon CACO2_Mock_D21/CACO2_Aza_D21

source_name: Control colon CACO2 Day21

source_name: AZA-treated colon CACO2 Day21


title: genomic dna from breast_SUM149_Mock_Day1


title: colon SW620 Mock/AZA Day10

description: colon SW620_Mock_D10/SW620_Aza_D10

source_name: Control colon SW620 Day10

source_name: AZA-treated colon SW620 Day10


title: colon CACO2 Mock/AZA Day14

description: colon CACO2_Mock_D14/CACO2_Aza_D14

source_name: Control colon CACO2 Day14

source_name: AZA-treated colon CACO2 Day14


title: colon CACO2 Mock/AZA Day10

description: colon CACO2_Mock_D10/CACO2_Aza_D10

source_name: Control colon CACO2 Day10

source_name: AZA-treated colon CACO2 Day10


title: colon SW620 Mock/AZA Day3

description: colon SW620_Mock_D3/SW620_Aza_D3

source_name: Control colon SW620 Day3

source_name: AZA-treated colon SW620 Day3


title: colon SW620 Mock/AZA Day7

description: colon SW620_Mock_D7/SW620_Aza_D7

source_name: Control colon SW620 Day7

source_name: AZA-treated colon SW620 Day7


title: colon CACO2 Mock/AZA Day7

description: colon CACO2_Mock_D7/CACO2_Aza_D7

source_name: Control colon CACO2 Day7

source_name: AZA-treated colon CACO2 Day7


title: genomic dna from breast_HCC38_AZA_Day10


title: Melanoma_Extracranial_Patient35

city: Houston

first: Guo

last: Chen

state: TX

address: 7435 Fannin Street

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: No replicates

hyb_protocol: Biotinylated cRNA was loaded onto Illumina Sentrix Beadchip Array Hum HT12_V4 arrays, hybridized at 58ºC in an Illumina Hybridization Oven (Cat# 198361, Illumina) for 17 hours, washed and incubated with straptavidin-Cy3.

scan_protocol: Arrays were dried and scanned with BeadArray Reader (Illumina, CA) under standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in R and converted to linear scale

label_protocol: Biotinylated cRNA was generated using Illumina® TotalPrep™ RNA Amplification Kit (AMIL1791, Life technologies) following manufactuer's instructions.

extract_protocol: Total RNA was extracted using mirVanaTM RNA extracrion kit (AM1560, Life technologies) following manufactuer's instructions.

