title: 2S121_M_CAU_Y_3_140_genotype

value: mononuclear


title: 2S118_M_CAU_N_1_119_genotype

status: Public on Nov 01 2017

type: genomic

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

country: USA

institute: The University of North Carolina at Chapel Hill

hyb_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).

data_processing:
CHP files were created from CEL file intensities using the Affymetrix Genotyping Console using the BIRDSEED V2 algorithm with default settings.
CHP files were imported into Partek Genomics Suite v6.6. Genotype Call (SNP call): AA, AB, BB, or NC (No Call).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood, mononuclear cell extract

extract_protocol: Blood was drawn early in the day from fasted subjects to minimize signals associated with nutritional and diurnal cycle and processed within fifteen minutes. Plasma samples were obtained and RNA and DNA recovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).

tag: tissue

value: blood

tag: cell type

tag: gender

value: M

value: CAU

tag: ancestry

value: N

tag: cad class

tag: cxcl5 rank

tag: bmi

tag: diabetes

tag: hyperlipid

value: Y

tag: hypertension


title: B. subtilis ccpA mutant_exponential growth_rep1

type: RNA

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 100 ng of Cy5-labeled cDNA and 100 ng of Cy3-labeled cDNAwere hybridized to the microarray following Agilent’s hybridization, washing and scanning protocol (Two-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing:
Data were extracted using the Agilent Feature Extraction software (version 10.5, Agilent Technologies).
The normalization/ dye bias correction method as defined by the Agilent Feature Extraction protocol for 2 color gene expression arrays (protocol GE2_105_Dec08) is: Linear and Lowess.  The normalization/ dye bias correction method is: Linear and Lowess.

molecule: total RNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol:
For cDNA synthesis, 5 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D
(final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye,
GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis 168 mutant strains were grown under vigorous agitation at 37 °C in C minimal medium (Faires et al., 1999; PMID 10941796) supplemented with glucose (5 g/l) and potassium glutamate (8g/l).

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

treatment_protocol: Samples were taken at OD600 of 1.0.

tag: control type

value: pooled reference

tag: strain

source_name: ccpA mutant_exponential growth

tag: genotype

value: Bacillus subtilis ccpA mutant


title: B. subtilis ccpA mutant_exponential growth_rep2


title: 2S119_M_CAU_N_1_136_genotype

scan_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).


title: 2S114_F_AA_Y_3_107_genotype

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by the DNA Array Core Facility at The Scripps Research Institute (Jupiter, FL).

value: F

value: AA


title: 2S010_M_CAU_Y_3_92

hyb_protocol: Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner.

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (v9.5.1.1 Agilent).The log expression ratios produced during the normalization step are provided.

source_name: Stratagene UHRR reference

label_protocol: 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

growth_protocol: Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw.  Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays.  The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD).  Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.

extract_protocol: RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).  RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions.  RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100.  RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.

value: pool of human cell line RNA

tag: batchid

value: E


title: NZO 3650

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

hyb_protocol: Fragmented cDNA samples were then hybridized to GeneChip Affymetrix GeneChip MOUSE GENE 430 2.0 (Affymetrix UK Ltd, Lahr, Germany).

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).  Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).  Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

organism: Mus musculus

source_name: liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2010, Affymetrix). All synthesis steps were monitored with an RNA 6000 nano kit (Agilent, Taufkirchen, Germany) for quality control.

growth_protocol: Mice were bred and maintained in a regular 12h light/dark cycle under constant temperature and humidity (22°C ± 1°C, 50% ± 5% humidity) with unrestricted access to water and standart chow.

extract_protocol: Total RNA was extracted from 50-100 mg liver tissue with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).  Total RNA was extracted from 50-100 mg epidydimal adipose tissue and gastrocnemius muscle with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).  Total RNA was extracted from 50-100 mg liver tissue with the RNeasy Mini Spin Kit protocol according to manufacturer’s recommendations (Qiagen, Hilden, Germany).

treatment_protocol: At 18 weeks of age male mice were sacrifced by CO2 asphyxation, liver was isolated and 100 mg aliquots were snap frozen in liquid nitrogen. Samples were stored at -80°C until processing.

value: male

tag: age

value: 18 weeks

value: NZO

value: liver


title: 2S108_M_CAU_Y_4_86_genotype


title: 2S009_M_CAU_Y_4_59


title: 2S105_F_CAU_N_1_48_genotype


title: 2S127_F_CAU_N_1_30_genotype


title: NZOm_1


title: 2S111_M_CAU_Y_3_115_genotype


title: 2S008_M_CAU_Y_4_120


title: 2S102_F_CAU_N_0_125_genotype


title: BKS wt_5

value: BKS


title: 2S007_F_CAU_Y_4_39

value: mononuclear


title: 2S120_M_CAU_Y_3_88_genotype

value: blood


title: 2S109_M_CAU_Y_2_127_genotype

value: M


title: 2S006_F_CAU_Y_3_55

value: CAU


title: 2S099_M_CAU_N_1_124_genotype

value: N


title: BKS wt_1


title: 2S098_M_CAU_N_1_102_genotype


title: 2S003_F_CAU_Y_4_135

value: Y


title: 2S004_M_AA_N_1_112


title: 2S005_F_CAU_Y_2_114


title: 2S103_M_CAU_Y_4_95_genotype


title: 2S101_F_CAU_N_1_110_genotype


title: 2S002_F_AA_Y_3_123


title: 2S001_F_CAU_N_1_43


title: 2S088_M_CAU_Y_2_69_genotype


title: 2S112_M_CAU_Y_3_40_genotype


title: WT neutrophils SP rep3

first: Claire

middle: M.

last: Doerschuk

address: Marsico Hall 7205 CB#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: mRNA expression data from mouse lung neutrophils

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

scan_protocol: Scanning of the Affymetrix peg plate arrays was carried out using the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control. A custom meta-probeset file was used to map probesets to genes based on netaffx 35 and ensembl81. Microarray data were preprocessed by RMA (Robust Multiarray Average) background correction, GC content and sequence correction, quantile normalization, and median polish summarization, and expression levels compared using ANOVA on log2 intensities to identify transcripts that were differentially expressed between genotype and treatment groups.  Differentially expressed (DE) mRNAs were filtered at Benjamini-Hochberg FDR < 0.05, and fold change > 2, and expression patterns of DE transcripts were visualized using hierarchical clustering.  Expression analyses were performed using Partek Genomics Suite (Partek Inc., St. Louis. MO, USA).  Gene Set Enrichment Analysis (GSEA) was performed according to the method described (12, 13).

source_name: Lung neutrophils isolated from WT mice given S. pneumoniae

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.  The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits.

extract_protocol: Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight. Neutrophils were isolated using MACS beads (Miltenyi, Auburn, CA) according to the manufacturer’s instructions. Briefly, single cell suspensions were prepared from dissected mouse lungs. The cells were washed with PBS containing 2 mM EDTA and 0.5% bovine serum albumin, and incubated with biotin-anti-Ly6G and magnetic beads coated with anti-biotin. The samples were passed through a column in a magnetic field, and cells bound to beads were collected for further analysis. Cells were kept at 4-8°C during staining and magnetic bead isolation.

value: Lung

value: neutrophils

value: Wild type (WT)

value: 6-12 weeks


title: WT neutrophils SP rep4


title: 2S139_F_CAU_Y_2_65_genotype

value: F


title: Aorta_Preeclampsia_rep5

city: Groningen

first: Marijke

last: Faas

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description: Gene expression data from the aorta from preeclamptic rat

hyb_protocol: Sample hybridization to chipsperformed according to the manufacturer's instructions.

scan_protocol: Sample image scanning was performed according to the manufacturer's instructions.

data_processing: Microarray analysis was performed using MADMAX pipeline for statistical analysis of microarray data. Quality control was performed and all arrays met our criteria. For further analysis a custom annotation was used based on reorganized oligonucleotide probes, which combines all individual probes for a gene (version 19.0.0: http://mbni.org/customcdf/19.0.0/entrezg.download/ragene11st_Rn_ENTREZG_19.0.0.zip). Only genes that had at least 5 probes present on the array were taken into account. Expression values were calculated using robust multichip average (RMA) method, which includes quantile normalisation. Significant differences in expression were assessed using paired Intensity-Based Moderated T-statistic (IBMT)

label: Biotin

organism: Rattus norvegicus

source_name: Aorta, preeclampsia

label_protocol: Total RNA (100 ng) was labelled using the Affymetrix WT plus reagent kit

growth_protocol: Wistar outbred rats (Harlan Inc, Horst, the Netherlands) were housed in a 12-hour light-dark cycle with food and water ad libitum.

extract_protocol: Total RNA was isolated from whole abdominal aortas with the use of TriReagent following the manufacturer’s instructions. An additional round of purification was performed with RNeasy Microkit columns. RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer.

treatment_protocol: A cannula was placed into the right jugular vein in animals at day 0 of pregnancy and also in age matched non-pregnant control animals while anesthetized with isoflurane/oxygen. Animals were infused with either LPS or saline 14 days after cannula placement. The infusion took place during 1 hour with 1 μg/kg bodyweight LPS dissolved in 2 ml saline and resulted in experimental preeclampsia. The healthy pregnant control animals received saline only (2 ml during 1h). At day 20 of pregnancy, the animals were terminated by decapitation and thoracic and abdominal aortas were isolated. From non-pregnant female rats with saline infusion aortas were also isolated. The aortas were placed in cold oxygenated Krebs solution and stored at -80°C until further use.

value: Wistar

value: Abdominal aorta

tag: gestational age

value: day 20

tag: infusion

value: LPS


title: 2S116_M_AA_Y_3_134_genotype

tag: tissue

value: AA


title: 2S100_F_CAU_Y_2_118_genotype

tag: cell type


title: 2S097_M_CAU_Y_4_90_genotype

tag: gender


title: 2S082_F_AA_Y_4_19_genotype

tag: ancestry


title: WT neutrophils SP rep2


title: Aorta_Preeclampsia_rep4


title: Aorta_Preeclampsia_rep3


title: Aorta_Preeclampsia_rep2


title: WT neutrophils SP rep1


title: 2S090_M_CAU_Y_4_53_genotype

tag: cad class


title: Aorta_Preeclampsia_rep1


title: WT neutrophils PBS rep3

source_name: Lung neutrophils isolated from WT mice given PBS


title: 2S087_M_CAU_Y_4_108_genotype

tag: cxcl5 rank


title: 2S078_M_CAU_Y_3_132_genotype

tag: bmi


title: Aorta_Pregnant_rep5

description: Gene expression data from the aorta from healthy pregnant rat

source_name: Aorta, pregnant

value: Saline


title: 2S092_F_AA_Y_4_85_genotype

value: mononuclear

tag: diabetes


title: 2S080_F_CAU_Y_2_128_genotype

value: blood

tag: hyperlipid


title: 2S073_M_CAU_N_1_45_genotype

value: M

tag: hypertension


title: BKS wt_4

value: male

value: 18 weeks

value: BKS

value: liver


title: Aorta_Pregnant_rep4


title: 2S074_F_CAU_N_0_83_genotype

value: CAU

value: N

value: Y


title: 2S075_F_AA_N_1_143_genotype

value: F


title: WT neutrophils PBS rep4

value: Lung

value: neutrophils

value: Wild type (WT)

value: 6-12 weeks


title: Aorta_Pregnant_rep2

value: Wistar

value: Abdominal aorta

value: day 20


title: WT neutrophils PBS rep1


title: WT neutrophils PBS rep2


title: Ctrl_8

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

hyb_protocol: For each sample, equal amount of enriched (Cy5-labeled) and reference (Cy3-labeled) DNAs were co-hybridized to the microarray platform.

scan_protocol: Arrays were scanned at 3µm resolution using an Agilent G2565CA scanner, and image data were processed using Feature Extraction version 10.7 with CGH-1200-Jun14 protocol (Agilent Technologies).

