title: Ctrl_Cmp302 10 µM

source_name: HMLE_Ctrl cells treated with 2 µM Cmp302 for 8 h

value: pBabe-shGFP retrovirus

value: 2 µM Cmp302 for 8 h


title: KDRRAS2.p1, biological rep1

status: Public on Apr 09 2014

type: RNA

city: Montpellier Cedex 05

first: Romain

middle: M

last: Larive

address: 1919, route de Mende

department: CRBM

country: France

institute: CNRS UMR5237

description:
Pool of RRAS2-deficient MDA-MB-231 cells generated by transducing the shRNA-encoding lentivirus TRCN0000047025.
Gene expression data from MDA-MB-231-Luc RRAS2-deficient cells.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231-Luc RRAS2-deficient

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were kept in exponential growing phase.

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

tag: cell line

tag: transduction


title: Liver_Female_LowEggProduction_rep3

city: Riverside

first: Jordan

last: Crago

state: CA

address: Science Lab 1

country: USA

institute: University California-Riverside

description: Gene expression after 28d reproduction cycle

hyb_protocol: Agilent's Gene Expression Hybridization Kit and Wash Buffer Kit (Agilent, Carlsad, CA) were used to hybridize and wash arrays per manufacturer's instructions. Briefly, 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 019597 custom fathead minnow 60mer  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned at 5 μm resolution using an Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA, USA)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent, Carlsbad, CA) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. and LOWESS normalization and analysis were performed using GeneSpring v.11 (Agilent). The criterion for conducting the analysis was a 2-way ANOVA using gender (male vs. female) and reproductive success (high vs. low total reproductive success from a stream) as components of this analysis. A Benjamini-Hochberg false discovery test was performed to correct for false discovery.  Gene probes needed to have greater than a 2-fold change or less than -2-fold changGene probes needed to have greater than a 2-fold change and be statistically significantly different (p < 0.05) after multiple test correction was performed. to be included in the analysis.

organism: Pimephales promelas

source_name: Pooled Liver of 6 females set in cages for 21-d, Low Reproduction Stream

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Agilent's One-Color Low Quick AmpLabelling Linear Amplification kit (Agilent, Carlsbad, CA) 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 liver samples using TriZol reagent (Invitrogen, Carlsbad, CA), following the instructions provided by the manufacturer. Samples were cleaned to remove any solvent contamination by precipitating RNA with a 1M NaCl aqueous solution, and washing the precipitate with ethanol. RNA was then dissolved in 40µL of water, and stored at -80 °C. RNA concentrations (ng/µL) were measured using a Nanodrop spectrophotometer (Thermo Fischer Scientific, Wilmington, DE). RNA degradation was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Degraded RNA samples were excluded from this study.

treatment_protocol: For the original study, cages of 6 reproductive pairs of FHM were placed in 6 streams across eastern Wisconsin during July and August of 2006-2007. Sites were selected to represent a full range of urban influence and coordinated with the US Geological.  Survey National Water-Quality Assessment Program Effects of Urbanization on Stream Ecosystems (EUSE) study. One reproductive pair was placed in each one of six breeding cages within a flow-through chamber constructed of polycarbonate plastic. A removable PVC spawning substrate was fastened to the bottom of each cage to allow for breeding. Cages were monitored daily to feed fish, remove and count eggs, and to assess fish condition. After 21 d, fish were collected and euthanized. Liver and blood plasma were collected and stored in 1.5 mL tubes at -80 °C.

tag: tissue

value: Liver

tag: gender

value: female

tag: age


title: Liver_Male_LowEggProduction_rep2

source_name: Pooled Liver of 6 males set in cages for 21-d, Low Reproduction Stream

value: male


title: Liver_Male_LowEggProduction_rep3

source_name: Pooled Liver of 6 males set in cages for 21-d, Low Reproduction, Stream


title: Liver_Male_HighEggProduction_rep2

source_name: Pooled Liver of 6 males set in cages for 21-d, High Reproduction Stream


title: Twist_Cmp302 5 µM

city: Cambridge

first: Yu-xiong

last: Feng

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Standard Affymetrix HG-U133 Plus2 arrays were hybridized with purified RNA samples.

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

data_processing: Raw CEL files were generated by Affymetrix GCOS 1.2 software, and the present/absent calls were defined with global scaling to target value of 500. By R software, the CEL files were normalized to a median-intensity array, and model-based expression values were calculated using PM/MM difference model.

source_name: HMLE_Twist cells treated with 2 µM Cmp302 for 4 h

label_protocol: All of the subsequent experimental procedures, including labeling, hybridization and scanning, were processed according to the standard Affymetrix protocols.

growth_protocol: HMLE cells were generated and maintained in a 1:1 mixture of DMEM + 10% FBS, insulin (10 μg/ml), hydrocortisone (0.5μg/ml), EGF (10 ng/ml) and MEGM

extract_protocol: Total RNA were extracted using Qiagen RNeasy kit, and the integrity and quality of the RNA met the quality requirements for Human Genome U133 Plus 2.0 arrays (Affymetrix, Inc., Santa Clara, CA) recommended by the company.

treatment_protocol: HMLE_ctrl and HMLE_Twist cells were treated with solvent control (DMSO), 5 µM or 10 µM of Cmp302 for 6 hours

value: HMLE

tag: infection

value: pBabe-Twist retrovirus

tag: treatment

value: 2 µM Cmp302 for 4 h


title: A2EN cells_Chlamydia G1V_4h_rep1

city: Durham

first: Raphael

middle: H

last: Valdivia

state: NC

address: 207 Research drive, Jones bldg 272

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridization was achieved in Affymetrix  GeneChip hybridization oven 645 according to standard Affymetrix GeneChip protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip protocol

data_processing: The data were analyzed with Partek Genomic Suite 6.6 using Affymetrix default analysis settings, quantile normalization and RMA background correction.

label: Biotin-UTP

source_name: Human A2EN_Chlamydia G1V_4 hrs

label_protocol: Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit from total RNA

growth_protocol: Human endocervical epithelial A2EN cells were maintained in keratinocyte-SFM medium supplemented with 10 % FBS, 0.5 ng/mL human recombinant epidermal growth factor and 50 μg/mL bovine pituitary extract.

extract_protocol: Samples were collected using QIAGEN RNeasy Plus Mini Kit as described by the manufacturer.

treatment_protocol: A2EN cells were infected with different strains of Chlamydia trachomatis at an MOI of 10 by spinning at 3000 rpm for 30 min at 10 degree and shift to 37 degree incubator for 4 hours.

tag: cell type

value: Human endocervical epithelial cells

tag: infected with

value: Chlamydia G1V mutant

tag: time point

value: 4 hr post infection


title: Twist_Cmp302 10 µM

source_name: HMLE_Twist cells treated with 2 µM Cmp302 for 8 h


title: KDRRAS2.p1, biological rep2


title: Vpr-Mac-Donor2

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip Operating Software (GCOS) were used for processing scanning data. Normalization was performed using the RMA method.

source_name: Healthy Donor 2

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

growth_protocol: Human PBMC were obtained using a standard Ficoll (Pharmacia ) gradient for heparinized blood extracted from two healthy individuals. CD14+ cells were isolated by positive selection using anti-human CD14+ magnetic beads (Miltenyi). Primary monocyte derived macrophages (MDMs) were generated by culturing CD14+ cells in RPMI (Sigma) medium supplemented with 10% FBS, 5% human AB serum, antibiotics and GlutaMax (Gibco) in the presence of recombinant human M-CSF (PeproTech).

extract_protocol: MDMs were washed three times with ice cold 1 x PBS, and total RNA was extracted using and RNeasy Mini Kit with DNase digestion, according to the manufacturer’s instructions (QIAgen).

treatment_protocol: MDMs were infected with adenovirus Vpr or ZsGreen1 at an MOI of 100. The cells were harvested for RNA extraction at 48 h post infection.

value: Monocyte Derived Macrophages (MDMs)

value: HIV-1 Vpr

tag: individual

value: healthy donor 2


title: AGS cells_SW 3.5μg/μl_24h_rep1

city: Beijing

first: tiantian

last: she

address: 52 Fucheng Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University Cancer Hospital & Institute

description: RMA expression value derived from Expression Console software; transcript analysis

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

source_name: human gastric cancer AGS cells,SW 3.5μg/μl,24h

label_protocol: Total RNA were amplified, labeled and purified by using Ambion  WT Expression Kit(Cat#411973， Ambion, US) and GeneChip  WT Terminal Labeling Kit (Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Cells were treated by solvent or SW for 24h before the RNA extraction

tag: Sex

tag: diagnosis

value: gastric cancer

value: AGS


title: A2EN cells_Mock infected_repl1

source_name: Mock infected human A2EN cells

value: none (mock)


title: A2EN cells_Chlamydia G1V_4h_rep2


title: KDRRAS2.p1, biological rep3


title: MDA-Control, biological rep3

description:
Human MDA-MB-231 breast cancer cells transduced with the shRNA-encoding lentivirus TRCN0000077750 (specific for the mouse Rras2 transcript and that it does not recognize the human RRAS2 mRNA). This cell line shows oncogenic mutations in KRAS and BRAF genes. In addition, it belongs to the triple negative Her2–, ER–, PR– breast cancer subtype. Other features are positivity for p53 and a mesenchymal phenotype.
Gene expression data from MDA-MB-231-Luc shControl cells.

source_name: MDA-MB-231-Luc shControl


title: A2EN cells_Chlamydia G1TEPP_4h_rep2

source_name: Human A2EN_Chlamydia G1TEPP_4 hrs

value: Chlamydia G1TEPP; complemented strain


title: Liver_Male_HighEggProduction_rep1


title: A2EN cells_Chlamydia G1TEPP_4h_rep1


title: Ctrl_DMSO

source_name: HMLE_Ctrl cells treated with DMSO

value: pBabe-shGFP retrovirus

value: DMSO


title: Ctrl_Cmp302 5 µM

source_name: HMLE_Ctrl cells treated with 2 µM Cmp302 for 4 h


title: MDA-Control, biological rep2


title: Liver_Male_LowEggProduction_rep1

value: Liver


title: R13_07d_Rep_5

status: Public on Apr 08 2014

city: Louisville

first: Jeffrey

middle: C

last: Petruska

state: KY

address: 511 S. Floyd St.

department: Department of Anatomical Sciences and Neurobiology

institute: University of Louisville

hyb_protocol: Each fragmented, biotin-labeled cRNA sample (30 μg) was hybridized to an Affymetrix rat 230 2.0 chip for 16 hours and rotated at 13 rpm at 50°C. The chips were washed and stained using a streptavidin–phycoerythrin conjugate (Molecular Probes, Eugene, OR), a goat IgG antibody, and then a second streptavidin–phycoerythrin stain.