tag: site

value: Lung

value: Melanoma metastases Extracranial

tag: individual


title: breast MDA175 Mock/AZA Day10

description: breast MDA175 Mock Day10/MDA175  AZA Day10

source_name: Control breast MDA175 Day10

source_name: AZA-treated breast MDA175 Day10


title: Melanoma_Extracranial_Patient43

description: No replicates

value: Liver


title: colon CACO2 Mock/AZA Day3

description: colon CACO2_Mock_D3/CACO2_Aza_D3

source_name: Control colon CACO2 Day3

value: Day 3

source_name: AZA-treated colon CACO2 Day3


title: Melanoma_Extracranial_Patient34

description: No replicates


title: breast MDA436 Mock/AZA Day10

description: breast MDA436 Mock Day10/MDA436  AZA Day10

source_name: Control breast MDA436 Day10

source_name: AZA-treated breast MDA436 Day10


title: breast MDA436 Mock/AZA Day7

description: breast MDA436  Mock Day7/MDA436  AZA Day7

source_name: Control breast MDA436 Day7

source_name: AZA-treated breast MDA436 Day7


title: breast MDA436 Mock/AZA Day3

description: breast MDA436  Mock Day3/MDA436  AZA Day3

source_name: Control breast MDA436 Day3

source_name: AZA-treated breast MDA436 Day3


title: breast MDA175 Mock/AZA Day3

description: breast MDA175  Mock Day3/MDA175  AZA Day3

source_name: Control breast MDA175 Day3

source_name: AZA-treated breast MDA175 Day3


title: breast MDA436 Mock/AZA Day1

description: breast MDA436 Mock Day1/MDA436  AZA Day1

source_name: Control breast MDA436 Day1

value: Day 1

source_name: AZA-treated breast MDA436 Day1


title: breast MDA175 Mock/AZA Day7

description: breast MDA175  Mock Day7/MDA175  AZA Day7

source_name: Control breast MDA175 Day7

source_name: AZA-treated breast MDA175 Day7


title: breast MDA175 Mock/AZA Day1

description: breast MDA175 Mock Day1/MDA175  AZA Day1

source_name: Control breast MDA175 Day1

source_name: AZA-treated breast MDA175 Day1


title: genomic dna from breast_HCC38_AZA_Day7


title: Melanoma_Extracranial_Patient33

description: No replicates


title: Melanoma_Extracranial_Patient32

description: No replicates

value: Lymph Node


title: Melanoma_Extracranial_Patient31

description: No replicates


title: genomic dna from breast_HCC38_Mock_Day7


title: genomic dna from breast_HCC38_AZA_Day3


title: genomic dna from breast_HCC38_Mock_Day10


title: breast SKBR3 Mock/AZA Day3

description: breast SKBR3  Mock Day3/SKBR3  AZA Day3

source_name: Control breast SKBR3 Day3

source_name: AZA-treated breast SKBR3 Day3


title: genomic dna from breast_HCC38_Mock_Day3


title: breast SKBR3 Mock/AZA Day1

description: breast SKBR3 Mock Day1/SKBR3  AZA Day1

source_name: Control breast SKBR3 Day1

source_name: AZA-treated breast SKBR3 Day1


title: breast MDA415 Mock/AZA Day7

description: breast MDA415  Mock Day7/MDA415  AZA Day7

source_name: Control breast MDA415 Day7

source_name: AZA-treated breast MDA415 Day7


title: breast SKBR3 Mock/AZA Day7

description: breast SKBR3  Mock Day7/SKBR3  AZA Day7

source_name: Control breast SKBR3 Day7

source_name: AZA-treated breast SKBR3 Day7


title: breast MDA415 Mock/AZA Day3

description: breast MDA415  Mock Day3/MDA415  AZA Day3

source_name: Control breast MDA415 Day3

source_name: AZA-treated breast MDA415 Day3


title: Melanoma_Extracranial_Patient28_Rep3

description: Replicate 3

value: Bone


title: genomic dna from breast_HCC38_AZA_Day1


title: breast MDA415 Mock/AZA Day10

description: breast MDA415 Mock Day10/MDA415  AZA Day10

source_name: Control breast MDA415 Day10

source_name: AZA-treated breast MDA415 Day10


title: genomic dna from breast_HCC38_Mock_Day1


title: breast SKBR3 Mock/AZA Day10

description: breast SKBR3  Mock Day10/SKBR3  AZA Day10

source_name: Control breast SKBR3 Day10

source_name: AZA-treated breast SKBR3 Day10


title: breast CAMA1 Mock/AZA Day10

description: breast CAMA1 Mock Day10/CAMA1  AZA Day10

source_name: Control breast CAMA1 Day10

source_name: AZA-treated breast CAMA1 Day10


title: genomic dna from breast_BT20_AZA_Day10


title: genomic dna from breast_BT20_Mock_Day10


title: breast CAMA1 Mock/AZA Day3

description: breast CAMA1  Mock Day3/CAMA1  AZA Day3

source_name: Control breast CAMA1 Day3

source_name: AZA-treated breast CAMA1 Day3


title: Melanoma_Extracranial_Patient30

description: No replicates


title: Melanoma_Extracranial_Patient28_Rep2

description: Replicate 2


title: breast HCC1419 Mock/AZA Day10

description: breast HCC1419 Mock Day10/HCC1419  AZA Day10

source_name: Control breast HCC1419 Day10

source_name: AZA-treated breast HCC1419 Day10


title: breast MDA415 Mock/AZA Day1

description: breast MDA415 Mock Day1/MDA415  AZA Day1

source_name: Control breast MDA415 Day1

source_name: AZA-treated breast MDA415 Day1


title: genomic dna from breast_BT20_AZA_Day7


title: breast CAMA1 Mock/AZA Day1

description: breast CAMA1  Mock Day1/CAMA1  AZA Day1

source_name: Control breast CAMA1 Day1

source_name: AZA-treated breast CAMA1 Day1


title: breast HCC1419 Mock/AZA Day7

description: breast HCC1419  Mock Day7/HCC1419  AZA Day7

source_name: Control breast HCC1419 Day7

source_name: AZA-treated breast HCC1419 Day7


title: breast CAMA1 Mock/AZA Day7

description: breast CAMA1  Mock Day7/CAMA1  AZA Day7

