title: HumanDC RNA Sample30 MTB-infected 18hours rep1


title: pTEN Deleted Early Tumor (21 Days), replicate 5

status: Public on Jan 17 2014

type: genomic

city: New York

first: Richard

last: Leung

state: NY

address: 1130 Saint Nicholas Avenue

department: Department of Neurosurgery

country: USA

institute: Columbia University

description: Sample name: PTEN21DPI-5

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scan protocol

data_processing:
Using R/-Bioconductor SnapCGH, samples were corrected by subtracting the background; zeros and negative intensities were set equal to half minimum of the positive corrected intensities for the array.  We performed a within array global median normalization and subsequent segmentation with smoothing using CBS.
Normalized processed data matrix contains log2(tumor/control) ratios for all samples.  See LogRatiosByProbe_MedianWithin_NotSegmented.txt linked as supplementary file on Series record.

molecule: genomic DNA

organism: Mus musculus

source_name: Brain tumor

label_protocol: Agilent SureTag Complete Enzymatic DNA Labeling Kit, Standard Protocol

growth_protocol: Retroviral vector PDGF-Ires-Cre was injected into the subcortical white matter of adult mice with lox sequences flanking p53 gene only, pTEN gene only, or both p53 and pTEN genes.  Animals were sacrificed at first sign of disease and tumor tissue was collected for genomic DNA extraction.

extract_protocol: Qiagen Mini DNA Extraction Kit, Standard Protocol for Tissue

treatment_protocol: No treatment

tag: disease state

value: Brain tumor

tag: genotype/variation

value: pTEN deleted

tag: disease stage

value: Early Tumor (21 Days)

source_name: Liver, control DNA

tag: sample type

value: control (liver)


title: HumanDC_totalRNA_IND3_Non-infected_24hrs_miR-29-Mimic-transfected_rep1

type: RNA

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

description: mRNA expression after 24hrs in Non-infected miR-29-Mimic-transfected DCs

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.10.0). It was vst transformed and quantile normalized.

molecule: total RNA

organism: Homo sapiens

source_name: Human dendritic cells, non-infected, miR29 mimic

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell type

value: dendritic cells

tag: infection

value: Non-infected

tag: miRNA

value: miR-29 mimic

tag: Sex

value: Male

tag: individual


title: HumanDC_totalRNA_IND3_MTB-infected_24hrs_miR-29-Inhibitor-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected miR-29-Inhibitor-transfected DCs

source_name: Human dendritic cells, MTB infected, miR29 inhibitor

value: MTB-infected

value: miR-29 inhibitor


title: HumanDC_totalRNA_IND4_Non-infected_24hrs_Control-Mimic-transfected_rep1

description: mRNA expression after 24hrs in Non-infected Control-Mimic-transfected DCs

source_name: Human dendritic cells, non-infected, control mimic

value: control mimic


title: HumanDC_totalRNA_IND3_Non-infected_24hrs_Control-Inhibitor-transfected_rep1

description: mRNA expression after 24hrs in Non-infected Control-Inhibitor-transfected DCs

source_name: Human dendritic cells, non-infected, control inhibitor

value: control inhibitor


title: HumanDC_totalRNA_IND2_MTB-infected_24hrs_Control-Inhibitor-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected Control-Inhibitor-transfected DCs

source_name: Human dendritic cells, MTB infected, control inhibitor

value: Female


title: pTEN Deleted Early Tumor (21 Days), replicate 4

description: Sample name: PTEN21DPI-4


title: HumanDC_totalRNA_IND1_Non-infected_24hrs_miR-29-Inhibitor-transfected_rep1

description: mRNA expression after 24hrs in Non-infected miR-29-Inhibitor-transfected DCs

source_name: Human dendritic cells, non-infected, miR29 inhibitor


title: HumanDC_totalRNA_IND4_MTB-infected_24hrs_Control-Mimic-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected Control-Mimic-transfected DCs

source_name: Human dendritic cells, MTB infected, control mimic


title: HumanDC_totalRNA_IND4_MTB-infected_24hrs_miR-29-Mimic-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected miR-29-Mimic-transfected DCs

source_name: Human dendritic cells, MTB infected, miR29 mimic


title: pTEN Deleted Early Tumor (21 Days), replicate 1

description: Sample name: PTEN21DPI-1


title: pTEN Deleted Early Tumor (21 Days), replicate 2

description: Sample name: PTEN21DPI-2


title: HumanDC_totalRNA_IND2_Non-infected_24hrs_Control-Mimic-transfected_rep1


title: pTEN Deleted Endstage, replicate 8

description: Sample name: PTEN7F

tag: gender

value: Endstage


title: pTEN Deleted Endstage, replicate 7

description: Sample name: PTEN6F


title: HumanDC RNA Sample5 MTB-infected 18hours rep1

description: microRNA expression after 18 hours MTB-infected DCs

hyb_protocol: As recommended by Agilent.

scan_protocol: As recommended by Agilent.

data_processing: Bioconductor package AgiMicrorna.

source_name: Human dendritic cells

label_protocol: As recommended by Agilent.

growth_protocol: Blood monocytes were purified from PBMCs by positive selection with magnetic CD14 MicroBeads. In order to derive dendritic cells, monocytes were cultured for 5 days in RPMI 1640  supplemented with 10% heat-inactivated FCS , L-glutamina, GM-CSF (20 ng/ml; Immunotools), and IL-4 (20 ng/ml; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol: Total RNA was extracted from the non-infected DCs and the MTB-infected DCs using the miRNeasy kit (Qiagen).

treatment_protocol: We infected DCs with an MTB strain expressing green-fluorescent protein (H37Rv)

tag: infection status


title: pTEN Deleted Endstage, replicate 6

description: Sample name: PTEN5F


title: pTEN Deleted Early Tumor (21 Days), replicate 3

description: Sample name: PTEN21DPI-3


title: HumanDC RNA Sample3 MTB-infected 18hours rep1


title: HumanDC RNA Sample6 Non-infected 18hours rep1

description: microRNA expression after 18 hours Non-infected DCs


title: HumanDC RNA Sample29 Non-infected 18hours rep1


title: pTEN Deleted Endstage, replicate 5

description: Sample name: PTEN3M


title: HumanDC RNA Sample2 MTB-infected 18hours rep1


title: HumanDC RNA Sample3 Non-infected 18hours rep1


title: Malek CLL-76-3-N

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing:
Affymetrix CEL files for each DNA sample were analyzed using Affymetrix's Genotyping Console software for initial quality control, followed by use of the Affymetrix “Birdseed” algorithm to determine final call rates and quality. Call rates for the entire group of samples included in this report were between 97.73% and 99.33%, with a mean call rate of 98.73%; none of the tumor DNA samples gave out-of-bounds results.   For the CLL CD3 samples employed as normals in this study, for sample call rate information, please refer to GEO accession number GSE30777.  Sample copy number heatmap displays were obtained from CEL files through use of the freely available software dChip adapted to operate in a 64-bit environment.    To generate functional and practical displays of LOH, a two-step, internally developed, Java-based software analysis system was employed. The Pre-LOH Unification Tool (PLUT) served to align all individual patient SNP calls to their respective dbSNP rs ID numbers and genomic physical positions prior to incorporation into the LOH tool version 2, an updated version of the LOH software tool able to accommodate Affy SNP 6.0 array data.  LOH analysis was only carried out using the SNP call files of the lymphoma samples.  The normal DNA derived from CLL patients were not used in any manner for LOH analysis.
dChip SNP software (www.dchip.org), build date Feb 25, 2009, compatible with 64-bit OS, analyzed the CEL files.  CEL files were normalized using the invariant set method, followed by model-based expression index calculations, and finally inferred copy number data were generated using the software's median-smoothing algorithm.

label: biotin

source_name: primary human: blood; FACS-sorted CD3+ cells

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol:
Cryopreserved cell suspensions made from lymphoma tissue or fine-needle aspirate samples were thawed and washed once in HBSS buffer with 1% fetal calf serum (FCS).   Cells were blocked with 200 µg/ml normal mouse IgG for 10 minutes.  Cells were then stained with the following: anti-human kappa and lambda light chain cocktail (Dako, Carpinteria, CA), anti-CD3 APC and either anti-CD20 PerCP-Cy5.5 or anti-CD19 PerCP-Cy5.5 (all from eBioscience, San Diego, CA).  The anti-CD19 antibody was used if cells were from patients who had undergone anti-CD20 immunotherapy within three months prior to sample procurement.  Cells were washed once, and DAPI (Molecular Probes) was added to a final concentration of 100ng/ml in order to discriminate dead cells.  Flow cytometry sorting was carried out on a Becton-Dickinson FACSAria IIu sorter.  The sorting schema was as follows:  cells were selected based on forward and side light scatter, a doublet discrimination gate, and negativity for DAPI.  These cells were then first interrogated for CD3 expression.  CD3-positive cells were sorted as a normal control for each patient.  CD3-negative cells were then interrogated for CD20 (or CD19) expression. CD20 (or CD19)-positive cells were subsequently interrogated for light-chain expression.  Both kappa and lambda single-positive populations were sorted and kappa to lambda ratios computed.  Either kappa or lambda was treated as tumor depending on the kappa to lambda ratio of the respective population within the sample.
Tumor and normal cells flow purified as above were digested overnight in 100 mM Tris pH 8.0, 50 mM EDTA, 50 mM NaCl, 0.5% SDS and 100 μg/ml of Proteinase K (Invitrogen) at 560C. DNA was extracted using phenol-chloroform and precipitated using ammonium acetate, ethanol and glycogen.