scan_protocol: Scanned on an Affymetrix GeneChip scanner.

data_processing: RMA normalized using R 3.0.1, Bioconductor 2.13.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: dorsal hairy skin; T9/10 dermatome; denervated 7 days

label_protocol: 5 µg of the extracted RNA was reverse transcribed (Superscript II, Invitrogen) to generate first-strand cDNA (by using a T7-linked-(dT)24 primer) per manufacturer’s recommendations. After second-strand synthesis, the double-stranded cDNA was purified by phase-lock gels, extracted using phenol/chloroform, precipitated in ethanol, and then used for in vitro transcription using the ENZO BioArray High-Yield RNA transcript labeling kit (ENZO Farmingdale, NY). Quality control indicated labelling was highly consistent with the expected range of transcript sizes centred on about 500 nt. The labeled cRNA was purified using the RNeasy kit (Qiagen, Valencia, CA) and was fragmented to approximately 25nt sequences by incubation at 94°C.

extract_protocol: Skin samples were trimmed to approximately 100 mg before extraction procedure. Skin was homogenized using a Polytron-style rotor-stator and then centrifuged at 12,000 g for 10 minutes at 4 degrees C. The supernatant was removed and RNA was extracted using 1.5 ml Trizol reagent (Invitrogen, Carlsbad, CA). RNA was resuspended in 50 ul DEPC water. Samples run on agarose gels (1%) verified that RNA was not degraded. Spectrometer values and 260/280 ratios for all samples ranged from 2.13 to 2.23. 50 µg total RNA was treated with DNase I (Qiagen) using RNeasy columns (Qiagen) per manufacturer’s recommendations.

treatment_protocol: Animals that underwent skin denervation surgery were anesthetized with 60mg/kg pentobarbital administered intraperitoneally. Body temperature was monitored with a rectal thermistor and was maintained at 35-37 degrees C with a heated water pad. EKG leads were also placed to monitor heart rate. Incision of the dorsal skin from T4 to L5 on the contralateral (right) side was performed to allow reflection of the skin over to the ipsilateral (left) side to expose dorsal and lateral cutaneous nerves (D/LCNs). Two areas of denervated skin were produced by transection of the T9/10 and T12/13 DCNs. Proximal nerve stumps were then sealed off with ligatures close to the body wall to prevent their regeneration. The T11 D/LCNs were left intact producing an island of intact innervation. Incisions were then sutured and stapled and the denervated areas mapped acutely, using permanent marker on the skin to define the border between innervated and denervated areas, by determining the ability of pinch applied to the skin to drive the cutaneous trunci muscle (CTM) reflex as previously described (Theriault and Diamond, 1988;Diamond et al., 1992;Petruska et al., 2013). Maps were maintained with regular re-application of border marks. After 7 or 14 days (corresponding to the initiation and maintenance phases, respectively, of axonal collateral sprouting), animals were euthanized with an overdose of pentobarbital and the rostral-most skin samples corresponding to the acutely mapped zones (i.e., those regions denervated by transection of the T9 and T10 cutaneous nerves) were removed and then trimmed to approximately 100 mg.

tag: strain

value: Sprague-Dawley

value: female

value: denervated, dorsal hairy skin

tag: time

value: 7 day


title: R20_14d_Rep_5

source_name: dorsal hairy skin; T9/10 dermatome; denervated 14 days

value: 14 day


title: R18_14d_Rep_3


title: MDA-Control, biological rep1


title: R08_07d_Rep_1


title: R14_14d_Rep_1


title: R15_14d_Rep_2


title: R12_07d_Rep_4


title: R09_07d_Rep_2


title: R11_07d_Rep_3


title: R19_14d_Rep_4


title: R04_N_Rep_4

source_name: dorsal hairy skin; T9/10 dermatome; naïve

value: naïve skin

value: control


title: R05_N_Rep_5


title: junctional epithelium 1

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

country: Japan

institute: Tokyo Dental College

description: comparison of gene expression between peri-implant epithelium and junctional epithelium sampled by LMD

hyb_protocol: Following fragmentation, aRNA products were hybridized on GeneChip® Rat Genome 230 2.0 Array Chips (Affymetrix) for 18 h at 45°C in a GeneChip® Hybridization Oven 640 (Affymetrix).

scan_protocol: Hybridized arrays were washed and stained by using a Gene Chip® Fluidics station 450 (Affymetrix), and the images were scanned by using a Genechip® scanner 3,000 (Affymetrix).

data_processing: CEL files were generated using the GeneChip® Operating Software version 1.2 (Affymetrix). Data analysis and normalization were performed using GeneSpring® GX software version 12 (Agilent Technologies, Foster City, CA, USA).

source_name: junctional epithelium

label_protocol: Total RNA was amplified using the Ovation RNA Amplification SystemV2 (NuGEN Technologies, San Carlos, CA, USA). The purified cDNA was fragmented and biotin-labeled using the NuGEN Encore Biotin Module Kit (NuGEN).

growth_protocol: Four-week-old male Sprague-Dawley rats were obtained from Japan SLC Inc.( Tokyo, Japan). After surgery the animals were housed in a room with controlled temperature and humidity and a 12 h light dark cycle and given freely water and diet until sacrificed after 4 weeks.

extract_protocol: Total RNA was extracted from the junctional epithelium and peri-implant epithelium using an RNeasy Micro Kit (Qiagen, Valencia, CA, USA) with complete removal of genomic DNA by RNase-free DNase I treatment (Qiagen).

treatment_protocol: Four weeks after implant placement, 20 rats were sacrificed under deep anesthesia. The peri-implant soft tissue and gingival soft tissue were carefully removed from the bone and implant or bone and tooth using a spoon excavator and knife under a substance microscope (SZ61; OLYMPUS, Tokyo, Japan). Briefly, all soft tissues were embedded in OCT compound (Sakura Finetek USA, Inc., Torrance, CA, USA), then frozen quickly in isopentane that had been refrigerated in liquid nitrogen. Frozen sections were cut at 10-m thickness and were mounted on PALM Membrane Slides (PALM. Microlaser Technologies, Bernried, Germany) on which films were mounted for laser microdissection. Cryosections were cut on the day of use with a cryostat (Cambridge Instruments, Heidelberg, Germany).

value: Sprague Dawley

value: male

value: Tooth extraction and implant placement

value: junctional epithelium


title: R06_N_Rep_6


title: R03_N_Rep_3


title: peri-implant epithelium 2

source_name: peri-implant epithelium

value: peri-implant epithelium


title: peri-implant epithelium 1


title: R02_N_Rep_2


title: junctional epithelium 2


title: E15.5 RPE_mutant_Rep3

city: Tel Aviv

first: Ruth

last: Ashery-Padan

state: Select a State or Province

address: Tel Aviv University

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

description: Gene expression

hyb_protocol: The labaled RNA was hybridized to Affymetrix GeneChip 1.0ST microarrays According to the instruction manual.

scan_protocol: According to the instruction manual, as described in the Affymetrix website

data_processing:
Microarray analysis was performed using Partek Genomics Suite (Partek Inc., MO, USA; www.partek.com).
Results were filtered further by fold-change (1.5) and p-value (0.05) [provided in the 'KOvsCON_processed data_p_0_05_FC_1_5.txt']

organism: Mus musculus

source_name: Pax6 negative_E15.5_RPE

label_protocol: Total RNA (300 ng) was used to generate sense strand cDNA, which was fragmented and biotin-labeled.

growth_protocol: animal work was conducted according to national and international guidelines and approved by the Tel Aviv University review board. Exact timed matings were performed by overnight cohabitation of an inbred Pax6loxP/loxP;DctCre male with Pax6loxP/loxP females.

extract_protocol: RNA was extracted using the QIAshredder and the RNeasy kits (QIAGEN).

treatment_protocol: Pregnant females were harvested on day E15.5 and the RPE of the embryos was dissected. RPEs were pooled into two separate tubes according to their pigmentation intensity, and tubes were stored at -80˚C. Tail cuts of the embryos were collected for genotype verification. Each tube was considered as one biological repeat

tag: strain background

value: Embryonic day 15.5

tag: genotype/variation

value: retinal pigmented epithelium (RPE)


title: R01_N_Rep_1


title: E15.5 RPE_control_Rep2

description: Gene expression


title: E15.5 RPE_control_Rep1

description: Gene expression


title: E15.5 RPE_mutant_Rep1

description: Gene expression


title: E15.5 RPE_mutant_Rep2

description: Gene expression


title: E15.5 RPE_control_Rep3

description: Gene expression


title: MCF7_6hrETP-45658_411_rep2

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: ETP-45658 411 B

hyb_protocol: Samples were hybridized to whole human genome microarray 4x44K (G4112F, Agilent Technologies). 1.65 μg of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx hybridization buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were then washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies) and dried out using a centrifuge.

scan_protocol: Next arrays were scanned at 5μm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format.

data_processing: Data extraction from images provided by the scanner were analyzed was carried out using feature extraction software (Agilent Technologies). Data analysis was performed in R statistical environment (http://www.r-project.org/) using different Bioconductor packages. The background data was normalised using quantile normalization method.

source_name: BreastCell line_6hrETP-45658

label_protocol: One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. Briefly, 800 ng of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

extract_protocol: Total RNA was prepared from cell lysates using the RNeasy total RNA Mini kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s protocol. The amount and purity of total RNA was determined using the NanoDrop and the integrity of the RNA was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Add DMSO or PI3K inhibitors in DMSO

tag: cell line

value: human breast adenocarcinoma cell

tag: cell line source

value: 69-year-old female

tag: treated with

value: ETP-45658 for 6hrs


title: MCF7_6hrPI-103_411_rep1

description: PI-103 411 A

source_name: BreastCell line_6hrPI-103

value: reference PI3K inhibitor PI-103 for 6hrs


title: MCF7_6hrETP-45658_411_rep1

description: ETP-45658 411 A


title: Severe Negative Energy Balance [spleen 11S]