source_name: Control breast CAMA1 Day7

source_name: AZA-treated breast CAMA1 Day7


title: breast HCC1419 Mock/AZA Day3

description: breast HCC1419  Mock Day3/HCC1419  AZA Day3

source_name: Control breast HCC1419 Day3

source_name: AZA-treated breast HCC1419 Day3


title: Melanoma_Extracranial_Patient27_Rep2

description: Replicate 2

value: Soft tissue


title: breast HCC1187 Mock/AZA Day10

description: breast HCC1187  Mock Day10/HCC1187  AZA Day10

source_name: Control breast HCC1187 Day10

source_name: AZA-treated breast HCC1187 Day10


title: Melanoma_Extracranial_Patient27_Rep3

description: Replicate 3


title: Melanoma_Extracranial_Patient27_Rep1

description: Replicate 1


title: Melanoma_Extracranial_Patient27_Rep4

description: Replicate 4


title: genomic dna from breast_ZR7530_AZA_Day1


title: breast HCC1187 Mock/AZA Day3

description: breast HCC1187  Mock Day3/HCC1187  AZA Day3

source_name: Control breast HCC1187 Day3

source_name: AZA-treated breast HCC1187 Day3


title: genomic dna from breast_BT20_Mock_Day3


title: genomic dna from breast_BT20_Mock_Day7


title: breast HCC1187 Mock/AZA Day7

description: breast HCC1187  Mock Day7/HCC1187  AZA Day7

source_name: Control breast HCC1187 Day7

source_name: AZA-treated breast HCC1187 Day7


title: Melanoma_Extracranial_Patient26_Rep1

description: Replicate 1

value: Lymph node


title: breast HCC1419 Mock/AZA Day1

description: breast HCC1419  Mock Day1/HCC1419  AZA Day1

source_name: Control breast HCC1419 Day1

source_name: AZA-treated breast HCC1419 Day1


title: genomic dna from breast_BT20_AZA_Day1


title: genomic dna from breast_BT20_Mock_Day1


title: breast EFM192A Mock/AZA Day10

description: breast EFM192A Mock Day10/EFM192A  AZA Day10

source_name: Control breast EFM192A Day10

source_name: AZA-treated breast EFM192A Day10


title: Melanoma_Extracranial_Patient26_Rep2

description: Replicate 2


title: breast EFM192A Mock/AZA Day7

description: breast EFM192A  Mock Day7/EFM192A  AZA Day7

source_name: Control breast EFM192A Day7

source_name: AZA-treated breast EFM192A Day7


title: breast EFM192A Mock/AZA Day3

description: breast EFM192A  Mock Day3/EFM192A  AZA Day3

source_name: Control breast EFM192A Day3

source_name: AZA-treated breast EFM192A Day3


title: genomic dna from breast_BT20_AZA_Day3


title: breast EFM192A Mock/AZA Day1

description: breast EFM192A Mock Day1/EFM192A  AZA Day1

source_name: Control breast EFM192A Day1

source_name: AZA-treated breast EFM192A Day1


title: breast BT474 Mock/AZA Day7

description: breast BT474 Mock Day7/BT474 AZA Day7

source_name: Control breast BT474 Day7

source_name: AZA-treated breast BT474 Day7


title: Melanoma_Extracranial_Patient25_Rep2

description: Replicate 2


title: Melanoma_Extracranial_Patient25_Rep1

description: Replicate 1


title: colon HT29 Mock/AZA Day7

description: colon HT29 mock D7/HT29 AZA D7

source_name: Control colon HT29 Day7

value: colon cancer cell line

source_name: AZA-treated colon HT29 Day7


title: genomic dna from breast_MCF7_AZA_Day21


title: Melanoma_Extracranial_Patient24_Rep1

description: Replicate 1

value: Spleen


title: breast BT474 Mock/AZA Day1

description: breast BT474 Mock Day1/BT474 AZA Day1

source_name: Control breast BT474 Day1

value: breast cancer cell line

source_name: AZA-treated breast BT474 Day1


title: breast BT474 Mock/AZA Day10

description: breast BT474 Mock Day10/BT474 AZA Day10

source_name: Control breast BT474 Day10

source_name: AZA-treated breast BT474 Day10


title: breast HCC1954 Mock/AZA Day3

description: breast HCC1954 Mock Day3/HCC1954 AZA Day3

source_name: Control breast HCC1954 Day3

source_name: AZA-treated breast HCC1954 Day3


title: breast HCC1954 Mock/AZA Day7

description: breast HCC1954 Mock Day7/HCC1954 AZA Day7

source_name: Control breast HCC1954 Day7

value: Day 7

source_name: AZA-treated breast HCC1954 Day7


title: genomic dna from breast_MCF7_Mock_Day21


title: breast HCC1954 Mock/AZA Day10

description: breast HCC1954 Mock Day10/HCC1954 AZA Day10

source_name: Control breast HCC1954 Day10

source_name: AZA-treated breast HCC1954 Day10


title: breast BT474 Mock/AZA Day3

description: breast BT474 Mock Day3/BT474 AZA Day3

source_name: Control breast BT474 Day3

source_name: AZA-treated breast BT474 Day3


title: genomic dna from breast_MCF7_AZA_Day10


title: Melanoma_Extracranial_Patient22_Rep2

description: Replicate 2


title: Melanoma_Extracranial_Patient23

description: No replicates

value: Adrenal


title: breast HCC1954 Mock/AZA Day1

description: breast HCC1954 Mock Day1/HCC1954 AZA Day1

source_name: Control breast HCC1954 Day1

source_name: AZA-treated breast HCC1954 Day1


title: breast ZR-75-30 Mock/AZA Day10

description: breast ZR-75-30 Mock Day10/ZR-75-30 AZA Day10

source_name: Control breast ZR-75-30 Day10

source_name: AZA-treated breast ZR-75-30 Day10


title: Melanoma_Extracranial_Patient28_Rep1

description: Replicate 1


title: Melanoma_Extracranial_Patient22_Rep1

description: Replicate 1


title: genomic dna from breast_MCF7_AZA_Day7


title: breast HCC1187 Mock/AZA Day1

description: breast HCC1187 Mock Day1/HCC1187  AZA Day1

source_name: Control breast HCC1187 Day1