treatment_protocol: Not applicable

tag: disease

value: normal


title: pTEN Deleted Endstage, replicate 4

description: Sample name: PTEN3F


title: HumanDC_totalRNA_IND1_Non-infected_24hrs_miR-29-Mimic-transfected_rep1


title: HumanDC RNA Sample14 MTB-infected 18hours rep1


title: HumanDC_totalRNA_IND3_MTB-infected_24hrs_Control-Inhibitor-transfected_rep1


title: pTEN Deleted Endstage, replicate 3

description: Sample name: PTEN2M


title: HumanDC RNA Sample14 Non-infected 18hours rep1


title: HumanDC RNA Sample13 MTB-infected 18hours rep1


title: pTEN Deleted Endstage, replicate 2

description: Sample name: PTEN2F


title: Malek CLL-146-3-N


title: HumanDC_totalRNA_IND4_Non-infected_24hrs_miR-29-Inhibitor-transfected_rep1


title: HumanDC_totalRNA_IND2_MTB-infected_24hrs_miR-29-Inhibitor-transfected_rep1


title: HumanDC_totalRNA_IND4_Non-infected_24hrs_Control-Inhibitor-transfected_rep1


title: HumanDC_totalRNA_IND3_MTB-infected_24hrs_Control-Mimic-transfected_rep1


title: HumanDC_totalRNA_IND1_MTB-infected_24hrs_miR-29-Mimic-transfected_rep1


title: HumanDC_totalRNA_IND2_Non-infected_24hrs_miR-29-Mimic-transfected_rep1


title: Malek CLL-145-3-N


title: HumanDC_totalRNA_IND3_Non-infected_24hrs_miR-29-Inhibitor-transfected_rep1


title: pTEN Deleted Endstage, replicate 1

description: Sample name: PTEN1M


title: HumanDC RNA Sample13 Non-infected 18hours rep1


title: HumanDC RNA Sample6 MTB-infected 18hours rep1


title: HumanDC RNA Sample28 MTB-infected 18hours rep1


title: HumanDC RNA Sample12 MTB-infected 18hours rep1


title: HumanDC RNA Sample12 Non-infected 18hours rep1


title: HumanDC_totalRNA_IND1_Non-infected_24hrs_Control-Mimic-transfected_rep1


title: HumanDC RNA Sample11 MTB-infected 18hours rep1


title: HumanDC_totalRNA_IND2_Non-infected_24hrs_Control-Inhibitor-transfected_rep1


title: HumanDC RNA Sample11 Non-infected 18hours rep1


title: 692D2_shield1_1000_rep3

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Ectopic c-MYC-high MKCLs

hyb_protocol: The labeled cDNA was fragmented using a Gene Expression Hybridization Kit (Agilent Technologies) and then hybridized at 65 ̊C for 17 h.

scan_protocol: Images were acquired using a DNA Microarray Scanner (Agilent Technologies). Data were numerized using FeatureExtraction.

data_processing: The raw intensity data were analyzed using dChip software (version 2010.01). The data was normalized based on an invariant data set, then spots with signal intensities near or below the background level were filtered out.

source_name: 692D2-derived MKCLs with 1000nM of Shield-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA-labeled cDNA was synthesized from 100 ng of RNA using aLow Input Quick Amp Labeling Kit, no dye kit , one-color kit, two-color kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: On day 14 of culture during hematopoietic differentiation from hESCs/hiPSCs, HPCs were collected and transduced with retroviral vectors harboring BMI1 and DD-tagged c-MYC in the absence of Shield-1.

extract_protocol: Total RNA was extracted using a RNeasy Micro-Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: 692D2-derived MKCLs cultured with 0 and 1,000 nM Shield-1 for 2 days were collected. Exposure of the cells to Shield-1 resulted in increasing ectopic c-MYC protein level.

tag: shield-1 concentration

tag: treatment

value: 692D2-derived MKCLs


title: HumanDC_totalRNA_IND4_MTB-infected_24hrs_miR-29-Inhibitor-transfected_rep1


title: HumanDC_totalRNA_IND1_MTB-infected_24hrs_Control-Inhibitor-transfected_rep1


title: 692D2_shield1_1000_rep2

description: Ectopic c-MYC-high MKCLs


title: HumanDC RNA Sample20 MTB-infected 18hours rep1


title: HumanDC RNA Sample22 MTB-infected 18hours rep1


title: Endometrioid ovarian tumor C053 vs. 19 OVCA tumor pool

city: Dunedin

first: Heather

middle: E.

last: Cunliffe

state: Otago

address: P O Box 913

department: Department of Pathology

country: New Zealand

institute: University of Otago, Dunedin School of Medicine

hyb_protocol: 1230 ng of labeled tumor RNA and 825 ng of labeled reference RNA were prepared and hybridized to Agilent 4x44K (V2) gene expression microarrays following manufacturer protocols (Agilent Technologies; Palo Alto, CA).

scan_protocol: Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment.

data_processing: Agilent Feature Extraction software (v10.5) was used for background subtraction and normalization. Array control features and control targets were removed. Data transformed from Log10 to Log2.

source_name: Fresh frozen SCCO primary tumor

label_protocol: 250 ng of RNA from each tumor sample were labeled with Cy3 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. For the reference, 200 ng of RNA from each of the 19 tumor samples were combined and labeled in batches of 500 ng with Cy5 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. Labeling efficiency was measured with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE).

extract_protocol: Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by addition of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. The RNA integrity and purity of all samples was measured using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) and a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). RIN# for all RNAs were >7.5

treatment_protocol: Primary ovarian tumor was preserved from chemo-naïve patients at the time of diagnostic surgery.

tag: tissue

value: Fresh frozen SCCO primary tumor

tag: diagnosis

value: Endometrioid carcinoma

tag: age at diagnosis

tag: ethnicity

value: European

tag: figo stage

value: IC

tag: grade

tag: hypercalcemia

value: Not Applicable

tag: excision to snap freeze (min)

source_name: Pool of all 19 tumors analyzed

value: Pool of all 19 tumors analyzed


title: 692D2_shield1_1000_rep1

description: Ectopic c-MYC-high MKCLs

tag: cell type


title: 692D2_shield1_0_rep3

description: Ectopic c-MYC-low MKCLs

source_name: 692D2-derived MKCLs without Shield-1


title: HumanDC RNA Sample22 Non-infected 18hours rep1

value: Non-infected


title: Serous ovarian tumor C044 vs. 19 OVCA tumor pool

value: Serous carcinoma

value: IIIC


title: HumanDC RNA Sample20 Non-infected 18hours rep1

value: Male


title: Serous ovarian tumor C038 vs. 19 OVCA tumor pool

value: Papillary serous adenocarcinoma


title: 692D2_shield1_0_rep2

description: Ectopic c-MYC-low MKCLs


title: Serous ovarian tumor C035 vs. 19 OVCA tumor pool

value: Serous adenocarcinoma


title: 692D2_shield1_0_rep1

description: Ectopic c-MYC-low MKCLs


title: HumanDC RNA Sample17 Non-infected 18hours rep1


title: HumanDC RNA Sample17 MTB-infected 18hours rep1

value: MTB-infected


title: Endometrioid ovarian tumor C018 vs. 19 OVCA tumor pool

value: Endometrioid adenocarcinoma


title: Serous ovarian tumor C023 vs.19 OVCA tumor pool


title: HumanDC RNA Sample16 MTB-infected 18hours rep1


title: Endometrioid ovarian tumor C031 vs. 19 OVCA tumor pool


title: HumanDC RNA Sample16 Non-infected 18hours rep1


title: Serous ovarian tumor C028 vs. 19 OVCA tumor pool


title: HumanDC RNA Sample10 MTB-infected 18hours rep1


title: Serous ovarian tumor C008 vs. 19 OVCA tumor pool


title: Endometrioid cancer tumor C011 vs. 19 OVCA tumor pool


title: Clear cell ovarian tumor C013 vs. 19 OVCA tumor pool

value: Clear cell adenocarcinoma

value: IA


title: HumanDC RNA Sample10 Non-infected 18hours rep1


title: HumanDC RNA Sample9 MTB-infected 18hours rep2


title: HumanDC RNA Sample8 MTB-infected 18hours rep1


title: Endometrioid ovarian tumor C001 vs. 19 OVCA tumor pool

value: IV


title: Endometrioid ovarian tumor C017 vs. 19 OVCA tumor pool

value: Fresh frozen SCCO primary tumor


title: Mucinous ovarian tumor A001 vs. 19 OVCA tumor pool

value: Mucinous adenocarcinoma

value: Hispanic


title: Clear cell ovarian tumor C007 vs. 19 OVCA tumor pool

value: Clear cell carcinoma


title: SCCO-015 tumor vs. 19 OVCA tumor pool

value: Small cell carcinoma of the ovary

value: African American

value: IIIA

value: Unknown


title: HumanDC RNA Sample8 Non-infected 18hours rep1

value: Non-infected


title: HumanDC RNA Sample7 MTB-infected 18hours rep1

value: Male


title: QSYQ_4

city: Hangzhou

first: Xiaohui

last: Fan

state: Zhejiang

address: Yuhangtang 866

country: China

institute: Zhejiang Univ.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Spike-in control transcripts were monitored to verify hybridization integrity.

organism: Rattus norvegicus

source_name: LAD ligation_QSYQ treated

label_protocol: Total RNA were amplified, labeled, and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The rats were maintained in air-conditioned rooms (temperature, 22-26 ºC; humidity, 40%-70%) with a 12-h light-dark cycle, and were acclimatized to the setting for 1 week.To provide comfortable conditions for rats, each cage contained 5 rats, and the sawdust in the bottom of the cage were renewed every 2 days. Rats were free to get fresh foods and water, and the water was renewed everyday.

extract_protocol: Total RNA was extracted using TRIZol Reagent (Invitrogen) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: All surgery was performed under 10% chloral hydrate anesthesia (300mg/kg), and all efforts were made to minimize suffering. Rat myocardial infarction was made by occlusion of left anterior descending coronary artery (LAD) according to Yamaguchi. Rats post-LAD ligation were intramuscular injected with penicillin sodium (300,000 Unit per rat) and the survived animals were injected penicillin sodium for another two days to avoid infection post-operation. Six surviving rats after LAD ligation were randomly divided into myocardial infarction group (MI) and QSYQ-treated group. Three sham-operated rats were treated in the same ways as the rats in MI group but without LAD ligation, which were served as control group (Control).In accordance with clinical recommendations, QSYQ was given intragastrically (i.g.) at a dose of 105.6 mg/kg once a day. Rats in control, and MI groups were administered with saline. Rats were sacrificed after 7 days of i.g. administration under 10% chloral hydrate anesthesia (300mg/kg). Blood samples were collected by abdominal aortic method, then the chest was carefully dissected and the heart was cut quickly. Three tissue samples on the border between infarct and non-infarct area were dissected from left ventricles of each group. The tissue samples were stored at -80℃ refrigerator.