data_processing: The MedianSignal of the probes was considered for data preprocessing.  Loess normalization was applied to correct for the Cy3/Cy5 dye bias for each dye. After quality control (QC) of the resulting log2 ratios, between-samples Quantile normalization was then applied to the QC-passed arrays (37 cDLBCLs and 7 controls). The median of the probe signal was calculated to retrieve the methylation levels of the target 672 CDS and 36,807 CpG regions.

organism: Canis lupus familiaris

source_name: Methylated fraction

label_protocol: Sample labeling was performed by using SureTag Complete DNA Labeling Kit (Agilent Technologies) following the manufacturer’s recommendations.

extract_protocol: Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (QIAGEN, CA, USA) according to the manufacturer’s instructions. Total DNA was enriched of methylated double-stranded DNA by using MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen).

value: lymph node

tag: disease state

value: control

source_name: Total gDNA (reference)


title: 2S071_M_CAU_N_0_67_genotype

value: blood

value: mononuclear

value: M


title: Aorta_Pregnant_rep1

tag: strain

value: Saline


title: Aorta_non pregnant_rep4

description: Gene expression data from the aorta from non pregnant rat

source_name: Aorta, non pregnant

value: Not pregnant


title: Ctrl_7


title: Aorta_non pregnant_rep3


title: Ctrl_5


title: 2S063_F_CAU_N_0_138_genotype

value: CAU

value: N


title: Ctrl_4


title: Aorta_non pregnant_rep2


title: 2S062_F_CAU_Y_2_122_genotype

value: F

value: Y


title: 2S076_M_CAU_Y_3_7_genotype


title: 2S079_M_CAU_Y_3_36_genotype


title: Ctrl_3


title: Ctrl_2


title: 2S058_F_CAU_Y_2_52_genotype


title: Aorta_non pregnant_rep1


title: 2S067_F_AA_Y_4_142_genotype

value: AA


title: 2S061_M_CAU_N_1_99_genotype


title: Ctrl_1


title: cDLBCL_37

value: cDLBCL


title: cDLBCL_39


title: cDLBCL_38


title: cDLBCL_35


title: cDLBCL_34


title: 2S057_F_CAU_Y_2_89_genotype


title: 2S052_F_AA_N_0_137_genotype


title: 2S065_F_AA_Y_4_61_genotype


title: cDLBCL_33


title: Aorta_Pregnant_rep3


title: 2S056_F_CAU_Y_2_81_genotype


title: 2S051_M_CAU_N_0_109_genotype


title: cDLBCL_32


title: microRNA profile of HV_S39

city: Guangzhou

first: Nuoqing

last: Weng

state: Guangdong

address: 651，Dongfengdong road

country: China

institute: State Key Laboratory of Oncology in South China,Sun Yat-sen University

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays, log 2 transformation of expression levels,EXPression Analyzer and DisplayER (EXPANDER) version 4.1 was used.

source_name: serum

label_protocol: 0.3μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY547 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Serum total RNA was isolated from serum samples using the Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Slurry Format) (Norgen Biotek Corporation, Thorold, Ontario, Canada) according to the manufacturer’s instructions.

tag: group

value: healthy volunteer


title: 2S066_F_CAU_Y_4_56_genotype


title: microRNA profile of HV_S36


title: 2S054_F_CAU_N_1_33_genotype


title: cDLBCL_36


title: cDLBCL_30


title: 2S049_M_CAU_N_1_104_genotype


title: 2S050_M_CAU_Y_4_103_genotype


title: microRNA profile of HV_S37


title: 2S042_F_CAU_N_1_131_genotype


title: 2S045_F_CAU_N_0_130_genotype


title: cDLBCL_29


title: microRNA profile of HV_S38


title: 2S040_M_CAU_N_0_13_genotype


title: cDLBCL_31


title: microRNA profile of HV_S34


title: 2S048_F_AA_N_0_141_genotype


title: 2S044_F_AA_N_1_75_genotype


title: cDLBCL_28


title: microRNA profile of HV_S40


title: cDLBCL_26


title: cDLBCL_25


title: microRNA profile of GBM_S41

value: glioblastoma multiforme patient


title: cDLBCL_24


title: microRNA profile of GBM_S35


title: microRNA profile of HV_S23


title: microRNA profile of GBM_S31


title: cDLBCL_27


title: cDLBCL_22


title: cDLBCL_23


title: 2S035_F_AA_N_1_106_genotype


title: 2S038_F_CAU_N_1_116_genotype


title: 2S033_M_CAU_N_1_64_genotype


title: microRNA profile of GBM_S28


title: microRNA profile of GBM_S27


title: 2S031_M_CAU_Y_3_27_genotype


title: microRNA profile of GBM_S20


title: microRNA profile of GBM_S30


title: cDLBCL_21


title: Iron supplemented_1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description:
Bacteria_LB_1 mM manganese_0.5 mM iron grown_1
Gene expression_Plus manganase_Plus iron_1

hyb_protocol: 2000ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent custom Microarray Gene expression 8x15k Array (AMADID: 068043). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Gene based analysis was performed.

organism: Escherichia coli

source_name: Bacteria grown in LB + 1mM manganese + 0.5mM iron

label_protocol: The samples for gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight culture of DmntP strain was diluted to 1:100 in Luria broth and grown in the presence or absence of MnCl2 (1 mM) or MnCl2 (1mM) supplemented with 0.5mM FeCl3 for 2 hours at 37°C. 2.5 ml stop solution (5% phenol in ethanol) was added in 25 ml of growing culture for 10 minutes to prevent the RNA degradation and the cell pellets were collected by centrifuging at 5000 rpm for 10 minutes at 4°C.

extract_protocol: RNA extraction was performed using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: The cells were grown in the presence or absence of MnCl2 (1 mM) or MnCl2 (1mM) supplemented with 0.5mM FeCl3 for 2 hours at 37°C.

tag: strain/background

value: DmntP

tag: growth media

value: LB + 1mM manganese + 0.5mM iron


title: cDLBCL_18

value: lymph node


title: cDLBCL_20


title: Manganese-fed_3

description:
Bacteria_LB_1 mM manganese grown_3
Gene expression_Plus manganase_3

source_name: Bacteria grown in LB + 1mM manganese

value: LB + 1mM manganese


title: microRNA profile of GBM_S18


title: microRNA profile of HV_S29


title: cDLBCL_17


title: microRNA profile of GBM_S17


title: Manganese-fed_1

description:
Bacteria_LB_1 mM manganese grown_1
Gene expression_Plus manganase_1


title: 2S039_M_CAU_Y_3_72_genotype

value: blood


title: 2S025_F_CAU_N_1_100_genotype

value: mononuclear


title: 2S060_M_CAU_Y_4_93_genotype

value: M


title: microRNA profile of GBM_S16


title: cDLBCL_15


title: cDLBCL_19


title: cDLBCL_16


title: 2S010_M_CAU_Y_3_92_genotype


title: Control 3_unfed

description:
Bacteria_LB grown_3
Gene expression_minus manganase_3

source_name: Bacteria grown in LB

value: LB


title: 2S029_M_CAU_Y_2_91_genotype


title: Control 2_unfed

description:
Bacteria_LB grown_2
Gene expression_minus manganase_2


title: microRNA profile of GBM_S14


title: 2S012_F_AA_Y_3_139_genotype


title: cDLBCL_14


title: Control 1_unfed

description:
Bacteria_LB grown_1
Gene expression_minus manganase_1


title: microRNA profile of GBM_S12


title: microRNA profile of GBM_S11


title: Iron supplemented_2

description:
Bacteria_LB_1 mM manganese_0.5 mM iron grown_2
Gene expression_Plus manganase_Plus iron_2


title: cDLBCL_13


title: microRNA profile of GBM_S13


title: microRNA profile of GBM_S7


title: cDLBCL_11


title: cDLBCL_9


title: cDLBCL_8


title: 2S004_M_AA_N_1_112_genotype


title: cDLBCL_12


title: microRNA profile of GBM_S8


title: microRNA profile of GBM_S6


title: microRNA profile of GBM_S3


title: microRNA profile of GBM_S2


title: cDLBCL_6


title: cDLBCL_4


title: Manganese-fed_2

description:
Bacteria_LB_1 mM manganese grown_2
Gene expression_Plus manganase_2


title: 2S037_F_CAU_Y_4_46_genotype


title: cDLBCL_5


title: microRNA profile of GBM_S1


title: 2S003_F_CAU_Y_4_135_genotype


title: 2S005_F_CAU_Y_2_114_genotype


title: Prostate_tumour_CPCG0576_rep1

status: Public on Aug 02 2017

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
Raw data were processed through Dasen
matrix processed value definition: Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Illumina Infinium HumanMethylation 450k BeadChip kits were used to assess global methylation, using 500 ng of input genomic DNA at the McGill University and Genome Quebec Innovation Centre (Montreal, QC)