source_name: AZA-treated breast HCC1187 Day1


title: genomic dna from breast_MCF7_Mock_Day7


title: breast ZR-75-30 Mock/AZA Day1

description: breast ZR-75-30 Mock Day1/ZR-75-30 AZA Day1

source_name: Control breast ZR-75-30 Day1

source_name: AZA-treated breast ZR-75-30 Day1


title: breast ZR-75-30 Mock/AZA Day7

description: breast ZR-75-30 Mock Day7/ZR-75-30 AZA Day7

source_name: Control breast ZR-75-30 Day7

source_name: AZA-treated breast ZR-75-30 Day7


title: breast HCC1500 Mock/AZA Day10

description: breast HCC1500 Mock Day10/HCC1500 AZA Day10

source_name: Control breast HCC1500 Day10

source_name: AZA-treated breast HCC1500 Day10


title: colon SW620 Mock/AZA Day28

description: colon SW620_Mock_D28/SW620_Aza_D28

source_name: Control colon SW620 Day28

value: Day 28

source_name: AZA-treated colon SW620 Day28


title: breast HCC1500 Mock/AZA Day7

description: breast HCC1500 Mock Day7/HCC1500 AZA Day7

source_name: Control breast HCC1500 Day7

source_name: AZA-treated breast HCC1500 Day7


title: breast ZR-75-30 Mock/AZA Day3

description: breast ZR-75-30 Mock Day3/ZR-75-30 AZA Day3

source_name: Control breast ZR-75-30 Day3

source_name: AZA-treated breast ZR-75-30 Day3


title: breast HCC1500 Mock/AZA Day3

description: breast HCC1500 Mock Day3/HCC1500 AZA Day3

source_name: Control breast HCC1500 Day3

source_name: AZA-treated breast HCC1500 Day3


title: Melanoma_Extracranial_Patient24_Rep2

description: Replicate 2


title: Melanoma_Extracranial_Patient17_Rep2

description: Replicate 2


title: Melanoma_Extracranial_Patient18

description: No replicates

value: Bowel


title: genomic dna from breast_MCF7_AZA_Day3


title: genomic dna from breast_MCF7_Mock_Day3


title: genomic dna from breast_MCF7_AZA_Day1


title: breast HCC1500 Mock/AZA Day1

description: breast HCC1500 Mock Day1/HCC1500 AZA Day1

source_name: Control breast HCC1500 Day1

source_name: AZA-treated breast HCC1500 Day1


title: Melanoma_Extracranial_Patient21

description: No replicates


title: genomic dna from breast_MCF7_Mock_Day1


title: breast SUM159 Mock/AZA Day3

description: breast SUM159 Mock Day3/SUM159 AZA Day3

source_name: Control breast SUM159 Day3

source_name: AZA-treated breast SUM159 Day3


title: genomic dna from breast_EFM19_AZA_Day10


title: breast SUM149 Mock/AZA Day1

description: breast SUM149 Mock Day1/SUM149 AZA Day1

source_name: Control breast SUM149 Day1

source_name: AZA-treated breast SUM149 Day1


title: genomic dna from breast_EFM19_Mock_Day10


title: breast HCC38 Mock/AZA Day10

description: breast HCC38 Mock Day10/HCC38 AZA Day10

source_name: Control breast HCC38 Day10

value: Day 10

source_name: AZA-treated breast HCC38 Day10


title: Melanoma_Extracranial_Patient10_Rep3

description: Replicate 3

value: Lung


title: breast SUM149 Mock/AZA Day10

description: breast SUM149 Mock Day10/SUM149 AZA Day10

source_name: Control breast SUM149 Day10

source_name: AZA-treated breast SUM149 Day10


title: Melanoma_Extracranial_Patient15

description: No replicates

value: Melanoma metastases Extracranial


title: Melanoma_Extracranial_Patient14_Rep1

description: Replicate 1


title: breast SUM149 Mock/AZA Day3

description: breast SUM149 Mock Day3/SUM149 AZA Day3

source_name: Control breast SUM149 Day3

source_name: AZA-treated breast SUM149 Day3


title: breast SUM149 Mock/AZA Day7

description: breast SUM149 Mock Day7/SUM149 AZA Day7

source_name: Control breast SUM149 Day7

source_name: AZA-treated breast SUM149 Day7


title: breast SUM159 Mock/AZA Day7

description: breast SUM159 Mock Day7/SUM159 AZA Day7

source_name: Control breast SUM159 Day7

source_name: AZA-treated breast SUM159 Day7


title: Melanoma_Extracranial_Patient17_Rep1

description: Replicate 1


title: breast SUM159 Mock/AZA Day1

description: breast SUM159 Mock Day1/SUM159 AZA Day1

source_name: Control breast SUM159 Day1

source_name: AZA-treated breast SUM159 Day1


title: breast SUM159 Mock/AZA Day10

description: breast SUM159 Mock Day10/SUM159 AZA Day10

source_name: Control breast SUM159 Day10

source_name: AZA-treated breast SUM159 Day10


title: Melanoma_Extracranial_Patient14_Rep2

description: Replicate 2


title: breast HCC38 Mock/AZA Day3

description: breast HCC38 Mock Day3/HCC38 AZA Day3

source_name: Control breast HCC38 Day3

source_name: AZA-treated breast HCC38 Day3


title: genomic dna from breast_EFM19_AZA_Day7


title: breast HCC38 Mock/AZA Day1

description: breast HCC38 Mock Day1/HCC38 AZA Day1

source_name: Control breast HCC38 Day1

source_name: AZA-treated breast HCC38 Day1


title: Melanoma_Extracranial_Patient10_Rep1

description: Replicate 1


title: breast HCC38 Mock/AZA Day7

description: breast HCC38 Mock Day7/HCC38 AZA Day7

source_name: Control breast HCC38 Day7

source_name: AZA-treated breast HCC38 Day7


title: genomic dna from breast_EFM19_Mock_Day7


title: breast MCF7 Mock/AZA Day10

description: breast MCF7  Mock Day10/MCF7  AZA Day10

source_name: Control breast MCF7 Day10

source_name: AZA-treated breast MCF7  Day10


title: breast MCF7 Mock/AZA Day21

description: breast MCF7  Mock Day21/MCF7  AZA Day21

source_name: Control breast MCF7 Day21

value: Day 21