tag: strain

value: Sprague Dawley

value: male

tag: rat weight

tag: surgery

value: left anterior descending coronary artery (LAD) ligation

tag: treated with

value: 105.6 mg/kg QSYQ

value: myocardium of left ventricles


title: QSYQ_3

description: tissue samples on the border between infarct and non-infarct area were dissected from left ventricles

tag: gender


title: Model_5

source_name: LAD ligation_saline treated

value: saline (control)


title: SCCO-014 tumor vs. 19 OVCA tumor pool

value: IIIC

value: Yes

value: Pool of all 19 tumors analyzed


title: QSYQ_2


title: ML090N_CD3

source_name: primary human: lymphoma tissue biopsy or FNA; flow-sorted CD3+ cells

tag: disease

value: normal


title: HumanDC RNA Sample23 MTB-infected 18hours rep1

tag: infection status

value: MTB-infected


title: ML090T_lambda

source_name: primary human: lymphoma tissue biopsy or FNA; flow-sorted tumor, determined by kappa:lambda ratio

value: tumor


title: SCCO-012 tumor vs. 19 OVCA tumor pool

source_name: Fresh frozen SCCO tumor recurrence

treatment_protocol: Primary ovarian tumors from non-SCCO patients were preserved from chemo-naïve patients at the time of diagnostic surgery.

value: Fresh frozen SCCO tumor recurrence

value: Small cell carcinoma of the ovary

value: European


title: ML093T_kappa


title: ML087N_CD3


title: HumanDC RNA Sample23 Non-infected 18hours rep1

value: Non-infected


title: SCCO-002 tumor vs. 19 OVCA tumor pool

value: IA

value: Unknown


title: Model_4

value: Sprague Dawley

value: male


title: HumanDC RNA Sample9 MTB-infected 18hours rep1

value: Male


title: ML087T_kappa


title: ML093N_CD3


title: HumanDC RNA Sample9 Non-infected 18hours rep1


title: SCCO-015 tumor vs. Normal ovary

label_protocol: 200 ng of RNA from each tumor sample were labeled with Cy3 using  Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. For the reference, 100 ng of RNA from each of the 2 commerical normal ovary samples were combined and labeled with Cy5 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. Labeling efficiency was measured with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE).

extract_protocol: Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by additiona of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. For the reference, normal ovarian RNA from 2 different individuals (32 and 37 years of age) was obtained from OriGene (Rockville, MD), catalog numbers CR562102, CR561549). The RNA integrity and purity of all samples was measured using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) and a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE).  RIN# for all RNAs were >8.

value: Fresh frozen SCCO primary tumor

value: African American

value: IIIA

tag: tumor size

value: 20 cm

source_name: Pool of 2 commercial normal ovary RNA samples

tag: age

tag: case diagnosis

value: Endometriosis, endometriosis

tag: supplier

value: OriGene Technologies

tag: catalog numbers

value: Normal ovary unaffected by endometriosis


title: ML079T_lambda

value: tumor


title: ML079N_CD3

value: normal


title: SCCO-012 tumor vs. Normal ovary

tag: tissue

value: Fresh frozen SCCO tumor recurrence

tag: diagnosis

value: Small cell carcinoma of the ovary

tag: age at diagnosis

tag: ethnicity

value: Yes

tag: figo stage

value: IIIC

value: 12 cm


title: Model_1

tag: strain

value: Sprague Dawley

value: left anterior descending coronary artery (LAD) ligation

value: saline (control)

value: myocardium of left ventricles


title: Sham_1

description: tissue samples on the corresponding area the same of that in model group were dissected from left ventricles

source_name: sham-operated_saline treated

value: male

tag: rat weight

value: sham-operated


title: Sham_2

tag: surgery


title: SCCO-002 tumor vs. Normal ovary

value: European

tag: hypercalcemia

value: IA

value: 17 cm


title: SCCO-014 tumor vs. Normal ovary

value: Fresh frozen SCCO primary tumor

value: African American

value: Unknown

value: Endometriosis, endometriosis

value: OriGene Technologies

value: Normal ovary unaffected by endometriosis


title: SUM44 24hr E2 C

status: Public on Jan 16 2014

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Gene expression data from hormone deprived SUM44 breast cancer cells following 24hr treatment with 1nM estradiol

hyb_protocol: cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA).

scan_protocol: cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility.

data_processing: The data is RMA normalized using 'affy' package in R-Bioconductor

source_name: Hormone deprived SUM44 cells in culture following treatment

label_protocol: cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies).

growth_protocol: Cells were hormone deprived by replacing growth medium with IMEM+10% charcoal stripped serum for 3 days.

extract_protocol: Following treatment, cells were lysed and RNA was harvested using the Illustra RNAspin Mini kit (GE Health)

treatment_protocol: Following deprivation, cells were treated for 3 or 24 hours with 1nM E2 or vehicle (0.01% EtOH).

value: Cell culture

tag: source

value: Asterand

tag: cell line

tag: treatment

value: baseline

tag: time


title: ML066T_CD19

tag: disease

value: tumor


title: Sham_3

value: Sprague Dawley

tag: gender

tag: treated with

value: saline (control)


title: ML047N_CD3

value: normal


title: SUM44 24hr E2 B


title: SUM44 24hr Vehicle B

description: Gene expression data from hormone deprived SUM44 breast cancer cells following 24hr treatment with 0.01% EtOH

value: vehicle


title: ML066N_CD3


title: SUM44 24hr Vehicle D


title: ML055T_lambda


title: SUM44 24hr Vehicle C


title: SUM44 3hr E2 D

description: Gene expression data from hormone deprived SUM44 breast cancer cells following 3hr treatment with 1nM estradiol


title: SUM44 24hr E2 A


title: SUM44 24hr Vehicle A


title: SUM44 3hr Vehicle A

description: Gene expression data from hormone deprived SUM44 breast cancer cells following 3hr treatment with 0.01% EtOH


title: SUM44 3hr E2 C


title: SUM44 3hr E2 A


title: SUM44 0hr D

description: Gene expression data from hormone deprived SUM44 breast cancer cells

source_name: Hormone deprived SUM44 cells in culture


title: SUM44 3hr Vehicle B


title: SUM44 3hr Vehicle C


title: ML030T_kappa_CD20


title: SUM44 3hr Vehicle D


title: ML051T_lambda


title: ML051N_CD3


title: SUM44 0hr A


title: MM134 24hr E2 C

description: Gene expression data from hormone deprived MM134 breast cancer cells following 24hr treatment with 1nM estradiol

source_name: Hormone deprived MM134 cells in culture following treatment

value: ATCC


title: SUM44 0hr B


title: ML055N_CD3


title: ML042N_CD3


title: ML042T_kappa


title: MM134 24hr E2 D


title: MM134 24hr E2 B


title: ML047T_lambda


title: MM134 24hr Vehicle D

description: Gene expression data from hormone deprived MM134 breast cancer cells following 24hr treatment with 0.01% EtOH


title: ML013T_lambda


title: MM134 24hr Vehicle B


title: MM134 3hr E2 C

description: Gene expression data from hormone deprived MM134 breast cancer cells following 3hr treatment with 1nM estradiol


title: MM134 3hr Vehicle B

description: Gene expression data from hormone deprived MM134 breast cancer cells following 3hr treatment with 0.01% EtOH


title: MM134 3hr E2 A


title: ML030N_CD3


title: MM134 24hr Vehicle C


title: ML013N_CD3


title: MM134 24hr E2 A


title: MM134 3hr Vehicle D


title: MM134 3hr E2 D


title: ML002T_kappa_CD20


title: MM134 3hr Vehicle C


title: MM134 3hr E2 B


title: MM134 0hr D

description: Gene expression data from hormone deprived MM134 breast cancer cells

source_name: Hormone deprived MM134 cells in culture


title: MM134 3hr Vehicle A


title: SUM44 24hr E2 D


title: MM134 0hr B


title: SUM44 0hr C


title: MM134 24hr Vehicle A


title: MM134 0hr A


title: ML002N_CD3


title: MM134 0hr C


title: mirna-5219n

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

hyb_protocol: Total labeled RNA was hybridized to the GeneChip Human Exon 1.0 ST (Affymetrix) array according to the manufacturer's recommendations.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. All chip probes were used for background estimation but only human probes were considered for normalization and summarization phases.

source_name: normal colon mucosa, sigmoid colon

label_protocol: 100 ng of total RNA from each sample were labeled with the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

extract_protocol: Total RNA was extracted from frozen samples using Trizol reagent (Invitrogen Life Technology Inc., USA) as recommended by the manufacturer. The concentration of RNA was quantified by NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Waltham, MA). RNA quality was evaluated by RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA) on the Agilent 2100 Bioanalyzer. The quality was measured by using RNA integrity number (RIN) and samples with RIN < 6 were excluded.