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

hyb_protocol: Gene expression was determined using a 24,027 probe set bovine oligonucleotide array (Affymetrix®), representing approximately 23,000 bovine transcripts based on the original mapping using Unigene build 57 (March 24, 2004). RNA from each cow was hybridised to a separate array.Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: All ten RNA samples were hybridised and scanned, by the German Resource Centre for Genomics Research, Germany (RZPD) according to the manufacturer’s instructions.GeneChips were scanned using GCOS v 1.x

data_processing: All microarray analysis including, pre-processing, normalisation and statistical analysis was carried out using R (R, 2007) version 2.6 and Bioconductor version 2.1.Data were quality assessed before and after normalisation using a number of in-built QC methods implemented in the Bioconductor affycoretools and associated packages to identify problems if they existed with array hybridisation, RNA degradation, and data normalisation. Microarray data was pre-processed using the mmgMOS normalisation method using the default settings and differential expression (DE) was analysed using the puma DE method both implemented in the Bioconductor package ‘puma’. The puma method uses a Bayesian hierarchical model to calculate the probability of positive likelihood ratio (PPLR). The PPLR associates probability values of being differentially expressed which is a measure of the false positive detection of differential expression to each ratio and generates lists of genes ranked by the probability of DE. This PPLR statistic was converted into p-like values using the recommended formula in the puma method prior to subsequent analysis.     As many of the original annotations for the Affymetrix® bovine chip are erroneous, Affyprobeminer re-defines the chip definition files (CDFs) for Affymetrix® chips, taking into account the most recent genomic sequence information. The re-mapped annotations were determined using the ‘bovineccdscdf’ cdf annotation file downloaded from the Affyprobeminer website which returned Entrez Gene gene name identifiers.     This re-mapped annotation include mappings to all RefSeq (mature RNA protein coding transcripts and validated complete coding sequences in GenBank  Annotations were also supplemented by interrogating the Ensembl bos-taurus database version 46 using the biomaRt package in Bioconductor and manual annotation where possible with recent entries in Entrez Gene.

organism: Bos taurus

source_name: spleen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (Genechip® Expression Analysis Technical Manual, 2005-2008, Affymetrix). cRNA was subjected to two rounds of linear amplification using the GeneChip® Expression 3’-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix Inc., Santa Clara, CA) according to the manufacturer’s instructions. cDNA was synthesized during the first cycle and biotin-labeled nucleotides were incorporated during the second in vitro transcription reaction.

extract_protocol: Total RNA was prepared from 100–200 mg of fragmented frozen spleen tissue using the TRIzol reagent (Sigma-Aldrich Chemical, Dorset, UK). Tissue samples  were homogenized in 3 ml of TRIzol reagent and chloroform and subsequently precipitated using isopropanol (Sigma-Aldrich). RNA samples were stored at  80°C. Twenty micrograms of total RNA from each sample was treated for genomic DNA contamination with the RNase-free DNase set (QIAGEN, Crawley, West Sussex, UK) and purified using the RNeasy mini kit in accordance with guidelines supplied (QIAGEN). RNA quality and quantity were assessed by automated capillary gel electrophoresis on a Bioanalyzer 2100 with RNA 6000 Nano Labchips according to manufacturers instructions (Agilent, Waldbronn, Germany).

treatment_protocol: At slaughter the entire spleen was removed and weighed, and samples weighing  1 g were dissected, rinsed in RNase-free phosphate buffer, snap frozen in liquid nitrogen, stored for 4 h in dry ice, and subsequently stored at  80°C

tag: breed

value: Holstein Friesian dairy

tag: animal tag no


title: MCF7_6hrPI-103_411_rep2

description: PI-103 411 B


title: MCF7_6hrDMSO_411_rep2

description: DMSO 411 B

source_name: BreastCell line_6hrDMSO

value: DMSO for 6hrs


title: MCF7_6hrDMSO_2810_rep2

description: DMSO 2810 B


title: Severe Negative Energy Balance [spleen 9S]


title: P0 Quadriceps Klhl40 KO 1

city: Dallas

first: Ankit

last: Garg

state: TX

address: 6000 Harry Hines Blvd, NA 8.500

department: Molecular Biology

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: KO 1 Quadriceps

label_protocol: Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: Klhl40 knock out

tag: age

value: 0 days

tag: tissue

value: muscle

tag: muscle type

value: Quadriceps


title: Mild Negative Energy Balance [spleen 5M]


title: MCF7_6hrETP-45658_2810_rep1

description: ETP-45658 2810 A

tag: cell type


title: MCF7_6hrETP-45658_2810_rep2

description: ETP-45658 2810 B


title: Severe Negative Energy Balance [spleen 8S]


title: Mild Negative Energy Balance [spleen 6M]


title: Severe Negative Energy Balance [spleen 12S]


title: P0 Quadriceps Klhl40 WT 2

source_name: WT 2 Quadriceps

value: wildtype


title: Severe Negative Energy Balance [spleen 10S]


title: P0 Quadriceps Klhl40 WT 1

source_name: WT 1 Quadriceps


title: MCF7_6hrDMSO_411_rep1

description: DMSO 411 A


title: MCF7_6hrPI-103_2810_rep1

description: PI-103 2810 A


title: P0 Quadriceps Klhl40 KO 3

source_name: KO 3 Quadriceps


title: MCF7_6hrDMSO_2810_rep1

description: DMSO 2810 A


title: P0 Quadriceps Klhl40 WT 3

source_name: WT 3 Quadriceps


title: MCF7_6hrPI-103_2810_rep2

description: PI-103 2810 B


title: Mild Negative Energy Balance [spleen 3M]


title: P0 Quadriceps Klhl40 KO 2

source_name: KO 2 Quadriceps


title: Mild Negative Energy Balance [spleen 2M]


title: Mild Negative Energy Balance [spleen 4M]


title: Severe Negative Energy Balance [liver 9S]

scan_protocol: All eleven RNA samples were hybridised and scanned, by the German Resource Centre for Genomics Research, Germany (RZPD) according to the manufacturer’s instructions.GeneChips were scanned using GCOS v 1.x

source_name: liver

extract_protocol: Total RNA was prepared from 100 to 200 mg of fragmented frozen liver tissue using the TRIzol reagent (Sigma-Aldrich Company Ltd., Dorset, UK). Tissue samples were homogenised in 3 ml of TRIzol® reagent and chloroform and subsequently precipitated using isopropanol (Sigma Chemical Co.). RNA samples were stored at –80oC. Twenty µg of total RNA from each sample was treated for genomic DNA contamination with the RNase-free DNase set (QIAGEN, Crawley, West Sussex, UK) and purified using the RNeasy mini kit in accordance with guidelines supplied (QIAGEN, Crawley, West Sussex, UK). RNA quality and quantity was assessed using automated capillary gel electrophoresis on a Bioanalyzer 2100 with RNA 6000 Nano Labchips according to manufacturer’s instructions (Agilent Technologies Ireland Ltd., Dublin, Ireland). Samples of RNA had 28S/18S ratios ranging from 1.8 to 2.0 and RIN values of between 8.0 and 10.0 which indicates that RNA samples are of high quality and suitable for microarray analysis.

treatment_protocol: The entire liver was removed within 15 to 30 min after slaughter and weighed. Samples weighing approximately 1 g were dissected, rinsed in RNase free phosphate buffer, snap frozen in liquid nitrogen and stored at -80ºC.


title: Severe Negative Energy Balance [liver 11S]


title: Mild Negative Energy Balance [liver 4M]


title: Mild Negative Energy Balance [liver 5M]


title: Severe Negative Energy Balance [liver 7S]


title: Severe Negative Energy Balance [liver 10S]


title: Severe Negative Energy Balance [liver 8S]


title: Mild Negative Energy Balance [liver 6M]


title: Mild Negative Energy Balance [liver 3M]


title: Mild Negative Energy Balance [liver 2M]


title: Severe Negative Energy Balance [liver 12S]


title: D79-3

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

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

scan_protocol: BeadChips were imaged using HiScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities+100). Probes with bad detection p-values were removed. Also removed were probes residing on X and Y chromosomes, probes cross-hybridizing with X, Y, and autosomal chromosome sites, and probes residing at SNP sites. Array normalization was performed in R using the built-in colour-correction and background subtraction, and quantile normalization functions of the lumi package with default settings followed by peak-based correction.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: peripheral mononuclear blood cells genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from peripheral blood mononuclear cells using the Isohelix DNA isolation kit following manufacturer's instructions.

value: M

tag: height (cm)

tag: ethnicity

value: Caucasian

value: peripheral mononuclear blood cells

tag: mass (kg)

tag: bmi

tag: fev1 % predicted

tag: atopy

value: yes

tag: asthma diagnosis

tag: methacholine responsive

tag: gstp1 genotype

value: G allele

tag: sample treatment

value: FAP

tag: time (hr)


title: D79-6

tag: Sex

value: DEP


title: D69-5


title: D76-6

value: F

value: no


title: D69-4


title: D76-3


title: D76-5


title: D69-6


title: D69-2


title: D69-3


title: D79-2


title: D68-6


title: D76-1


title: D68-5


title: D76-4


title: D79-5


title: D69-1


title: D68-1


title: D68-3


title: D76-2


title: D79-1


title: D66-5

value: South Asian

value: A allele


title: D66-1


title: D66-4


title: D68-4


title: D66-2


title: D66-3


title: D68-2


title: D79-4


title: D66-6


title: D63-5


title: Fibroblast_64y_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Labeled cRNA was hybridized to the Agilent SurePrint G3 Human gene expression 8x60K microarray according to the manufacturer's protocol.

scan_protocol: The arrays were scanned using Agilent Microarray Scanner (G2565BA, Agilent Technologies).

data_processing: Signal intensities were calculated using Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies). GeneSpring GX software (Vers. 11.5.1; Agilent Technologies) was used fordata analysis. Probe signal intensities were quantile normalized across all samples. Input data pre-processing was concluded by baseline transformation to the median of all samples and genes annotated using the A-GEOD-14550 probe annotation package from EBI ArrayExress.

source_name: bottom epidermis of female breast

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions.

growth_protocol: Human dermal fibroblasts were isolated from skin specimen removed in the course of cosmetic surgery from the bottom side of female breast. Isolation and primary culture of the cells followed published procedures (Tigges et al J Invest Dermatol. 2013). Cells were not expanded beyond 12 population doublings, while replicative cell cycle arrest was determined to not occur before 40 population doublings.

extract_protocol: Total RNA was prepared using TotalRNA Easy (Quiagen, Hilden, Germany). RNA integrity numbers  determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany) were > 9.7. RNA was quantified by photometric measurement using a Nanodrop device (Thermo Scientific, Wilmington, DE, USA).