title: Prostate_tumour_CPCG0582_rep1


title: Prostate_tumour_CPCG0578_rep1


title: Prostate_tumour_CPCG0577_rep1


title: Prostate_tumour_CPCG0580_rep1


title: Prostate_tumour_CPCG0581_rep1


title: Prostate_tumour_CPCG0396_rep3


title: Prostate_tumour_CPCG0448_rep3


title: Prostate_tumour_CPCG0396_rep4


title: Prostate_tumour_CPCG0452_rep3


title: cDLBCL_3


title: cDLBCL_2


title: Prostate_tumour_CPCG0235_rep3


title: Prostate_tumour_CPCG0459_rep2


title: Prostate_tumour_CPCG0235_rep2


title: Prostate_tumour_CPCG0335_rep2


title: 2S008_M_CAU_Y_4_120_genotype


title: Prostate_tumour_CPCG0471_rep1


title: Prostate_tumour_CPCG0470_rep1


title: Prostate_tumour_CPCG0271_rep2


title: Prostate_tumour_CPCG0468_rep1


title: Prostate_tumour_CPCG0467_rep1


title: Prostate_tumour_CPCG0459_rep1


title: Prostate_tumour_CPCG0458_rep1


title: Prostate_tumour_CPCG0465_rep1


title: Prostate_tumour_CPCG0457_rep2


title: Prostate_tumour_CPCG0466_rep2


title: Prostate_tumour_CPCG0456_rep2


title: Prostate_tumour_CPCG0462_rep1


title: Prostate_tumour_CPCG0454_rep2


title: Prostate_tumour_CPCG0464_rep1


title: 2S007_F_CAU_Y_4_39_genotype


title: Prostate_tumour_CPCG0100_rep2


title: Prostate_tumour_CPCG0466_rep1


title: Prostate_tumour_CPCG0463_rep1


title: Prostate_tumour_CPCG0451_rep2


title: Prostate_tumour_CPCG0455_rep2


title: Prostate_tumour_CPCG0453_rep2


title: Prostate_tumour_CPCG0452_rep2


title: 2S001_F_CAU_N_1_43_genotype


title: Prostate_tumour_CPCG0439_rep2


title: Prostate_tumour_CPCG0448_rep2


title: Prostate_tumour_CPCG0445_rep1


title: Prostate_tumour_CPCG0435_rep2


title: Prostate_tumour_CPCG0434_rep2


title: Prostate_tumour_CPCG0418_rep2


title: Prostate_tumour_CPCG0428_rep1


title: Prostate_tumour_CPCG0397_rep2


title: Prostate_tumour_CPCG0398_rep3


title: Prostate_tumour_CPCG0406_rep2


title: Prostate_tumour_CPCG0396_rep2


title: Prostate_tumour_CPCG0395_rep2


title: Prostate_tumour_CPCG0423_rep2


title: Prostate_tumour_CPCG0328_rep1


title: Prostate_tumour_CPCG0320_rep1


title: Prostate_tumour_CPCG0317_rep2


title: Prostate_tumour_CPCG0321_rep1


title: Prostate_tumour_CPCG0313_rep1


title: Prostate_tumour_CPCG0402_rep1


title: Prostate_tumour_CPCG0322_rep1


title: Prostate_tumour_CPCG0315_rep2


title: microRNA profile of GBM_S19


title: Prostate_tumour_CPCG0314_rep1


title: Prostate_tumour_CPCG0312_rep2


title: 2S023_F_AA_Y_3_101_genotype


title: microRNA profile of GBM_S9


title: Prostate_tumour_CPCG0323_rep1


title: 2S002_F_AA_Y_3_123_genotype


title: Prostate_tumour_CPCG0304_rep2


title: Prostate_tumour_CPCG0302_rep2


title: Prostate_tumour_CPCG0301_rep2


title: Prostate_tumour_CPCG0310_rep2


title: Prostate_tumour_CPCG0306_rep2


title: cDLBCL_7


title: Prostate_tumour_CPCG0300_rep2


title: Prostate_tumour_CPCG0297_rep1


title: Prostate_tumour_CPCG0299_rep2


title: Prostate_tumour_CPCG0295_rep1


title: Prostate_tumour_CPCG0296_rep2


title: Prostate_tumour_CPCG0292_rep1


title: Prostate_tumour_CPCG0298_rep2


title: Prostate_tumour_CPCG0290_rep2


title: Prostate_tumour_CPCG0291_rep1


title: Prostate_tumour_CPCG0293_rep1


title: Prostate_tumour_CPCG0289_rep1


title: Prostate_tumour_CPCG0287_rep1


title: Prostate_tumour_CPCG0288_rep2


title: Prostate_tumour_CPCG0317_rep1


title: Prostate_tumour_CPCG0315_rep1


title: Prostate_tumour_CPCG0310_rep1


title: Prostate_tumour_CPCG0007_rep1


title: Prostate_tumour_CPCG0306_rep1


title: Prostate_tumour_CPCG0307_rep1


title: Prostate_tumour_CPCG0304_rep1


title: Prostate_tumour_CPCG0302_rep1


title: Prostate_tumour_CPCG0312_rep1


title: Prostate_tumour_CPCG0296_rep1


title: Prostate_tumour_CPCG0300_rep1


title: Prostate_tumour_CPCG0290_rep1


title: Prostate_tumour_CPCG0288_rep1


title: Prostate_tumour_CPCG0418_rep1


title: Prostate_tumour_CPCG0457_rep1


title: Prostate_tumour_CPCG0298_rep1


title: Prostate_tumour_CPCG0435_rep1


title: Prostate_tumour_CPCG0434_rep1


title: Prostate_tumour_CPCG0455_rep1


title: Prostate_tumour_CPCG0454_rep1


title: Prostate_tumour_CPCG0453_rep1


title: Prostate_tumour_CPCG0456_rep1


title: Prostate_tumour_CPCG0452_rep1


title: Prostate_tumour_CPCG0451_rep1


title: Prostate_tumour_CPCG0448_rep1


title: Prostate_tumour_CPCG0439_rep1


title: Prostate_tumour_CPCG0398_rep2


title: Prostate_tumour_CPCG0423_rep1


title: Prostate_tumour_CPCG0406_rep1


title: Prostate_tumour_CPCG0398_rep1


title: Prostate_tumour_CPCG0396_rep1


title: Prostate_tumour_CPCG0397_rep1


title: Prostate_tumour_CPCG0299_rep1


title: Prostate_tumour_CPCG0301_rep1


title: Prostate_tumour_CPCG0282_rep3


title: Prostate_tumour_CPCG0333_rep2


title: Prostate_tumour_CPCG0382_rep2


title: Prostate_tumour_CPCG0415_rep1


title: Prostate_tumour_CPCG0408_rep1


title: Prostate_tumour_CPCG0416_rep1


title: Prostate_tumour_CPCG0382_rep1


title: Prostate_tumour_CPCG0377_rep1


title: Prostate_tumour_CPCG0333_rep1


title: Prostate_tumour_CPCG0335_rep1


title: Prostate_tumour_CPCG0271_rep1


title: Prostate_tumour_CPCG0349_rep1


title: Prostate_tumour_CPCG0282_rep2


title: Prostate_tumour_CPCG0188_rep1


title: Prostate_tumour_CPCG0282_rep1


title: Prostate_tumour_CPCG0281_rep1


title: Prostate_tumour_CPCG0285_rep1


title: Prostate_tumour_CPCG0279_rep1


title: Prostate_tumour_CPCG0240_rep1


title: Prostate_tumour_CPCG0187_rep1


title: Prostate_tumour_CPCG0395_rep1


title: Prostate_tumour_CPCG0286_rep1


title: Prostate_tumour_CPCG0200_rep1


title: Prostate_tumour_CPCG0203_rep1


title: Prostate_tumour_CPCG0100_rep1


title: Prostate_tumour_CPCG0072_rep1


title: Prostate_tumour_CPCG0132_rep1


title: Prostate_tumour_CPCG0227_rep1


title: Prostate_tumour_CPCG0235_rep1


title: Sporadic_prostate_tumour_CPCG0391_rep2

status: Public on Jan 10 2017

data_processing: Raw data were processed through Dasen. The Unmethylated and methylated signal intensities are available in the file Non-normalized_data.txt on the series record and in the .idat files.