source_name: AZA-treated breast MCF7 Day21


title: Melanoma_Extracranial_Patient10_Rep2

description: Replicate 2


title: breast MCF7 Mock/AZA Day3

description: breast MCF7  Mock Day3/MCF7  AZA Day3

source_name: Control breast MCF7 Day3

value: Day 3

source_name: AZA-treated breast MCF7  Day3


title: Melanoma_Extracranial_Patient06_Rep2

description: Replicate 2

value: Small Intestine


title: breast MCF7 Mock/AZA Day7

description: breast MCF7  Mock Day7/MCF7  AZA Day7

source_name: Control breast MCF7 Day7

source_name: AZA-treated breast MCF7  Day7


title: genomic dna from breast_EFM19_AZA_Day3


title: genomic dna from breast_EFM19_AZA_Day1


title: Melanoma_Extracranial_Patient06_Rep1

description: Replicate 1


title: genomic dna from breast_EFM19_Mock_Day3


title: genomic dna from breast_EFM19_Mock_Day1


title: breast EFM19 Mock/AZA Day10

description: breast EFM19  Mock Day10/EFM19  AZA Day10

source_name: Control breast EFM19 Day10

source_name: AZA-treated breast EFM19 Day10


title: genomic dna from breast_T47D_AZA_Day10


title: genomic dna from breast_T47D_Mock_Day10


title: genomic dna from breast_T47D_AZA_Day7


title: genomic dna from breast_T47D_Mock_Day7


title: genomic dna from breast_T47D_AZA_Day3


title: breast MCF7 Mock/AZA Day1

description: breast MCF7 Mock Day1/MCF7  AZA Day1

source_name: Control breast MCF7 Day1

value: Day 1

source_name: AZA-treated breast MCF7  Day1


title: breast EFM19 Mock/AZA Day7

description: breast EFM19  Mock Day7/EFM19  AZA Day7

source_name: Control breast EFM19 Day7

source_name: AZA-treated breast EFM19 Day7


title: genomic dna from breast_T47D_Mock_Day3


title: Melanoma_Extracranial_Patient05

description: No replicates


title: breast HCC1569 Mock/AZA Day10

description: breast HCC1569 Mock Day10/HCC1569 AZA Day10

source_name: Control breast HCC1569 Day10

source_name: AZA-treated breast HCC1569 Day10


title: breast HCC1937 Mock/AZA Day10

description: breast HCC1937 Mock Day10/HCC1937 AZA Day10

source_name: Control breast HCC1937 Day10

source_name: AZA-treated breast HCC1937 Day10


title: genomic dna from breast_T47D_AZA_Day1


title: Melanoma_Extracranial_Patient04_Rep2

description: Replicate 2


title: Melanoma_Extracranial_Patient04_Rep1

description: Replicate 1


title: breast EFM19 Mock/AZA Day3

description: breast EFM19  Mock Day3/EFM19  AZA Day3

source_name: Control breast EFM19 Day3

source_name: AZA-treated breast EFM19 Day3


title: genomic dna from breast_MCF7_Mock_Day10


title: Melanoma_Extracranial_Patient03_Rep2

description: Replicate 2


title: breast HCC1569 Mock/AZA Day7

description: breast HCC1569 Mock Day7/HCC1569 AZA Day7

source_name: Control breast HCC1569 Day7

source_name: AZA-treated breast HCC1569 Day7


title: breast MDA468 Mock/AZA Day1

description: breast MDA468 Mock Day1/MDA468 AZA Day1

source_name: Control breast MDA468 Day1

source_name: AZA-treated breast MDA468 Day1


title: breast HCC1569 Mock/AZA Day3

description: breast HCC1569 Mock Day3/HCC1569 AZA Day3

source_name: Control breast HCC1569 Day3

source_name: AZA-treated breast HCC1569 Day3


title: breast MDA468 Mock/AZA Day10

description: breast MDA468 Mock Day10/MDA468 AZA Day10

source_name: Control breast MDA468 Day10

source_name: AZA-treated breast MDA468 Day10


title: genomic dna from breast_HCC1569_AZA_Day10


title: Melanoma_Extracranial_Patient02_Rep2

description: Replicate 2


title: breast HCC1937 Mock/AZA Day1

description: breast HCC1937 Mock Day1/HCC1937 AZA Day1

source_name: Control breast HCC1937 Day1

source_name: AZA-treated breast HCC1937 Day1


title: genomic dna from breast_T47D_Mock_Day1


title: breast HCC1569 Mock/AZA Day1

description: breast HCC1569 Mock Day1/HCC1569 AZA Day1

source_name: Control breast HCC1569 Day1

source_name: AZA-treated breast HCC1569 Day1


title: Melanoma_Extracranial_Patient03_Rep3

description: Replicate 3


title: Melanoma_Brain_Patient53

description: No replicates

value: Brain

value: Melanoma metastases Brain


title: breast MDA453 Mock/AZA Day10

description: breast MDA453 Mock Day10/MDA453 AZA Day10

source_name: Control breast MDA453 Day10

source_name: AZA-treated breast MDA453 Day10


title: breast MDA468 Mock/AZA Day3

description: breast MDA468 Mock Day3/MDA468 AZA Day3

source_name: Control breast MDA468 Day3

source_name: AZA-treated breast MDA468 Day3


title: breast HCC1937 Mock/AZA Day3

description: breast HCC1937 Mock Day3/HCC1937 AZA Day3

source_name: Control breast HCC1937 Day3

source_name: AZA-treated breast HCC1937 Day3


title: Melanoma_Brain_Patient55

description: No replicates


title: Melanoma_Extracranial_Patient03_Rep1

description: Replicate 1

value: Soft tissue


title: genomic dna from breast_HCC1569_AZA_Day7


title: breast MDA231 Mock/AZA Day7

description: breast MDA231 Mock Day7/MDA231 AZA Day7

source_name: Control breast MDA231 Day7

source_name: AZA-treated breast MDA231 Day7


title: genomic dna from breast_HCC1569_Mock_Day10


title: breast MDA453 Mock/AZA Day3

description: breast MDA453 Mock Day3/MDA453 AZA Day3

source_name: Control breast MDA453 Day3

source_name: AZA-treated breast MDA453 Day3


title: breast MDA453 Mock/AZA Day7

