title: A549  infected and intervened by Flutide 24h d2

city: Beijing

first: zhenpeng

last: li

address: Taiping Road, Haidian District

country: China

institute: Beijing Institute of Radiation Medicine

hyb_protocol: Hybridization was performed overnight on a  µParaflo™ microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by  in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100  μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Detection used fluorescence labeling using tag-specific Cy3 and Cy5 dyes.  Hybridization images were collected using a  laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). or two color experiments, the ratio of the two sets   of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially   detected signals were those with less than 0.01 p-values.

label_protocol: Five µg of total RNA sample was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3＇-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: A549 cells were cultured in F12K medium containing 10% FBS with 50 U/ml Gentamicin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted from infected A549 cells using mirVana miRNA Isolation Kit (ambion)  according to the manufacturer’s protocol.

treatment_protocol: A549 cells were infected with influenza virus A /JingFang/86-1(H1N1) for 4 and 24 hours and intervented by Flutide

tag: infection

value: influenza A virus

value: Flutide

tag: time

value: 24 h infection


title: A549  infected 4h B2

status: Public on Jul 07 2011

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: 4 h infection


title: A549 non-infected A2

value: uninfected


title: leaves_HLB-inoculated plant, biological rep2

city: Lake Alfred

first: Fred

middle: G.

last: Gmitter

email: fgmitter@ufl.edu, fanjing7758@126.com

address: 700 Experiment Station Rd

country: USA

institute: University of Florida

description: Gene expression data from HLB-inoculated sweet orange at 7 months after inoculation

hyb_protocol: The biotin-labeled aRNA was then purified and fragmented. Samples were hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip® Citrus Genome Arrays. The arrays were washed and stained with the reagents supplied in GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: The array data were analyzed using BioConductor (http://www.bioconductor.org), which is primarily based on the R programming language. Data normalization was performed by the Robust Multichip Analysis (RMA) approach in an R package, Affy.

label: biotin

organism: Citrus sinensis

source_name: HLB-inoculated plant

label_protocol: Biotin-labeled aRNA was prepared from 250 ng of total RNA according to the manufacturer's instructions of the GeneChip® 3’ IVT Express kit (Affymetrix, Inc).

growth_protocol: Plants were kept under controlled conditions in a U.S. Department of Agriculture-APHIS/CDC-approved and secured greenhouse at University of Florida, Citrus Research and Education Center, Lake Alfred, FL.

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

treatment_protocol: Two-year-old seedlings of ‘Madam Vinous’ sweet orange (Citrus sinensis L. Osbeck) were inoculated by grafting with bud sticks from HLB-diseased, PCR positive sweet orange plants. For mock-inoculated controls, the same types of plants were grafted with bud sticks from HLB-free, PCR negative sweet orange. Leaf samples were collected at 7 months after inoculation.

tag: tissue

value: mature leaf

tag: Stage

value: 7 months after inoculation

tag: treatment

value: HLB


title: blood 4g T25 ppD

city: Maastricht

first: marlon

last: jetten

address: universiteitssingel 50

country: Netherlands

institute: maastricht university

description:
globin reduced total RNA
sample 4g APAP exposure

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: All samples were normalized by RMA algorithm and analyzed by SAM (FC>1.5 and FDR<10%).

source_name: blood 4g T25 ppD

label_protocol: We used standard Affymetrix labeling protocols

extract_protocol: Total RNA was isolated using the PAXgene Blood RNA kit (PreAnalytiX/Qiagen) according to the manufacturers protocol (including Dnase) and was globin reduced using the GLOBINclear kit (Ambion) according to the manufacturers protocol

tag: donor

value: D

tag: Sex

value: M

value: blood

value: 4g APAP exposure


title: A549  infected 24h C2


title: blood 4g T0 ppF

description:
globin reduced total RNA
control sample (unexposed)

source_name: blood 4g T0 ppF

value: F

value: control  (unexposed)


title: blood 4g T25 ppE

source_name: blood 4g T25 ppE

value: E


title: leaves_mock-inoculated control, biological rep3

description: Gene expression data from mock-inoculated sweet orange at 7 months after inoculation

source_name: mock-inoculated control

value: mock


title: leaves_mock-inoculated control, biological rep2


title: blood 4g T25 ppC

source_name: blood 4g T25 ppC

value: C


title: blood 4g T25 ppA

source_name: blood 4g T25 ppA

value: A


title: leaves_HLB-inoculated plant, biological rep1


title: blood 4g T25 ppB

source_name: blood 4g T25 ppB

value: B


title: leaves_HLB-inoculated plant, biological rep3


title: blood 4g T0 ppB

source_name: blood 4g T0 ppB


title: blood 4g T25 ppF

source_name: blood 4g T25 ppF


title: blood 4g T0 ppC

source_name: blood 4g T0 ppC


title: blood 4g T0 ppD

source_name: blood 4g T0 ppD


title: blood 4g T0 ppE

source_name: blood 4g T0 ppE


title: Maturing DCs, technical replicate 2

status: Public on Jul 08 2011

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

description: Gene expression data from monocyte-derived DCs stimulated with LPS 6hr

hyb_protocol: 17 hours at 45 degrees Celsius in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using using Stain cocktails included in the Affymetrix 3' IVT Express Kit

scan_protocol: GeneChip scanner 3000 7G

data_processing: GCRMA (in Bioconductor version 2.6.1) using R version 2.10.1 on Mac OS X 10.4.11 (PPC), and the Bioconductor packages gcrma (version 2.18.1) and affy (version 1.24.2).

label: Biotin

source_name: DCs derived from CD14+ monocytes from adult human blood, stimulated with LPS for 6 hr

label_protocol: Biotin labeling using Affymetrix 3' IVT Express Kit, following manufacturer's directions

extract_protocol: RNeasy column purification

tag: cell type

value: DCs derived from CD14+ blood monocytes cultured for 6 days in the presence of IL4 and GGM-CSF