tag: gender

value: female

value: 64 years

tag: age group

value: old

value: bottom epidermis of female breast

value: dermal fibroblast


title: Fibroblast_62y_rep1

tag: age

value: 62 years

tag: tissue


title: D63-3

tag: cell type


title: Fibroblast_49y_rep1

value: 49 years

value: middle aged


title: Fibroblast_60y_rep1

value: 60 years


title: Fibroblast_41y_rep1

value: 41 years


title: Fibroblast_42y_rep1

value: 42 years


title: Fibroblast_63y_rep1

value: 63 years


title: Fibroblast_67y_rep1

value: 67 years


title: D59-2

value: F

tag: height (cm)

value: Caucasian

value: peripheral mononuclear blood cells

value: yes

value: G allele

value: FAP


title: Fibroblast_43y_rep1

value: female

value: 43 years


title: D59-1

tag: ethnicity

value: no


title: Fibroblast_40y_rep1

value: 40 years

value: bottom epidermis of female breast

value: dermal fibroblast


title: D63-6

tag: mass (kg)

value: A allele

value: DEP


title: D63-4

tag: bmi


title: Fibroblast_26y_rep2

value: 26 years

value: young


title: D59-5

tag: fev1 % predicted


title: Fibroblast_26y_rep1


title: Fibroblast_21y_rep1

value: 21 years


title: D63-2

value: F

tag: atopy


title: Fibroblast_23y_rep1

value: 23 years


title: D51-4

value: Caucasian

value: peripheral mononuclear blood cells

tag: asthma diagnosis


title: PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human SOST biological rep3

city: Livermore

first: Gabriela

last: Loots

address: 7000 East Avenue

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Laboratory

description: gene expression data from PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human SOST

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

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

data_processing: Microarray data analysis was conducted using Bioconductor. Data preprocessing and normalization were performed using Robust Multi-chip Average (RMA) protocol. Genes differentially expressed between different conditions were identified using the empirical Bayes method implemented in Linear Models for MicroArray package.

label: Biotin

source_name: PC3 co cultured with WT OB and rhSOST

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PC3 cells were grown in DMEM/F12 growth media supplemented with 0.1%penicillin and streptomycin for 48 hours under speciefied conditions. Fresh media was added at T0hrs.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini columns performed according to the manufacturer's instructions.

treatment_protocol: Coculture osteoblast cells were grown on BD falcon cell culture inserts and placed in PC3 seeded wells at T0hrs. Recombinant human DKK1 and SOST were supplemented to media for a final concentration of 100ng/ml.

tag: cell line

tag: treatment

value: co culture with mouse WT osteoblasts and 100ng/ml recombinant human SOST


title: Fibroblast_20y_rep1

value: 20 years


title: D59-3

value: yes

tag: methacholine responsive

tag: gstp1 genotype

value: G allele

tag: sample treatment

value: FAP


title: D59-6

tag: Sex

value: no

tag: time (hr)


title: D51-5

tag: age


title: D51-3


title: D51-2


title: D51-6


title: D63-1


title: D51-1


title: PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human SOST biological rep1


title: D49-5

value: M

value: Asian


title: D59-4


title: D49-6

value: A allele


title: D49-1


title: D49-2


title: D49-4

value: DEP


title: untreated PC3 cells biological rep1

description: gene expression data from untreated PC3 cells


title: PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human SOST biological rep2


title: PC3 cells cocultured with mouse SostKO osteoblasts biological rep1

description: gene expression data from PC3 cells cocultured with mouse SostKO osteoblasts

source_name: PC3 co cultured with SostKO OB

value: co culture with mouse SostKO osteoblasts


title: PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human DKK1 biological rep1

description: gene expression data from PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human DKK1

source_name: PC3 co cultured with WT OB and rhDKK1

value: co culture with mouse WT osteoblasts and 100ng/ml recombinant human DKK1


title: D49-3


title: PC3 cells cocultured with mouse WT osteoblasts with 100ng/ml recombinant human DKK1 biological rep2


title: PC3 cells cocultured with mouse SostKO osteoblasts biological rep2


title: untreated PC3 cells biological rep2


title: Vector-ORF6_rep3

city: Los Angeles

first: Nicholas

middle: Alexander

last: Graham

address: 570 Westwood Blvd, CNSI 4338

department: Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description: MCF10A cells induced to accutely express empty vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy H133 PLUS 2.0 Genome Array.  The Genechip was wasted and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Array was scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: cell line

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

growth_protocol: MCF10A Human breast epithelial cells were plated in triplicated and incubated in DMEM/F12 media containing 5% horse serum, 10 ug/ml insulin, 0.5 ug/ml hydrocortisone, 20ng/ml EGF, 10ug/ml cholera toxin for 24 hours.

extract_protocol: Total RNA was extracted using Qiagen RNeasy

treatment_protocol: To induce expression of E4 ORF1, cells were treated with 100 ng/mL doxycyline for an additional 24 hours.

tag: vector type

value: Empty


title: D40-3

tag: cell type


title: D40-2

tag: height (cm)


title: D40-5

tag: ethnicity


title: Vector-ORF6_rep1


title: D40-4

tag: mass (kg)


title: Vector-ORF6_rep2


title: D39-6

value: F

tag: bmi


title: D40-6

tag: fev1 % predicted


title: ORF1-ORF6_rep3

description: MCF10A cells induced to accutely express ORF1.


title: Mit1 [py4144_2-pombe1.0FR]

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Biotinylated cDNA was hybridized to an Affymetrix GeneChip S.pombe Tiling 1.0FR array for 16 hours at 45 C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Data were analyzed using the Affymetrix Tiling Analysis Software v1.1.02 (2006). The genomic map file used was Sp20b_M_v04.bpmap, and the GRC file used was Sp20b_M_v04.grc from the 2004 genome build of S. pombe.  Probe signals on the arrays were quantile normalized and scaled to an average value of 500. Comparison between Mit1-deletion and WT samples were performed using duplicate samples. A two-sided Wilcoxon signed-rank test was performed using probes  summarized over a window of 101 nucleotides (software setting: bandwith = 50). BAR files of the summarized log2 signal differences and -10logP of the Wilcoxon signed-rank test are provided. Text (TXT) files of the summarized log2 signal differences and -10logP of the Wilcoxon signed-rank test are also provided.
Mit1_vs_WT_log2ratio.txt,    Mit1_vs_WT_pvalue.txt,    Mit1_vs_WT_2fold_up.bed,    Mit1_vs_WT_2fold_down.bed,    Mit1_vs_WT_p05.bed
Mit1_vs_WT_log2ratio.txt and Mit1_vs_WT_pvalue.txt are TEXT versions of the BAR files generated in the Tiling Analysis Software. Following summarization of signal differences, genomic interval analysis was also performed using the Tiling Analysis Software. The thresholds for significance were set to greater than 2-fold difference (up-regulated or down-regulated) or with p-value <0.05 by the 2-sided Wilcoson signed-rank test. The distance thresholds applied were maximum gap <100 bases and minimum run of >150 bases. The BED files contain regions across the genome that passed these thresholds. A separate BED file is provided for up-regulated regions (Mit1_vs_WT_2fold_up.bed), down-regulated regions (Mit1_vs_WT_2fold_down.bed), and significant regions (Mit1_vs_WT_p05.bed).

organism: Schizosaccharomyces pombe

source_name: Mit1 deletion

label_protocol: Seven micrograms of total RNA was converted to cDNA, fragmented and biotin-labeled according to the Affymetrix Eukaryotic Double Strand Whole Transcript protocol for yeast tiling arrays (Affymetrix P/N703064 Rev1).

growth_protocol: Yeast were grown to exponential growth phase at 30°C in YES media.

extract_protocol: RNA was extracted by hot phenol:chloroform method.

treatment_protocol: Not appplicable.

tag: strain

value: h- mit1D::NatMX6 ade6-210 arg3-D4 his3-D1 leu1-32 ura4-D18


title: ORF1-ORF6_rep2


title: Mit1 [py4144-pombe1.0FR]


title: WT [py42_2-pombe1.0FR]

source_name: WT


title: D39-5

tag: atopy

tag: asthma diagnosis


title: ORF1-ORF6_rep1

tag: cell line


title: D39-3

tag: methacholine responsive


title: D39-1

tag: gstp1 genotype


title: D39-4

tag: sample treatment


title: Macrophage-VitaminD-Subject17Post

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
RMA background correction was done to generate log 2 quantile normalized expression values (PartekGS v6.12.1011)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility.  Briefly, 50 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v2 (NuGEN Technologies, San Carlos, CA, Cat. #3302) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: not applicable

extract_protocol: RNA was extracted from alveolar macrophages obtained by bronchoalveolar lavage using the mirVana RNA isolation kit from Applied Biosystems

treatment_protocol: 1000 international units per day for three months of vitamin D3 (cholecalciferol) in human subjects

tag: individual

tag: treatment

value: Post-VitaminD

value: macrophage


title: Macrophage-VitaminD-Subject21Post


title: Macrophage-VitaminD-Subject16Post


title: D36-3

tag: Sex

tag: age

value: Caucasian

value: peripheral mononuclear blood cells

tag: time (hr)


title: D36-2

tag: height (cm)

tag: cell type

value: yes


title: Macrophage-VitaminD-Subject19Post


title: Macrophage-VitaminD-Subject20Post


title: Macrophage-VitaminD-Subject18Post


title: D36-4

tag: ethnicity

tag: mass (kg)

value: G allele


title: Macrophage-VitaminD-Subject22Post


title: D40-1

tag: bmi

tag: fev1 % predicted

value: FAP


title: D36-1

tag: atopy

value: no


title: Macrophage-VitaminD-Subject11Post


title: D39-2

tag: asthma diagnosis


title: D35-5

value: M


title: WT [py42-pombe1.0FR]

tag: strain


title: Macrophage-VitaminD-Subject14Post


title: D31-5

tag: methacholine responsive


title: D36-6

tag: gstp1 genotype


title: Macrophage-VitaminD-Subject15Post


title: D35-3

tag: sample treatment


title: D36-5


title: D35-6


title: D35-2


title: Macrophage-VitaminD-Subject10Post

tag: individual


title: D31-6


title: D35-4


title: D35-1


title: Macrophage-VitaminD-Subject9Post

tag: treatment


title: C19.3

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: MWRI - OBGYN and Reproductive Sciences

institute: University of Pittsburgh

description: Gene expression profiles in C19MC transfected HTR-8/SVeo cells

hyb_protocol: The hybridization was performed using  Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit from Agilent following the manufacturer's instructions

scan_protocol: Slides were scanned on the Agilent G4900DA SureScan Microarray Scanner System using the protocol GE1_1100_Jul11 (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMI gain is set to100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028004_D_F_20120411)