description: breast MDA453 Mock Day7/MDA453 AZA Day7

source_name: Control breast MDA453 Day7

source_name: AZA-treated breast MDA453 Day7


title: breast MDA453 Mock/AZA Day1

description: breast MDA453 Mock Day1/MDA453 AZA Day1

source_name: Control breast MDA453 Day1

source_name: AZA-treated breast MDA453 Day1


title: breast EFM19 Mock/AZA Day1

description: breast EFM19 Mock Day1/EFM19  AZA Day1

source_name: Control breast EFM19 Day1

source_name: AZA-treated breast EFM19 Day1


title: genomic dna from breast_HCC1569_Mock_Day7


title: Melanoma_Extracranial_Patient02_Rep1

description: Replicate 1

value: Lymph node


title: Melanoma_Brain_Patient52

description: No replicates


title: breast HCC1937 Mock/AZA Day7

description: breast HCC1937 Mock Day7/HCC1937 AZA Day7

source_name: Control breast HCC1937 Day7

source_name: AZA-treated breast HCC1937 Day7


title: breast MDA231 Mock/AZA Day1

description: breast MDA231 Mock Day1/MDA231 AZA Day1

source_name: Control breast MDA231 Day1

source_name: AZA-treated breast MDA231 Day1


title: genomic dna from breast_HCC1569_AZA_Day3


title: breast MDA468 Mock/AZA Day7

description: breast MDA468 Mock Day7/MDA468 AZA Day7

source_name: Control breast MDA468 Day7

source_name: AZA-treated breast MDA468 Day7


title: breast MDA231 Mock/AZA Day3

description: breast MDA231 Mock Day3/MDA231 AZA Day3

source_name: Control breast MDA231 Day3

source_name: AZA-treated breast MDA231 Day3


title: breast MDA231 Mock/AZA Day10

description: breast MDA231 Mock Day10/MDA231 AZA Day10

source_name: Control breast MDA231 Day10

source_name: AZA-treated breast MDA231 Day10


title: breast MDA361 Mock/AZA Day10

description: breast MDA361Mock Day10/MDA361AZA Day10

source_name: Control breast MDA361 Day10

source_name: AZA-treated breast MDA361 Day10


title: genomic dna from breast_HCC1569_Mock_Day3


title: Melanoma_Brain_Patient51

description: No replicates


title: breast MDA361 Mock/AZA Day3

description: breast MDA361Mock Day3/MDA361AZA Day3

source_name: Control breast MDA361 Day3

source_name: AZA-treated breast MDA361 Day3


title: Melanoma_Brain_Patient50

description: No replicates


title: Melanoma_Brain_Patient54

description: No replicates


title: Melanoma_Brain_Patient49

description: No replicates


title: genomic dna from breast_HCC1569_AZA_Day1


title: Melanoma_Brain_Patient48

description: No replicates


title: genomic dna from breast_HCC1569_Mock_Day1


title: genomic dna from breast_MDA453_Mock_day10


title: genomic dna from breast_MDA453_AZA_day10


title: breast ZR-75-1 Mock/AZA Day10

description: breast ZR-75-1 Mock Day10/ZR-75-1 AZA Day10

source_name: Control breast ZR-75-1 Day10

source_name: AZA-treated breast ZR-75-1 Day10


title: breast MDA361 Mock/AZA Day1

description: breast MDA361Mock Day1/MDA361AZA Day1

source_name: Control breast MDA361 Day1

source_name: AZA-treated breast MDA361 Day1


title: genomic dna from breast_MDA453_AZA_day7


title: breast MDA361 Mock/AZA Day7

description: breast MDA361Mock Day7/MDA361AZA Day7

source_name: Control breast MDA361 Day7

source_name: AZA-treated breast MDA361 Day7


title: genomic dna from breast_MDA453_Mock_day7


title: breast ZR-75-1 Mock/AZA Day3

description: breast ZR-75-1 Mock Day3/ZR-75-1 AZA Day3

source_name: Control breast ZR-75-1 Day3

source_name: AZA-treated breast ZR-75-1 Day3


title: breast T47D AZA/Mock Day14

description: breast T47D AZA Day14/T47D Mock Day14

source_name: AZA treated breast T47D Day14

value: Day 14

source_name: Control breast T47D Day14


title: breast T47D AZA/Mock Day3

description: breast T47D AZA Day3/T47D Mock Day3

source_name: AZA treated breast T47D Day3

value: breast cancer cell line

source_name: Control breast T47D Day3


title: Melanoma_Brain_Patient46

description: No replicates


title: breast T47D AZA/Mock Day7

description: breast T47D AZA Day7/T47D Mock Day7

source_name: AZA treated breast T47D Day7

value: Day 7

source_name: Control breast T47D Day7


title: breast ZR-75-1 Mock/AZA Day7

description: breast ZR-75-1 Mock Day7/ZR-75-1 AZA Day7

source_name: Control breast ZR-75-1 Day7

source_name: AZA-treated breast ZR-75-1 Day7


title: breast T47D AZA/Mock Day1

description: breast T47D AZA Day1/T47D Mock Day1

source_name: AZA treated breast T47D Day1

source_name: Control breast T47D Day1


title: Melanoma_Brain_Patient44

description: No replicates


title: genomic dna from breast_MDA453_AZA_day3


title: Melanoma_Brain_Patient39

description: No replicates


title: Melanoma_Brain_Patient40

description: No replicates


title: breast ZR-75-1 Mock/AZA Day1

description: breast ZR-75-1 Mock Day1/ZR-75-1 AZA Day1

source_name: Control breast ZR-75-1 Day1

source_name: AZA-treated breast ZR-75-1 Day1


title: Old_HSC_24h_repl2

city: Stanford

first: Jun

last: Seita

state: CA

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: Sample name: 701_2425_Old_HSC_24h

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

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036.

data_processing: Each data was normalized individually using RMA method against the common reference on Gene Expression Commons system (http://gexc.stanford.edu/)