tag: stimulus

value: LPS 6 hr


title: blood 4g T0 ppA

source_name: blood 4g T0 ppA


title: blood 2g T7 ppF

description:
globin reduced total RNA
sample 2g APAP exposure

source_name: blood 2g T7 ppF

value: 2g APAP exposure


title: leaves_mock-inoculated control, biological rep1

value: mature leaf


title: blood 2g T25 ppE

source_name: blood 2g T25 ppE


title: blood 2g T25 ppB

source_name: blood 2g T25 ppB


title: blood 2g T25 ppC

source_name: blood 2g T25 ppC


title: blood 2g T25 ppD

source_name: blood 2g T25 ppD


title: blood 2g T25 ppA

source_name: blood 2g T25 ppA


title: blood 2g T25 ppF

source_name: blood 2g T25 ppF


title: blood 2g T7 ppE

source_name: blood 2g T7 ppE


title: blood 2g T1 ppE

source_name: blood 2g T1 ppE


title: blood 2g T7 ppC

source_name: blood 2g T7 ppC


title: blood 2g T1 ppB

source_name: blood 2g T1 ppB


title: blood 2g T1 ppF

source_name: blood 2g T1 ppF


title: blood 2g T1 ppD

source_name: blood 2g T1 ppD


title: blood 2g T7 ppB

source_name: blood 2g T7 ppB


title: blood 2g T7 ppA

source_name: blood 2g T7 ppA


title: blood 2g T0 ppB

source_name: blood 2g T0 ppB


title: blood 2g T0 ppF

source_name: blood 2g T0 ppF


title: blood 2g T0 ppC

source_name: blood 2g T0 ppC


title: blood 2g T0 ppD

source_name: blood 2g T0 ppD


title: blood 2g T1 ppA

source_name: blood 2g T1 ppA


title: blood 2g T1 ppC

source_name: blood 2g T1 ppC


title: blood 0.5g T25 ppA

description:
globin reduced total RNA
sample 0.5g APAP exposure

source_name: blood 0.5g T25 ppA

value: 0.5g APAP exposure


title: blood 2g T0 ppA

source_name: blood 2g T0 ppA


title: blood 2g T7 ppD

source_name: blood 2g T7 ppD


title: blood 2g T0 ppE

source_name: blood 2g T0 ppE


title: blood 0.5g T25 ppC

source_name: blood 0.5g T25 ppC


title: blood 0.5g T25 ppB

source_name: blood 0.5g T25 ppB


title: blood 0.5g T25 ppE

source_name: blood 0.5g T25 ppE


title: blood 0.5g T7 ppF

source_name: blood 0.5g T7 ppF


title: blood 0.5g T7 ppE

source_name: blood 0.5g T7 ppE


title: blood  0.5g T25 ppD

source_name: blood  0.5g T25 ppD


title: blood 0.5g T1 ppF

source_name: blood 0.5g T1 ppF


title: blood 0.5g T7 ppA

source_name: blood 0.5g T7 ppA


title: blood 0.5g T7 ppD

source_name: blood 0.5g T7 ppD


title: blood 0.5g T7 ppC

source_name: blood 0.5g T7 ppC


title: blood 0.5g T1 ppE

source_name: blood 0.5g T1 ppE


title: blood 0.5g T25 ppF

source_name: blood 0.5g T25 ppF


title: blood 0.5g T7 ppB

source_name: blood 0.5g T7 ppB


title: blood 0.5g T1 ppC

source_name: blood 0.5g T1 ppC


title: blood 0.5g T1 ppD

source_name: blood 0.5g T1 ppD


title: Fat_Pt57_HIV+_No_ART

city: Frederick

first: Richard

middle: A

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

hyb_protocol: Labeled cRNA was hybridized to the Affymetrix FATMITO1a520158F microarray according to the manufacturer's recommended standard protocol.

scan_protocol: Hybridized huMITOchips were scanned according to the Affymetrix recommended standard protocol.

data_processing: Partek Genomics Software 2.3 (Partek, St. Louis, MO) was used for statistical analysis. The raw data were normalized using the quantile normalization method. To neutralize variation by tissue, the normalized gene expression values in each tissue type were further standardized with a median-shift strategy (i.e., subtracting each gene expression value from the median expression value of the corresponding cohort).  A two-way ANOVA model (i.e., tissue, disease group) was designed to identify differentially expressed genes with absolute fold change >0.5 (log2 scale) and p values <0.05. Selected genes were clustered by hierarchical clustering.

source_name: HIV positive without ART, fat

label_protocol: cRNA was labelled according  to the Affymetrix recommended standard protocol.

extract_protocol: Tissue samples were disrupted in a TissueLyser (Qiagen, Valencia, CA) prior to RNA extraction. Total RNA was isolated from PBMCs using the RNeasy Mini QIAshredder Kit, from adipose tissue using the RNeasy Lipid Tissue Mini Kit, and from muscle using the RNeasy Fibrous Tissue Mini Kit (Qiagen).

treatment_protocol: Three groups of volunteers 18 to 55 years old were enrolled in the study: HIV-infected adults receiving ART, HIV-infected adults not receiving ART, and healthy, HIV-negative adults. ART recipients were required to have received a stable regimen containing three drugs, including at least two nucleoside or nucleotide analogues, for a minimum of 12 consecutive months prior to study entry.  Patients receiving protease inhibitor therapy were excluded to minimize potential confounding effects. HIV-infected participants not receiving ART could not have received any ART in the 12 months preceding study entry.  Patients with a history of muscle disorder or diabetes were excluded.

value: fat

tag: hiv status

value: positive

tag: art treatment

value: without

tag: patient


title: Fat_Pt6_HIV_Neg

source_name: HIV negative, fat

value: negative


title: Fat_Pt59_HIV+_No_ART


title: Fat_Pt9_HIV+_ART

source_name: HIV positive with ART, fat

value: with


title: blood 0.5g T0 ppD

source_name: blood 0.5g T0 ppD

value: D

value: M

value: blood


title: Fat_Pt59_dup_HIV+_No_ART


title: blood 0.5g T0 ppE

source_name: blood 0.5g T0 ppE

value: E

value: F

value: control  (unexposed)


title: Fat_Pt8_HIV_Neg


title: blood 0.5g T0 ppA

source_name: blood 0.5g T0 ppA

value: A


title: Fat_Pt60_HIV+_ART


title: blood 0.5g T1 ppB

source_name: blood 0.5g T1 ppB

value: B


title: Fat_Pt58_dup_HIV+_No_ART


title: blood 0.5g T0 ppB

source_name: blood 0.5g T0 ppB


title: Fat_Pt57_dup_HIV+_No_ART


title: Fat_Pt58_HIV+_No_ART


title: Fat_Pt56_HIV+_No_ART


title: blood 0.5g T0 ppF

source_name: blood 0.5g T0 ppF


title: Fat_Pt55_HIV+_ART


title: Fat_Pt54_HIV+_No_ART


title: Fat_Pt53_HIV+_ART


title: Fat_Pt52_HIV+_No_ART


title: Fat_Pt51_HIV+_No_ART


title: blood 0.5g T1 ppA

source_name: blood 0.5g T1 ppA


title: Fat_Pt50_HIV+_No_ART


title: Fat_Pt7_HIV+_ART


title: Fat_Pt5_HIV+_ART


title: blood 0.5g T0 ppC

source_name: blood 0.5g T0 ppC

value: C


title: Fat_Pt49_HIV+_No_ART


title: Fat_Pt47_HIV+_No_ART


title: Fat_Pt4_HIV_Neg


title: Fat_Pt23_HIV+_ART


title: Fat_Pt12_HIV_Neg


title: Fat_Pt11_HIV+_ART


title: Fat_Pt3_HIV+_ART


title: Fat_Pt21_HIV_Neg


title: Fat_Pt19_HIV_Neg


title: Fat_Pt10_HIV+_ART


title: Fat_Pt15_HIV+_No_ART


title: Fat_Pt22_HIV+_ART


title: Muscle_Pt5_duplicate_HIV+_ART

source_name: HIV positive with ART, muscle

value: muscle


title: Fat_Pt16_HIV+_ART


title: Muscle_Pt49_HIV+_No_ART

source_name: HIV positive without ART, muscle


title: Fat_Pt14_HIV+_No_ART


title: Muscle_Pt10_duplicate_HIV+_ART

description: CCL060215_muscle_Pt10_duplicate_HIV+_ART


title: Muscle_Pt10_HIV+_ART


title: Muscle_Pt15_HIV+_No_ART


title: Muscle_Pt5_HIV+_ART


title: Fat_Pt18_HIV_Neg


title: Fat_Pt2_HIV+_ART


title: Fat_Pt20_HIV+_ART


title: Muscle_Pt9_HIV+_ART


title: Muscle_Pt7_HIV+_ART


title: Muscle_Pt61_HIV+_No_ART


title: Muscle_Pt8_HIV_Neg

source_name: HIV negative, muscle


title: Muscle_Pt60_HIV+_ART


title: Muscle_Pt15_duplicate_HIV+_No_ART

description: CCL060215_muscle_Pt15_duplicate_HIV+_No_ART


title: Muscle_Pt6_HIV_Neg


title: Muscle_Pt57_HIV+_No_ART


title: Muscle_Pt56_HIV+_No_ART


title: In vivo infected 3

type: other

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

description: Measured on both negative and positive ionization modes, with duplicate acquisition, resulting in 4 files.