value: prostate tumor

value: Sporadic


title: Sporadic_prostate_tumour_CPCG0267_rep1


title: Sporadic_prostate_tumour_CPCG0258_rep1


title: Sporadic_prostate_tumour_CPCG0374_rep2


title: Sporadic_prostate_tumour_CPCG0362_rep2


title: Sporadic_prostate_tumour_CPCG0258_rep2


title: Sporadic_prostate_tumour_CPCG0353_rep2


title: Sporadic_prostate_tumour_CPCG0375_rep2


title: Sporadic_prostate_tumour_CPCG0267_rep2


title: Sporadic_prostate_tumour_CPCG0414_rep1


title: Sporadic_prostate_tumour_CPCG0265_rep2


title: Sporadic_prostate_tumour_CPCG0388_rep3


title: Sporadic_prostate_tumour_CPCG0334_rep3


title: Sporadic_prostate_tumour_CPCG0189_rep2


title: Sporadic_prostate_tumour_CPCG0366_rep3


title: Sporadic_prostate_tumour_CPCG0189_rep3


title: Sporadic_prostate_tumour_CPCG0242_rep3


title: Sporadic_prostate_tumour_CPCG0255_rep2


title: Sporadic_prostate_tumour_CPCG0184_rep2


title: Sporadic_prostate_tumour_CPCG0411_rep1


title: Sporadic_prostate_tumour_CPCG0368_rep2


title: Sporadic_prostate_tumour_CPCG0365_rep3


title: Sporadic_prostate_tumour_CPCG0360_rep2


title: Sporadic_prostate_tumour_CPCG0381_rep2


title: Sporadic_prostate_tumour_CPCG0346_rep3


title: Sporadic_prostate_tumour_CPCG0344_rep2


title: Sporadic_prostate_tumour_CPCG0242_rep2


title: Sporadic_prostate_tumour_CPCG0365_rep4


title: Sporadic_prostate_tumour_CPCG0345_rep3


title: Sporadic_prostate_tumour_CPCG0345_rep4


title: Sporadic_prostate_tumour_CPCG0411_rep2


title: Sporadic_prostate_tumour_CPCG0388_rep2


title: Sporadic_prostate_tumour_CPCG0392_rep3


title: Sporadic_prostate_tumour_CPCG0256_rep3


title: Sporadic_prostate_tumour_CPCG0404_rep2


title: Sporadic_prostate_tumour_CPCG0256_rep2


title: Sporadic_prostate_tumour_CPCG0087_rep1


title: Sporadic_prostate_tumour_CPCG0073_rep2


title: Sporadic_prostate_tumour_CPCG0256_rep1


title: Sporadic_prostate_tumour_CPCG0364_rep2


title: Sporadic_prostate_tumour_CPCG0366_rep2


title: Sporadic_prostate_tumour_CPCG0345_rep1


title: Sporadic_prostate_tumour_CPCG0379_rep2


title: Sporadic_prostate_tumour_CPCG0078_rep1


title: Sporadic_prostate_tumour_CPCG0388_rep1


title: Sporadic_prostate_tumour_CPCG0392_rep1


title: Sporadic_prostate_tumour_CPCG0345_rep2


title: Sporadic_prostate_tumour_CPCG0392_rep2


title: Sporadic_prostate_tumour_CPCG0365_rep2


title: Sporadic_prostate_tumour_CPCG0404_rep1


title: Sporadic_prostate_tumour_CPCG0243_rep1


title: Sporadic_prostate_tumour_CPCG0127_rep1


title: Sporadic_prostate_tumour_CPCG0073_rep1


title: Sporadic_prostate_tumour_CPCG0361_rep2


title: Sporadic_prostate_tumour_CPCG0357_rep2


title: Sporadic_prostate_tumour_CPCG0117_rep1


title: Sporadic_prostate_tumour_CPCG0346_rep2


title: Sporadic_prostate_tumour_CPCG0341_rep2


title: Sporadic_prostate_tumour_CPCG0040_rep2


title: Sporadic_prostate_tumour_CPCG0040_rep1


title: Sporadic_prostate_tumour_CPCG0027_rep1


title: Sporadic_prostate_tumour_CPCG0078_rep2


title: Sporadic_prostate_tumour_CPCG0266_rep2


title: Sporadic_prostate_tumour_CPCG0340_rep2


title: Sporadic_prostate_tumour_CPCG0410_rep1


title: Sporadic_prostate_tumour_CPCG0409_rep1


title: Sporadic_prostate_tumour_CPCG0401_rep1


title: Sporadic_prostate_tumour_CPCG0336_rep2


title: Sporadic_prostate_tumour_CPCG0387_rep1


title: Sporadic_prostate_tumour_CPCG0413_rep1


title: Sporadic_prostate_tumour_CPCG0379_rep1


title: Sporadic_prostate_tumour_CPCG0380_rep1


title: Sporadic_prostate_tumour_CPCG0373_rep1


title: Sporadic_prostate_tumour_CPCG0324_rep2


title: Sporadic_prostate_tumour_CPCG0375_rep1


title: Sporadic_prostate_tumour_CPCG0381_rep1


title: Sporadic_prostate_tumour_CPCG0334_rep2


title: Sporadic_prostate_tumour_CPCG0374_rep1


title: Sporadic_prostate_tumour_CPCG0391_rep1


title: Sporadic_prostate_tumour_CPCG0372_rep1


title: Sporadic_prostate_tumour_CPCG0366_rep1


title: Sporadic_prostate_tumour_CPCG0371_rep1


title: Sporadic_prostate_tumour_CPCG0369_rep1


title: Sporadic_prostate_tumour_CPCG0412_rep1


title: Sporadic_prostate_tumour_CPCG0360_rep1


title: Sporadic_prostate_tumour_CPCG0365_rep1


title: Sporadic_prostate_tumour_CPCG0407_rep1


title: Sporadic_prostate_tumour_CPCG0358_rep1


title: Sporadic_prostate_tumour_CPCG0364_rep1


title: Sporadic_prostate_tumour_CPCG0361_rep1


title: Sporadic_prostate_tumour_CPCG0357_rep1


title: Sporadic_prostate_tumour_CPCG0363_rep1


title: Sporadic_prostate_tumour_CPCG0368_rep1


title: Sporadic_prostate_tumour_CPCG0352_rep1


title: Sporadic_prostate_tumour_CPCG0362_rep1


title: Sporadic_prostate_tumour_CPCG0378_rep1


title: Sporadic_prostate_tumour_CPCG0354_rep1


title: Sporadic_prostate_tumour_CPCG0355_rep1


title: Sporadic_prostate_tumour_CPCG0346_rep1


title: Sporadic_prostate_tumour_CPCG0353_rep1


title: Sporadic_prostate_tumour_CPCG0341_rep1


title: Sporadic_prostate_tumour_CPCG0342_rep1


title: Sporadic_prostate_tumour_CPCG0350_rep1


title: Sporadic_prostate_tumour_CPCG0344_rep1


title: Sporadic_prostate_tumour_CPCG0356_rep1


title: Sporadic_prostate_tumour_CPCG0331_rep1


title: Sporadic_prostate_tumour_CPCG0334_rep1


title: Sporadic_prostate_tumour_CPCG0339_rep1


title: Sporadic_prostate_tumour_CPCG0348_rep1


title: Sporadic_prostate_tumour_CPCG0336_rep1


title: Sporadic_prostate_tumour_CPCG0340_rep1


title: Sporadic_prostate_tumour_CPCG0269_rep1


title: Sporadic_prostate_tumour_CPCG0255_rep1


title: Sporadic_prostate_tumour_CPCG0266_rep1


title: Sporadic_prostate_tumour_CPCG0263_rep1


title: Sporadic_prostate_tumour_CPCG0268_rep1


title: Sporadic_prostate_tumour_CPCG0324_rep1


title: Sporadic_prostate_tumour_CPCG0251_rep1


title: Sporadic_prostate_tumour_CPCG0265_rep1


title: Sporadic_prostate_tumour_CPCG0250_rep1


title: Sporadic_prostate_tumour_CPCG0246_rep1


title: Sporadic_prostate_tumour_CPCG0248_rep1


title: Sporadic_prostate_tumour_CPCG0190_rep1


title: Sporadic_prostate_tumour_CPCG0182_rep1


title: Sporadic_prostate_tumour_CPCG0196_rep2


title: Sporadic_prostate_tumour_CPCG0242_rep1


title: Sporadic_prostate_tumour_CPCG0208_rep2


title: Sporadic_prostate_tumour_CPCG0191_rep2


title: Sporadic_prostate_tumour_CPCG0210_rep2


title: Sporadic_prostate_tumour_CPCG0154_rep1


title: Sporadic_prostate_tumour_CPCG0236_rep1


title: Sporadic_prostate_tumour_CPCG0189_rep1


title: Sporadic_prostate_tumour_CPCG0233_rep2


title: Sporadic_prostate_tumour_CPCG0185_rep1


title: Sporadic_prostate_tumour_CPCG0232_rep2


title: Sporadic_prostate_tumour_CPCG0213_rep1


title: Sporadic_prostate_tumour_CPCG0217_rep1


title: Sporadic_prostate_tumour_CPCG0047_rep1


title: Sporadic_prostate_tumour_CPCG0241_rep1


title: Sporadic_prostate_tumour_CPCG0094_rep1


title: Sporadic_prostate_tumour_CPCG0262_rep1


title: Sporadic_prostate_tumour_CPCG0057_rep1


title: Sporadic_prostate_tumour_CPCG0249_rep1


title: Sporadic_prostate_tumour_CPCG0260_rep1


title: Sporadic_prostate_tumour_CPCG0238_rep1


title: Sporadic_prostate_tumour_CPCG0048_rep1


title: WAT, CNOT3KO mouse_2

status: Public on Jan 01 2017

city: Onna

first: Toru

last: Suzuki

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Instutue of Science and Technology Graduate University

description: Gene expression data from white adipose tissue in adipose tissue-specific Cnot3-deficient mouse

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: WAT from CNOT3KO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Genetically modified mice are bred in SPF condition.

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

treatment_protocol: Epididymal white adipose tissues are picked up from mice grown up to 8 weeks after birth

value: white adipose tissue

tag: genotype

value: CNOT3 knockout

tag: age

value: 8 weeks


title: Sporadic_prostate_tumour_CPCG0083_rep1

tag: tissue


title: WAT, CNOT3KO mouse_3


title: Sporadic_prostate_tumour_CPCG0259_rep1


title: WAT, WT mouse_1

description: Gene expression data from white adipose tissue in control mouse

source_name: WAT from wild type mouse

value: wild type


title: Sporadic_prostate_tumour_CPCG0114_rep1


title: WAT, WT mouse_3


title: P_1_5d_shoot_rep1

status: Public on Aug 12 2015

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description: Gene expression of rice shoot at 5 days after control treatment for phosphorus deficiency treatment

hyb_protocol: 1,650 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with R

organism: Oryza sativa Japonica Group

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and 1% (v/v) sodium hypochlorite solution, imbibed in distilled water in the dark at 28°C for 2 days, and transferred onto a nylon net floated in distilled water in a growth chamber (60% humidity; 14.5 h light period at 28°C and 9.5 h dark period at 23°C). After 3 days of germination, the seedlings were transferred in Yoshida nutrient solution (5-fold dilution, pH 5.5) and allowed to grow for another 4 days. The pH of the nutrient solution was adjusted using 1N NaOH and maintained using MES (buffer). The solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from the each sample with a RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The 7-day old seedlings were exposed to N, P, and K deficiency treatments (1/4, 1/16 and 1/64 of normal concentration) and control conditions, respectively. Shoot samples were collected at 5 days after nutrient starvation. To exclude potential effects of osmotic pressure, NaCl and Na2SO4 were added into the low P and K treatment solutions, respectively, and the osmotic level was adjusted to the same level as the control.

tag: cultivar

value: Nipponbare

tag: organ

value: Shoot

tag: nutrient

value: Phosphorus

tag: treatment

value: Control (1)


title: K_1_5d_shoot_rep2

description: Gene expression of rice shoot at 5 days after control treatment for potassium deficiency treatment

value: Potassium


title: N_1_5d_shoot_rep2

description: Gene expression of rice shoot at 5 days after control treatment for nitrogen deficiency treatment

value: Nitrogen


title: N_1_5d_shoot_rep3


title: Sporadic_prostate_tumour_CPCG0208_rep1


title: K_1_5d_shoot_rep3


title: WAT, WT mouse_2


title: Sporadic_prostate_tumour_CPCG0196_rep1


title: P_1_5d_shoot_rep3


title: Sporadic_prostate_tumour_CPCG0183_rep1


title: Sporadic_prostate_tumour_CPCG0184_rep1


title: Sporadic_prostate_tumour_CPCG0233_rep1


title: Sporadic_prostate_tumour_CPCG0191_rep1


title: N_1_5d_shoot_rep1


title: WAT, CNOT3KO mouse_1


title: Sporadic_prostate_tumour_CPCG0102_rep1


title: Sporadic_prostate_tumour_CPCG0099_rep1


title: Sporadic_prostate_tumour_CPCG0210_rep1


title: Sporadic_prostate_tumour_CPCG0158_rep1


title: P_1_5d_shoot_rep2


title: K_1_5d_shoot_rep1


title: Sporadic_prostate_tumour_CPCG0232_rep1


title: BCFD404

status: Public on Jun 18 2015

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

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

country: United Kingdom

institute: University College London

description:
Normal breast, normal-adjacent and breast cancer tissue samples
***WARNING: incomplete metadata supplied for this study***

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

data_processing: idat files processed using minfi V1.8.9 and BMIQ v1.4

source_name: genomic DNA from breast sample BCFD404

label_protocol: Standard Illumina Protocol for Infinium 450k Chip

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: molecule subtype

value: bi-sulphite converted genomic DNA from BCFD404

tag: status(0=normal 1=normal-adjacent 2=breast cancer 3=normal-brca1 4=cancer-brca1)