source_name: bone marrow

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

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

value: 24 months

value: male

value: HSC

tag: time


title: Old_HSC_12h_repl2

description: Sample name: 700_2423_Old_HSC_12h


title: Melanoma_Brain_Patient47

description: No replicates


title: Melanoma_Brain_Patient41

description: No replicates


title: Melanoma_Brain_Patient42

description: No replicates


title: Old_HSC_24h_repl1

description: Sample name: 701_2424_Old_HSC_24h


title: Melanoma_Brain_Patient38

description: No replicates


title: genomic dna from breast_MDA453_AZA_day1


title: Melanoma_Brain_Patient45

description: No replicates


title: Old_HSC_6h_repl1

description: Sample name: 699_2420_Old_HSC_6h


title: genomic dna from breast_MDA453_Mock_day1


title: genomic dna from breast_MDA453_Mock_day3


title: genomic dna from breast_MDA468_AZA_day10


title: Old_HSC_12h_repl1

description: Sample name: 700_2422_Old_HSC_12h


title: Old_HSC_3h_repl1

description: Sample name: 698_2418_Old_HSC_3h


title: Old_HSC_6h_repl2

description: Sample name: 699_2421_Old_HSC_6h


title: HSC_24h_repl2

description: Sample name: 697_2417_HSC_24h

value: 3 months


title: HSC_12h_repl2

description: Sample name: 696_2415_HSC_12h


title: Old_HSC_3h_repl2

description: Sample name: 698_2419_Old_HSC_3h


title: genomic dna from breast_MDA468_AZA_day7


title: HSC_24h_repl1

description: Sample name: 697_2416_HSC_24h


title: HSC_6h_repl1

description: Sample name: 695_2412_HSC_6h


title: genomic dna from breast_MDA468_Mock_day10


title: Melanoma_Brain_Patient27_Rep1

description: Replicate 1


title: genomic dna from breast_MDA468_Mock_day7


title: HSC_6h_repl2

description: Sample name: 695_2413_HSC_6h


title: genomic dna from breast_MDA468_AZA_day3


title: HSC_3h_repl2

description: Sample name: 694_2411_HSC_3h


title: HSC_12h_repl1

description: Sample name: 696_2414_HSC_12h


title: Old_preplroB_repl2

description: Sample name: 893_3201_Old_preproB

value: preproB


title: Melanoma_Brain_Patient27_Rep2

description: Replicate 2


title: Melanoma_Brain_Patient36

description: No replicates


title: HSC_3h_repl1

description: Sample name: 694_2410_HSC_3h


title: Old_preplroB_repl1

description: Sample name: 893_3200_Old_preproB


title: Old_preplroB_repl3

description: Sample name: 893_3202_Old_preproB


title: genomic dna from breast_MDA468_AZA_day1


title: Old_BLP_repl2

description: Sample name: 892_3198_Old_BLP

value: BLP


title: Melanoma_Brain_Patient20

description: No replicates


title: Melanoma_Brain_Patient14_Rep2

description: Replicate 2


title: Old_BLP_repl3

description: Sample name: 892_3199_Old_BLP


title: genomic dna from breast_MDA468_Mock_day1


title: genomic dna from breast_MDA468_Mock_day3


title: genomic dna from breast_MDA231_Mock_day10


title: Melanoma_Brain_Patient13

description: No replicates


title: Old_CLP_repl1

description: Sample name: 891_3194_Old_CLP

value: CLP


title: genomic dna from breast_MDA231_AZA_day10


title: Melanoma_Brain_Patient15

description: No replicates


title: Melanoma_Brain_Patient03

description: No replicates


title: Old_CLP_repl2

description: Sample name: 891_3195_Old_CLP


title: Melanoma_Brain_Patient14_Rep1

description: Replicate 1


title: genomic dna from breast_MDA231_AZA_day7


title: Old_BLP_repl1

description: Sample name: 892_3197_Old_BLP


title: Old_MEP_repl3

description: Sample name: 847_3041_Old_MEP

value: MEP


title: Old_GMP_repl3

description: Sample name: 848_3044_Old_GMP

value: GMP


title: Old_GMP_repl1

description: Sample name: 848_3042_Old_GMP


title: genomic dna from breast_MDA231_Mock_day7


title: Old_CMP_repl3

description: Sample name: 846_3038_Old_CMP

value: CMP


title: Old_CMP_repl2

description: Sample name: 846_3037_Old_CMP


title: Old_CMP_repl1

description: Sample name: 846_3036_Old_CMP


title: Old_CLP_repl3

description: Sample name: 891_3196_Old_CLP


title: 10T1/2; M-fraction

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

description: C3H10T1/2 cells co-infected with Myc-MyoD and HA-PPARg and then fractionated according to size (myotube-enriched fraction)

hyb_protocol: Following fragmentation, hybridization to the Mouse Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with RMA (robust multi-array analysis) algorithm.

source_name: C3H10T1/2 cells; M-fraction

label_protocol: cDNA was synthesized using Ambion WT expression kit according to the manufacture's instruction. Labeling was performed with GeneChip WT Terminal Labeling kit according to Affymetrix protocols.

growth_protocol: C3H10T1/2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (10% FBS).

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: Lentiviral infection was performed when cells were 40-60% confluent. Cells were harvested 4 days after infection for microarray assay

value: C3H10T1/2 cells

tag: treatment

value: Myc-MyoD and HA-PPARg

tag: fraction

value: myotube-enriched fraction


title: Old_MEP_repl2

description: Sample name: 847_3040_Old_MEP

tag: age


title: genomic dna from breast_MDA231_AZA_day3


title: Melanoma_Brain_Patient05

description: No replicates

value: Brain

value: Melanoma metastases Brain


title: genomic dna from breast_MDA231_Mock_day3

value: breast cancer cell line


title: Old_MPP_Flk2+_repl2

description: Sample name: 845_3034_Old_MPP_Flk2+


title: 10T1/2; A-fraction

description: C3H10T1/2 cells co-infected with Myc-MyoD and HA-PPARg and then fractionated according to size (adipocyte-enriched fraction)

source_name: C3H10T1/2 cells; A-fraction

value: adipocyte-enriched fraction


title: Old_GMP_repl2

description: Sample name: 848_3043_Old_GMP

value: 24 months


title: genomic dna from breast_MDA231_Mock_day1


title: Old_MPP_Flk2+_repl1

description: Sample name: 845_3033_Old_MPP_Flk2+

value: male


title: Old_MEP_repl1

description: Sample name: 847_3039_Old_MEP


title: Old_MPP_Flk2-_repl1

description: Sample name: 1388_5271_Old_MPP_Flk2-


title: Old_MPP_Flk2+_repl3

description: Sample name: 845_3035_Old_MPP_Flk2+


title: Melanoma_Brain_Patient02

description: No replicates


title: 10T1/2; non-infected

description: C3H10T1/2 cells grown in 10% FBS

source_name: C3H10T1/2 cells; non-infected


title: Old_MPP_Flk2-_repl2

description: Sample name: 1388_5272_Old_MPP_Flk2-


title: WTp53, exp f [control]

city: Boulder

first: Shih-chieh

last: Lin

address: 215 UCB

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

description:
control: WTp53, exp f
Gene expression data from transfected cell, 40hours after transfection

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

scan_protocol: examination with an Affymetrix GeneChip Scanner 3000

data_processing: Normalized RMA sketch were calculated by Expression Console

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

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

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

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

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

tag: transfection

value: WTp53 in GFP vectors (pIRES-2EGFP)


title: Old_MPP_Flk2-_repl3

description: Sample name: 1388_5273_Old_MPP_Flk2-


title: CMP_repl1

description: Sample name: 754_2616_CMP

value: 3 months


title: genomic dna from breast_MDA231_AZA_day1


title: 10T1/2; HA-PPARg-infected

description: C3H10T1/2 cells were infected with lentivirus containing HA-PPARg

source_name: C3H10T1/2 cells; HA-PPARg-infected

value: lentivirus containing HA-PPARg


title: CMP_repl2

description: Sample name: 754_2617_CMP


title: MPP_Flk2+_repl3

description: Sample name: 752_2612_MPP_Flk2+


title: 10T1/2; control lentivirus-infected

description: C3H10T1/2 cells were infected with lentivirus containing empty vector

source_name: C3H10T1/2 cells; control lentivirus-infected

value: lentivirus containing empty vector


title: WTp53, exp d [control]

description:
control: WTp53, exp d
Gene expression data from transfected cell, 40hours after transfection


title: MPP_Flk2-_repl5

description: Sample name: 751_2609_MPP_Flk2-


title: Melanoma_Brain_Patient37

description: No replicates


title: MPP_Flk2+_repl1

description: Sample name: 752_2610_MPP_Flk2+


title: MPP_Flk2-_repl2

description: Sample name: 751_2606_MPP_Flk2-


title: Control 1B

type: other

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

description: Goat anti-mouse IgG biotinylated secondary antibody was added followed by streptavidin conjugated with AlexaFluor 647.