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 3

label_protocol: The labeling was performed using  Low Input Quick Amp Labeling Kit, One-Color  from Agilent following the manufacturer's instructions

growth_protocol: HTR-8/SVeo cells were cultured in DMEM with 5% BGS (Bovine Growth Serum, Hyclone) and 1% Pen/Strep. Primary trophoblasts were isolated from third trimester placentas after Trypsin/Dispase/DNaseI digestion followed by purification on a Percoll gradient. Primary trophoblasts were cultured for 48h  to 72h in DMEM supplemented with 10% FBS (Fetal Bovine Serum), 20 mM Hepes ph 7.4, and a mixture of penicilin-streptomycin-fungizone. Cells were maintained at 37ºC/5% CO2

extract_protocol: Total RNA were prepared using miRNeasy Mini Kit following the manufacturer's instructions

treatment_protocol: HTR-8/SVeo were transfected with a BAC (RP11-1055O17) that was modified by recombineering in order to insert a GFP-zeocin cassette. After transfection using PEI (Polyethylenimine), selection was carried out for two weeks with 200 μg/ml Zeocin. Resistant clones were selected and expanded.

tag: tissue

value: Placenta


title: C19.2

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 2


title: D31-2

tag: Sex

tag: age

value: A allele


title: Macrophage-VitaminD-Subject3Post


title: D31-3

tag: height (cm)

tag: time (hr)


title: D31-4

tag: ethnicity

tag: cell type

value: DEP


title: Macrophage-VitaminD-Subject12Post


title: Macrophage-VitaminD-Subject8Post


title: Macrophage-VitaminD-Subject13Post


title: C19.6

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 6


title: Macrophage-VitaminD-Subject7Post


title: Macrophage-VitaminD-Subject5Post


title: Macrophage-VitaminD-Subject6Post


title: WT

description: Gene expression profiles in parental HTR-8/SVeo cells

source_name: HTR-8/SVeo cell line, not transfected

value: not transfected


title: Macrophage-VitaminD-Subject22Pre

value: Pre-VitaminD


title: D30-6

tag: mass (kg)

tag: bmi


title: D31-1

tag: fev1 % predicted

tag: atopy


title: C19.1

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 1


title: Macrophage-VitaminD-Subject4Post


title: D30-3

tag: asthma diagnosis


title: C19.pool

source_name: HTR-8/SVeo cell line, transfected with modified BAC, mixed population


title: D30-4

tag: methacholine responsive


title: Macrophage-VitaminD-Subject21Pre


title: Cal 27 erlotinib 5uM 48hr replicate 3

description:
replicate 3
06_Cal 27 erl 3

hyb_protocol: Standard Illumina Hybridization protocol

data_processing: The data was quantile normalized in Genome Studio (v2011.1).

source_name: Cal 27 cultured 48 hr  5uM erlotinib in 0.01%DMSO

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

growth_protocol: Cell lines were maintained in DMEM (11965-092 Gibco) media containing 10% Hyclone Fetal Bovine Serum and supplemented with 5mM Sodium Pyruvate.

extract_protocol: RNA was extracted  and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was was performed with Agilent Bioanalyser.

treatment_protocol: To the cell lines either 5uM Erlotinib in DMSO or DMSO (vehicle) was added 48 hours prior to RNA harvest (100,000 cells cultured for 48 hr + 0.01%DMSO (veh) or + 5uM erlotinib in DMSO)

tag: cell line

value: Cal 27

value: tongue, squamous cell carcinoma cells

tag: treated with

value: 5uM Erlotinib for 48h


title: PHT

description: Gene expression profiles in primary human trophoblast cells

source_name: Primary human trophoblast third trimester


title: D25-4

value: F

value: Middle Eastern

tag: gstp1 genotype

tag: sample treatment


title: Macrophage-VitaminD-Subject2Post

tag: individual

tag: treatment

value: Post-VitaminD

value: macrophage


title: Macrophage-VitaminD-Subject1Post


title: Cal 27  0.01% DMSO 48 hr-replicate 3

description:
replicate 3
03_Cal 27 veh 3

source_name: Cal 27 cultured 48 hr 0.01% DMSO (veh)

value: 0.01% DMSO (veh) for 48h


title: Cal 27 erlotinib 5uM 48hr replicate 1

description:
replicate 1
04_Cal 27 erl 1


title: D30-2

source_name: peripheral mononuclear blood cells genomic DNA

tag: Sex

tag: age

value: Caucasian

value: peripheral mononuclear blood cells

value: yes

value: G allele


title: control (0238B)

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

institute: IDIBAPS

description: Gene expression data from human colon biopsies; non-inflammatory control

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (version 2.15.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).

source_name: Human colon biopsies from non-inflammatory control

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

extract_protocol: Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

tag: tissue

value: colon biopsy

tag: biopsy

value: non-inflammatory control

tag: gender

value: female


title: Macrophage-VitaminD-Subject17Pre

tag: cell type


title: D30-5

tag: height (cm)

tag: ethnicity

tag: mass (kg)

tag: bmi

value: no

value: DEP

tag: time (hr)


title: Cal 27  0.01% DMSO 48 hr-replicate 1

description:
replicate 1
01_Cal 27 veh 1

tag: cell line

value: Cal 27


title: D30-1

tag: fev1 % predicted

tag: atopy

tag: asthma diagnosis

tag: methacholine responsive

value: FAP


title: FADU erlotinib 5uM 48hr replicate 3

description:
replicate 3
12_FADUERL-3

source_name: FADU cultured 48 hr  5uM erlotinib in 0.01%DMSO

value: FADU

value: pharynx, squamous cell carcinoma cells

tag: treated with

value: 5uM Erlotinib for 48h


title: D25-6

tag: Sex

value: F

value: Middle Eastern

tag: gstp1 genotype

tag: sample treatment


title: control (0213B)

tag: tissue

tag: biopsy

tag: age


title: Cal 27 erlotinib 5uM 48hr replicate 2

description:
replicate 2
05_Cal 27 erl 2

tag: cell type

value: tongue, squamous cell carcinoma cells


title: Macrophage-VitaminD-Subject14Pre

tag: individual

tag: treatment

value: Pre-VitaminD

value: macrophage


title: Cal 27  0.01% DMSO 48 hr-replicate 2

description:
replicate 2
02_Cal 27 veh 2

value: 0.01% DMSO (veh) for 48h


title: control (0378B)

tag: gender


title: Macrophage-VitaminD-Subject19Pre


title: control (0212B)

value: male


title: Macrophage-VitaminD-Subject20Pre


title: FADU erlotinib 5uM 48hr replicate 2

description:
replicate 2
11_FADUERL-2


title: D25-5

tag: height (cm)

tag: ethnicity

value: peripheral mononuclear blood cells

tag: mass (kg)

tag: bmi

value: yes

value: G allele

tag: time (hr)


title: Macrophage-VitaminD-Subject18Pre


title: control (0210B)

value: colon biopsy

value: non-inflammatory control

value: female


title: control (0205B)


title: Macrophage-VitaminD-Subject13Pre


title: control (0218B)


title: Macrophage-VitaminD-Subject10Pre


title: Macrophage-VitaminD-Subject16Pre


title: control (0376B)


title: control (0204B)


title: Macrophage-VitaminD-Subject9Pre


title: Macrophage-VitaminD-Subject11Pre


title: Macrophage-VitaminD-Subject15Pre


title: control (0211B)


title: SQ20B erlotinib 5uM 48hr replicate 2

description:
replicate 2
05_SQ20BERL-2

source_name: SQ20B cultured 48 hr  5uM erlotinib in 0.01%DMSO

tag: cell line

value: Larynx, squamous cell carcinoma cells


title: FADU erlotinib 5uM 48hr replicate 1

description:
replicate 1
10_FADUERL-1

value: FADU

tag: treated with


title: D25-3

tag: Sex

tag: fev1 % predicted

tag: atopy

value: no

tag: asthma diagnosis

tag: methacholine responsive

value: FAP


title: FADU  0.01% DMSO 48 hr-replicate 3

description:
replicate 3
09_FADU-3

source_name: FADU cultured 48 hr 0.01% DMSO (veh)

value: pharynx, squamous cell carcinoma cells


title: D25-2

value: F

tag: age

value: Middle Eastern

tag: gstp1 genotype

tag: sample treatment


title: D25-1

tag: cell type


title: FADU  0.01% DMSO 48 hr-replicate 2

description:
replicate 2
08_FADU-2


title: Macrophage-VitaminD-Subject12Pre

tag: individual

tag: treatment

value: Pre-VitaminD


title: FADU  0.01% DMSO 48 hr-replicate 1

description:
replicate 1
07_FADU-1


title: Macrophage-VitaminD-Subject6Pre

value: macrophage


title: SQ20B  0.01% DMSO 48 hr-replicate 3

description:
replicate 3
03_SQ20B-3

source_name: SQ20B cultured 48 hr 0.01% DMSO (veh)

value: 0.01% DMSO (veh) for 48h


title: SQ20B  0.01% DMSO 48 hr-replicate 1

description:
replicate 1
01_SQ20B-1


title: SQ20B erlotinib 5uM 48hr replicate 3

description:
replicate 3
06_SQ20BERL-3

value: 5uM Erlotinib for 48h


title: control (0196B)

tag: tissue

tag: biopsy

tag: gender

value: male


title: Macrophage-VitaminD-Subject7Pre


title: SQ20B erlotinib 5uM 48hr replicate 1

description:
replicate 1
04_SQ20BERL-1


title: Macrophage-VitaminD-Subject5Pre


title: Macrophage-VitaminD-Subject8Pre


title: Macrophage-VitaminD-Subject4Pre


title: control (0203B)


title: trt-B13GB8

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description:
SAMPLE 23
colonies_IAPV_Brood
Cy3-050109-B13GB8:Signal Median

hyb_protocol: The Cy5- or Cy3-labeled cRNA were mixed in the same amount and hybridized to honey bee oligonucleotide microarray fabricated at the University of Illinois, Keck Center microarray.

scan_protocol: Scan protocal was according to honey bee oligonucleotide microarray fabricated at the University of Illinois, Keck Center microarray.

data_processing: 'Signal Median' raw data was used for ANOVA by software Partek 6.0. Only value of Signal median was used for the data analysis.

organism: Apis mellifera

label_protocol: The cDNA was labeled with Cytidine 3 (Cy3) and Cytidine 5 (Cy5), respectively, and vice versa for the dye-swap analysis.

growth_protocol: Bee colonies maintained in USDA-ARS BRL’s apiaries were divided into healthy and weak groups based on the size of adult populations, amount of sealed brood, and presence of food stores.