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing:
Raw mass spectrometry data were processed using a custom-developed software package, as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). Mass spectra were batch-processed using a custom VBA script, within the instrument vendor’s data processing software package, DataAnalysis®. First, all the raw mass spectra acquired in positive and negative ion modes were internally calibrated with the reference masses of the spiked standard compounds and a ubiquitous known contaminant, N-butylbenzensulfonamide. Monoisotopic peaks corresponding to the isotopic distribution patterns were then automatically determined and those with signal-to-noise ratios above 3 were picked. The m/z values were subsequently converted to neutral masses by subtracting 1.007276 for positive ion mode or adding 1.007276 for negative ion mode. Next, the resulting mass lists from the individual mass spectra within each paired sample group were further processed with another custom software program developed with LabVIEW® (National Instruments, Austin, USA). The first step of this program is to remove the adduct ions, e.g., (M+Na)+ and/or (M+K)+ in positive ion mode and (M+Cl)- in negative ion mode, from the mass lists based on the expected mass differences for these ions within 2 ppm. Next, the peak intensity of each unique monoisotopic neutral mass was normalized to the intra-spectrum total ion intensity. Masses observed in at least 50% of the spectra from each paired sample group were aligned into unique masses (metabolite features) from the masses that matched within 2 ppm. Finally, a two-dimensional data matrix (neutral mass vs. peak intensity) was generated for each group and saved in a tab-delimited text format. To detect metabolite differences between the different sample groups, the masses were filtered in each list for metabolites that were present on one set of samples, but not the other. Additionally, the intensities were averaged of each unique mass in each set of biological replicates and calculated the ratio between the sample groups. To assign possible metabolite identities to the masses present only in one set or showing at least 2-fold changes, the monoisotopic neutral masses of interest were queried against the Human Metabolome Database (HMDB, http://www.hmdb.ca), with a tolerance of 0.001 Da.
Masses (daltons) with relative intensity

label: Not applicable

molecule: other

organism: Mus musculus

source_name: Bile

label_protocol: Not applicable

growth_protocol: For in vitro growth studies, an overnight culture of Salmonella enterica serovar Typhimurium SL1344 was used to inoculate 10 μL of bile at an approximate density of 5x10^6 cells/mL. Samples were incubated for 24 hours at 37 oC with shaking, and were then extracted as described.

extract_protocol: After appropriate incubation, bile samples were centrifuged for 5-10 minutes at 13,000 g and 7 μL of the supernatant was removed and dried at room temperature in a centrifuge equipped with a vacuum pump. Dried extracts were then suspended in a mixture of acetonitrile and water (200 μL, 50% acetonitrile for in vitro samples; 400 μL, 75%  acetonitrile for in vivo samples), vortexed and cleared by centrifugation. All extracts were kept at -80˚C until further use.

treatment_protocol: For in vivo studies, C57BL/6 mice were infected with approximately 10^8 cells of Salmonella enterica serovar Typhimurium SL1344 by oral gavage.

tag: strain

value: Salmonella enterica serovar Typhimurium SL1344 in vivo

tag: sample type

value: bile


title: In vivo uninfected 2


title: In vivo uninfected 3


title: Muscle_Pt59_HIV+_No_ART


title: In vivo infected 2


title: In vivo infected 1


title: In vivo uninfected 1


title: In vitro infected 2

value: Salmonella enterica serovar Typhimurium SL1344 in vitro


title: Muscle_Pt50_HIV+_No_ART

value: positive


title: In vitro infected 1


title: Muscle_Pt52_HIV+_No_ART

value: without


title: Muscle_Pt53_HIV+_ART


title: In vitro uninfected 2


title: Muscle_Pt55_HIV+_ART


title: Muscle_Pt45_HIV+_ART


title: Muscle_Pt54_HIV+_No_ART


title: In vitro uninfected 1


title: Muscle_Pt48_HIV+_No_ART


title: Muscle_Pt47_HIV+_No_ART


title: Muscle_Pt44_HIV+_No_ART


title: Muscle_Pt51_HIV+_No_ART


title: Muscle_Pt43_HIV+_ART


title: Muscle_Pt41_HIV+_ART


title: Muscle_Pt42_HIV+_ART


title: Muscle_Pt37_HIV_Neg

value: negative


title: Muscle_Pt46_HIV+_ART

value: with


title: Muscle_Pt36_HIV+_ART


title: Muscle_Pt40_HIV+_No_ART


title: Muscle_Pt38_HIV+_ART


title: Muscle_Pt4_HIV_Neg


title: Muscle_Pt39_HIV+_No_ART


title: Muscle_Pt34_HIV+_ART


title: Muscle_Pt30_HIV+_ART


title: Muscle_Pt29_HIV_Neg


title: Muscle_Pt28_HIV_Neg


title: Muscle_Pt33_HIV+_ART


title: Muscle_Pt3_HIV+_ART


title: Muscle_Pt27_HIV+_ART


title: 13T rep1

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: 13T replicate 1

hyb_protocol: A total hybridisation volume of 15ul is prepared for each sample and    15ul loaded into a single array on the Sentrix Human-HT12v4 Beadchip.     A total of 12 different labelled samples can be loaded into 12    individual arrays per beadchip.  The chip is hybridised at 58C for 16    hours in an oven with a rocking platform.  After hybridisation, the    chip is washed using the appropriate protocols as outlined in the    illumina manual.  Upon completion of the washing, the chips are then    coupled with Cy3 and scanned in the illumina BeadArray Reader.

scan_protocol: Arrays were scanned in the Illumina BeadArray Reader.

data_processing: The scanner operating software, GenomeStudio, converts the signal on the    array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.

source_name: xenograft tumor

label_protocol: Human total RNA was quality ascertained using the Agilent Bioanalyser    2100 using the NanoChip protocol.  A total of 500ng was labelled using    the Ambion Total Prep RNA amplification kit (Cat. No. IL1791).  The    quantity of labelled product was ascertained using the Agilent    Bioanalyser 2100 using the NanoChip protocol.  A total of 750ng of    labelled cRNA was then prepared for hybridisation to the Sentrix Human-   HT12v4 Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that    includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).

extract_protocol: RNA was extracted using Invotrogen Trizol Reagent    in accordance with the prescribed protocol provided with the kit.    DNase treatment was performed using the QIAGEN RNase free DNase Set    prior to RNA purification using the QIAGEN RNAeasy kit in accordance    with the prescribed protocol provided with the kit. Quality control    was performed with Agilent Bioanalyser.

tag: tumor id

tag: tumor type

value: human breast tumor xenograft


title: 806T rep1

description: 806T replicate 1


title: 24T rep2

description: 24T replicate 2


title: 13T rep2

description: 13T replicate 2


title: 13T rep3

description: 13T replicate 3


title: 806T rep2

description: 806T replicate 2


title: Muscle_Pt32_HIV+_ART


title: Muscle_Pt31_HIV_Neg


title: Muscle_Pt35_HIV_Neg


title: 806T rep3

description: 806T replicate 3


title: 24T rep3

description: 24T replicate 3


title: 24T rep1

description: 24T replicate 1


title: Muscle_Pt26_HIV_Neg


title: Muscle_Pt24_HIV+_ART


title: Muscle_Pt25_HIV_Neg


title: Muscle_Pt23_HIV+_ART


title: Muscle_Pt22_HIV+_ART


title: Muscle_Pt21_HIV_Neg


title: Muscle_Pt20_HIV+_ART


title: Human Hepatocytes (HL33) infected with Foxa1 Adenovirus (5 MOI)

city: Valencia

first: RAMIRO

last: JOVER

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

hyb_protocol: Labeled ssDNA (5.5 ug) was combined with hybridization and spike controls, and hybridized with a pre-equilibrated Affymetrix chip for 16-18 h. Following hybridization, arrays were washed and stained with a streptavidin phycoerythrin conjugate (SAPE) using an automated GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned with a GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.

data_processing:
Microarray quality control assessment and data acquisition were performed with the GeneChip Operating Software (Affymetrix).
Normalization among the different microarray data files was performed by using robust multiarray analysis (RMA). We applied a conservative probe filtering step excluding those probes not reaching a log2 expression value of 5 in at least one sample, which resulted in the selection of a total of 14,833 probes out of the original 32,320 set.