tag: ChIP

tag: er

tag: pr

tag: sentrix id


title: BCFD406

source_name: genomic DNA from breast sample BCFD406

value: bi-sulphite converted genomic DNA from BCFD406


title: BCFD402

source_name: genomic DNA from breast sample BCFD402

value: bi-sulphite converted genomic DNA from BCFD402


title: BCFD405

source_name: genomic DNA from breast sample BCFD405

value: bi-sulphite converted genomic DNA from BCFD405


title: BCFD407

source_name: genomic DNA from breast sample BCFD407

value: bi-sulphite converted genomic DNA from BCFD407


title: BCFD399

source_name: genomic DNA from breast sample BCFD399

value: bi-sulphite converted genomic DNA from BCFD399


title: BCFD403

source_name: genomic DNA from breast sample BCFD403

value: bi-sulphite converted genomic DNA from BCFD403


title: BCFD400

source_name: genomic DNA from breast sample BCFD400

value: bi-sulphite converted genomic DNA from BCFD400


title: BCFD398

source_name: genomic DNA from breast sample BCFD398

value: bi-sulphite converted genomic DNA from BCFD398


title: BCFD395

source_name: genomic DNA from breast sample BCFD395

value: bi-sulphite converted genomic DNA from BCFD395


title: BCFD393

source_name: genomic DNA from breast sample BCFD393

value: bi-sulphite converted genomic DNA from BCFD393


title: BCFD390

source_name: genomic DNA from breast sample BCFD390

value: bi-sulphite converted genomic DNA from BCFD390


title: BCFD397

source_name: genomic DNA from breast sample BCFD397

value: bi-sulphite converted genomic DNA from BCFD397


title: BCFD388

source_name: genomic DNA from breast sample BCFD388

value: bi-sulphite converted genomic DNA from BCFD388


title: BCFD391

source_name: genomic DNA from breast sample BCFD391

value: bi-sulphite converted genomic DNA from BCFD391


title: BCFD389

source_name: genomic DNA from breast sample BCFD389

value: bi-sulphite converted genomic DNA from BCFD389


title: BCFD385

source_name: genomic DNA from breast sample BCFD385

value: bi-sulphite converted genomic DNA from BCFD385


title: BCFD386

source_name: genomic DNA from breast sample BCFD386

value: bi-sulphite converted genomic DNA from BCFD386


title: BCFD396

source_name: genomic DNA from breast sample BCFD396

value: bi-sulphite converted genomic DNA from BCFD396


title: BCFD394

source_name: genomic DNA from breast sample BCFD394

value: bi-sulphite converted genomic DNA from BCFD394


title: BCFD379

source_name: genomic DNA from breast sample BCFD379

value: bi-sulphite converted genomic DNA from BCFD379


title: BCFD382

source_name: genomic DNA from breast sample BCFD382

value: bi-sulphite converted genomic DNA from BCFD382


title: BCFD387

source_name: genomic DNA from breast sample BCFD387

value: bi-sulphite converted genomic DNA from BCFD387


title: BCFD401

source_name: genomic DNA from breast sample BCFD401

value: bi-sulphite converted genomic DNA from BCFD401


title: BCFD383

source_name: genomic DNA from breast sample BCFD383

value: bi-sulphite converted genomic DNA from BCFD383


title: BCFD392

source_name: genomic DNA from breast sample BCFD392

value: bi-sulphite converted genomic DNA from BCFD392


title: BCFD380

source_name: genomic DNA from breast sample BCFD380

value: bi-sulphite converted genomic DNA from BCFD380


title: BCFD381

source_name: genomic DNA from breast sample BCFD381

value: bi-sulphite converted genomic DNA from BCFD381


title: BCFD384

source_name: genomic DNA from breast sample BCFD384

value: bi-sulphite converted genomic DNA from BCFD384


title: BCFD378

source_name: genomic DNA from breast sample BCFD378

value: bi-sulphite converted genomic DNA from BCFD378


title: BCFD377

source_name: genomic DNA from breast sample BCFD377

value: bi-sulphite converted genomic DNA from BCFD377


title: BCFD373

source_name: genomic DNA from breast sample BCFD373

value: bi-sulphite converted genomic DNA from BCFD373


title: BCFD376

source_name: genomic DNA from breast sample BCFD376

value: bi-sulphite converted genomic DNA from BCFD376


title: BCFD369

source_name: genomic DNA from breast sample BCFD369

value: bi-sulphite converted genomic DNA from BCFD369


title: BCFD371

source_name: genomic DNA from breast sample BCFD371

value: bi-sulphite converted genomic DNA from BCFD371


title: BCFD370

source_name: genomic DNA from breast sample BCFD370

value: bi-sulphite converted genomic DNA from BCFD370


title: BCFD367

source_name: genomic DNA from breast sample BCFD367

value: bi-sulphite converted genomic DNA from BCFD367


title: BCFD374

source_name: genomic DNA from breast sample BCFD374

value: bi-sulphite converted genomic DNA from BCFD374


title: BCFD361

source_name: genomic DNA from breast sample BCFD361

value: bi-sulphite converted genomic DNA from BCFD361


title: BCFD355

source_name: genomic DNA from breast sample BCFD355

value: bi-sulphite converted genomic DNA from BCFD355


title: BCFD372

source_name: genomic DNA from breast sample BCFD372

value: bi-sulphite converted genomic DNA from BCFD372


title: BCFD357

source_name: genomic DNA from breast sample BCFD357

value: bi-sulphite converted genomic DNA from BCFD357


title: BCFD375

source_name: genomic DNA from breast sample BCFD375

value: bi-sulphite converted genomic DNA from BCFD375


title: BCFD352

source_name: genomic DNA from breast sample BCFD352

value: bi-sulphite converted genomic DNA from BCFD352


title: BCFD365

source_name: genomic DNA from breast sample BCFD365

value: bi-sulphite converted genomic DNA from BCFD365


title: BCFD368

source_name: genomic DNA from breast sample BCFD368

value: bi-sulphite converted genomic DNA from BCFD368


title: BCFD366

source_name: genomic DNA from breast sample BCFD366

value: bi-sulphite converted genomic DNA from BCFD366


title: BCFD350

source_name: genomic DNA from breast sample BCFD350

value: bi-sulphite converted genomic DNA from BCFD350


title: BCFD360

source_name: genomic DNA from breast sample BCFD360

value: bi-sulphite converted genomic DNA from BCFD360


title: BCFD348

source_name: genomic DNA from breast sample BCFD348

value: bi-sulphite converted genomic DNA from BCFD348


title: BCFD349

source_name: genomic DNA from breast sample BCFD349

value: bi-sulphite converted genomic DNA from BCFD349


title: BCFD364

source_name: genomic DNA from breast sample BCFD364

value: bi-sulphite converted genomic DNA from BCFD364


title: BCFD351

source_name: genomic DNA from breast sample BCFD351

value: bi-sulphite converted genomic DNA from BCFD351


title: BCFD359

source_name: genomic DNA from breast sample BCFD359

value: bi-sulphite converted genomic DNA from BCFD359


title: BCFD362

source_name: genomic DNA from breast sample BCFD362

value: bi-sulphite converted genomic DNA from BCFD362


title: BCFD358

source_name: genomic DNA from breast sample BCFD358

value: bi-sulphite converted genomic DNA from BCFD358


title: BCFD363

source_name: genomic DNA from breast sample BCFD363

value: bi-sulphite converted genomic DNA from BCFD363


title: BCFD356

source_name: genomic DNA from breast sample BCFD356

value: bi-sulphite converted genomic DNA from BCFD356


title: BCFD353

source_name: genomic DNA from breast sample BCFD353

value: bi-sulphite converted genomic DNA from BCFD353


title: BCFD354

source_name: genomic DNA from breast sample BCFD354

value: bi-sulphite converted genomic DNA from BCFD354


title: BCFD347

source_name: genomic DNA from breast sample BCFD347

value: bi-sulphite converted genomic DNA from BCFD347


title: BCFD346

source_name: genomic DNA from breast sample BCFD346

value: bi-sulphite converted genomic DNA from BCFD346


title: BCFD343

source_name: genomic DNA from breast sample BCFD343

value: bi-sulphite converted genomic DNA from BCFD343


title: BCFD345

source_name: genomic DNA from breast sample BCFD345

value: bi-sulphite converted genomic DNA from BCFD345


title: BCFD344

source_name: genomic DNA from breast sample BCFD344

value: bi-sulphite converted genomic DNA from BCFD344


title: BCFD335

source_name: genomic DNA from breast sample BCFD335

value: bi-sulphite converted genomic DNA from BCFD335


title: BCFD337

source_name: genomic DNA from breast sample BCFD337

value: bi-sulphite converted genomic DNA from BCFD337


title: BCFD340

source_name: genomic DNA from breast sample BCFD340

value: bi-sulphite converted genomic DNA from BCFD340


title: BCFD339

source_name: genomic DNA from breast sample BCFD339

value: bi-sulphite converted genomic DNA from BCFD339


title: BCFD326

source_name: genomic DNA from breast sample BCFD326

value: bi-sulphite converted genomic DNA from BCFD326


title: BCFD341

source_name: genomic DNA from breast sample BCFD341

value: bi-sulphite converted genomic DNA from BCFD341


title: BCFD331

source_name: genomic DNA from breast sample BCFD331

value: bi-sulphite converted genomic DNA from BCFD331


title: BCFD330

source_name: genomic DNA from breast sample BCFD330

value: bi-sulphite converted genomic DNA from BCFD330


title: BCFD323

source_name: genomic DNA from breast sample BCFD323

value: bi-sulphite converted genomic DNA from BCFD323


title: BCFD329

source_name: genomic DNA from breast sample BCFD329

value: bi-sulphite converted genomic DNA from BCFD329


title: BCFD332

source_name: genomic DNA from breast sample BCFD332

value: bi-sulphite converted genomic DNA from BCFD332


title: BCFD334

source_name: genomic DNA from breast sample BCFD334

value: bi-sulphite converted genomic DNA from BCFD334


title: BCFD338

source_name: genomic DNA from breast sample BCFD338

value: bi-sulphite converted genomic DNA from BCFD338


title: BCFD336

source_name: genomic DNA from breast sample BCFD336

value: bi-sulphite converted genomic DNA from BCFD336


title: BCFD333

source_name: genomic DNA from breast sample BCFD333

value: bi-sulphite converted genomic DNA from BCFD333


title: BCFD322

source_name: genomic DNA from breast sample BCFD322

value: bi-sulphite converted genomic DNA from BCFD322


title: BCFD327

source_name: genomic DNA from breast sample BCFD327

value: bi-sulphite converted genomic DNA from BCFD327


title: BCFD328

source_name: genomic DNA from breast sample BCFD328

value: bi-sulphite converted genomic DNA from BCFD328


title: BCFD319

source_name: genomic DNA from breast sample BCFD319

value: bi-sulphite converted genomic DNA from BCFD319


title: BCFD321

source_name: genomic DNA from breast sample BCFD321

value: bi-sulphite converted genomic DNA from BCFD321


title: BCFD318

source_name: genomic DNA from breast sample BCFD318

value: bi-sulphite converted genomic DNA from BCFD318


title: BCFD317

source_name: genomic DNA from breast sample BCFD317

value: bi-sulphite converted genomic DNA from BCFD317


title: BCFD325

source_name: genomic DNA from breast sample BCFD325

value: bi-sulphite converted genomic DNA from BCFD325


title: BCFD316

source_name: genomic DNA from breast sample BCFD316

value: bi-sulphite converted genomic DNA from BCFD316


title: BCFD320

source_name: genomic DNA from breast sample BCFD320

value: bi-sulphite converted genomic DNA from BCFD320


title: BCFD342

source_name: genomic DNA from breast sample BCFD342

value: bi-sulphite converted genomic DNA from BCFD342


title: BCFD314

source_name: genomic DNA from breast sample BCFD314

value: bi-sulphite converted genomic DNA from BCFD314


title: BCFD315

source_name: genomic DNA from breast sample BCFD315

value: bi-sulphite converted genomic DNA from BCFD315


title: BCFD313

source_name: genomic DNA from breast sample BCFD313

value: bi-sulphite converted genomic DNA from BCFD313


title: BCFD308

source_name: genomic DNA from breast sample BCFD308

value: bi-sulphite converted genomic DNA from BCFD308


title: BCFD324

source_name: genomic DNA from breast sample BCFD324

value: bi-sulphite converted genomic DNA from BCFD324


title: BCFD309

source_name: genomic DNA from breast sample BCFD309

value: bi-sulphite converted genomic DNA from BCFD309


title: BCFD307

source_name: genomic DNA from breast sample BCFD307

value: bi-sulphite converted genomic DNA from BCFD307


title: BCFD303

source_name: genomic DNA from breast sample BCFD303

value: bi-sulphite converted genomic DNA from BCFD303


title: BCFD305

source_name: genomic DNA from breast sample BCFD305

value: bi-sulphite converted genomic DNA from BCFD305


title: BCFD304

source_name: genomic DNA from breast sample BCFD304

value: bi-sulphite converted genomic DNA from BCFD304


title: BCFD312

source_name: genomic DNA from breast sample BCFD312

value: bi-sulphite converted genomic DNA from BCFD312


title: BCFD302

source_name: genomic DNA from breast sample BCFD302