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

treatment_protocol: The ubiquitous presence of DWV in both IAPV-positive and IAPV-negative bees was considered as a background infection  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: developmental stage

value: Brood

tag: infection

value: IAPV


title: control (0195B)

value: colon biopsy


title: control (0167B)

value: non-inflammatory control


title: control (0140B)

value: female


title: Macrophage-VitaminD-Subject3Pre


title: control (0153B)


title: trt-B12GB7

description:
SAMPLE 24
colonies_IAPV_Brood
Cy3-050109-B12GB7:Signal Median


title: SQ20B  0.01% DMSO 48 hr-replicate 2

description:
replicate 2
02_SQ20B-2

tag: cell line

value: Larynx, squamous cell carcinoma cells

tag: treated with


title: control (0138B)


title: trt-B5GB5

description:
SAMPLE 22
colonies_IAPV_Brood
Cy3-050109-B5GB5:Signal Median


title: Active CD with anti-TNF (0366B)

description: Gene expression data from human colon biopsies; active CD patient with anti-TNF therapy

source_name: Human colon biopsies from active CD patient with anti-TNF therapy

value: active CD patient with anti-TNF therapy

tag: patient

tag: cd evolution time (years)

tag: cdeis


title: Macrophage-VitaminD-Subject1Pre


title: Macrophage-VitaminD-Subject2Pre


title: Active CD with anti-TNF (0081B)


title: trt-B1GB1

description:
SAMPLE 21
colonies_IAPV_Brood
Cy5-050109-B1GB1:Signal Median


title: Active CD with anti-TNF (0244B)


title: trt-B2GB2

description:
SAMPLE 20
colonies_IAPV_Brood
Cy5-050109-B2GB2:Signal Median


title: Active CD with anti-TNF (0143B)


title: Inactive CD with anti-TNF (0197B)

description: Gene expression data from human colon biopsies; inactive CD patient with anti-TNF therapy

source_name: Human colon biopsies from inactive CD patient with anti-TNF therapy


title: Active CD with anti-TNF (0127B)


title: ck-B1GB1

description:
SAMPLE 18
health colonies without IAPV_Brood
Cy3-050109-B1GB1:Signal Median

value: without IAPV


title: ck-B2GB2

description:
SAMPLE 17
health colonies without IAPV_Brood
Cy3-050109-B2GB2:Signal Median


title: Inactive CD with anti-TNF (0061B)

value: inactive CD patient with anti-TNF therapy


title: Inactive CD with anti-TNF (0178B)


title: Inactive CD with anti-TNF (0051B)


title: Inactive CD with anti-TNF (0179B)


title: trt-B4GB4

description:
SAMPLE 19
colonies_IAPV_Brood
Cy5-050109-B4GB4:Signal Median


title: ck-B13GB8

description:
SAMPLE 14
health colonies without IAPV_Brood
Cy5-050109-B13GB8:Signal Median


title: ck-B12GB7

description:
SAMPLE 15
health colonies without IAPV_Brood
Cy5-050109-B12GB7:Signal Median


title: Lmono5923_4h_cclA_rep3

city: Edmonton

first: Lynn

last: McMullen

state: Alberta

address: 410 Ag/For

institute: University of Alberta

hyb_protocol: Hybridization was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using NimbleScan v2.6. 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 pac

organism: Listeria monocytogenes 08-5923

source_name: L. monocytogenes 08-5923 treated

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Tryptic Soy Broth at 21°C

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an A

treatment_protocol: 7 μg/mL purified carnocyclin A (cclA)

tag: genotype

value: Wild-type

tag: phenotype

value: normal

value: carnocyclin A


title: Lmono5923_4h_cclA_rep2


title: Lmono5923_4h_TSB_rep3

source_name: L. monocytogenes 08-5923 untreated

value: untreated


title: ck-B4GB4

description:
SAMPLE 16
health colonies without IAPV_Brood
Cy3-050109-B4GB4:Signal Median


title: ck-B5GB5

description:
SAMPLE 13
health colonies without IAPV_Brood
Cy5-050109-B5GB5:Signal Median


title: 042909-F6C4-trt_VA

description:
SAMPLE 11
colonies_IAPV_Adult
Cy5-042909-F6C4:Signal Median

value: Adult


title: Active CD without anti-TNF (0172B)

description: Gene expression data from human colon biopsies;  active CD patient without anti-TNF therapy

source_name: Human colon biopsies from active CD patient without anti-TNF therapy

tag: age


title: Inactive CD with anti-TNF (0176B)


title: 042909-F4C3-trt_VA

description:
SAMPLE 10
colonies_IAPV_Adult
Cy5-042909-F4C3:Signal Median


title: 042909-F9C6-trt_VA

description:
SAMPLE 12
colonies_IAPV_Adult
Cy3-042909-F9C6:Signal Median


title: 042909-F12C10-trt_VA

description:
SAMPLE 8
colonies_IAPV_Adult
Cy3-042909-F12C10:Signal Median


title: Inactive CD with anti-TNF (0170B)


title: 042909-F1C1-trt_VA

description:
SAMPLE 9
colonies_IAPV_Adult
Cy5-042909-F1C1:Signal Median


title: 042909-F10C7-trt_VA

description:
SAMPLE 7
colonies_IAPV_Adult
Cy3-042909-F10C7:Signal Median


title: Active CD without anti-TNF (0026B)

value: active CD patient without anti-TNF therapy


title: Lmono5923_4h_cclA_rep1


title: Lmono5923_4h_TSB_rep2


title: Active CD without anti-TNF (0070B)


title: Lmono5923_4h_TSB_rep1


title: C19.3

description: miRNA expression in C19MC transfected cells

hyb_protocol: The hybridization was performed using  "miRNA Microarray System with miRNA Complete Labeling and Hyb Kit" from Agilent following the manufacturer's instructions

scan_protocol: Slides were scanned on the Agilent G4900DA SureScan Microarray Scanner System using the protocol miRNA_1100_Jul11 (Scan Region Agilent HD (61 × 21.6 mm), Scan resolution 5 um, Dye channel is set to Green and Green PMI gain is set to100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol miRNA_1100_Jul11 and Grid: 021827_D_F_20121224)

label: total RNA

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 3

label_protocol: The labeling was performed using  "miRNA Microarray System with miRNA Complete Labeling and Hyb Kit" from Agilent following the manufacturer's instructions

value: Placenta


title: Active CD without anti-TNF (0108B)

value: male


title: Ferment_S5-5_#14

city: Berkeley

first: Ulas

last: Karaoz

address: 1 Cyclotron Rd.

institute: LBNL

description: This sample is a fermentative aquifer community from Hanford 100H

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

scan_protocol: Scanned at 532 nm using a GenePix 4200A scanner (Molecular Devices, Sunnyvale, CA, USA). The images were gridded and pair files generated using the Nimblescan software version 2.4 (Roche-Nimblegen)

data_processing: Data from NimbleGen array scans were analyzed by building a custom array annotation package with the R makePdInfoPackage function and normalizing probe-level data using the Robust Multi-array Average (RMA) approach with the R rma function available in Bioconductor, pdInfoBuilder, and oligo libraries, respectively.

organism: mixed sample

source_name: Fermentative column S5-5, day 281

label_protocol: Labeled with Cy3 9-mers using One color DNA labeling kit (Roche-Nimblegen, Madison, WI, USA)

growth_protocol: Anaerobic incubation in 6-mL columns continuously infused with Hanford 100H synthetic groundwater including 5 mM lactate and 5 uM chromate

extract_protocol: CTAB phenol:chloroform:isoamylalcohol with Qiagen AllPrep purification. DNA-free RNA (50 ng) was amplified using the Sigma Whole-Transcriptome Amplification 2 kit (Sigma-Aldrich, St Louis, MO, USA)

treatment_protocol: Samples differed with respect to electron acceptor present in groundwater (nitrate or sulfate)

tag: source

value: effluent

tag: electron acceptor

value: sulfate


title: Active CD without anti-TNF (0013B)

value: colon biopsy


title: 042909-F9C6-ck_VA

description:
SAMPLE 6
health colonies without IAPV_Adult
Cy5-042909-F9C6:Signal Median


title: 042909-F6C4-ck_VA

description:
SAMPLE 5
health colonies without IAPV_Adult
Cy3-042909-F6C4:Signal Median


title: C19.2

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 2

tag: cell type


title: C19.6

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 6

tag: treatment


title: Active CD without anti-TNF (0011-2B)

tag: tissue


title: Denit_N5-4_#12

description: This sample is a denitrifying aquifer community from Hanford 100H

source_name: Denitrifying column N5-4, day 295

value: nitrate


title: Active CD without anti-TNF (0010B)

tag: biopsy


title: C19.1

source_name: HTR-8/SVeo cell line, transfected with modified BAC, clone # 1


title: Active CD without anti-TNF (0009B)

tag: gender

value: female


title: 042909-F1C1-ck_VA

description:
SAMPLE 3
health colonies without IAPV_Adult
Cy3-042909-F1C1:Signal Median

tag: developmental stage


title: Active CD without anti-TNF (0008B)


title: Active CD without anti-TNF (0003B)


title: 042909-F4C3-ck_VA

description:
SAMPLE 4
health colonies without IAPV_Adult
Cy3-042909-F4C3:Signal Median

tag: infection


title: PHT

description: miRNA expression in primary trophoblasts

source_name: Primary human trophoblast third trimester


title: 042909-F10C7-ck_VA

description:
SAMPLE 1
health colonies without IAPV_Adult
Cy5-042909-F10C7:Signal Median


title: 042909-F12C10-ck_VA

description:
SAMPLE 2
health colonies without IAPV_Adult
Cy5-042909-F12C10:Signal Median


title: C19.pool

source_name: HTR-8/SVeo cell line, transfected with modified BAC, mixed population


title: WT

description: miRNA expression in WT cells

source_name: HTR-8/SVeo cell line, not transfected

value: not transfected


title: Chromosomal distribution of Cnp1 in rpt3-1mutant, 2

status: Public on Apr 07 2014

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with GFP-cnp1 (Cy5) from the Schizosaccharomyces pombe proteasome mutant strain.

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the KU-LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 (Agilent Technologies) according to the manufacturer's instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer's instructions (Agilent Technologies), in ozone-depleted surroundings.

scan_protocol: Microarray slides were scanned using the Agilent Microarray Scanner G2505B and Scan Control Software G2565BA, followed by extraction of information from the probe features using Agilent Feature Extraction Software 9.5.1.1.