source_name: Human hepatocytes from liver donor 33 infected with a Foxa1 adenovirus (5 MOI)

label_protocol: Amplified and biotinylated sense-strand DNA was generated from total RNA according to the Affymetrix Whole Transcript Sense Target Labeling Assay.

growth_protocol: Human hepatocytes were isolated from nonsteatotic biopsies (1–4 g) using a two-step perfusion technique.

extract_protocol: Total RNA was extracted with TRIzol Reagent from Invitrogen and re-purified using the RNeasy Plus Mini Kit from Qiagen. The amount and integrity of purified RNA was estimated by micro-capillary electrophoresis (2100 Bioanalyzer, Agilent Technologies), and purity was assessed by the ratio A260/A280.

value: liver

value: cultured hepatocytes from liver donor

tag: transfection

tag: moi

tag: identifier of donor


title: Human Hepatocytes (HL29) infected with Foxa1 Adenovirus (5 MOI)

source_name: Human hepatocytes from liver donor 29 infected with a Foxa1 adenovirus (5 MOI)

tag: tissue


title: Human Hepatocytes (HLH1) infected with adenovirus control (5 MOI)

source_name: Human hepatocytes from liver donor H1 infected with a control adenovirus (insertless Ad-pACC)

value: control adenovirus


title: Human Hepatocytes(HL27) infected with Foxa1 Adenovirus (5 MOI)

source_name: Human hepatocytes from liver donor 27 infected with a Foxa1 adenovirus (5 MOI)


title: Muscle_Pt18_HIV_Neg


title: Muscle_Pt2_HIV+_ART


title: Human Hepatocytes (HL33) infected with adenovirus control (5 MOI)

source_name: Human hepatocytes from liver donor 33 infected with a control adenovirus (insertless Ad-pACC)


title: Muscle_Pt19_HIV_Neg


title: Human Hepatocytes (HLH1)infected with Foxa1 Adenovirus (5 MOI)

source_name: Human hepatocytes from liver donor H1 infected with a Foxa1 adenovirus (5 MOI)


title: Human Hepatocytes (HL27) infected with adenovirus control (5 MOI)

source_name: Human hepatocytes from liver donor 27 infected with a control adenovirus (insertless Ad-pACC)


title: Human Hepatocytes (HL29) infected with adenovirus control (5 MOI)

source_name: Human hepatocytes from liver donor 29 infected with a control adenovirus (insertless Ad-pACC)


title: Muscle_Pt16_HIV+_ART


title: Muscle_Pt17_HIV+_ART


title: Muscle_Pt13_HIV_Neg


title: Muscle_Pt12_HIV_Neg


title: Muscle_Pt11_HIV+_ART


title: HepG2 control, replicate 8

source_name: HepG2 infected with a control adenovirus (insertless Ad-pACC) passage 15

tag: cell line

value: liver hepatocellular carcinoma cells

tag: passage


title: HepG2 infected with Foxa 1 Adenovirus, replicate 8

source_name: HepG2 infected with Foxa1 adenovirus passage 15


title: HepG2 infected with Foxa 1 Adenovirus, replicate 6

source_name: HepG2 infected with Foxa1 adenovirus passage 14


title: HepG2 control, replicate 7


title: Muscle_Pt14_HIV+_No_ART


title: PBMC_Pt6_2nd_HIV_Neg

source_name: HIV negative, PBMC

value: peripheral blood mononuclear cell (PBMC)


title: HepG2 infected with Foxa 1 Adenovirus, replicate 5


title: HepG2 control, replicate 5

source_name: HepG2 infected with a control adenovirus (insertless Ad-pACC) passage 14


title: PBMC_Pt5_duplicate_HIV+_ART

source_name: HIV positive with ART, PBMC


title: PBMC_Pt6_HIV_Neg


title: HepG2 infected with Foxa 1 Adenovirus, replicate 4

source_name: HepG2 infected with Foxa1 adenovirus passage 11


title: HepG2 control, replicate 6


title: PBMC_Pt18_HIV_Neg


title: HepG2 infected with Foxa 1 Adenovirus, replicate 7


title: PBMC_Pt5_HIV+_ART


title: HepG2 infected with Foxa 1 Adenovirus, replicate 3


title: Muscle_Pt1_HIV+_No_ART

source_name: HIV positive without ART, muscle


title: PBMC_Pt15_HIV+_No_ART

source_name: HIV positive without ART, PBMC


title: HepG2 control, replicate 4

source_name: HepG2 infected with a control adenovirus (insertless Ad-pACC) passage 11


title: PBMC_Pt15_duplicate.CEL


title: PBMC_Pt21_2nd_HIV_Neg


title: HepG2 control, replicate 3


title: HepG2 control, replicate 2

source_name: HepG2 infected with a control adenovirus (insertless Ad-pACC) passage 10


title: HepG2 infected with Foxa 1 Adenovirus, replicate 1

source_name: HepG2 infected with Foxa1 adenovirus passage 10


title: HepG2 control, replicate 1


title: HepG2 infected with Foxa 1 Adenovirus, replicate 2


title: PBMC_Pt21_HIV_Neg


title: PBMC_Pt13_2nd_HIV_Neg


title: PBMC_Pt13_HIV_Neg


title: PBMC_Pt12_2nd_HIV_Neg


title: pulmonary artery clipping right ventricle_6wk_1

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

country: Germany

institute: Max Planck Institut for Heart and Lung Research

description: PAC.6wk.RV1 : 6 weeks after operation

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.  Heat cocktails at 99C for 5 minutes, then 42C for 5 minutes centrifuge at max speed for 1 minute, Transfer 200ul of hyb solution to each array, then tape holes, Hybridize 17 hours at 45C at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalized gene expression values from Affymetrix Power Tools
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Animals were kept on ad libitum food and water schedules throughout the experiment.

extract_protocol: Hearts were isolated at defined timepoints, perfused with buffer and dissected into three parts for further analysis: LV, septum (SP) and RV.

treatment_protocol: Model of pressure-induced remodeling of RV and LV, Weck haemoclips were closed around PA or the aorta, respectively.

tag: gender

value: male

tag: age

value: 18 weeks

tag: tissue origin

value: heart

value: right ventricle


title: pulmonary artery clipping right ventricle_6wk_2

description: PAC.6wk.RV2 : 6 weeks after operation


title: PBMC_Pt18_2nd_HIV_Neg


title: pulmonary artery clipping right ventricle_3wk_2

description: PAC.3wk.RV2 : 3 weeks after operation

value: 15 weeks


title: sham right ventricle_3wk_1

description: Sham.3wk.RV1 : 3 weeks after operation

source_name: sham right ventricle_3wk


title: PBMC_Pt9_HIV+_ART


title: PBMC_Pt10_duplicate_HIV+_ART


title: PBMC_Pt10_HIV+_ART


title: sham right ventricle_3wk_2

description: Sham.3wk.RV2 : 3 weeks after operation


title: PBMC_Pt12_HIV_Neg


title: PBMC_Pt8_HIV_Neg


title: PBMC_Pt7_HIV+_ART


title: PBMC_Pt61_HIV+_No_ART


title: PBMC_Pt58_HIV+_No_ART


title: PBMC_Pt60_HIV+_ART


title: PBMC_Pt57_HIV+_No_ART


title: pulmonary artery clipping right ventricle_1wk_1

description: PAC.1wk.RV1 : 1 weeks after operation

value: 13 weeks


title: pulmonary artery clipping right ventricle_3wk_1

description: PAC.3wk.RV1 : 3 weeks after operation


title: sham left ventricle_3wk_1

description: Sham.3wk.LV1 : 3 weeks after operation

source_name: sham left ventricle_3wk

value: left ventricle


title: Transaortic constriction left ventricle_3wk_ 1

description: TAC.3wk.LV1 : 3 weeks after operation


title: SeAx_E47myc_transfected_rep2

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Gene expression after transfection with myc-tagged E47 expression construct

hyb_protocol: Samples were hybridized on a Whole Human Genome Microarray 4x44K G4112F (Agilent). For detailed instructions see the One-Color Microarray-Based Gene Expression Analysis Protocol (Qick Amp Labeling) Version 5.7 (G4140-90040v5.7; Agilent) including the Gene Expression Hybridization Kit (Agilent).