value: F

tag: site

value: sigmoid colon

tag: age

tag: grading

tag: tnm

value: synchronous


title: mirna-3388n

source_name: normal colon mucosa, colon ascending

value: M

value: colon ascending

value: metachronous


title: mirna-5092t

source_name: colon cancer, colon

value: colon


title: mirna-4470n


title: mirna-11140m

source_name: colon cancer metastasis (liver), synchronous

value: transverse colon


title: mirna-4096t

source_name: colon cancer, rectum

value: rectum


title: mirna-7392t

source_name: colon cancer, sigmoid colon


title: mirna-3831m


title: mirna-4254t


title: mirna-1150n

source_name: normal colon mucosa, rectum


title: mirna-5007m


title: mirna-10016m


title: mirna-1240n


title: mirna-7077t


title: mirna-7392m

source_name: colon cancer metastasis (liver), metachronous


title: mirna-7392n


title: mirna-11140t

source_name: colon cancer, transverse colon


title: mirna-10566m


title: mirna-6661n


title: mirna-7349n


title: mirna-6661m


title: mirna-9527t

source_name: colon cancer, cecum

value: cecum


title: mirna-9201m


title: mirna-9201n


title: mirna-3385n


title: mirna-5219t


title: mirna-6218n


title: mirna-8981m


title: mirna-6236n

source_name: normal colon mucosa, cecum


title: mirna-7077m


title: SUM44 3hr E2 B

tag: tissue

value: Cell culture

value: Asterand


title: mirna-6536n


title: mirna-6536t


title: mirna-9984n


title: mirna-9212t


title: mirna-3385t


title: mirna-11769m


title: mirna-7349t


title: mirna-8932m


title: mirna-4424n


title: mirna-5647t


title: mirna-5881t


title: mirna-5007t

source_name: colon cancer, colon ascending


title: mirna-3976n


title: mirna-9597t

source_name: colon cancer, colon descending

value: colon descending


title: mirna-5773n


title: mirna-6661t


title: mirna-5647m


title: mirna-3976m


title: mirna-9984m


title: mirna-6021n

source_name: normal colon mucosa, splenic [left] flexure

value: splenic [left] flexure


title: mirna-9527n


title: mirna-5773m


title: mirna-3976t


title: mirna-9597n

source_name: normal colon mucosa, colon descending


title: mirna-10397m


title: mirna-9913m


title: mirna-5525m


title: mirna-10008t


title: mirna-12188m


title: mirna-9821n


title: mirna-9821m


title: mirna-5647n


title: mirna-5881m


title: mirna-12188t

source_name: colon cancer, splenic [left] flexure


title: mirna-9984t


title: mirna-3388m


title: mirna-2936t


title: mirna-5700t


title: mirna-10566t


title: mirna-5773t


title: mirna-5527t


title: mirna-3388t


title: mirna-6233n


title: mirna-10397t


title: mirna-6021t


title: mirna-5525t


title: mirna-6236m


title: mirna-9821t


title: Xenograft_HumanBreastCancer_MAS98.06

city: Oslo

first: Einar

middle: Andreas

last: Rødland

address: Montebello

department: Institute for Cancer Research

country: Norway

institute: Oslo University Hospital HF - Radiumhospitalet

description: Gene expression from mouse xenograft of human breast cancer

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol (Agilent One-Color Microarray-Based Gene Expression Analysis v6.5) using 600 ng cy3-labeled cRNA per sample and SurePrint G3 Human Gene Expression 8x60K Microarrays.

scan_protocol: The microarrays were scanned using Agilent Technologies Microarray Scanner (G2505C). Data were extracted from the scanned images using Feature Extraction software (Agilent Technologies), version 10.7 and protocol GE1-107-Sep09 for mRNA, using default settings and FULL text output.

data_processing: Raw intensities were corrected for spatial variation using the multiplicative correction factor provided by the Agilent Feature Extraction software and subsequently log2-transformed. Control features were removed. Features flagged as non-uniform outliers were excluded. For replicated probes, features flagged as population outliers were removed, and the average over features containing the same probe computed to represent the probe signal (log2-transformed). The log2-transformed signals, one value per probe per sample, were then quantile normalised, resulting in normalised log2-transformed signal intensities. Local least square imputation (method llsImpute from the R package pcaMethods with parameter k=20) was used to impute missing values, i.e. those excluded as non-uniform outliers. The normalised data with missing values imputed is made available as the main data set. And additional data set (see GSE44666-linked supplementary file: hbcx_probe_qnorm_missimp_cent2_log2.dat.txt), used for determining cancer subtypes, has been gene centered by subtracting the average expression from a population representative cohort of 152 breast cancers normalised by the same procedure.

source_name: mouse xenograft of human breast cancer

label_protocol: 100-125 ng total RNA was amplified and labeled with cy3-CTP following Agilent Low Input Quick Amplification Labeling Kit protocol for One-Color Microarray-Based Gene Expression Analysis

extract_protocol: Total RNA from snap frozen xenograft tissue samples was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA concentration was measured using NanoDrop (NanoDrop Technologies) and the quality was evaluated using 2100 Bioanalyzer (Agilent Technologies).

value: Patient-derived breast cancer xenograft

tag: cancer subtype

value: Luminal B

tag: xenograft host

value: mouse


title: Xenograft_HumanBreastCancer_HBCx-39

value: Basal


title: Xenograft_HumanBreastCancer_HBCx-41


title: Xenograft_HumanBreastCancer_HBCx-30


title: Xenograft_HumanBreastCancer_HBCx-40

value: HER2 enriched


title: Xenograft_HumanBreastCancer_HBCx-4B


title: Xenograft_HumanBreastCancer_HBCx-26


title: Xenograft_HumanBreastCancer_MAS98.12


title: Xenograft_HumanBreastCancer_HBCx-24


title: Xenograft_HumanBreastCancer_HBCx-21

value: Luminal A


title: Xenograft_HumanBreastCancer_HBCx-3


title: Xenograft_HumanBreastCancer_HBCx-31


title: Xenograft_HumanBreastCancer_HBCx-27


title: Xenograft_HumanBreastCancer_HBCx-34


title: Xenograft_HumanBreastCancer_HBCx-28


title: Xenograft_HumanBreastCancer_HBCx-14


title: Xenograft_HumanBreastCancer_HBCx-13B


title: Xenograft_HumanBreastCancer_HBCx-12A


title: Xenograft_HumanBreastCancer_HBCx-16


title: Xenograft_HumanBreastCancer_HBCx-17


title: Xenograft_HumanBreastCancer_HBCx-8


title: Xenograft_HumanBreastCancer_HBCx-10


title: Xenograft_HumanBreastCancer_HBCx-7


title: Xenograft_HumanBreastCancer_HBCx-12B


title: Xenograft_HumanBreastCancer_HBCx-9


title: Xenograft_HumanBreastCancer_HBCx-13A


title: Xenograft_HumanBreastCancer_HBCx-1


title: Xenograft_HumanBreastCancer_HBCx-15


title: MRC-5-2

city: Dallas

first: Chun-Li

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern

description:
replicate 2
MRC2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genome Studio software (v.2011.1).

source_name: fetal lung fibroblasts

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

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

value: male

value: 14 weeks gestation

value: lung

tag: cell/tissue type

value: fetal lung fibroblasts


title: Xenograft_HumanBreastCancer_HBCx-19


title: Xenograft_HumanBreastCancer_HBCx-5


title: Spinal cord2

description:
replicate 2
SC2

source_name: spinal cord

value: pool

value: 20-59 years old

value: spinal cord

tag: sample type

value: Commercially available total RNAs (control)


title: Spinal cord1

description:
replicate 1
SC1


title: exon-4470n

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package using the Dai custom CDF package: HuEx10stv2_Hs_ENTREZG

source_name: normal colon mucosa, sigmoid colon

value: F

value: sigmoid colon

value: synchronous


title: IMR-90-N2-21d

description:
replicate 2
IMR-N2

source_name: NGN2-converted cells from IMR-90 fibroblasts at 21 days post viral transduction

value: converted cholinergic neurons


title: CNS_FruMCpupae_Exp1

city: Oxford

first: Megan

last: Neville

address: South Park Road

department: DPAG

country: United Kingdom

institute: University of Oxford

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Drosophila melanogaster

source_name: DamFruMC

label_protocol: standard Nimblegen protocol

growth_protocol: Sexed L3 'wandering larvae were grown on Oxford media for 46 hr.

extract_protocol: Larvae: L3 ‘wandering’ larvae were collected and sexed. Male CNSs were dissected in DamID buffer (5 mM EDTA, 100 mM Tris-HCl pH 8.5, 137 mM NaCl), and flash frozen on dry ice (~ 45 larval CNSs were used per experimental replicate). Pupae: L3 wandering larvae were sexed and males were collected and transferred to a Petri dish lined with Whatman paper soaked in 1xPBS. After 46 hrs, pupal CNSs were dissected in DamID buffer and flash frozen on dry ice (~ 45 pupal CNSs were used per experimental replicate). Adult: Virgin males were isolated from females and left to mature in small groups of 3-5 for 48 hrs. At this point, the flies were anesthetised with CO2 gas, and dipped briefly in ethanol before CNSs were dissected in DamID buffer, and flash frozen on dry ice (~ 30 adult brains and VNC were used per experimental replicate). DNA was extracted from pooled dissected CNSs using the Qiagen DNEasy Blood and Tissue kit. Due to our inclusion of EDTA in the DamID dissection buffer (used to inhibit DNase activity), RNaseA was omitted from the initial DNA extraction procedure, and was instead added after genomic DNA was ethanol precipitated and resuspended in 100µl dH2O (containing 0.5µg/ml RNaseA).  Digestion and Genomic DNA processing for DamID  For selective PCR amplification of methylated DNA fragments, 2.5 μg of genomic DNA for each replicate was digested for 16 hr at 37°C with ten units DpnI (NEB) in a total volume of 100 μl buffer 4 (NEB). After inactivation of DpnI at 80°C for 20 min, DpnI and RNaseA were removed using the QIAquick PCR purification kit (Qiagen) and eluted in 30 µl dH2O. 1.25 μg of the DpnI digested genomic DNA was ligated to 40 pmol of a double-stranded unphosphorylated adaptor (top strand, 5′-CTA ATA CGA CTC ACT ATA GGG CAG CGT GGT CGC GGC CGA GGA-3′; bottom strand, 5′-TCC TGC GCC-3′) for 16 hr at 16°C with five units T4-DNA Ligase (Roche) in a total volume of 20μl ligation buffer (Roche). To prevent amplification of DNA fragments containing unmethylated GATCs, the adaptor-ligated DNA was cut with five units DpnII (NEB) for 1 hour at 37°C in a total volume of 80 μl DpnII buffer (NEB). Next, amplification was performed with 20 μl DpnII-cut DNA (313 ng), 1.6 μl PCR Advantage enzyme mix (Clontech), 16 nmoles of dNTPs and 100 pmoles primer (5′-GGT CGC GGC CGA GGA tc-3′) in 80 μl total volume of PCR Advantage reaction buffer under the following cycling conditions: activation of the polymerase and nick translation for 10 min at 68°C, followed by one cycle of 1 min at 94°C, 5 min at 65°C, and 15 min at 68°C; three cycles of 1 min at 94°C, 1 min at 65°C, and 10 min at 68°C; and 19 cycles of 1 min at 94°C, 1 min at 65°C, and 2 min at 68°C. Final PCR samples were pooled and purified (Qiaquick PCR purification). Samples were eluted in 25µl dH2O and quantified using a NanoDrop (Thermo Scientific). Amplified DNA from experimental and Dam-only controls were labelled with either Cy3 or Cy5 and co-hybridized to NimbleGen 2.1M Drosophila whole genome tiling arrays (performed at Roche NimbleGen, Inc., USA). The exception being FruMC pupae, which was the first experiment to be completed, and was done so on a customised tiling array (van Steensel and Henikoff, 2000). For the 2.1 M arrays, probe length was 45bp, for the custom array they were 60bp. In each instance, one of the three replicates was dye swapped.     Larvae: L3 ‘wandering’ larvae were collected and sexed. Male CNSs were dissected in DamID buffer (5 mM EDTA, 100 mM Tris-HCl pH 8.5, 137 mM NaCl), and flash frozen on dry ice (~ 45 larval CNSs were used per experimental replicate). Pupae: L3 wandering larvae were sexed and males were collected and transferred to a Petri dish lined with Whatman paper soaked in 1xPBS. After 46 hrs, pupal CNSs were dissected in DamID buffer and flash frozen on dry ice (~ 45 pupal CNSs were used per experimental replicate). Adult: Virgin males were isolated from females and left to mature in small groups of 3-5 for 48 hrs. At this point, the flies were anesthetised with CO2 gas, and dipped briefly in ethanol before CNSs were dissected in DamID buffer, and flash frozen on dry ice (~ 30 adult brains and VNC were used per experimental replicate). DNA was extracted from pooled dissected CNSs using the Qiagen DNEasy Blood and Tissue kit. Due to our inclusion of EDTA in the DamID dissection buffer (used to inhibit DNase activity), RNaseA was omitted from the initial DNA extraction procedure, and was instead added after genomic DNA was ethanol precipitated and resuspended in 100µl dH2O (containing 0.5µg/ml RNaseA).For selective PCR amplification of methylated DNA fragments, 2.5 μg of genomic DNA for each replicate was digested for 16 hr at 37°C with ten units DpnI (NEB) in a total volume of 100 μl buffer 4 (NEB). After inactivation of DpnI at 80°C for 20 min, DpnI and RNaseA were removed using the QIAquick PCR purification kit (Qiagen) and eluted in 30 µl dH2O. 1.25 μg of the DpnI digested genomic DNA was ligated to 40 pmol of a double-stranded unphosphorylated adaptor (top strand, 5′-CTA ATA CGA CTC ACT ATA GGG CAG CGT GGT CGC GGC CGA GGA-3′; bottom strand, 5′-TCC TGC GCC-3′) for 16 hr at 16°C with five units T4-DNA Ligase (Roche) in a total volume of 20μl ligation buffer (Roche). To prevent amplification of DNA fragments containing unmethylated GATCs, the adaptor-ligated DNA was cut with five units DpnII (NEB) for 1 hour at 37°C in a total volume of 80 μl DpnII buffer (NEB). Next, amplification was performed with 20 μl DpnII-cut DNA (313 ng), 1.6 μl PCR Advantage enzyme mix (Clontech), 16 nmoles of dNTPs and 100 pmoles primer (5′-GGT CGC GGC CGA GGA tc-3′) in 80 μl total volume of PCR Advantage reaction buffer under the following cycling conditions: activation of the polymerase and nick translation for 10 min at 68°C, followed by one cycle of 1 min at 94°C, 5 min at 65°C, and 15 min at 68°C; three cycles of 1 min at 94°C, 1 min at 65°C, and 10 min at 68°C; and 19 cycles of 1 min at 94°C, 1 min at 65°C, and 2 min at 68°C. Final PCR samples were pooled and purified (Qiaquick PCR purification). Samples were eluted in 25µl dH2O and quantified using a NanoDrop (Thermo Scientific). Amplified DNA from experimental and Dam-only controls were labelled with either Cy3 or Cy5 and co-hybridized to NimbleGen 2.1M Drosophila whole genome tiling arrays (performed at Roche NimbleGen, Inc., USA). The exception being FruMC pupae, which was the first experiment to be completed, and was done so on a customised tiling array (van Steensel and Henikoff, 2000). For the 2.1 M arrays, probe length was 45bp, for the custom array they were 60bp. In each instance, one of the three replicates was dye swapped.