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy5) signals over corresponding WCE (Cy3) signals.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for GFP-cnp1, rpt3-1 mutant

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: Cells were fixed with 3% formaldehyde at 18 °C for 35 min, and the fixation reaction was terminated by adding 330 mM final concentration of glycine and incubating for 10 min; the cells were collected by centrifugation and washed 3 times with 1x PBS.

extract_protocol:
Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100. To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.
ChIP was performed using anti-GFP antibody (Roche, cat. No. 11 814 460 001, lot 10744900).

treatment_protocol: Exponentially growing fission yeast cells were asynchronously cultured for 18h at 33 °C in EMM2+Leucine-Thiamine, and transferred to 18 °C for 2 h prior to fixation.

tag: strain

value: mutant cell; h- leu1-32 lys1::nmt1 GFP-cnp1+-lys1+ rpt3-1 strain

tag: chip antibody

value: anti-GFP

source_name: Chromatin-input DNA (WCE) for GFP-cnp1, rpt3-1 mutant

label_protocol: WCE DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.


title: Chromosomal distribution of Cnp1 in WT, 2

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with GFP-cnp1 (Cy5) from the Schizosaccharomyces pombe WT strain.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for GFP-cnp1, wild-type

value: wild-type cell; h- leu1-32 lys1::nmt1 GFP-cnp1+-lys1+ strain

source_name: Chromatin-input DNA (WCE) for GFP-cnp1, wild-type

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100. To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.


title: Chromosomal distribution of Cnp1 in rpt3-1mutant, 1

treatment_protocol: Exponentially growing fission yeast cells were asynchronously cultured for 18h at 33 °C in EMM2+Leucine+Thiamine, and transferred to 18 °C for 2 h prior to fixation.


title: Uhrf1 +/+ Treg

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Gene expression data of Uhrf1 +/+ Treg

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

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

data_processing: The data were analyzed with mas5 algorithm included in affy package of R. Log2 of MAS5 values were normalized using quantile normalization algorithm.

source_name: Uhrf1 +/+ regulatory T-cell

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

extract_protocol: TRIZOL with Etachinemate

treatment_protocol: Sorted

value: SPF C57BL/6

value: Treg

tag: genotype/variation

value: Uhrf1 +/+


title: GF Treg

description: Gene expression data of GF Treg

source_name: WT regulatory T-cell from germ-free mouse

value: GF

value: Wild type


title: MBzP - 24 h - 4.41 mM - nr5

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Next, 0.0375 ng/ul of cRNA was hybridized on the Affymetrix HT MG-430 PM array. After hybridization, washing and staining was performed with the Affymetrix HWS Kit (#901530).

scan_protocol: The Array plates were scanned via the Affymetrix GeneTitan scanner. Data quality was checked by Affymetrix Expression Console software.

data_processing: Data was normalized using the Robust Multichip Average (RMA) algorithm, using an MBNI custom CDF version (http://brainarray.mbni.med.umich.edu) version 13.

source_name: ESCs_MBzP_24 h_4.41 mM

label_protocol: Samples were randomized, blinded and further processed for array analysis at ServiceXS (Leiden, The Netherlands) using Affymetrix HT MG 430 PM array plates. Array analysis methods were according to manufacturer’s protocols. For each individual sample 100 ng RNA was  used for the labelling reaction. The Affymetrix 3 IVT-Express labelling kit (#901229) was used to synthesize biotin-labelled cRNA. Subsequently, 7.5 ug cRNA of each sample was fragmented using a hybridization cocktail.

growth_protocol: ES-D3 (ATCC) pluripotent embryonic stem cells (ESC) were cultured in complete medium (CM), consisting of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% foetal bovine serum, 1% non-essential amino acids, 2 mM l-glutamine, 1% 5000 IU/ml penicillin/5000 ug/ml streptomycin , and 0.1 mM b-mercaptoethanol . ESC pluripotency was maintained by adding leukaemia inhibitory factor (LIF), 1000 units/ml to the culture medium. ESC were kept for a maximum of 25 passages and are passaged every other day. Differentiation was initiated by culturing the cells via the ‘hanging drop method’ in which approximately 750 cells/drop were cultured in 56 droplets of 20 ul of CM, on the inner side of a lid of a Petri dish (94 mm × 16 mm), containing 5 ml phosphate buffered saline (PBS), Ca2+ and Mg2+ free . ESC were cultured in a humidified atmosphere (37 ◦C, 5% CO2) for three days during which the cells proliferated and formed cell aggregates (i.e. embryoid bodies (EB)). EB were transferred to a bacterial Petri dish (60 mm × 15 mm) containing 5 ml CM and cultured in a humidified atmosphere (37 ◦C, 5% CO2) for two days. Subsequently each individual EB was transferred to a single well of a 24-wells plate , containing 1 ml CM. Within 5 days aggregates further differentiated and displayed spontaneously contracting cell foci. At day 10, all wells were microscopically examined and scored based on the presence or absence of contracting cells.

extract_protocol: RNA was extracted by using the RNA Mini-extraction kit (Qiagen).The concentration of the RNA was measured by Nanodrop (Thermo Scientific). The quality of the RNA was checked using the 2100 Bio-Analyzer (Agilent) and Shimadzu MultiNA. Samples with a RNA Integrity Number (RIN) ≥ 8 were used for microarray analysis.

treatment_protocol: ESC were exposed to phthalate monoesters (MEHP, MBuP, MBzP, or MMP) in 0.3% DMSO during the differentiation protocol from day 3 onwards (time 0 h). Phthalates were dissolved in DMSO and tested in a concentration-response fashion (0.00441, 0.0143, 0.0441, 0.143, 0.441, 1.43 and 4.41 mM). Concurrent solvent control cultures (0.3% DMSO) were exposed from day 3 onward, and collected after 24 h (day 4, time 24 h). All groups contained 7–8 replicates, individually cultured. EB were collected in RNA protect in a 15 ml tube (Qiagen #76526) and stored at −20 ◦C prior to RNA extraction.

tag: cell line

value: ES-D3 (ATCC)

value: murine pluripotent embryonic stem cells (ESC)

tag: time

tag: exposured to

value: monobenzyl phthalate

tag: concentration


title: Chromosomal distribution of Cnp1 in WT, 1

tag: genotype


title: Uhrf1 fl/fl Tconv

description: Gene expression data of Uhrf1 fl/fl Tconv

source_name: Uhrf1 -/- conventional T-cell

value: Non-Treg

value: Uhrf1 -/-


title: MBzP - 24 h - 4.41 mM - nr3


title: MBzP - 24 h - 4.41 mM - nr6


title: SPF Treg

description: Gene expression data of SPF Treg

source_name: WT regulatory T-cell from SPF mouse

value: SPF IQI


title: MBzP - 24 h - 4.41 mM - nr4


title: MBzP - 24 h - 4.41 mM - nr7


title: GF Tconv

description: Gene expression data of GF Tconv

source_name: WT conventional T-cell from germ-free mouse


title: MBzP - 24 h - 4.41 mM - nr2


title: MBzP - 24 h - 1.43 mM - nr5

source_name: ESCs_MBzP_24 h_1.43 mM


title: MBzP - 24 h - 1.43 mM - nr6


title: MBzP - 24 h - 4.41 mM - nr1


title: MBzP - 24 h - 1.43 mM - nr1


title: MBzP - 24 h - 1.43 mM - nr2


title: MBzP - 24 h - 1.43 mM - nr4


title: MBzP - 24 h - 1.43 mM - nr3


title: MBzP - 24 h - 0.441 mM - nr7

source_name: ESCs_MBzP_24 h_0.441 mM


title: MBzP - 24 h - 1.43 mM - nr7


title: Uhrf1 fl/fl Treg

description: Gene expression data of Uhrf1 fl/fl Treg

source_name: Uhrf1 -/- regulatory T-cell


title: Uhrf1 +/+ Tconv

description: Gene expression data of Uhrf1 +/+ Tconv

source_name: Uhrf1 +/+ conventional T-cell


title: MBzP - 24 h - 0.441 mM - nr3


title: MBzP - 24 h - 0.143 mM - nr3

source_name: ESCs_MBzP_24 h_0.143 mM


title: SPF Tconv

description: Gene expression data of SPF Tconv

source_name: WT conventional T-cell from SPF mouse


title: MBzP - 24 h - 0.441 mM - nr5


title: MBzP - 24 h - 0.441 mM - nr4


title: MBzP - 24 h - 0.143 mM - nr7


title: MBzP - 24 h - 0.0441 mM - nr6

source_name: ESCs_MBzP_24 h_0.0441 mM


title: MBzP - 24 h - 0.441 mM - nr6


title: MBzP - 24 h - 0.143 mM - nr5


title: MBzP - 24 h - 0.143 mM - nr4


title: MBzP - 24 h - 0.143 mM - nr6


title: MBzP - 24 h - 0.441 mM - nr1


title: MBzP - 24 h - 0.143 mM - nr8


title: MBzP - 24 h - 0.0441 mM - nr3


title: MBzP - 24 h - 0.143 mM - nr2


title: MBzP - 24 h - 0.441 mM - nr2


title: MBzP - 24 h - 0.143 mM - nr1


title: MBzP - 24 h - 0.0441 mM - nr5


title: MBzP - 24 h - 0.0441 mM - nr7


title: MBzP - 24 h - 0.0143 mM - nr7

source_name: ESCs_MBzP_24 h_0.0143 mM


title: MBzP - 24 h - 0.0143 mM - nr5


title: MBzP - 24 h - 0.0143 mM - nr6


title: MBzP - 24 h - 0.0441 mM - nr4


title: MBzP - 24 h - 0.0441 mM - nr2


title: MBzP - 24 h - 0.0143 mM - nr4


title: MBzP - 24 h - 0.0143 mM - nr2


title: NCTC8325 2810::ermB

city: He Fei

first: Haipeng

last: Sun

state: An Hui

address: Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: Gene expression in SAOUHSC_02810 mutated strain

hyb_protocol: total of 600 ng cy5-labeled cDNA was used for hybridization sample using Gene Expression Hybridization Kit (Agilent p/n5188-4242) following the manufacturer’s instruction. 40 ul of the hybridization samples were added onto the microarray slide and hybridized in an Agilent hybridization oven to rotate at 10 rpm at 65 °C for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan resolution 5 um, Dye channel is set to Red and Red PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Quantity normalization were analyzed with GENESPRING 11.5 (Agilent).