hyb_protocol: Each slide was blocked with buffer containing mercaptohexanol for one hour followed by a one hour incubation with each monoclonal antibody.  The slides were washed with TBST and then incubated with 6.67μM of goat anti-mouse IgG biotinylated secondary antibody at 37oC for one hour.  5nM of streptavidin conjugated with AlexaFluor 647 was added to the slides, the slides were washed and then spun dry before scanning.

scan_protocol: A Perkin Elmer Scan Array laser Scanner was used to scanned the slides (543nm emission, 565 nm absorption, 75% PMT, 100% laser power).

data_processing: GenePix Pro 6.0 was used to produce a gpr file that was analyzed in GeneSpring 7.3.1.

label: Alexafluor 647

molecule: other

source_name: BRAA from B-Cells isolated from Mouse Spleen Cells

label_protocol: Brain-reactive autoantibodies bound to the arrays were detected using goat anti-mouse IgG biotinylated secondary antibody followed by streptavidin conjugated with AlexaFluor 647.

growth_protocol: Brain-reactive autoantibodies were created using hybridoma technology.  The B-cells from an autoimmune mouse and myeloma cells were fused and cultured.

extract_protocol: The antibodies produced in the supernant from these hybridomas were tested for reactivity to brain antigen using ELISA and those antibodies that displayed reactivity above 0.1 OD were retained for testing on microarray.

treatment_protocol: Not applicable

value: MRL/lpr

value: B cell

tag: antigenic target

value: Autoreactive to brain antigen


title: Empty vector, exp d [control]

description:
control: Empty vector, exp d
Gene expression data from transfected cell, 40hours after transfection

value: GFP vector (pIRES-2EGFP)


title: MPP_Flk2-_repl4

description: Sample name: 751_2608_MPP_Flk2-

tag: strain


title: WTp53, exp e [control]

description:
control: WTp53, exp e
Gene expression data from transfected cell, 40hours after transfection


title: Empty vector, exp e [control]

description:
control: Empty vector, exp e
Gene expression data from transfected cell, 40hours after transfection


title: tethered WTp53, exp f [control]

description:
control: tethered p53, exp f
Gene expression data from transfected cell, 40hours after transfection

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


title: Control


title: Empty vector, exp f [control]

description:
control: Empty vector, exp f
Gene expression data from transfected cell, 40hours after transfection


title: CMP_repl3

description: Sample name: 754_2618_CMP

value: CMP


title: BRAA D9B


title: MPP_Flk2-_repl3

description: Sample name: 751_2607_MPP_Flk2-


title: MPP_Flk2+_repl2

description: Sample name: 752_2611_MPP_Flk2+


title: Middle aged 4

city: Boston

first: Amy

middle: J

last: Wagers

state: MA

address: One Joslin place

department: Stem Cell and Regenerative Biology

institute: Joslin diabetes center and Harvard University

description: Gene expression data from middle aged mouse skeletal muscle precursor cells

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

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

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

source_name: Skeletal muscle

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

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

value: skeletal muscle precursor cells

tag: cell surface markers

tag: developmental stage

value: Middle aged (12 months)

tag: genetic background


title: MPP_Flk2-_repl1

description: Sample name: 751_2605_MPP_Flk2-

tag: cell type


title: tethered WTp53, exp d [control]

description:
control: tethered p53, exp d
Gene expression data from transfected cell, 40hours after transfection

tag: cell line


title: Aged 1

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

value: Aged (24 months)


title: Aged 5


title: BRAA D1B


title: BRAA D1


title: Aged 4


title: WTp53, exp 4

description:
Taatjes_WTG_4th
Gene expression data from transfected cell, 40hours after transfection

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

tag: transfected with


title: Middle aged 2


title: BRAA D9


title: BRAA G4B


title: Young 5

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

value: young (2 months)


title: Empty vector, exp 5

description:
Taatjes_VG_5th_2
Gene expression data from transfected cell, 40hours after transfection

source_name: H1299_Empty vector


title: tethered WTp53, exp e [control]

description:
control: tethered p53, exp e
Gene expression data from transfected cell, 40hours after transfection


title: Middle aged 3


title: Aged 2


title: WTp53, exp 5

description:
Taatjes_WTG_5th
Gene expression data from transfected cell, 40hours after transfection


title: WTp53, exp 0

description:
Taatjes_WTG_0th
Gene expression data from transfected cell, 40hours after transfection


title: Middle aged 1


title: BRAA G4


title: ΔNp53:WTp53, exp 5

description:
Taatjes_23AG_5th
Gene expression data from transfected cell, 40hours after transfection


title: Empty vector, exp 4

description:
Taatjes_VG_4th
Gene expression data from transfected cell, 40hours after transfection


title: Aged 3


title: Young 4


title: BRAA G10B

description: Goat anti-mouse IgG biotinylated secondary antibody was added followed by streptavidin conjugated with AlexaFluor 647.


title: ΔNp53:WTp53, exp 4

description:
Taatjes_23AG_4th
Gene expression data from transfected cell, 40hours after transfection


title: Empty vector, exp 0

description:
Taatjes_VG_0th
Gene expression data from transfected cell, 40hours after transfection


title: Young 3


title: BRAA G10


title: BRAA F9B


title: BRAA F9


title: Young 2