treatment_protocol: 46 hr. pupae were dissected out of their pupae casings.

value: CNS

tag: developmental stage

value: pupae

source_name: CNS DNA from Dam control line

tag: tag


title: exon-3388n

source_name: normal colon mucosa, colon ascending

value: M

value: colon ascending

value: metachronous


title: exon-5219n


title: exon-5092t

source_name: colon cancer, colon

value: colon


title: IMR-90-N1-21d

description:
replicate 1
IMR-N1


title: MRC-5-N1-21d

description:
replicate 1
MRC-N1

source_name: NGN2-converted cells from MRC-5 fibroblasts at 21 days post viral transduction


title: Brain2

description:
replicate 2
Brain2

source_name: whole brain

value: male

value: 43 years old

value: whole brain


title: MRC-5-N2-21d

description:
replicate 2
MRC-N2


title: MRC-5-1

description:
replicate 1
MRC1

value: 14 weeks gestation

value: lung

value: fetal lung fibroblasts


title: Brain1

description:
replicate 1
Brain1

value: Commercially available total RNAs (control)


title: CNS_FruMCpupae_Exp2


title: IMR-90-1

description:
replicate 1
IMR1

value: female

value: 16 weeks gestation


title: exon-7392t

source_name: colon cancer, sigmoid colon

value: F

value: sigmoid colon


title: exon-1240n

source_name: normal colon mucosa, rectum

value: rectum

value: synchronous


title: exon-1150n


title: exon-4096t

source_name: colon cancer, rectum

value: M


title: exon-4254t


title: exon-5007m

source_name: colon cancer metastasis (liver), synchronous

value: colon ascending


title: exon-11140m

value: transverse colon


title: exon-10566m


title: exon-6661n


title: exon-9201m


title: exon-11140t

source_name: colon cancer, transverse colon


title: exon-3831m


title: exon-7077t


title: Control Replicate 4

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

description:
con_4
Array 10

hyb_protocol: This was performed following protocols from Agilent. Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and  hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida.

data_processing:
Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis.
Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays.  To identify the genes that were differentially regulated (DR) between the treated and control fetuses, the normalized and transformed intensities were analyzed by one-way ANOVA (p<0.01).   All the statistical procedures were carried out using JMP Genomics 5 software (SAS Institute Inc, Cary, NC, USA).

organism: Ovis aries

source_name: hypothalamus 60 min after onset of 30 min normoxia

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.0 to 12.8 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the hypothalamus using Trizol (Invitrogen, Carlsbad, CA) , followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA).The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.  RNA Integrity Number (RIN) values ranged from 7.4 to 8.4.

treatment_protocol: Chronically catheterized late gestation fetal sheep were subjected to transient (30 min) maternal ventilatory hypoxia (n=3) or normoxia (n=4) followed by 30 min normoxia.  Hypothalami were collected at the end of normoxia recovery period, and compared to hypothalami from age-matched controls not subjected to hypoxia.

value: fetal

tag: stress

value: Control

value: hypothalamus


title: exon-10016m


title: Control Replicate 1

description:
con_1
Array 7


title: Hypoxia Replicate 3

description:
VH_3
Array 3

source_name: hypothalamus 60 min after onset of 30 min hypoxia

value: Hypoxia


title: Hypoxia Replicate 2

description:
VH_2
Array 2


title: Control Replicate 2

description:
con_2
Array 8


title: exon-7392n

value: metachronous


title: exon-7392m

source_name: colon cancer metastasis (liver), metachronous


title: Hypoxia Replicate 1

description:
VH_1
Array 1


title: exon-3385n


title: exon-6661m


title: mesenteric, visceral adipose tissue, repA

city: Boston

first: Paul

last: Cohen

state: MA

address: 450 Brookline Ave, CLSB11118

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C to Affymetrix mouse genome 430A v2.0 arrays, according to established methods.

scan_protocol: Labeling, hybridization, and scanning were performed by the Dana-Farber Cancer Institute Microarray Core Facility using established methods.

data_processing: The data were normalized and analyzed usig the dChip software.

source_name: mesenteric visceral adipose tissue, RNA pooled from 3 mice

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

growth_protocol: Mice were housed in standard conditions and few a rodent chow diet

extract_protocol: Total RNA was isolated with Trizol and purified using Qiagen RNEasy mini columns according to the manufacturer's instructions.

value: 8-10 wk old

tag: Sex

value: male

tag: strain

value: mesenteric visceral adipose tissue


title: exon-7349n

source_name: normal colon mucosa, sigmoid colon


title: axillary, subcutaneous adipose tissue, repB

source_name: axillary subcutaneous adipose tissue, RNA pooled from 3 mice

value: axillary subcutaneous adipose tissue


title: mesenteric, visceral adipose tissue, repC


title: axillary, subcutaneous adipose tissue, repC


title: exon-5219t


title: mesenteric, visceral adipose tissue, repB


title: axillary, subcutaneous adipose tissue, repA


title: exon-9201n


title: epididymal, visceral adipose tissue, repA

source_name: epididymal visceral adipose tissue, RNA pooled from 3 mice

value: epididymal visceral adipose tissue


title: inguinal, subcutaneous adipose tissue, repA

source_name: inguinal subcutaneous adipose tissue, RNA pooled from 3 mice

value: inguinal subcutaneous adipose tissue


title: epididymal, visceral adipose tissue, repB


title: exon-6218n


title: epididymal, visceral adipose tissue, repC


title: exon-8981m


title: inguinal, subcutaneous adipose tissue, repB


title: exon-6536n

value: sigmoid colon


title: exon-6236n

source_name: normal colon mucosa, cecum

value: F

value: cecum


title: inguinal, subcutaneous adipose tissue, repC


title: exon-4424n

source_name: normal colon mucosa, colon ascending

value: M

value: synchronous


title: exon-9597m

value: colon descending


title: exon-9527t

source_name: colon cancer, cecum


title: Foxa2_NPCs_rep1

city: Seoul

first: Sang-Hun

last: Lee

address: 222 Wangsimni-ro, Seongdong-gu

department: biochemistry and molecular biology

country: South Korea

institute: College of medicine, Hanyang University

description: replicate 1

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. Array probes that have detection p-value > 0.05 (similar to signal to noise) in over 50% samples were filtered out before normalization. (We applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05) Selected gene signal value was transformed by logarithm and normalized by quantile method.

source_name: NPCs treated retrovirus Foxa2

growth_protocol: Neural precursor cells (NPCs) were isolated and cultured from mouse cortices at embryonic days 12. NPCs were proliferated with bFGF (20 ng/m) and EGF (20 ng/ml) in serum-free N2 medium supplemented with ascorbic acid and B27 for expasion. Viral transductions were carried out in the proliferating cultures as described in the treatment protocol. Differentiation of transduced NPCs was induced by withdrawing bFGF and EGF for 2 days.

extract_protocol: Total RNA was extracted with Trizol reagent according to the instructions of manufacturer.