scan_protocol: The slide was scanned on an Agilent DNA Microarray Scanner G2565BA with following settings:  Scan region: 61 x 21.6 mm   Scan resolution: 5µm  Extended Dynamic range: selected  TIFF: 16 bit  Dye channel: green - with Green PMT XDR Hi: 100% and Green PMT XDR Lo: 10%

data_processing: TIFF image was processed with Agilent Feature Extraction v10.5.1.1 using the GE1_105_Dec08 protocol.

source_name: SeAx cell line, E47myc

label_protocol: starting amount of total RNA: 500ng; for detailed instructions see the One-Color Microarray-Based Gene Expression Analysis Protocol (Qick Amp Labeling) Version 5.7 (G4140-90040v5.7; Agilent) including the One-Color RNA Spike-In Kit (Agilent), Quick Amp Labeling Kit (Agilent) and RNeasy Mini Kit (Qiagen)

growth_protocol: The human SS-derived cell line Se-Ax (Kaltoft et al, Dermatol Res. 1987) was cultured as described (Mathas et al, Immunol. 2006) apart from adding 100 U/ml recombinant human IL-2 (Sigma-Aldrich, Germany) to Se-Ax cell culture medium.

extract_protocol: Total RNA was extracted using RNeasy Mini-Kit from QIAGEN according to the manufacturer's recommendations.

treatment_protocol: Cells were transfected with 30 µg myc-tagged E47 or E47-forced dimer expression constructs or 30 µg control plasmid pcDNA3.1 (Invitrogen) along with 10 µg of pEGFP-N3. 48 to 72 hours after transfection, GFP+ cells were enriched by FACS sorting, and enriched cells were used for RNA preparation.

value: SeAx

tag: transfection with

value: myc-tagged E47 expression construct

tag: replicate


title: PBMC_Pt56_HIV+_No_ART

tag: hiv status

value: positive

tag: art treatment

value: without


title: sham left ventricle_3wk_2

description: Sham.3wk.LV2 : 3 weeks after operation

tag: strain


title: PBMC_Pt59_HIV+_No_ART

tag: patient


title: SeAx_Mock2_transfected_rep2

description: Gene expression after transfection with control plasmid - negative control for E47myc transfected replicate 2

source_name: SeAx cell line, Mock

value: control plasmid pcDNA3.1


title: Transaortic constriction left ventricle_3wk_ 2

description: TAC.3wk.LV2 : 3 weeks after operation


title: SeAx_E47dimer_transfected_rep2

description: Gene expression after transfection with E47 forced dimer expression construct

source_name: SeAx cell line, E47dimer

value: E47 forced dimer expression construct


title: PBMC_Pt55_HIV+_ART

value: with


title: PBMC_Pt54_HIV+_No_ART


title: PBMC_Pt52_HIV+_No_ART


title: pulmonary artery clipping right ventricle_1wk_2

description: PAC.1wk.RV2 : 1 weeks after operation


title: PBMC_Pt50_HIV+_No_ART


title: PBMC_Pt51_HIV+_No_ART


title: SeAx_Mock2_transfected_rep1

description: Gene expression after transfection with control plasmid - negative control for E47myc transfected replicate 1


title: SeAx_E47myc_transfected_rep1


title: PBMC_Pt53_HIV+_ART


title: FPP accumulation M9 reg 14hr 4

city: Emeryville

first: Robert

last: Dahl

state: CA

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

description:
Regular MgSO4
Technical replicate 4 of 4
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.

hyb_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.

scan_protocol: Arrays were scanned with an Axon 4200 scanner acquiped with GenePix Pro6.0

data_processing: Feature fluorescence intensities [F532 media-B532 and F635media-B635] were extracted with GenePix Pro6.0.  Local hybridization and intensity-dependent artifacts were removed with Lowess normalization using Standardization and Normalization of Microarray Data (SNOMAD, http://pevsnerlab.kennedykrieger.org/snomadinput.html).  The three replicate spots for each gene were averaged and variance calculated.

organism: Escherichia coli

source_name: 14 hr, FPP

growth_protocol:
Individual clones of E. coli DH1 transformed with pMBIS/pADS or pMBIS/pADSmut were grown in 200 mL M9 in 1 L flasks.  At OD ~ 0.3, 20 mM mevalonate and 0.5 mM IPTG were added to each culture.
Regular Mg M9 recipe is as follows: 1x M9 salts (Difco) (1 g/L NH4Cl, 0.5 g/L NaCl, 6.6 g/L Na2HPO4 (anhydrous), 3 g/L KH2PO4), 2 mM MgSO4, 100 mM CaCl2, 40 mM MOPS, 1x trace metal containing (3x10-6 mM (NH4)6(MO7)24, 4x10-4 mM HBO3, 3x10-5 mM CoCl2, 10-5 mM CuSO4, 8x10-5 mM MnCl2, 10-5 mM ZnSO4), 4.5 mg/ml thiamine, 0.01 mM FeSO4 (heptahydrate), and 1% glucose.  Low Mg M9 is the same recipe, but with 10 mM MgSO4

extract_protocol: Biomass was snap frozen in liquid nitrogen and stored at -80 C prior to extraction with Qiagen Rneasy Midi kits.  RNA integrity was verified with a 2100 Bioanalyzer (Agilent)

treatment_protocol: 20 mM Mevalonate and 0.5 mM IPTG added

tag: sample type

value: E. coli DH1, pMBIS/pADSmut, 14 hr

tag: genetic background

tag: genotype

value: pMBIS/pADSmut

tag: time

value: 14 hr

tag: media

value: Regular MgSO4

source_name: 14 hr, amorphadiene

value: pMBIS/pADS

value: E. coli DH1, pMBIS/pADS, 14 hr


title: FPP accumulation M9 reg 14hr 3

description:
Regular MgSO4
Technical replicate 3 of 4
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.

label_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.


title: SeAx_Mock1_transfected_rep2

description: Gene expression after transfection with control plasmid - negative control for E47dimer transfected replicate 2


title: SeAx_E47dimer_transfected_rep1

description: Gene expression after transfection of SeAx cells with E47 forced dimer expression construct


title: PBMC_Pt49_HIV+_No_ART

tag: tissue

value: peripheral blood mononuclear cell (PBMC)


title: FPP accumulation M9 reg 14hr 2

description:
Regular MgSO4
Technical replicate 2 of 4
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.


title: PBMC_Pt47_HIV+_No_ART


title: SeAx_Mock1_transfected_rep1

description: Gene expression after transfection of SeAx cells with control plasmid - negative control for E47dimer transfected replicate 1

tag: cell line


title: PBMC_Pt48_HIV+_No_ART


title: FPP accumulation M9 reg 10hr 2

description:
Regular MgSO4
Technical replicate 2 of 2
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.

source_name: 10 hr, FPP

value: E. coli DH1, pMBIS/pADSmut, 10 hr

value: 10 hr

source_name: 10 hr, amorphadiene

value: E. coli DH1, pMBIS/pADS, 10 hr


title: FPP accumulation M9 Lo 26.5hr 2

description:
Low MgSO4
Technical replicate 2 of 2
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.

source_name: 26.5 hr, FPP

value: E. coli DH1, pMBIS/pADSmut, 26.5 hr

value: Low MgSO4

source_name: 26.5 hr, amorphadiene

value: E. coli DH1, pMBIS/pADS, 26.5 hr


title: FPP accumulation M9 reg 14hr 1

description:
Regular MgSO4
Technical replicate 1 of 4
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.