value: bi-sulphite converted genomic DNA from BCFD302


title: BCFD301

source_name: genomic DNA from breast sample BCFD301

value: bi-sulphite converted genomic DNA from BCFD301


title: BCFD300

source_name: genomic DNA from breast sample BCFD300

value: bi-sulphite converted genomic DNA from BCFD300


title: BCFD306

source_name: genomic DNA from breast sample BCFD306

value: bi-sulphite converted genomic DNA from BCFD306


title: BCFD311

source_name: genomic DNA from breast sample BCFD311

value: bi-sulphite converted genomic DNA from BCFD311


title: BCFD297

source_name: genomic DNA from breast sample BCFD297

value: bi-sulphite converted genomic DNA from BCFD297


title: BCFD296

source_name: genomic DNA from breast sample BCFD296

value: bi-sulphite converted genomic DNA from BCFD296


title: BCFD310

source_name: genomic DNA from breast sample BCFD310

value: bi-sulphite converted genomic DNA from BCFD310


title: BCFD292

source_name: genomic DNA from breast sample BCFD292

value: bi-sulphite converted genomic DNA from BCFD292


title: BCFD294

source_name: genomic DNA from breast sample BCFD294

value: bi-sulphite converted genomic DNA from BCFD294


title: BCFD289

source_name: genomic DNA from breast sample BCFD289

value: bi-sulphite converted genomic DNA from BCFD289


title: BCFD298

source_name: genomic DNA from breast sample BCFD298

value: bi-sulphite converted genomic DNA from BCFD298


title: BCFD295

source_name: genomic DNA from breast sample BCFD295

value: bi-sulphite converted genomic DNA from BCFD295


title: BCFD285

source_name: genomic DNA from breast sample BCFD285

value: bi-sulphite converted genomic DNA from BCFD285


title: BCFD299

source_name: genomic DNA from breast sample BCFD299

value: bi-sulphite converted genomic DNA from BCFD299


title: BCFD288

source_name: genomic DNA from breast sample BCFD288

value: bi-sulphite converted genomic DNA from BCFD288


title: BCFD291

source_name: genomic DNA from breast sample BCFD291

value: bi-sulphite converted genomic DNA from BCFD291


title: BCFD293

source_name: genomic DNA from breast sample BCFD293

value: bi-sulphite converted genomic DNA from BCFD293


title: BCFD284

source_name: genomic DNA from breast sample BCFD284

value: bi-sulphite converted genomic DNA from BCFD284


title: BCFD286

source_name: genomic DNA from breast sample BCFD286

value: bi-sulphite converted genomic DNA from BCFD286


title: BCFD287

source_name: genomic DNA from breast sample BCFD287

value: bi-sulphite converted genomic DNA from BCFD287


title: BCFD282

source_name: genomic DNA from breast sample BCFD282

value: bi-sulphite converted genomic DNA from BCFD282


title: BCFD283

source_name: genomic DNA from breast sample BCFD283

value: bi-sulphite converted genomic DNA from BCFD283


title: BCFD290

source_name: genomic DNA from breast sample BCFD290

value: bi-sulphite converted genomic DNA from BCFD290


title: BCFD280

source_name: genomic DNA from breast sample BCFD280

value: bi-sulphite converted genomic DNA from BCFD280


title: BCFD281

source_name: genomic DNA from breast sample BCFD281

value: bi-sulphite converted genomic DNA from BCFD281


title: BCFD274

source_name: genomic DNA from breast sample BCFD274

value: bi-sulphite converted genomic DNA from BCFD274


title: BCFD269

source_name: genomic DNA from breast sample BCFD269

value: bi-sulphite converted genomic DNA from BCFD269


title: BCFD270

source_name: genomic DNA from breast sample BCFD270

value: bi-sulphite converted genomic DNA from BCFD270


title: BCFD277

source_name: genomic DNA from breast sample BCFD277

value: bi-sulphite converted genomic DNA from BCFD277


title: BCFD259

source_name: genomic DNA from breast sample BCFD259

value: bi-sulphite converted genomic DNA from BCFD259


title: BCFD265

source_name: genomic DNA from breast sample BCFD265

value: bi-sulphite converted genomic DNA from BCFD265


title: BCFD267

source_name: genomic DNA from breast sample BCFD267

value: bi-sulphite converted genomic DNA from BCFD267


title: BCFD263

source_name: genomic DNA from breast sample BCFD263

value: bi-sulphite converted genomic DNA from BCFD263


title: BCFD271

source_name: genomic DNA from breast sample BCFD271

value: bi-sulphite converted genomic DNA from BCFD271


title: BCFD262

source_name: genomic DNA from breast sample BCFD262

value: bi-sulphite converted genomic DNA from BCFD262


title: BCFD275

source_name: genomic DNA from breast sample BCFD275

value: bi-sulphite converted genomic DNA from BCFD275


title: BCFD260

source_name: genomic DNA from breast sample BCFD260

value: bi-sulphite converted genomic DNA from BCFD260


title: BCFD278

source_name: genomic DNA from breast sample BCFD278

value: bi-sulphite converted genomic DNA from BCFD278


title: BCFD268

source_name: genomic DNA from breast sample BCFD268

value: bi-sulphite converted genomic DNA from BCFD268


title: BCFD261

source_name: genomic DNA from breast sample BCFD261

value: bi-sulphite converted genomic DNA from BCFD261


title: BCFD266

source_name: genomic DNA from breast sample BCFD266

value: bi-sulphite converted genomic DNA from BCFD266


title: BCFD256

source_name: genomic DNA from breast sample BCFD256

value: bi-sulphite converted genomic DNA from BCFD256


title: BCFD273

source_name: genomic DNA from breast sample BCFD273

value: bi-sulphite converted genomic DNA from BCFD273


title: BCFD264

source_name: genomic DNA from breast sample BCFD264

value: bi-sulphite converted genomic DNA from BCFD264


title: BCFD254

source_name: genomic DNA from breast sample BCFD254

value: bi-sulphite converted genomic DNA from BCFD254


title: BCFD255

source_name: genomic DNA from breast sample BCFD255

value: bi-sulphite converted genomic DNA from BCFD255


title: BCFD258

source_name: genomic DNA from breast sample BCFD258

value: bi-sulphite converted genomic DNA from BCFD258


title: BCFD252

source_name: genomic DNA from breast sample BCFD252

value: bi-sulphite converted genomic DNA from BCFD252


title: BCFD279

source_name: genomic DNA from breast sample BCFD279

value: bi-sulphite converted genomic DNA from BCFD279


title: BCFD272

source_name: genomic DNA from breast sample BCFD272

value: bi-sulphite converted genomic DNA from BCFD272


title: BCFD257

source_name: genomic DNA from breast sample BCFD257

value: bi-sulphite converted genomic DNA from BCFD257


title: BCFD251

source_name: genomic DNA from breast sample BCFD251

value: bi-sulphite converted genomic DNA from BCFD251


title: BCFD250

source_name: genomic DNA from breast sample BCFD250

value: bi-sulphite converted genomic DNA from BCFD250


title: BCFD248

source_name: genomic DNA from breast sample BCFD248

value: bi-sulphite converted genomic DNA from BCFD248


title: BCFD276

source_name: genomic DNA from breast sample BCFD276

value: bi-sulphite converted genomic DNA from BCFD276


title: BCFD253

source_name: genomic DNA from breast sample BCFD253

value: bi-sulphite converted genomic DNA from BCFD253


title: BCFD240

source_name: genomic DNA from breast sample BCFD240

value: bi-sulphite converted genomic DNA from BCFD240


title: BCFD244

source_name: genomic DNA from breast sample BCFD244

value: bi-sulphite converted genomic DNA from BCFD244


title: BCFD243

source_name: genomic DNA from breast sample BCFD243

value: bi-sulphite converted genomic DNA from BCFD243


title: BCFD242

source_name: genomic DNA from breast sample BCFD242

value: bi-sulphite converted genomic DNA from BCFD242


title: BCFD233

source_name: genomic DNA from breast sample BCFD233

value: bi-sulphite converted genomic DNA from BCFD233


title: BCFD236

source_name: genomic DNA from breast sample BCFD236

value: bi-sulphite converted genomic DNA from BCFD236


title: BCFD241

source_name: genomic DNA from breast sample BCFD241

value: bi-sulphite converted genomic DNA from BCFD241


title: BCFD247

source_name: genomic DNA from breast sample BCFD247

value: bi-sulphite converted genomic DNA from BCFD247


title: BCFD238

source_name: genomic DNA from breast sample BCFD238

value: bi-sulphite converted genomic DNA from BCFD238


title: BCFD235

source_name: genomic DNA from breast sample BCFD235

value: bi-sulphite converted genomic DNA from BCFD235


title: BCFD231

source_name: genomic DNA from breast sample BCFD231

value: bi-sulphite converted genomic DNA from BCFD231


title: BCFD224

source_name: genomic DNA from breast sample BCFD224

value: bi-sulphite converted genomic DNA from BCFD224


title: BCFD226

source_name: genomic DNA from breast sample BCFD226

value: bi-sulphite converted genomic DNA from BCFD226


title: BCFD245

source_name: genomic DNA from breast sample BCFD245

value: bi-sulphite converted genomic DNA from BCFD245


title: BCFD228

source_name: genomic DNA from breast sample BCFD228

value: bi-sulphite converted genomic DNA from BCFD228


title: BCFD229

source_name: genomic DNA from breast sample BCFD229

value: bi-sulphite converted genomic DNA from BCFD229


title: BCFD234

source_name: genomic DNA from breast sample BCFD234

value: bi-sulphite converted genomic DNA from BCFD234


title: BCFD246

source_name: genomic DNA from breast sample BCFD246

value: bi-sulphite converted genomic DNA from BCFD246


title: BCFD237

source_name: genomic DNA from breast sample BCFD237

value: bi-sulphite converted genomic DNA from BCFD237


title: BCFD230

source_name: genomic DNA from breast sample BCFD230

value: bi-sulphite converted genomic DNA from BCFD230


title: BCFD222

source_name: genomic DNA from breast sample BCFD222

value: bi-sulphite converted genomic DNA from BCFD222


title: BCFD232

source_name: genomic DNA from breast sample BCFD232

value: bi-sulphite converted genomic DNA from BCFD232


title: BCFD218

source_name: genomic DNA from breast sample BCFD218

value: bi-sulphite converted genomic DNA from BCFD218


title: BCFD217

source_name: genomic DNA from breast sample BCFD217

value: bi-sulphite converted genomic DNA from BCFD217


title: BCFD223

source_name: genomic DNA from breast sample BCFD223

value: bi-sulphite converted genomic DNA from BCFD223


title: BCFD221

source_name: genomic DNA from breast sample BCFD221

value: bi-sulphite converted genomic DNA from BCFD221


title: BCFD212

source_name: genomic DNA from breast sample BCFD212

value: bi-sulphite converted genomic DNA from BCFD212


title: BCFD213

source_name: genomic DNA from breast sample BCFD213

value: bi-sulphite converted genomic DNA from BCFD213


title: BCFD215

source_name: genomic DNA from breast sample BCFD215

value: bi-sulphite converted genomic DNA from BCFD215


title: BCFD211

source_name: genomic DNA from breast sample BCFD211

value: bi-sulphite converted genomic DNA from BCFD211


title: BCFD225

source_name: genomic DNA from breast sample BCFD225

value: bi-sulphite converted genomic DNA from BCFD225


title: BCFD210

source_name: genomic DNA from breast sample BCFD210

value: bi-sulphite converted genomic DNA from BCFD210


title: BCFD216

source_name: genomic DNA from breast sample BCFD216

value: bi-sulphite converted genomic DNA from BCFD216


title: BCFD208

source_name: genomic DNA from breast sample BCFD208

value: bi-sulphite converted genomic DNA from BCFD208


title: BCFD203

source_name: genomic DNA from breast sample BCFD203

value: bi-sulphite converted genomic DNA from BCFD203


title: BCFD205

source_name: genomic DNA from breast sample BCFD205

value: bi-sulphite converted genomic DNA from BCFD205


title: BCFD209

source_name: genomic DNA from breast sample BCFD209

value: bi-sulphite converted genomic DNA from BCFD209


title: BCFD202

source_name: genomic DNA from breast sample BCFD202

value: bi-sulphite converted genomic DNA from BCFD202


title: BCFD214

source_name: genomic DNA from breast sample BCFD214

value: bi-sulphite converted genomic DNA from BCFD214


title: BCFD198

source_name: genomic DNA from breast sample BCFD198

value: bi-sulphite converted genomic DNA from BCFD198


title: BCFD249

source_name: genomic DNA from breast sample BCFD249

value: bi-sulphite converted genomic DNA from BCFD249


title: BCFD239

source_name: genomic DNA from breast sample BCFD239

value: bi-sulphite converted genomic DNA from BCFD239


title: BCFD219

source_name: genomic DNA from breast sample BCFD219

value: bi-sulphite converted genomic DNA from BCFD219


title: BCFD204

source_name: genomic DNA from breast sample BCFD204

value: bi-sulphite converted genomic DNA from BCFD204


title: BCFD206

source_name: genomic DNA from breast sample BCFD206

value: bi-sulphite converted genomic DNA from BCFD206


title: BCFD227

source_name: genomic DNA from breast sample BCFD227

value: bi-sulphite converted genomic DNA from BCFD227