treatment_protocol: Retroviral vectors expressing Nurr1 or Foxa2 were constructed by inserting the respective cDNA into pCL. The empty pCL vector was used as a negative control. For viral transduction, NPCs cultured in vitro were incubated with the viral supernatant for 2 hours, followed by a medium change.

value: ICR

value: embryonic day 12

value: embryonic cortical brain


title: Nurr1+Foxa2_NPCs_rep1

description: replicate 1

source_name: NPCs treated retrovirus Nurr1-Foxa2


title: exon-7077m

value: rectum


title: exon-11769m


title: Nurr1_NPCs_rep1

description: replicate 1

source_name: NPCs treated retrovirus Nurr1


title: exon-6536t

source_name: colon cancer, sigmoid colon


title: exon-9527n

value: metachronous


title: exon-9984n

source_name: normal colon mucosa, rectum


title: Control_NPCs_rep1

description: replicate 1

source_name: NPCs treated retrovirus control


title: exon-9212t

source_name: colon cancer, rectum


title: exon-3385t


title: exon-7349t


title: exon-8932m

source_name: colon cancer metastasis (liver), synchronous


title: exon-5647t


title: Pooled_P. vivax_complicated malaria samples and one P. vivax_un-complicated malaria sample (Cy3/background intensity)

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

hyb_protocol: The labeled cRNA samples were hybridized to Plasmodium vivax Custom 244k Array designed by Genotypic Technology Private Limited and Prof.Ashis K Das (AMADID:019103) with Gene Expression Hybridization Kit (Agilent Technologies, part number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Gene Expression wash buffers (Agilent Technologies, Part No: 5188-5327).

scan_protocol: Scanning was performed using the Agilent Microarray Scanner (Agilent, Palo Alto, CA, G Model G2565BA) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software (Agilent Technologies). Channel split Analysis was performed. Data was analyzed separately for complicated (Cy5) and un-complicated (Cy 3) samples. The raw signal intensities and back ground intensities were obtained from the raw data files for each channel. Based on the annotation and probe orientation the probes were classified as sense and antisense probes. Ratio was calculated by taking the raw signal intensity vs. background signal intensity for each of the probes.

organism: Plasmodium vivax

source_name: P. vivax parasites from patients blood

label_protocol: The one un-complicated P. vivax RNA sample and the seven complicated parasite samples (pooled) were labeled in equimolar amounts. The labeling was performed using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technolgies). 500ng each of the pooled complicated (test) samples and one un-complicated (control) sample were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The double stranded cDNA was used as template for cRNA generation. This was performed by in vitro transcription and during this process Cy3 and Cy5 CTP dyes (Agilent) were incorporated for un-complicated and complicated malaria samples respectively. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: P. vivax isolates collected directly from infected patients with differing clinical symptoms

extract_protocol: Total RNA extracted using TriReagent (Sigma Aldrich, USA) following manufacturer's instructions

treatment_protocol: Blood was immediately (Within 15 minutes of collection) subjected to density gradient based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the Peripheral Blood Mononuclear Cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with Phosphate buffered saline (PBS) twice and lysed using 4 volumes of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

tag: clinical presentation

value: un-complicated malaria

tag: age (1#pvu_1)

value: complicated malaria (pooled 7 samples)

tag: age (1#pvc_1)

tag: gender (1#pvc_1)

tag: age (2#pvc_2)

tag: gender (2#pvc_2)

tag: age (3# pvc_3)

tag: gender (3# pvc_3)

tag: age (4#pvc_4)

tag: gender (4#pvc_4)

tag: age (5#pvc_5)

tag: gender (5#pvc_5)

tag: age (6#pvc_6)

tag: gender (6#pvc_6)

tag: age (7# pvc_7)

tag: gender (7# pvc_7)


title: exon-9597t

source_name: colon cancer, colon descending

tag: gender

tag: site

tag: age

tag: grading

tag: tnm


title: exon-6661t


title: Pooled_P. vivax_complicated malaria samples and one P. vivax_un-complicated malaria sample (Cy5/background intensity)

tag: clinical presentation

tag: age (1#pvu_1)

tag: age (1#pvc_1)

tag: gender (1#pvc_1)

tag: age (2#pvc_2)


title: exon-8850m

value: splenic [left] flexure


title: exon-5773n


title: exon-3976n


title: exon-5007t

source_name: colon cancer, colon ascending

value: colon ascending


title: Control Replicate 3

description:
con_3
Array 9

source_name: hypothalamus 60 min after onset of 30 min normoxia

tag: developmental stage

value: fetal

tag: stress

value: Control

tag: tissue

value: hypothalamus


title: exon-12188m


title: exon-5881t

value: sigmoid colon


title: exon-9597n

source_name: normal colon mucosa, colon descending


title: exon-10008t


title: exon-7349m


title: exon-5881m

source_name: colon cancer metastasis (liver), metachronous


title: exon-3976t


title: exon-5773m

value: F

value: cecum


title: exon-5647m

value: M

value: synchronous


title: exon-3976m


title: exon-5647n

source_name: normal colon mucosa, sigmoid colon


title: Hu_VN1203_pCalu3_7h_4

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: After control probes filtering : 58,717 probes including 8118 duplicated probes 3. After SUMMARIZATION OF non-CTRL PROBES: 50,599 probes 4. Filtering of probes: we require that the probes pass the following QC in at least 100% samples of 1 infected time-point: gIsFound, gIsWellAboveBG, gIsSaturated: no probe was excluded based on that criteria, gIsFeatNonUnifOL, and gIsFeatPopnOL. Probes passing qc: 29,382 probes only.

source_name: Human, virus, polarized calu-3 cells, timepoint, replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The human bronchial epithelial cell line Calu-3 was originally derived from subbronchial epithelium of a lung adenocarcinoma (ATCC) and cells were grown in Eagle's minimal essential medium (MEM) supplemented with 2 mM l-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 1.5 g/liter sodium bicarbonate, and 10% fetal bovine serum. Calu-3 cells (5 × 105) were seeded onto Corning 24-mm-diameter semipermeable membrane inserts with a 0.4-μm pore size (Corning, NY) and cultured for 1 week with the addition of fresh culture medium every 2 to 3 days.  Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

tag: cell line

value: polarized Calu3 cells

tag: infection

tag: time


title: exon-9821n

source_name: normal colon mucosa, colon ascending


title: Hu_VN1203_pCalu3_7h_2

treatment_protocol: Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.


title: exon-9984m


title: Hu_VN1203_pCalu3_7h_3


title: exon-10397m


title: Hu_VN1203_pCalu3_7h_1


title: Hu_VN1203_pCalu3_3h_4


title: Hu_VN1203_pCalu3_3h_3


title: exon-6021n

source_name: normal colon mucosa, splenic [left] flexure


title: exon-9913m


title: exon-5525m


title: exon-9821m


title: CNS_FruMClarvae_Exp3

hyb_protocol: Performed by Nimblegen

scan_protocol: Performed by Nimblegen

source_name: DamFruMC

label_protocol: Performed by Nimblegen

growth_protocol: Freshly laid eggs were grown on Oxford media until they reached L3 'wandering' larvae stage

treatment_protocol: L3 'wandering' larvae were sexed through observation of gonads, the CNS was dissected out.

value: male

value: CNS

value: larvae

source_name: CNS DNA from Dam control line


title: Hu_VN1203_pCalu3_24h_4


title: CNS_FruMClarvae_Exp2


title: CNS_FruMBadult_Exp1

source_name: DamFruMB

growth_protocol: Virgin males were grown on Oxford media for 48 hr.

treatment_protocol: CNS were dissected from 48 hr. males.

value: adult


title: CNS_FruMCadult_Exp2


title: CNS_FruMBpupae_Exp3

value: pupae


title: Hu_VN1203_pCalu3_24h_3


title: exon-9984t

value: rectum


title: CNS_FruMBadult_Exp3


title: exon-3388m

value: metachronous


title: CNS_FruMAadult_Exp1

source_name: DamFruMA


title: CNS_FruMBpupae_Exp2


title: Hu_VN1203_pCalu3_24h_2


title: Hu_VN1203_pCalu3_24h_1


title: Hu_VN1203_pCalu3_3h_2


title: exon-12188t

source_name: colon cancer, splenic [left] flexure

value: splenic [left] flexure


title: Hu_VN1203_pCalu3_12h_3


title: exon-2936t

value: colon descending


title: Hu_VN1203_pCalu3_12h_2


title: CNS_FruMCadult_Exp3


title: exon-10566t

source_name: colon cancer, rectum


title: exon-5527t

source_name: colon cancer, sigmoid colon


title: CNS_FruMCadult_Exp1


title: CNS_FruMClarvae_Exp1


title: exon-6021t


title: exon-6236m

source_name: colon cancer metastasis (liver), synchronous


title: CNS_FruMBlarvae_Exp3


title: Hu_Pan99_pCalu3_7h_4


title: exon-5700t


title: CNS_FruMBpupae_Exp1


title: Hu_Pan99_pCalu3_7h_3


title: CNS_FruMApupae_Exp2


title: NaB treated exp 5

city: Scranton

last: Bordonaro

address: 525 Pine Street

department: Basic Sciences

institute: The Commonwealth Medical College

description:
Gene expression
NaB Exp 5

hyb_protocol: cRNA was fragmented to uniform size and hybridized to Agilent Human v2 Whole Genome 4x44K arrays (Design ID 026652).

scan_protocol: Slides were washed and scanned on the Agilent G2565 Microarray Scanner.

data_processing:
Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).
Analytical approach:
The overall analytical approach was to use human whole genome microarray analyses to first identify the identity of all genes whose expression was up- or downregulated by butyrate, in a statistically significant manner, by two-fold or more, in the absence of doxycycline induction of DN-Tcf4.  We then repeated the analysis in the presence of doxycycline, and considered those genes whose expression was modulated by butyrate in the absence of doxycycline (fully intact Wnt signaling) but not similarly modulated in the presence of doxycycline (repressed Wnt signaling).
Thus, we were interested in identifying those genes that are differentially expressed (> two-fold, P< 0.01) in the NaB vs. Ctrl comparison but not differentially expressed (> two-fold, P< 0.01) in the Doxy + NaB vs. Doxy comparison.  The NaB vs., Ctrl comparison yields all genes differentially expressed after exposure to 5 mM butyrate, while the Doxy + NaB vs. Doxy comparison yields all butyrate-modulated genes except those that are Wnt targets, since the doxycycline induction combined with butyrate treatment efficiently results in DN-Tcf4 expression, which inhibits Wnt signaling and Wnt-dependent gene expression.
Analyzed_data_Differentially_Expressed_Genes.xls is linked as a supplementary file on the Series record.

source_name: transfected HCT-116 cells

label_protocol: First and second strand cDNA was prepared from the total RNA samples. cRNA  target was prepared from the DNA template and verified on the Bioanalyzer.