title: FPP accumulation M9 Lo 26.5hr 1

description:
Low MgSO4
Technical replicate 1 of 2
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.


title: FPP accumulation M9 Lo 14hr 2


title: FPP accumulation M9 Lo 14hr 1


title: PBMC_Pt45_HIV+_ART

source_name: HIV positive with ART, PBMC

value: positive


title: PBMC_Pt43_HIV+_ART


title: PBMC_Pt44_HIV+_No_ART

value: without


title: FPP accumulation M9 reg 10hr 1

description:
Regular MgSO4
Technical replicate 1 of 2
The strain accumulating FPP (pMBIS/pADSmut) is considered the treatment while the strain producing the non-toxic amorphadiene is considered the control.


title: PBMC_Pt42_HIV+_ART


title: PBMC_Pt41_HIV+_ART


title: FPP accumulation M9 Lo 10hr 1


title: PBMC_Pt46_HIV+_ART


title: FPP accumulation M9 Lo 10hr 2


title: PBMC_Pt37_HIV_Neg

source_name: HIV negative, PBMC

value: negative


title: PBMC_Pt36_HIV+_ART

value: with


title: PBMC_Pt4_HIV_Neg


title: PBMC_Pt34_HIV+_ART


title: PBMC_Pt40_HIV+_No_ART

source_name: HIV positive without ART, PBMC


title: PBMC_Pt35_HIV_Neg


title: PBMC_Pt33_HIV+_ART


title: PBMC_Pt38_HIV+_ART


title: PBMC_Pt32_HIV+_ART


title: PBMC_Pt3_HIV+_ART


title: PBMC_Pt31_HIV_Neg


title: PBMC_Pt30_HIV+_ART


title: C24 x C24  day 6 vs. C24 x C24 day 4 C24-DAS4-C24-DAS6

city: Dummerstorf

first: Dirk

last: Repsilber

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology

hyb_protocol: ATH1 GeneChip hybridizations, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

scan_protocol: washing, staining, and scanning, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

data_processing: column LogRatio in raw data files: log(REDsignal/GREENsignal) (base 10) per feature (processed signals from Agilent feature extraction file were used)

organism: Arabidopsis thaliana

source_name: pool of whole seedlings

label_protocol: preparation and biotin labeling of cRNA, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

growth_protocol: For early timepoints 4-6 days after sawing (DAS) seeds were sown onto nylon mesh (pore size 200 µm) covering 80 ml of a 1:1 mixture of GS90 soil (Gebrüder Patzer, Sinntal-Jossa, Germany) and vermiculite (Deutsche Vermiculite Dämmstoff, Sprockhövel, Germany) moistened with 40 ml tap water in 15 cm Petri dishes. Each Petri dish was divided in four equal-sized quarters, marked with pencil on the nylon mesh. Approximately 50 seeds of the four tested genotypes Col-0, C24, Col-0xC24-F1 and C24xCol-0-F1 were placed in one quarter each. The Petri dishes were sealed with micropore surgical tape (3M, Neuss, Germany). Seedlings were grown in four independent replicates in  a controlled reach-in growth chamber under long-day conditions (16/8 hr photoperiod with 20°/19°C at 120 µmol m-2 s-1). For later time points (10, 15, 20, 25, and 30 DAS) five plants of each genotype were grown in pots (16 cm diameter) in a controlled walk-in phytotron under the same conditions as described above, in four independent replicates. Samples were harvested into liquid nitrogen in the middle of the light period between 11 am to 1 pm. This experiment was repeated four times and the RNA obtained from the four extractions per genotype and time point was pooled for the hybridization on Ath1- Affymetrix expression arrays.

extract_protocol: innu PREP Plant RNA kit (845-KS-2060250, Analytik Jena)

treatment_protocol: stable 16/8 hr photoperiod with 20°/19°C at 120 µmol m-2 s-1

tag: days after sowing

tag: date of crna synthesis

value: whole seedling


title: C24 x Col-0  day 30 vs. C24 x Col-0 day 25 C24Col-DAS25-C24Col-DAS30

value: C24 x Col-0


title: Col-0 x Col-0  day 25 vs. Col-0 x Col-0 day 20 Col-DAS20-Col-DAS25

value: Col-0 x Col-0


title: PBMC_Pt28_HIV_Neg


title: Col-0 x C24  day 4 vs. Col-0 x C24 day 30 ColC24-DAS30-ColC24-DAS4

value: Col-0 x C24


title: C24 x Col-0  day 10 vs. C24 x Col-0 day 6 C24Col-DAS6-C24Col-DAS10


title: C24 x Col-0  day 15 vs. C24 x Col-0 day 10 C24Col-DAS10-C24Col-DAS15


title: Col-0 x Col-0  day 10 vs. Col-0 x Col-0 day 6 Col-DAS6-Col-DAS10


title: PBMC_Pt27_HIV+_ART


title: C24 x C24  day 4 vs. Col-0 x C24 day 4 ColC24-DAS4-C24-DAS4


title: PBMC_Pt25_HIV_Neg


title: PBMC_Pt26_HIV_Neg


title: C24 x C24  day 15 vs. C24 x C24 day 10 C24-DAS10-C24-DAS15


title: C24 x C24  day 30 vs. C24 x C24 day 25 C24-DAS25-C24-DAS30


title: PBMC_Pt23_HIV+_ART


title: PBMC_Pt24_HIV+_ART


title: Col-0 x Col-0  day 20 vs. C24 x C24 day 20 C24-DAS20-Col-DAS20


title: C24 x C24  day 10 vs. Col-0 x C24 day 10 ColC24-DAS10-C24-DAS10


title: Col-0 x Col-0  day 4 vs. Col-0 x Col-0 day 30 Col-DAS30-Col-DAS4


title: C24 x Col-0  day 10 vs. Col-0 x Col-0 day 10 Col-DAS10-C24Col-DAS10


title: Col-0 x C24  day 25 vs. Col-0 x C24 day 20 ColC24-DAS20-ColC24-DAS25


title: Col-0 x C24  day 20 vs. C24 x Col-0 day 20 C24Col-DAS20-ColC24-DAS20


title: Col-0 x C24  day 30 vs. C24 x Col-0 day 30 C24Col-DAS30-ColC24-DAS30


title: C24 x C24  day 30 vs. Col-0 x C24 day 30 ColC24-DAS30-C24-DAS30


title: PBMC_Pt22_HIV+_ART


title: C24 x C24  day 20 vs. Col-0 x C24 day 20 ColC24-DAS20-C24-DAS20


title: PBMC_Pt2_HIV+_ART


title: PBMC_Pt20_HIV+_ART


title: PBMC_Pt19_HIV_Neg


title: Col-0 x C24  day 10 vs. C24 x Col-0 day 10 C24Col-DAS10-ColC24-DAS10


title: Col-0 x Col-0  day 10 vs. C24 x C24 day 10 C24-DAS10-Col-DAS10


title: PBMC_Pt17_HIV+_ART


title: PBMC_Pt1_HIV+_No_ART


title: PBMC_Pt16_HIV+_ART


title: PBMC_Pt11_HIV+_ART


title: PBMC_Pt14_HIV+_No_ART


title: Col-0 x Col-0  day 30 vs. C24 x C24 day 30 C24-DAS30-Col-DAS30


title: UHRF1_sh2

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

description: Gene expression data from HCT116 cells treated with UHRF1 shRNA-2 and selected with puromycin.

hyb_protocol: Hybridization was performed according to the manufacturer's instructions at Expression Analysis, Inc. (http://www.expressionanalysis.com).

scan_protocol: Scanning was performed at Expression Analysis, Inc. (http://www.expressionanalysis.com).