title: BCFD195

source_name: genomic DNA from breast sample BCFD195

value: bi-sulphite converted genomic DNA from BCFD195


title: BCFD207

source_name: genomic DNA from breast sample BCFD207

value: bi-sulphite converted genomic DNA from BCFD207


title: BCFD197

source_name: genomic DNA from breast sample BCFD197

value: bi-sulphite converted genomic DNA from BCFD197


title: BCFD220

source_name: genomic DNA from breast sample BCFD220

value: bi-sulphite converted genomic DNA from BCFD220


title: BCFD199

source_name: genomic DNA from breast sample BCFD199

value: bi-sulphite converted genomic DNA from BCFD199


title: BCFD201

source_name: genomic DNA from breast sample BCFD201

value: bi-sulphite converted genomic DNA from BCFD201


title: BCFD188

source_name: genomic DNA from breast sample BCFD188

value: bi-sulphite converted genomic DNA from BCFD188


title: BCFD192

source_name: genomic DNA from breast sample BCFD192

value: bi-sulphite converted genomic DNA from BCFD192


title: BCFD193

source_name: genomic DNA from breast sample BCFD193

value: bi-sulphite converted genomic DNA from BCFD193


title: BCFD190

source_name: genomic DNA from breast sample BCFD190

value: bi-sulphite converted genomic DNA from BCFD190


title: BCFD186

source_name: genomic DNA from breast sample BCFD186

value: bi-sulphite converted genomic DNA from BCFD186


title: BCFD187

source_name: genomic DNA from breast sample BCFD187

value: bi-sulphite converted genomic DNA from BCFD187


title: BCFD191

source_name: genomic DNA from breast sample BCFD191

value: bi-sulphite converted genomic DNA from BCFD191


title: BCFD194

source_name: genomic DNA from breast sample BCFD194

value: bi-sulphite converted genomic DNA from BCFD194


title: BCFD200

source_name: genomic DNA from breast sample BCFD200

value: bi-sulphite converted genomic DNA from BCFD200


title: BCFD180

source_name: genomic DNA from breast sample BCFD180

value: bi-sulphite converted genomic DNA from BCFD180


title: BCFD178

source_name: genomic DNA from breast sample BCFD178

value: bi-sulphite converted genomic DNA from BCFD178


title: BCFD174

source_name: genomic DNA from breast sample BCFD174

value: bi-sulphite converted genomic DNA from BCFD174


title: BCFD184

source_name: genomic DNA from breast sample BCFD184

value: bi-sulphite converted genomic DNA from BCFD184


title: BCFD181

source_name: genomic DNA from breast sample BCFD181

value: bi-sulphite converted genomic DNA from BCFD181


title: BCFD183

source_name: genomic DNA from breast sample BCFD183

value: bi-sulphite converted genomic DNA from BCFD183


title: BCFD177

source_name: genomic DNA from breast sample BCFD177

value: bi-sulphite converted genomic DNA from BCFD177


title: BCFD179

source_name: genomic DNA from breast sample BCFD179

value: bi-sulphite converted genomic DNA from BCFD179


title: BCFD175

source_name: genomic DNA from breast sample BCFD175

value: bi-sulphite converted genomic DNA from BCFD175


title: BCFD182

source_name: genomic DNA from breast sample BCFD182

value: bi-sulphite converted genomic DNA from BCFD182


title: BCFD169

source_name: genomic DNA from breast sample BCFD169

value: bi-sulphite converted genomic DNA from BCFD169


title: BCFD172

source_name: genomic DNA from breast sample BCFD172

value: bi-sulphite converted genomic DNA from BCFD172


title: BCFD185

source_name: genomic DNA from breast sample BCFD185

value: bi-sulphite converted genomic DNA from BCFD185


title: BCFD171

source_name: genomic DNA from breast sample BCFD171

value: bi-sulphite converted genomic DNA from BCFD171


title: BCFD189

source_name: genomic DNA from breast sample BCFD189

value: bi-sulphite converted genomic DNA from BCFD189


title: BCFD176

source_name: genomic DNA from breast sample BCFD176

value: bi-sulphite converted genomic DNA from BCFD176


title: BCFD196

source_name: genomic DNA from breast sample BCFD196

value: bi-sulphite converted genomic DNA from BCFD196


title: BCFD168

source_name: genomic DNA from breast sample BCFD168

value: bi-sulphite converted genomic DNA from BCFD168


title: BCFD160

source_name: genomic DNA from breast sample BCFD160

value: bi-sulphite converted genomic DNA from BCFD160


title: BCFD156

source_name: genomic DNA from breast sample BCFD156

value: bi-sulphite converted genomic DNA from BCFD156


title: BCFD164

source_name: genomic DNA from breast sample BCFD164

value: bi-sulphite converted genomic DNA from BCFD164


title: BCFD170

source_name: genomic DNA from breast sample BCFD170

value: bi-sulphite converted genomic DNA from BCFD170


title: BCFD173

source_name: genomic DNA from breast sample BCFD173

value: bi-sulphite converted genomic DNA from BCFD173


title: BCFD159

source_name: genomic DNA from breast sample BCFD159

value: bi-sulphite converted genomic DNA from BCFD159


title: BCFD166

source_name: genomic DNA from breast sample BCFD166

value: bi-sulphite converted genomic DNA from BCFD166


title: BCFD161

source_name: genomic DNA from breast sample BCFD161

value: bi-sulphite converted genomic DNA from BCFD161


title: BCFD163

source_name: genomic DNA from breast sample BCFD163

value: bi-sulphite converted genomic DNA from BCFD163


title: BCFD167

source_name: genomic DNA from breast sample BCFD167

value: bi-sulphite converted genomic DNA from BCFD167


title: BCFD151

source_name: genomic DNA from breast sample BCFD151

value: bi-sulphite converted genomic DNA from BCFD151


title: BCFD155

source_name: genomic DNA from breast sample BCFD155

value: bi-sulphite converted genomic DNA from BCFD155


title: BCFD157

source_name: genomic DNA from breast sample BCFD157

value: bi-sulphite converted genomic DNA from BCFD157


title: BCFD153

source_name: genomic DNA from breast sample BCFD153

value: bi-sulphite converted genomic DNA from BCFD153


title: BCFD165

source_name: genomic DNA from breast sample BCFD165

value: bi-sulphite converted genomic DNA from BCFD165


title: BCFD145

source_name: genomic DNA from breast sample BCFD145

value: bi-sulphite converted genomic DNA from BCFD145


title: BCFD154

source_name: genomic DNA from breast sample BCFD154

value: bi-sulphite converted genomic DNA from BCFD154


title: BCFD148

source_name: genomic DNA from breast sample BCFD148

value: bi-sulphite converted genomic DNA from BCFD148


title: BCFD149

source_name: genomic DNA from breast sample BCFD149

value: bi-sulphite converted genomic DNA from BCFD149


title: BCFD162

source_name: genomic DNA from breast sample BCFD162

value: bi-sulphite converted genomic DNA from BCFD162


title: BCFD158

source_name: genomic DNA from breast sample BCFD158

value: bi-sulphite converted genomic DNA from BCFD158


title: BCFD144

source_name: genomic DNA from breast sample BCFD144

value: bi-sulphite converted genomic DNA from BCFD144


title: BCFD152

source_name: genomic DNA from breast sample BCFD152

value: bi-sulphite converted genomic DNA from BCFD152


title: BCFD150

source_name: genomic DNA from breast sample BCFD150

value: bi-sulphite converted genomic DNA from BCFD150


title: BCFD140

source_name: genomic DNA from breast sample BCFD140

value: bi-sulphite converted genomic DNA from BCFD140


title: BCFD143

source_name: genomic DNA from breast sample BCFD143

value: bi-sulphite converted genomic DNA from BCFD143


title: BCFD142

source_name: genomic DNA from breast sample BCFD142

value: bi-sulphite converted genomic DNA from BCFD142


title: BCFD146

source_name: genomic DNA from breast sample BCFD146

value: bi-sulphite converted genomic DNA from BCFD146


title: BCFD141

source_name: genomic DNA from breast sample BCFD141

value: bi-sulphite converted genomic DNA from BCFD141


title: BCFD139

source_name: genomic DNA from breast sample BCFD139

value: bi-sulphite converted genomic DNA from BCFD139


title: BCFD137

source_name: genomic DNA from breast sample BCFD137

value: bi-sulphite converted genomic DNA from BCFD137


title: BCFD138

source_name: genomic DNA from breast sample BCFD138

value: bi-sulphite converted genomic DNA from BCFD138


title: BCFD136

source_name: genomic DNA from breast sample BCFD136

value: bi-sulphite converted genomic DNA from BCFD136


title: BCFD130

source_name: genomic DNA from breast sample BCFD130

value: bi-sulphite converted genomic DNA from BCFD130


title: BCFD132

source_name: genomic DNA from breast sample BCFD132

value: bi-sulphite converted genomic DNA from BCFD132


title: BCFD131

source_name: genomic DNA from breast sample BCFD131

value: bi-sulphite converted genomic DNA from BCFD131


title: BCFD147

source_name: genomic DNA from breast sample BCFD147

value: bi-sulphite converted genomic DNA from BCFD147


title: BCFD122

source_name: genomic DNA from breast sample BCFD122

value: bi-sulphite converted genomic DNA from BCFD122


title: BCFD135

source_name: genomic DNA from breast sample BCFD135

value: bi-sulphite converted genomic DNA from BCFD135


title: BCFD128

source_name: genomic DNA from breast sample BCFD128

value: bi-sulphite converted genomic DNA from BCFD128


title: BCFD127

source_name: genomic DNA from breast sample BCFD127

value: bi-sulphite converted genomic DNA from BCFD127


title: BCFD125

source_name: genomic DNA from breast sample BCFD125

value: bi-sulphite converted genomic DNA from BCFD125


title: BCFD123

source_name: genomic DNA from breast sample BCFD123

value: bi-sulphite converted genomic DNA from BCFD123


title: BCFD134

source_name: genomic DNA from breast sample BCFD134

value: bi-sulphite converted genomic DNA from BCFD134


title: BCFD133

source_name: genomic DNA from breast sample BCFD133

value: bi-sulphite converted genomic DNA from BCFD133


title: BCFD124

source_name: genomic DNA from breast sample BCFD124

value: bi-sulphite converted genomic DNA from BCFD124


title: BCFD121

source_name: genomic DNA from breast sample BCFD121

value: bi-sulphite converted genomic DNA from BCFD121


title: BCFD119

source_name: genomic DNA from breast sample BCFD119

value: bi-sulphite converted genomic DNA from BCFD119


title: BCFD126

source_name: genomic DNA from breast sample BCFD126

value: bi-sulphite converted genomic DNA from BCFD126


title: BCFD120

source_name: genomic DNA from breast sample BCFD120

value: bi-sulphite converted genomic DNA from BCFD120


title: BCFD117

source_name: genomic DNA from breast sample BCFD117

value: bi-sulphite converted genomic DNA from BCFD117


title: BCFD129

source_name: genomic DNA from breast sample BCFD129

value: bi-sulphite converted genomic DNA from BCFD129


title: BCFD114

source_name: genomic DNA from breast sample BCFD114

value: bi-sulphite converted genomic DNA from BCFD114


title: BCFD115

source_name: genomic DNA from breast sample BCFD115

value: bi-sulphite converted genomic DNA from BCFD115


title: BCFD116

source_name: genomic DNA from breast sample BCFD116

value: bi-sulphite converted genomic DNA from BCFD116


title: BCFD113

source_name: genomic DNA from breast sample BCFD113

value: bi-sulphite converted genomic DNA from BCFD113


title: BCFD118

source_name: genomic DNA from breast sample BCFD118

value: bi-sulphite converted genomic DNA from BCFD118


title: BCFD108

source_name: genomic DNA from breast sample BCFD108

value: bi-sulphite converted genomic DNA from BCFD108


title: BCFD111

source_name: genomic DNA from breast sample BCFD111

value: bi-sulphite converted genomic DNA from BCFD111


title: BCFD110

source_name: genomic DNA from breast sample BCFD110

value: bi-sulphite converted genomic DNA from BCFD110


title: BCFD112

source_name: genomic DNA from breast sample BCFD112

value: bi-sulphite converted genomic DNA from BCFD112


title: BCFD106

source_name: genomic DNA from breast sample BCFD106

value: bi-sulphite converted genomic DNA from BCFD106


title: BCFD107

source_name: genomic DNA from breast sample BCFD107

value: bi-sulphite converted genomic DNA from BCFD107


title: BCFD109

source_name: genomic DNA from breast sample BCFD109

value: bi-sulphite converted genomic DNA from BCFD109


title: BCFD96

source_name: genomic DNA from breast sample BCFD96

value: bi-sulphite converted genomic DNA from BCFD96


title: BCFD105

source_name: genomic DNA from breast sample BCFD105

value: bi-sulphite converted genomic DNA from BCFD105


title: BCFD99

source_name: genomic DNA from breast sample BCFD99

value: bi-sulphite converted genomic DNA from BCFD99


title: BCFD97

source_name: genomic DNA from breast sample BCFD97

value: bi-sulphite converted genomic DNA from BCFD97


title: BCFD101

source_name: genomic DNA from breast sample BCFD101

value: bi-sulphite converted genomic DNA from BCFD101