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.  RNA was purified using Ribopure (Ambion) RNA isolation kit. Total RNA samples were quantitated by UV spectrophotometry (OD260/280). Quality of the total RNA was assessed by using and Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: treatment was for 17.5 hr +/- 4 ug/ml doxycycline and/or 5 mM sodium butyrate

tag: treatment

value: control

tag: agent

value: sodium butyrate


title: CNS_FruMBlarvae_Exp2

tag: gender


title: exon-6233n

tag: site

value: sigmoid colon

tag: age


title: CNS_FruMAadult_Exp2


title: CNS_FruMAadult_Exp3


title: CNS_FruMBlarvae_Exp1


title: CNS_FruMApupae_Exp3


title: CNS_FruMApupae_Exp1


title: CNS_FruMAlarvae_Exp2


title: CNS_FruMAlarvae_Exp3


title: CNS_FruMBadult_Exp2


title: Hu_Pan99_pCalu3_7h_2


title: CNS_FruMAlarvae_Exp1


title: exon-5525t

tag: grading

tag: tnm


title: Hu_Pan99_pCalu3_7h_1


title: NaB treated exp 3

description:
Gene expression
NaB Exp 3


title: NaB treated exp 2

description:
Gene expression
NaB Exp 2


title: NaB treated exp 1

description:
Gene expression
NaB Exp 1


title: exon-9821t

source_name: colon cancer, colon ascending

value: colon ascending


title: Hu_VN1203_pCalu3_12h_1


title: double treated exp 6

description:
Gene expression
Doxy/NaB Exp 6

value: dox-induced DN-Tcf4 expression to repress Wnt signaling


title: Hu_Pan99_pCalu3_3h_4


title: double treated exp 4

description:
Gene expression
Doxy/NaB Exp 4


title: Hu_Pan99_pCalu3_3h_2


title: double treated exp 1

description:
Gene expression
Doxy/NaB Exp 1


title: double treated exp 2

description:
Gene expression
Doxy/NaB Exp 2


title: double treated exp 3

description:
Gene expression
Doxy/NaB Exp 3


title: doxy treated exp 6

description:
Gene expression
Doxy Exp 6

value: mock-treated


title: double treated exp 5

description:
Gene expression
Doxy/NaB Exp 5


title: EL RA 6_20d 0106011728(13)

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

description:
EL RA 6_20d 0106011728(13) 106011728(13)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

hyb_protocol: signal quantification of hybridized PIQORTM cDNA arrays were performed with the ScanArray3000 (GSI Lumonics, Watertown, MA).

scan_protocol: images were quantified and analysed by ImaGene software version 4.1 (Bio Discovery, Los Angeles, CA)

data_processing: LOWESS normalization

source_name: vehicle

label_protocol: 2 µl of FluoroLinkTM Cy3and Cy5-dCTP (Amersham Pharmacia Biotech, Freiburg, Germany), 4 µl of 0.1 M DTT and 1 µl of RNasin (20–40 U) (Promega), One µl (200 U) of Superscript TM II enzyme was added, incubated at 42°C for 30 min followed by the addition of a further 1 µl of SSII enzyme and again incubated in the same conditions.50 µl of  equal volume of 2x hybridization solution (MEMOREC) pre-warmed to 42°C was added to the cy3 and cy5 labelled samples. Hybridization was performed according to manufacturer's guidelines (MEMOREC) using a Gene TACTM hybridization station (Perkin Elmer, Langen, Germany).

growth_protocol: Pregnant female Wistar rats were dosed daily with either EMD 82571 (50 or 150 mg/kg/day, low and high dose of EMD, respectively) or retinoic acid (12 mg/kg/day) on gestational days 6-11 and 6-17, respectively.

extract_protocol: The mRNA was then reverse-transcribed by adding it to a mix consisting of 8 µl of 5x first-strand buffer (Invitrogen), 2 µl of Primer-Mix [oligo (dT) and randomeres] (MEMOREC, Köln, Germany), 2 µl of low C dNTPs (10 mM dATP, 10 mM dGTP, 10 mM dTTP, 4 mM dCTP).

treatment_protocol: One hundred µg of total RNA was combined with control RNA consisting of an in vitro-transcribed Escherichia coli genomic DNA fragment carrying a 30 nucleotide poly(A)+tail (CR1) and the resulting mRNA was subsequently isolated using Oligotex mRNA Mini Kit (Qiagen).

value: Embryo Liver

value: vehicle

tag: strain

value: Wistar

source_name: Embryo Liver 20mg RA 20day

value: 20mg RA


title: ML RA 6_20d 0106011728(18)

description:
ML RA 6_20d 0106011728(18) 106011728(18)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: Maternal Liver

source_name: Maternal Liver  20mg RA 20day


title: ML RA 6_20d 0106011728(17)

description:
ML RA 6_20d 0106011728(17) 106011728(17)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: NaB treated exp 6

description:
Gene expression
NaB Exp 6


title: Hu_Pan99_pCalu3_3h_1

value: polarized Calu3 cells


title: EL RA 6_20d 0106011728(12)

description:
EL RA 6_20d 0106011728(12) 106011728(12)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: EB RA 6_20d 2905010941(20)

description:
EB RA 6_20d 2905010941(20) 2905010941(20)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: Embryo Bone

source_name: Embryo Bone 20mg RA 20day


title: doxy treated exp 3

description:
Gene expression
Doxy Exp 3


title: Hu_VN1203_pCalu3_12h_4

source_name: Human, virus, polarized calu-3 cells, timepoint, replicate


title: doxy treated exp 4

description:
Gene expression
Doxy Exp 4


title: EB RA 6_20d 2905010941(19)

description:
EB RA 6_20d 2905010941(19) 2905010941(19)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: doxy treated exp 5

description:
Gene expression
Doxy Exp 5


title: untreated exp 4

description:
Gene expression
Ctrl Exp 4


title: doxy treated exp 2

description:
Gene expression
Doxy Exp 2


title: untreated exp 6

description:
Gene expression
Ctrl Exp 6


title: untreated exp 5

description:
Gene expression
Ctrl Exp 5


title: Hu_Pan99_pCalu3_12h_3


title: doxy treated exp 1

description:
Gene expression
Doxy Exp 1


title: EMD_EB_150_20d 2905010941(15)

description:
EMD_EB_150_20d 2905010941(15) 2905010941(15)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Embryo Bone 150mg EMD 20day

value: 150mg EMD


title: untreated exp 3

description:
Gene expression
Ctrl Exp 3


title: Hu_Pan99_pCalu3_24h_2


title: exon-10397t

value: M

value: synchronous


title: Hu_Pan99_pCalu3_24h_1


title: untreated exp 1

description:
Gene expression
Ctrl Exp 1


title: EMD_EB_50_20d 2905010941(14)

description:
EMD_EB_50_20d 2905010941(14) 2905010941(14)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Embryo Bone 50mg EMD 20day

value: 50mg EMD


title: untreated exp 2

description:
Gene expression
Ctrl Exp 2

value: control


title: Hu_Pan99_pCalu3_24h_3


title: EMD_EL_150_20d 2905010941(13)

description:
EMD_EL_150_20d 2905010941(13) 2905010941(13)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Embryo Liver 150mg EMD 20day


title: EMD_ML_150_20d 2905010941(11)

description:
EMD_ML_150_20d 2905010941(11) 2905010941(11)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Maternal Liver 150mg EMD 20day


title: EMD_EL_50_20d 2905010941(12)

description:
EMD_EL_50_20d 2905010941(12) 2905010941(12)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Embryo Liver 50mg EMD 20day


title: Hu_Pan99_pCalu3_12h_4


title: Hu_Pan99_pCalu3_12h_1


title: Hu_Pan99_pCalu3_12h_2


title: CBX8-shRNA

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

description: Gene expression in HepG2 cells with constructs expressing shRNA that specifically targets CBX8.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from shLuc, shEZH2, shSUZ12, shCBX8 and shBMI1 HepG2 cells using TRIzol (Invitrogen). The RNA samples were hybridized to the microarray according to the manufacturer’s protocol. For each experimental sample, Cy5- and Cy3-labeled samples were co-hybridized to a cDNA microarray containing 41,000 human cDNAs (Agilent Technologies).

treatment_protocol: The HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco)  supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% penicillin–streptomycin.


title: SUZ12-shRNA

description: Gene expression in HepG2 cells with constructs expressing shRNA that specifically targets SUZ12.


title: EMD_EB_50_20d 2905010941(08)

description:
EMD_EB_50_20d 2905010941(08) 2905010941(08)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: EMD_EB_150_20d 2905010941(09)

description:
EMD_EB_150_20d 2905010941(09) 2905010941(09)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: BMI1-shRNA

description: Gene expression in HepG2 cells with constructs expressing shRNA that specifically targets BMI1.


title: EZH2-shRNA

description: Gene expression in HepG2 cells with constructs expressing shRNA that specifically targets EZH2.


title: RetroQ

description: Gene expression in HepG2 cells with RetroQ vector

source_name: RetroQ


title: Hu_NL219_pCalu3_7h_2


title: Hu_NL219_pCalu3_7h_3


title: p53Ab8 monoclonal

type: other

city: Tempe

first: Phillip

last: Stafford

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

description: Alexa-647 conjugated Streptavidin tertiary

hyb_protocol: No hybridization was done, but antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, Physical characterization of the Immunosignaturing Effect, MCP 11(4), 2012).

scan_protocol: Scanning was done on an Innopsys Innoscan 910 at 10um resolution, high laser power, 70% PMT, autofocus ON, 545nm.

data_processing: Median normalization per slide was done, and any negative values were adjusted to 0.01.

label: biotinylated anti-mouse IgG

molecule: other

label_protocol: Alexafluor 647-labeled Streptavidin was used to detect biotinylated anti-mouse secondary antibody.