data_processing: The data were analyzed with Expression Console software (RMA), which is produced by Affymetrix.

source_name: colorectal carcinoma cells, UHRF1 shRNA

label_protocol: Biotinylated cRNA were prepared using the Affymetrix One Cycle kit according to the standard Affymetrix protocol at Expression Analysis, Inc. (http://www.expressionanalysis.com).

growth_protocol: HCT116 cells were cultured with McCoy’s 5A medium containing 10% fetal bovine serum (FBS; Hyclone) and 1% Pen-Strep.

extract_protocol: Total RNA was extracted by Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse-free DNase I.

treatment_protocol: HCT116 cells were infected with Scr shRNA, UHRF1 shRNA-2 or UHRF1 shRNA-5 containing lentivirus and harvested after 6-days selection with puromycin.

tag: cell type

value: colorectal carcinoma cells

tag: shRNA

value: UHRF1 shRNA-2


title: C24 x Col-0  day 6 vs. C24 x Col-0 day 4 C24Col-DAS4-C24Col-DAS6


title: C24 x Col-0  day 20 vs. Col-0 x Col-0 day 20 Col-DAS20-C24Col-DAS20


title: C24 x Col-0  day 30 vs. Col-0 x Col-0 day 30 Col-DAS30-C24Col-DAS30


title: C24 x C24  day 10 vs. C24 x C24 day 6 C24-DAS6-C24-DAS10


title: Penicillum_24hr_rep1

city: Shinjuku-ku

first: TSUYOSHI

last: OGUMA

state: Tokyo

address: 35 Shinanomachi

department: Department of Medicine

country: Japan

institute: Keio University School of Medicine

description: Gene expression after 24 hours in NCI-H294 cells stimulated with the P. notatum extracts

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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 DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. gProcessed Signal intensity is provided in the Sample Table below.
Values below 0.01 were set to 0.01. Each mesurement was divided by the 50.0th percentile of all mesurements in that sample. Specific samples were normalized to one another: Sample (s) 2-4 were normalized against the median of the control sample 1. Each meseaurements for each gene in those specific sample were divided by that gene's mesurements in the corresponding control sample. Ratio data is provided in a supplementary file available on the Series record.

label_protocol: 1000ng total RNA labeled Cyanine-3 (Cy3) using the One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NCI-H292 (CRL-1848, American Tissue Culture Collection), a human bronchial epithelial cell line originating from lung mucoepidermoid carcinoma, was cultured in RPMI1640 medium (Invitrogen, Carlsbad, CA) containing 10% FBS (Invitrogen) in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using TRIzol® (Invitrogen) and RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Confluent cells were stimulated with fungal extracts of A. fumigatus, P. notatum, A. alternata, or Candida albicans (C. albicans) obtained from Greer laboratories (Lenoir, NC) at concentrations of 1000 protein nitrogen unit (PNU)/ml for 24 hours.

tag: agent

value: Penicillum

value: airway epithelial cells


title: C24 x Col-0  day 4 vs. Col-0 x Col-0 day 4 Col-DAS4-C24Col-DAS4


title: Col-0 x Col-0  day 6 vs. Col-0 x Col-0 day 4 Col-DAS4-Col-DAS6


title: Alternaria_24hr_rep1

description: Gene expression after 24 hours in NCI-H293 cells stimulated with the A. alternata extracts

value: Alternaria


title: Col-0 x C24  day 30 vs. Col-0 x C24 day 25 ColC24-DAS25-ColC24-DAS30


title: UHRF1_sh5

description: Gene expression data from HCT116 cells treated with UHRF1 shRNA-5 and selected with puromycin.

value: UHRF1 shRNA-5


title: Myotubes-FSHD-2-patient1

city: monza

first: raffaella

last: meneveri

state: italia

address: via cadore 48

department: Dept of Experimental Medicine

country: Italy

institute: Univ. Milano Bicocca

description:
12/M
FSHD_FENO1_DAY_8.CEL

hyb_protocol: Washing and staining steps were carried out using GeneChip Fluidics Station 450

scan_protocol: The arrays were scanned in the Affymetrix® GeneChip® scanner 3000 7G. Affymetrix® GeneChip® operating software was used for acquisition, management and initial processing of the expression data, while arrays quality control was performed using Affymetrix® Expression Console™.

data_processing: RMA signal estimates obtained with Affymetrix Power Tools (APT) software

source_name: Quadriceps femoris

label_protocol: Fragmented biotin-labeled cDNAs were hybridized to Affymetrix® human exon 1.0 ST arrays at 45°C for 17 hours, as described in Affymetrix® Users Manual.

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM) containing 20% fetal bovine serum (FBS), L-glutamine (1%), penicillin and streptomycin (1%) (Euroclone), insulin 10mg/ml (Sigma), human fibroblast growth factor (hFGF) 25 ng/ml and human epidermal growth factor (hEGF) 10ng/ml (Peprotech)

extract_protocol: Total RNA was isolated from sub confluent cell cultures using the RNeasy Mini Kit (Qiagen), and the purified RNA was treated with RNase-free DNase (Qiagen) to remove any residual DNA.

treatment_protocol: Myotubes were obtained after treatment in DMEM supplemented with 2% horse serum (Euroclone) and 1% insulin (Sigma), for 8 days (differentiating medium).

value: Myotubes

tag: patient type

value: phenotypic FSHD patient

tag: patient/donor number


title: Myoblasts-FSHD-2-patient1

description:
12/M
FSHD_FENO1_DAY_0.CEL

value: Myoblasts


title: Scr_shRNA

description: Gene expression data from HCT116 cells treated with scramble shRNA and selected with puromycin.

source_name: colorectal carcinoma cells, scrambled shRNA control

value: scrambled shRNA


title: Aspergillus_24hr_rep1

description: Gene expression after 24 hours in NCI-H292 cells stimulated with the A. fumigatus extracts

value: Aspergillus


title: C24 x Col-0  day 20 vs. C24 x Col-0 day 15 C24Col-DAS15-C24Col-DAS20


title: Col-0 x C24  day 10 vs. Col-0 x C24 day 6 ColC24-DAS6-ColC24-DAS10


title: C24 x Col-0  day 25 vs. C24 x Col-0 day 20 C24Col-DAS20-C24Col-DAS25


title: Myoblasts-FSHD-2-patient2

description:
17/M
FSHD_FENO2_DAY_0.CEL


title: Myblasts-FSHD-2-patient2

description:
17/M
FSHD_FENO2_DAY_8.CEL


title: Control_24hr_rep1

description: Gene expression after 24 hours in NCI-H292 cells stimulated with vehicle

value: Control


title: Myotubes-FSHD-1-patient2

description:
5/M
FSHD8_DAY_8.CEL

value: 4q linked FSHD patient


title: Myotubes-FSHD-1-patient3

description:
71/F
FSHD10_DAY_8.CEL


title: Col-0 x C24  day 4 vs. C24 x Col-0 day 4 C24Col-DAS4-ColC24-DAS4

value: whole seedling


title: Myotubes-FSHD-1-patient1

description:
35/M
FSHD7_DAY_8.CEL


title: Col-0 x C24  day 20 vs. Col-0 x C24 day 15 ColC24-DAS15-ColC24-DAS20


title: 100Hz_NR_Arc1 rat

first: ke

last: wang

address: 151 Libing Road

institute: Shanghai Biochip Co., Ltd.

description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA).

hyb_protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42?  for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning.

scan_protocol: Axon GenePix 4000B

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed test/reference

organism: Rattus norvegicus

source_name: arcuate nucleus of 100Hz electroacupuncture non responder(NR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each Arc which come from rats received 100Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.

extract_protocol: Total RNA was prepared from Arc using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

treatment_protocol: Sprague-Dawley rats were received 100Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's Arc was then collected for transcript profiling analysis.