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: S. aureus growth culture, OD600=2.0

label_protocol: 5 ug RNA was used to synthesize cDNA, and labeled with cy5. This process was accomplished using FairPlay III Microarray Labeling Kit (Aglilent p/n252012). Labeled cDNA was purified and quantified with NanoDrop Spectrophotometer (Thermo G2939A).

growth_protocol: Overnight culture were diluted 1:100 in TSB and grow until OD600=2.0.

extract_protocol: Total RNA was prepared using mirVana RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer’s instruction.

treatment_protocol: In order to lysis the cell wall, cells were collected and incubated in 37°C with 10 mg/ml lysozyme and 40 ug/ml lysostaphin for 5 minutes. Then, cells were centrifuged and resuspended in TRIzol immediately.

value: staphylococcus aureus NCTC8325 and its derivative strain


title: MBzP - 24 h - 0.0143 mM - nr3


title: MBzP - 24 h - 0.0441 mM - nr1


title: MBzP - 24 h - 0.00441 mM - nr6


title: MBzP - 24 h - 0.0143 mM - nr1


title: MBuP - 24 h - 4.41 mM - nr4

source_name: ESCs_MBuP_24 h_4.41 mM

value: monobutyl phthalate


title: MBzP - 24 h - 0.00441 mM - nr7


title: MBuP - 24 h - 4.41 mM - nr5


title: MBuP - 24 h - 4.41 mM - nr6


title: MBuP - 24 h - 4.41 mM - nr3


title: MBzP - 24 h - 0.00441 mM - nr4


title: MBzP - 24 h - 0.00441 mM - nr1


title: MBuP - 24 h - 4.41 mM - nr7


title: MBuP - 24 h - 4.41 mM - nr1


title: MBzP - 24 h - 0.00441 mM - nr2


title: MBuP - 24 h - 1.43 mM - nr7

source_name: ESCs_MBuP_24 h_1.43 mM


title: MBzP - 24 h - 0.00441 mM - nr3


title: MBuP - 24 h - 4.41 mM - nr2


title: MBzP - 24 h - 0.00441 mM - nr5


title: MBuP - 24 h - 1.43 mM - nr5


title: MBuP - 24 h - 1.43 mM - nr4


title: MBuP - 24 h - 1.43 mM - nr3


title: HCT116 PEA15 shRNA#2replicate 1

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (lumi package in R/Bioconductor)

source_name: HCT116 cell line

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

growth_protocol: HCT116 NS shRNA, HCT16 PEA15 shRNA#1 and HCT116 PEA15 shRNA #2 cell lines were grown in DEMEM media with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: HCT116 cells that either expressed Non-silencing shRNA (NS shRNA) or shRNAs targeting PEA15  (PEA15 shRNA #1 and PEA15 shRNA #2 were used for preparing the total RNA and to perfrom gene expression array.

tag: shRNA

value: shRNA targeting PEA15  (PEA15 shRNA #2)


title: HCT116 PEA15 shRNA#1replicate 2

description: SAMPLE 4

value: shRNA targeting PEA15  (PEA15 shRNA #1)


title: HCT116 PEA15 shRNA#2replicate 2

description: SAMPLE 6


title: HCT116 NS shRNA replicate 1

description: SAMPLE 1

value: Non-silencing shRNA (NS shRNA)


title: HCT116 NS shRNA replicate 2

description: SAMPLE 2


title: cerv5

city: Kyoto

first: Aya

last: Nakajima

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Radiation Oncology

institute: Kyoto University

description: Gene expression of CTOSs embedded in Matrigel Matrix and cultured in StemPro hESC

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Microarray Scanner using one color scan setting for 8x60K array slides (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent), then imported to GeneSpring GX and normalized (Per Chip: Normalized to 75 percentie).

source_name: radio-resistant CTOS, cerv5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: CTOSs were embedded in Matrigel Matrix and cultured with StemPro hESC for 24 hours.

extract_protocol: Total RNA was extracted from CTOSs using TRIzol Reagent (Life Technologies) and purified by RNeasy Mini Kit (QIAGEN).

value: patient-derived sphere culture from small cell carcinoa of cervix uteri

value: female


title: MBuP - 24 h - 0.441 mM - nr6

source_name: ESCs_MBuP_24 h_0.441 mM


title: MBuP - 24 h - 0.441 mM - nr7


title: HCT116 PEA15 shRNA#1replicate 1

description: SAMPLE 3


title: MBuP - 24 h - 1.43 mM - nr2


title: MBuP - 24 h - 1.43 mM - nr1


title: MBuP - 24 h - 0.441 mM - nr5


title: MBuP - 24 h - 1.43 mM - nr6


title: MBuP - 24 h - 0.441 mM - nr4


title: cerv9

source_name: radio-sensitive CTOS, cerv9


title: MBuP - 24 h - 0.441 mM - nr3


title: MBuP - 24 h - 0.441 mM - nr1


title: MBuP - 24 h - 0.441 mM - nr2


title: sputum_106

city: New Haven

middle: L.

last: Chupp

address: 300 Cedar St, S441

department: Department of Internal Medicine

institute: Section of Pulmonary, Critical Care and Sleep Medicine

description: Gene expression from sputum

hyb_protocol: See manufacturer's protocol

scan_protocol: See manufacturer's protocol

data_processing: RMA was used to background correct, quantile normalize and summarize the gene expression levels across all arrays. Blood and sputum arrays were processed separately. Principal component analysis (PCA) was used to visualize the data and remove outliers. The batch effect was adjusted using Combat and the RIN number was adjusted using linear regression model.

source_name: sputum

label_protocol: Purified RNA from the sputum or blood was processed for gene expression using the Affymetrix HuGene 1.0 ST gene arrays following manufacturer’s protocols.

growth_protocol: Sputum induction was performed with hypertonic saline, as previously described. Simply, by using a microscope, mucus plugs (cellular parts) from the sputum sample were dissected, separated and collected from aqueous compartments. Processing of the collected cellular part was done by mixing with  1 X Sputolysin Reagent (Calbiochem, cat# 560000) at a ratio of 1:4 (weight:volume), followed by vortexings at high speed for 30 seconds and low speed for 15 min, adding equal volume of PBS and a cell strainer filtration. Total cell count, viability, and differential, were determined by hemocytometer, trypan blue exclusion, and Wright-Geimsa stain, respectively. After centrifuged at 3,500 x g for 5 min, cell pellets were lysed in lysis solution of All-in-One Purification Kit (Product# 24200, Norgen Biotek Co, Thorhold, CAN) and stored at -80C until use.

extract_protocol: 10 ng of sputum RNA was amplified using the WT-Ovation Pico RNA amplification System (NuGen, San Carlos, CA) and processed per Affymetrix protocols. Total RNA from the blood was isolated using a column-based system (total-RNA kit, Norgen) and if needed, DNA contamination was removed using a DNA clear kit (Qiagen).  Hemoglobin reduction of blood samples was used to remove hemoglobin gene transcripts (GLOBINclear Kit, Ambion, Austin, TX) and samples were checked by Agilent bioanalyzer.

treatment_protocol: Sputum cell pellets were processed using the All-in-One purification kit (Norgen Biotek, Thorhold, CAN), checked on an Agilent bioanalyzer and, if needed, treated again to remove DNA contamination (Qiagen, Gaithersberg, MD).

tag: cluster assignment

value: CONTROL


title: sputum_110

description: Gene expression from sputum


title: sputum_109

description: Gene expression from sputum


title: sputum_107

description: Gene expression from sputum


title: sputum_112

description: Gene expression from sputum


title: sputum_104

description: Gene expression from sputum


title: sputum_111

description: Gene expression from sputum


title: MBuP - 24 h - 0.143 mM - nr7

source_name: ESCs_MBuP_24 h_0.143 mM

tag: cell type


title: sputum_105

description: Gene expression from sputum


title: sputum_103

description: Gene expression from sputum


title: sputum_108

description: Gene expression from sputum


title: MBuP - 24 h - 0.0441 mM - nr7

source_name: ESCs_MBuP_24 h_0.0441 mM


title: MBuP - 24 h - 0.143 mM - nr1


title: MBuP - 24 h - 0.143 mM - nr6


title: MBuP - 24 h - 0.143 mM - nr4


title: MBuP - 24 h - 0.0441 mM - nr6


title: MBuP - 24 h - 0.143 mM - nr2


title: MBuP - 24 h - 0.0441 mM - nr5


title: sputum_95

description: Gene expression from sputum


title: sputum_96

description: Gene expression from sputum


title: sputum_102

description: Gene expression from sputum


title: MBuP - 24 h - 0.143 mM - nr5


title: sputum_100

description: Gene expression from sputum


title: MBuP - 24 h - 0.143 mM - nr3


title: sputum_101

description: Gene expression from sputum


title: sputum_99

description: Gene expression from sputum


title: sputum_98

description: Gene expression from sputum


title: MBuP - 24 h - 0.0441 mM - nr4


title: sputum_97

description: Gene expression from sputum


title: sputum_94

description: Gene expression from sputum


title: sputum_90

description: Gene expression from sputum


title: sputum_91

description: Gene expression from sputum


title: sputum_93

description: Gene expression from sputum


title: MBuP - 24 h - 0.0441 mM - nr1


title: sputum_92

description: Gene expression from sputum


title: sputum_88

description: Gene expression from sputum


title: MBuP - 24 h - 0.0441 mM - nr3


title: sputum_87

description: Gene expression from sputum


title: MBuP - 24 h - 0.0143 mM - nr5

source_name: ESCs_MBuP_24 h_0.0143 mM


title: MBuP - 24 h - 0.0441 mM - nr2


title: MBuP - 24 h - 0.0143 mM - nr4


title: MBuP - 24 h - 0.0143 mM - nr3


title: sputum_86

description: Gene expression from sputum


title: sputum_89

description: Gene expression from sputum


title: MBuP - 24 h - 0.0143 mM - nr2


title: sputum_85

description: Gene expression from sputum


title: MBuP - 24 h - 0.0143 mM - nr6


title: MBuP - 24 h - 0.0143 mM - nr7


title: sputum_84

description: Gene expression from sputum


title: MBuP - 24 h - 0.00441 mM - nr7


title: MBuP - 24 h - 0.00441 mM - nr6


title: sputum_80

description: Gene expression from sputum


title: sputum_83

description: Gene expression from sputum


title: MBuP - 24 h - 0.0143 mM - nr1


title: sputum_79

description: Gene expression from sputum


title: MBuP - 24 h - 0.00441 mM - nr3


title: sputum_78

description: Gene expression from sputum


title: sputum_82

description: Gene expression from sputum


title: MBuP - 24 h - 0.00441 mM - nr2


title: sputum_81

description: Gene expression from sputum


title: MBuP - 24 h - 0.00441 mM - nr5


title: MBuP - 24 h - 0.00441 mM - nr1


title: MBuP - 24 h - 0.00441 mM - nr4


title: MMP - 24 h - 4.41 mM - nr7

source_name: ESCs_MMP_24 h_4.41 mM

value: monomethyl phthalate


title: MMP - 24 h - 4.41 mM - nr6


title: sputum_77

description: Gene expression from sputum


title: MMP - 24 h - 4.41 mM - nr5


title: MMP - 24 h - 4.41 mM - nr4