tag: antibody

value: p53Ab8 monoclonal


title: Hu_NL219_pCalu3_7h_1


title: EMD_EL_150_20d 2905010941(07)

description:
EMD_EL_150_20d 2905010941(07) 2905010941(07)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: DM1A monoclonal

value: DM1A monoclonal


title: HA monoclonal

source_name: HA

value: HA monoclonal


title: FLAG monoclonal

source_name: FLAG

value: FLAG monoclonal


title: NaB treated exp 4

description:
Gene expression
NaB Exp 4

value: sodium butyrate


title: exon-5773t

source_name: colon cancer, cecum

value: F

value: cecum

value: metachronous


title: A10 monoclonal

value: A10 monoclonal


title: p53Ab1 monoclonal

value: p53Ab1 monoclonal


title: Hu_NL219_pCalu3_3h_2

value: polarized Calu3 cells


title: Hu_NL219_pCalu3_3h_3


title: EMD_ML_50_20d 2905010941(03)

description:
EMD_ML_50_20d 2905010941(03) 2905010941(03)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: Maternal Liver

value: vehicle

value: Wistar

source_name: Maternal Liver 50mg EMD 20day


title: EMD_ML_150_20d 2905010941(04)

description:
EMD_ML_150_20d 2905010941(04) 2905010941(04)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: 150mg EMD


title: EMD_ML_50_20d 2905010941(02)

description:
EMD_ML_50_20d 2905010941(02) 2905010941(02)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: 50mg EMD


title: 2C11 monoclonal

value: 2C11 monoclonal


title: E RA 6_12d 0106011728(16)

description:
E RA 6_12d 0106011728(16) 106011728(16)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

value: Whole Embryo

source_name: Whole Embryo 20mg RA 12day

value: 20mg RA


title: 4C1 monoclonal

value: 4C1 monoclonal


title: E RA 6_12d 0106011728(14)

description:
E RA 6_12d 0106011728(14) 106011728(14)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Hu_NL219_pCalu3_3h_1


title: Wildtype sample T50

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from 3-4 murine wildtype forelimbs at stage E11.5

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: A Custom CDF Version 17 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

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

growth_protocol: murine embryonic forelimb tissue was dissected at stage E11.5

extract_protocol: For total RNA isolation by TRIzol® (Invitrogen), samples from embryonic limbs (E11.5) of the same genotype (wildtype and Shox2 knockout) were pooled. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue was stored at -80°C until RNA preparation

tag: genotype/variation

value: WT


title: Hu_NL219_pCalu3_3h_4


title: Hu_NL219_pCalu3_24h_2


title: SHOX2-KO sample T50

description: Gene expression data from 3-4 murine knockout forelimbs at stage E11.5


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_254

city: Beijing

first: Yongfei

last: Hu

address: NO.1 West Beichen Road, Chaoyang District

department: CAS key Laboratory of Pathogenic Microbiology and Immunology

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Group SC

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: human gut metagenome

source_name: School Children_Fecal

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

growth_protocol: All fecal samples were collected from healthy volunteers in Hangzhou,China. All the volunteers were required not to take any antibiotic agent in the past three months.

extract_protocol: DNA from gut microbiomes was extracted directly from each fecal sample using QIAamp DNA stool mini kit according to the manufacturer’s suggested protocol.

treatment_protocol: All the fecal samples were stored in -80°C ultra low temperature refrigerator before DNA extracton.

value: Femal

tag: molecule type

value: Metagenomic DNA


title: Hu_NL219_pCalu3_24h_4


title: SHOX2-KO sample T48

source_name: 3-4 murine knockout forelimbs at stage E11.5


title: Hu_NL219_pCalu3_24h_3


title: Wildtype sample T48

source_name: 3-4 murine wildtype forelimbs at stage E11.5


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_253

description: Group SC

value: Male


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_255

description: Group SC


title: ML RA 6_12d 0106011728(11)

description:
ML RA 6_12d 0106011728(11) 106011728(11)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: vehicle

source_name: Maternal Liver 20mg RA 12day


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_252

description: Group SC


title: ML RA_12d 1209011725(15)

description:
ML RA_12d 1209011725(15) 1209011725(15)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: ML RA_12d 1209011725(16)

description:
ML RA_12d 1209011725(16) 1209011725(16)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_257

description: Group SC


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_251

description: Group SC


title: Hu_NL219_pCalu3_24h_1

source_name: Human, virus, polarized calu-3 cells, timepoint, replicate


title: Hu_NL219_pCalu3_12h_4


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_250

description: Group SC


title: Hu_NL219_pCalu3_12h_3


title: Hu_NL219_pCalu3_12h_1


title: Hu_NL219_pCalu3_12h_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_249

description: Group SC


title: ML 150_12d 1209011725(14)

description:
ML 150_12d 1209011725(14) 1209011725(14)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Maternal Liver 150mg EMD 12day


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_247

description: Group SC


title: Hu_Mock_pCalu3_7h_4

value: Mock Infection


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_246

description: Group SC


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_245

description: Group SC


title: ML 50_12d 1209011725(12)

description:
ML 50_12d 1209011725(12) 1209011725(12)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Maternal Liver 50mg EMD 12day


title: ML 50_12d 1209011725(11)

description:
ML 50_12d 1209011725(11) 1209011725(11)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Hu_Mock_pCalu3_7h_3


title: E 20 RA_12d 1209011725(10)

description:
E 20 RA_12d 1209011725(10) 1209011725(10)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: ML 150_12d 1209011725(13)

description:
ML 150_12d 1209011725(13) 1209011725(13)_1b
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_243

description: Group SC


title: E 150_12d 1209011725(08)

description:
E 150_12d 1209011725(08) 1209011725(08)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Whole Embryo 150mg EMD 12day


title: Hu_Mock_pCalu3_7h_1


title: Hu_Mock_pCalu3_7h_2


title: E 50_12d 1209011725(04)

description:
E 50_12d 1209011725(04) 1209011725(04)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name

source_name: Whole Embryo 50mg EMD 12day


title: E 150_12d 1209011725(05)

description:
E 150_12d 1209011725(05) 1209011725(05)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Hu_Mock_pCalu3_3h_4


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_241

description: Group SC


title: Hu_Mock_pCalu3_3h_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_239

description: Group SC


title: E 20 RA_12d 1209011725(09)

description:
E 20 RA_12d 1209011725(09) 1209011725(09)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_237

description: Group SC


title: Hu_Mock_pCalu3_3h_3


title: E 50_12d 1209011725(03)

description:
E 50_12d 1209011725(03) 1209011725(03)
Cy3-channel pictures and correspondig raw data are marked by an 1b at the end of the file name
Cy5-channel pictures and correspondig raw data are marked by an 2b at the end of the file name


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_238

description: Group SC


title: Hu_Mock_pCalu3_3h_1


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_240

description: Group SC


title: Hu_Mock_pCalu3_24h_4


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_236

description: Group SC


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_235

description: Group SC


title: Hu_Pan99_pCalu3_24h_4


title: Yellow Fever monoclonal Yellow Fever_2

type: protein

description:
Alexa-647 conjugated Streptavidin tertiary
Yellow Fever_2

hyb_protocol: Antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, Physical characterization of the Immunosignaturing Effect, MCP 11(4), 2012).

molecule: protein

source_name: Yellow Fever

value: Yellow Fever monoclonal


title: Yellow Fever monoclonal Yellow Fever_1

description:
Alexa-647 conjugated Streptavidin tertiary
Yellow Fever_1


title: Y. pestis monoclonal Y. pestis_2

description:
Alexa-647 conjugated Streptavidin tertiary
Y. pestis_2

source_name: Y. pestis

value: Y. pestis monoclonal


title: Hu_Mock_pCalu3_24h_3

value: polarized Calu3 cells


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_233

description: Group SC


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_232

description: Group SC


title: VEE monoclonal VEE_1

description:
Alexa-647 conjugated Streptavidin tertiary
VEE_1

source_name: VEE

value: VEE monoclonal


title: Hu_Mock_pCalu3_24h_2


title: Hu_Mock_pCalu3_24h_1


title: VEE monoclonal VEE_2

description:
Alexa-647 conjugated Streptavidin tertiary
VEE_2


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_231

description: Group SC


title: Hu_Mock_pCalu3_12h_3


title: Human_intestinal_Metagenome_Drug-resistance_Gene_Study_230

description: Group SC


title: Hu_Mock_pCalu3_12h_4


title: Tularensis monoclonal Tularensis_3

description:
Alexa-647 conjugated Streptavidin tertiary
Tularensis_3

source_name: Tularensis

value: Tularensis monoclonal


title: Hu_Mock_pCalu3_12h_2


title: Tularensis monoclonal Tularensis_4

description:
Alexa-647 conjugated Streptavidin tertiary
Tularensis_4


title: Y. pestis monoclonal Y. pestis_1

description:
Alexa-647 conjugated Streptavidin tertiary
Y. pestis_1


title: LTNP8

city: Sydney

first: daniel

last: murray

address: cnr West and Boundary Streets

country: Australia

institute: Kirby Institute

description: MicroRNA profile of monocytes

hyb_protocol: Cy3 labelled RNA was hybridized to the slide overnight in rotating incubator at 37 degrees celsius

scan_protocol: Scanning was performed using an agilent G2505B scanner

data_processing: Data was uploaded to CaArray by the Peter Wills Bioinformatics centre at the Garvan Institute before it was analyzed on the online bioinformatics program Genepattern. Data was first filtered for miRNA expressed in more than 4 patients across all patient groups before being run on the Limma and Comparative Marker Selection Modules which determine statistical difference while accounting for multiple testing.

source_name: miRNA extracted from monocytes

label_protocol: 100ng total RNA used, dephosphorylated and labelled with Cy3 as per manufacturer's recommendations

extract_protocol: Monocytes were extracted from PBMCs by positive selection using MACS CD14 magnetic beads and separation columns (Miltenyi Biotec, Cologne area, Germany. RNA was then extracted using a miRNeasy mini kit (Qiagen, Hilden, Germany)

tag: cell type

value: Monocytes

tag: disease status

value: Long-term nonprogressor


title: HC7

description: MicroRNA profile of monocytes

value: healthy control


title: CHI8

description: MicroRNA profile of monocytes

value: Chronic HIV patient


title: LTNP7

description: MicroRNA profile of monocytes


title: Hu_Anhui01_pCalu3_7h_3


title: Hu_NL219_pCalu3_7h_4


title: Hu_Mock_pCalu3_12h_1