title: BCFD93

source_name: genomic DNA from breast sample BCFD93

value: bi-sulphite converted genomic DNA from BCFD93


title: BCFD89

source_name: genomic DNA from breast sample BCFD89

value: bi-sulphite converted genomic DNA from BCFD89


title: BCFD94

source_name: genomic DNA from breast sample BCFD94

value: bi-sulphite converted genomic DNA from BCFD94


title: BCFD98

source_name: genomic DNA from breast sample BCFD98

value: bi-sulphite converted genomic DNA from BCFD98


title: BCFD103

source_name: genomic DNA from breast sample BCFD103

value: bi-sulphite converted genomic DNA from BCFD103


title: BCFD104

source_name: genomic DNA from breast sample BCFD104

value: bi-sulphite converted genomic DNA from BCFD104


title: BCFD95

source_name: genomic DNA from breast sample BCFD95

value: bi-sulphite converted genomic DNA from BCFD95


title: BCFD100

source_name: genomic DNA from breast sample BCFD100

value: bi-sulphite converted genomic DNA from BCFD100


title: BCFD91

source_name: genomic DNA from breast sample BCFD91

value: bi-sulphite converted genomic DNA from BCFD91


title: BCFD86

source_name: genomic DNA from breast sample BCFD86

value: bi-sulphite converted genomic DNA from BCFD86


title: BCFD92

source_name: genomic DNA from breast sample BCFD92

value: bi-sulphite converted genomic DNA from BCFD92


title: BCFD83

source_name: genomic DNA from breast sample BCFD83

value: bi-sulphite converted genomic DNA from BCFD83


title: BCFD102

source_name: genomic DNA from breast sample BCFD102

value: bi-sulphite converted genomic DNA from BCFD102


title: BCFD87

source_name: genomic DNA from breast sample BCFD87

value: bi-sulphite converted genomic DNA from BCFD87


title: BCFD84

source_name: genomic DNA from breast sample BCFD84

value: bi-sulphite converted genomic DNA from BCFD84


title: BCFD80

source_name: genomic DNA from breast sample BCFD80

value: bi-sulphite converted genomic DNA from BCFD80


title: BCFD88

source_name: genomic DNA from breast sample BCFD88

value: bi-sulphite converted genomic DNA from BCFD88


title: BCFD85

source_name: genomic DNA from breast sample BCFD85

value: bi-sulphite converted genomic DNA from BCFD85


title: BCFD90

source_name: genomic DNA from breast sample BCFD90

value: bi-sulphite converted genomic DNA from BCFD90


title: BCFD77

source_name: genomic DNA from breast sample BCFD77

value: bi-sulphite converted genomic DNA from BCFD77


title: BCFD81

source_name: genomic DNA from breast sample BCFD81

value: bi-sulphite converted genomic DNA from BCFD81


title: BCFD78

source_name: genomic DNA from breast sample BCFD78

value: bi-sulphite converted genomic DNA from BCFD78


title: BCFD82

source_name: genomic DNA from breast sample BCFD82

value: bi-sulphite converted genomic DNA from BCFD82


title: BCFD73

source_name: genomic DNA from breast sample BCFD73

value: bi-sulphite converted genomic DNA from BCFD73


title: BCFD72

source_name: genomic DNA from breast sample BCFD72

value: bi-sulphite converted genomic DNA from BCFD72


title: BCFD79

source_name: genomic DNA from breast sample BCFD79

value: bi-sulphite converted genomic DNA from BCFD79


title: BCFD76

source_name: genomic DNA from breast sample BCFD76

value: bi-sulphite converted genomic DNA from BCFD76


title: BCFD70

source_name: genomic DNA from breast sample BCFD70

value: bi-sulphite converted genomic DNA from BCFD70


title: BCFD69

source_name: genomic DNA from breast sample BCFD69

value: bi-sulphite converted genomic DNA from BCFD69


title: BCFD67

source_name: genomic DNA from breast sample BCFD67

value: bi-sulphite converted genomic DNA from BCFD67


title: BCFD65

source_name: genomic DNA from breast sample BCFD65

value: bi-sulphite converted genomic DNA from BCFD65


title: BCFD68

source_name: genomic DNA from breast sample BCFD68

value: bi-sulphite converted genomic DNA from BCFD68


title: BCFD64

source_name: genomic DNA from breast sample BCFD64

value: bi-sulphite converted genomic DNA from BCFD64


title: BCFD62

source_name: genomic DNA from breast sample BCFD62

value: bi-sulphite converted genomic DNA from BCFD62


title: BCFD63

source_name: genomic DNA from breast sample BCFD63

value: bi-sulphite converted genomic DNA from BCFD63


title: BCFD71

source_name: genomic DNA from breast sample BCFD71

value: bi-sulphite converted genomic DNA from BCFD71


title: BCFD59

source_name: genomic DNA from breast sample BCFD59

value: bi-sulphite converted genomic DNA from BCFD59


title: BCFD60

source_name: genomic DNA from breast sample BCFD60

value: bi-sulphite converted genomic DNA from BCFD60


title: BCFD75

source_name: genomic DNA from breast sample BCFD75

value: bi-sulphite converted genomic DNA from BCFD75


title: BCFD52

source_name: genomic DNA from breast sample BCFD52

value: bi-sulphite converted genomic DNA from BCFD52


title: BCFD57

source_name: genomic DNA from breast sample BCFD57

value: bi-sulphite converted genomic DNA from BCFD57


title: BCFD53

source_name: genomic DNA from breast sample BCFD53

value: bi-sulphite converted genomic DNA from BCFD53


title: BCFD54

source_name: genomic DNA from breast sample BCFD54

value: bi-sulphite converted genomic DNA from BCFD54


title: BCFD55

source_name: genomic DNA from breast sample BCFD55

value: bi-sulphite converted genomic DNA from BCFD55


title: BCFD51

source_name: genomic DNA from breast sample BCFD51

value: bi-sulphite converted genomic DNA from BCFD51


title: BCFD48

source_name: genomic DNA from breast sample BCFD48

value: bi-sulphite converted genomic DNA from BCFD48


title: BCFD47

source_name: genomic DNA from breast sample BCFD47

value: bi-sulphite converted genomic DNA from BCFD47


title: BCFD50

source_name: genomic DNA from breast sample BCFD50

value: bi-sulphite converted genomic DNA from BCFD50


title: BCFD58

source_name: genomic DNA from breast sample BCFD58

value: bi-sulphite converted genomic DNA from BCFD58


title: BCFD45

source_name: genomic DNA from breast sample BCFD45

value: bi-sulphite converted genomic DNA from BCFD45


title: BCFD40

source_name: genomic DNA from breast sample BCFD40

value: bi-sulphite converted genomic DNA from BCFD40


title: BCFD56

source_name: genomic DNA from breast sample BCFD56

value: bi-sulphite converted genomic DNA from BCFD56


title: BCFD46

source_name: genomic DNA from breast sample BCFD46

value: bi-sulphite converted genomic DNA from BCFD46


title: BCFD33

source_name: genomic DNA from breast sample BCFD33

value: bi-sulphite converted genomic DNA from BCFD33


title: BCFD43

source_name: genomic DNA from breast sample BCFD43

value: bi-sulphite converted genomic DNA from BCFD43


title: BCFD37

source_name: genomic DNA from breast sample BCFD37

value: bi-sulphite converted genomic DNA from BCFD37


title: BCFD41

source_name: genomic DNA from breast sample BCFD41

value: bi-sulphite converted genomic DNA from BCFD41


title: BCFD74

source_name: genomic DNA from breast sample BCFD74

value: bi-sulphite converted genomic DNA from BCFD74


title: BCFD66

source_name: genomic DNA from breast sample BCFD66

value: bi-sulphite converted genomic DNA from BCFD66


title: BCFD34

source_name: genomic DNA from breast sample BCFD34

value: bi-sulphite converted genomic DNA from BCFD34


title: BCFD36

source_name: genomic DNA from breast sample BCFD36

value: bi-sulphite converted genomic DNA from BCFD36


title: BCFD38

source_name: genomic DNA from breast sample BCFD38

value: bi-sulphite converted genomic DNA from BCFD38


title: BCFD35

source_name: genomic DNA from breast sample BCFD35

value: bi-sulphite converted genomic DNA from BCFD35


title: BCFD39

source_name: genomic DNA from breast sample BCFD39

value: bi-sulphite converted genomic DNA from BCFD39


title: BCFD29

source_name: genomic DNA from breast sample BCFD29

value: bi-sulphite converted genomic DNA from BCFD29


title: BCFD32

source_name: genomic DNA from breast sample BCFD32

value: bi-sulphite converted genomic DNA from BCFD32


title: BCFD42

source_name: genomic DNA from breast sample BCFD42

value: bi-sulphite converted genomic DNA from BCFD42


title: BCFD30

source_name: genomic DNA from breast sample BCFD30

value: bi-sulphite converted genomic DNA from BCFD30


title: BCFD28

source_name: genomic DNA from breast sample BCFD28

value: bi-sulphite converted genomic DNA from BCFD28


title: BCFD26

source_name: genomic DNA from breast sample BCFD26

value: bi-sulphite converted genomic DNA from BCFD26


title: BCFD61

source_name: genomic DNA from breast sample BCFD61

value: bi-sulphite converted genomic DNA from BCFD61


title: BCFD25

source_name: genomic DNA from breast sample BCFD25

value: bi-sulphite converted genomic DNA from BCFD25


title: BCFD24

source_name: genomic DNA from breast sample BCFD24

value: bi-sulphite converted genomic DNA from BCFD24


title: BCFD23

source_name: genomic DNA from breast sample BCFD23

value: bi-sulphite converted genomic DNA from BCFD23


title: BCFD21

source_name: genomic DNA from breast sample BCFD21

value: bi-sulphite converted genomic DNA from BCFD21


title: BCFD11

source_name: genomic DNA from breast sample BCFD11

value: bi-sulphite converted genomic DNA from BCFD11


title: BCFD19

source_name: genomic DNA from breast sample BCFD19

value: bi-sulphite converted genomic DNA from BCFD19


title: BCFD22

source_name: genomic DNA from breast sample BCFD22

value: bi-sulphite converted genomic DNA from BCFD22


title: TRIB-76

status: Public on Dec 01 2014

city: Sao Paulo

first: Karina

middle: Lumi

last: Mine

address: Rua Loefgreen, 1235

department: Instituto de Imunogenetica

country: Brazil

institute: AFIP

description: preimplantation kidney biopsy from deceased donor 76

hyb_protocol: cDNA was added to the hybridization cocktail and hybridized to the array for 16 hours at 45°C using Hybrization oven 640 (Affymetrix).

scan_protocol: After the incubation the arrays were washed using the Affymetrix Fluidics Station 450 and images were acquired using the GeneChip Scanner 3000 (both from Affymetrix).

data_processing: The data analyses were performed using BRB-ArrayTools version 4.2.1 developed by Dr. Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html). We applied the Robust Multiarray Analysis (RMA) algorithm for data summarization and background correction, and quantile normalization.

source_name: preimplantation kidney biopsy

label_protocol: Briefly, 200 ng of total RNA underwent first- and second-strand cDNA synthesis. Complementary RNA was generated and used to produce sense-strand cDNA. All these steps were performed using The Ambion® WT Expression kit (Life Technologies), following manufacturer’s instructions. 5.5 ug of single-stranded cDNA samples were fragmented and end-labeled with the GeneChip® WT Terminal Labeling and Hybridization Kit (Affymetrix).

extract_protocol: Biopsy fragments were homogenized (Multipro; Dremel, Racine, WI) before total RNA extraction with RNeasy Minikit® (QIAGEN, Valencia, CA), according to manufacturer’s instructions.

tag: donor

tag: tissue type

value: preimplantation kidney biopsy

tag: dgf occurrence

value: DGF

tag: dgf lasting more than 14 days

value: no

tag: egfr

value: High


title: TRIB-293

description: preimplantation kidney biopsy from deceased donor 293

value: without DGF

value: Low


title: BCFD20

source_name: genomic DNA from breast sample BCFD20

value: bi-sulphite converted genomic DNA from BCFD20


title: BCFD17

source_name: genomic DNA from breast sample BCFD17

value: bi-sulphite converted genomic DNA from BCFD17


title: TRIB-19

description: preimplantation kidney biopsy from deceased donor 19

value: yes


title: TRIB-173

description: preimplantation kidney biopsy from deceased donor 173


title: BCFD15

source_name: genomic DNA from breast sample BCFD15

value: bi-sulphite converted genomic DNA from BCFD15


title: BCFD6

source_name: genomic DNA from breast sample BCFD6

value: bi-sulphite converted genomic DNA from BCFD6


title: BCFD31

source_name: genomic DNA from breast sample BCFD31

value: bi-sulphite converted genomic DNA from BCFD31


title: BCFD7

source_name: genomic DNA from breast sample BCFD7

value: bi-sulphite converted genomic DNA from BCFD7


title: BCFD14

source_name: genomic DNA from breast sample BCFD14

value: bi-sulphite converted genomic DNA from BCFD14


title: BCFD16

source_name: genomic DNA from breast sample BCFD16

value: bi-sulphite converted genomic DNA from BCFD16


title: TRIB-294

description: preimplantation kidney biopsy from deceased donor 294


title: BCFD4

source_name: genomic DNA from breast sample BCFD4

value: bi-sulphite converted genomic DNA from BCFD4