value: Sprague-Dawley

tag: electroacupuncture

tag: responder

value: no

source_name: Arc of control rats

extract_protocol: Total RNA was prepared from DH of control rats using Trizol reagent (Invitrogen,USA), and further purified with an QIAGEN RNeasy Kit

treatment_protocol: Sprague-Dawley rats were sacrificed after stayed in their home cages without receiving electroacupuncture stimulation.the RNA of Arc were collected for transcript profilinf analysis

value: control


title: 100Hz_NR_Arc2 rat

tag: strain


title: Col-0 x C24  day 6 vs. Col-0 x C24 day 4 ColC24-DAS4-ColC24-DAS6

value: Col-0 x C24


title: 100Hz_NR_Arc3 rat

tag: sample type


title: 100Hz_HR_Arc3 rat

source_name: arcuate nucleus of 100Hz electroacupuncture high responder(HR) rats

value: high


title: Myoblasts-FSHD-1-patient3

description:
71/F
FSHD10_DAY_0.CEL


title: Col-0 x Col-0  day 30 vs. Col-0 x Col-0 day 25 Col-DAS25-Col-DAS30

value: Col-0 x Col-0


title: C24 x C24  day 4 vs. C24 x C24 day 30 C24-DAS30-C24-DAS4


title: Col-0 x C24  day 15 vs. Col-0 x C24 day 10 ColC24-DAS10-ColC24-DAS15


title: Myoblasts-FSHD-1-patient1

description:
35/M
FSHD7_DAY_0.CEL


title: 100Hz_HR_Arc1 rat


title: 2Hz_NR_Arc2 rat

source_name: arcuate nucleus of 2Hz electroacupuncture non responder(NR) rats

label_protocol: Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65? for 10 min, then reversed transcribed at 40? for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each Arc which come from rats received 2Hz electroacupuncture for 30 min, nociceptive testing, returned to home cages for 1 hours and sensitivity on  electroacupuncture analgesia was labeled with Cy3.

treatment_protocol: Sprague-Dawley rats were received 2Hz electroacupuncture for 30 min, nociceptive testing and returned to home cages for 1 hours before sacrificed.These rats were sensitivity on  EA analgesia. It's Arc was then collected for transcript profiling analysis.


title: 2Hz_NR_Arc3 rat


title: 2Hz_NR_Arc1 rat


title: 100Hz_HR_Arc2 rat


title: Myoblasts-FSHD-1-patient2

description:
5/M
FSHD8_DAY_0.CEL


title: Myotubes-normal-donor1

description:
62/F
CN7_DAY_8.CEL

value: healthy donor


title: C24 x C24  day 20 vs. C24 x C24 day 15 C24-DAS15-C24-DAS20

description: 9% of the array surface was covered by an air bubble


title: Myotubes-normal-donor2

description:
77/M
CN9_DAY_8.CEL


title: Col-0 x Col-0  day 4 vs. C24 x C24 day 4 C24-DAS4-Col-DAS4


title: C24 x Col-0  day 4 vs. C24 x Col-0 day 30 C24Col-DAS30-C24Col-DAS4

value: C24 x Col-0


title: 2Hz_HR_Arc3 rat

source_name: arcuate nucleus of 2Hz electroacupuncture high responder(HR) rats


title: 2Hz_HR_Arc2 rat


title: Myotubes-normal-donor3

description:
55/F
CN10_DAY_8.CEL


title: Myoblasts-normal-donor3

description:
55/F
CN10_DAY_0.CEL


title: Col-0 x Col-0  day 20 vs. Col-0 x Col-0 day 15 Col-DAS15-Col-DAS20


title: Myoblasts-normal-donor2

description:
77/M
CN9_DAY_0.CEL


title: 2Hz_HR_Arc1 rat


title: Myoblasts-normal-donor1

description:
62/F
CN7_DAY_0.CEL


title: C24 x C24  day 25 vs. C24 x C24 day 20 C24-DAS20-C24-DAS25


title: Col-0 x Col-0  day 15 vs. Col-0 x Col-0 day 10 Col-DAS10-Col-DAS15


title: WHJSC culture at passage 8, biological rep2

status: Public on Jul 06 2011

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

institute: UNIVERSITY OF GRANADA

description: Gene expression data from WHJSC cultures

hyb_protocol: Following fragmentation, 10 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 400.

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

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

source_name: WHJSC culture at passage 8

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: Cells were isolated from WHJSC fragments using collagenase I. Then, cells were cultured using AMNIOMAX® cell culture medium at 37ºC until subconfluence and furtherly subcultured to new culture flasks until passage 10

extract_protocol: QIAgen RNAeasy extraction kit, following manufacturer's recommendations

value: Umbilical cord Wharton's jelly stem cells culture

tag: passage


title: WHJSC culture at passage 10, biological rep2

source_name: WHJSC culture at passage 10


title: WHJSC culture at passage 8, biological rep1


title: WHJSC culture at passage 5, biological rep1

source_name: WHJSC culture at passage 5


title: WHJSC culture at passage 10, biological rep1


title: WHJSC culture at passage 7, biological rep2

source_name: WHJSC culture at passage 7


title: WHJSC culture at passage 6, biological rep2

source_name: WHJSC culture at passage 6


title: WHJSC culture at passage 3, biological rep3

source_name: WHJSC culture at passage 3


title: WHJSC culture at passage 2, biological rep3

source_name: WHJSC culture at passage 2


title: WHJSC culture at passage 4, biological rep2

source_name: WHJSC culture at passage 4


title: WHJSC culture at passage 7, biological rep1


title: WHJSC culture at passage 10, biological rep3


title: WHJSC culture at passage 8, biological rep3


title: WHJSC culture at passage 4, biological rep1


title: WHJSC culture at passage 9, biological rep1

source_name: WHJSC culture at passage 9


title: WHJSC culture at passage 2, biological rep2


title: WHJSC culture at passage 9, biological rep2


title: WHJSC culture at passage 7, biological rep3


title: WHJSC culture at passage 5, biological rep2


title: WHJSC culture at passage 3, biological rep1


title: WHJSC culture at passage 3, biological rep2


title: WHJSC culture at passage 6, biological rep3


title: WHJSC culture at passage 1, biological rep1

source_name: WHJSC culture at passage 1


title: WHJSC culture at passage 2, biological rep1


title: WHJSC culture at passage 5, biological rep3


title: WHJSC culture at passage 6, biological rep1


title: WHJSC culture at passage 1, biological rep3


title: WHJSC culture at passage 4, biological rep3


title: WHJSC culture at passage 1, biological rep2


title: WHJSC culture at passage 9, biological rep3


title: CUTLL1 DNMAML1 GSIwash4h-rep3

city: Boston

first: James

last: Zou

state: MA

address: 185 Cambridge St.

institute: Harvard University

description: Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 4 hours

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: Affymetrix expression data were normalized using the standard robust multichip average (RMA) package in R.

source_name: CUTLL1 DNMAML1 GSIwash4h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7-10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CUTLL1 cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, penicillin and streptomycin.

extract_protocol: Total RNA prepared with RNeasy Mini kit (Qiagen) was subjected to expression profiling in triplicate on Affymetrix human genome U133 plus 2.0 arrays.

value: CUTLL1 (T lymphoblastic leukemia / lymphoma)


title: CUTLL1 DNMAML1 GSI-rep2

description: Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days

source_name: CUTLL1 DNMAML1 GSI


title: CUTLL1 DNMAML1 GSIwash4h-rep1


title: CUTLL1 DNMAML1 GSIwash4h-rep2


title: CUTLL1 DNMAML1 GSI-rep3


title: CUTLL1 DNMAML1 GSI-rep1


title: CUTLL1 DNMAML1 GSIwash2h-rep2

description: Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 2 hours

source_name: CUTLL1 DNMAML1 GSIwash2h


title: CUTLL1 MigR1 GSIwash4h-rep3

description: Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days and washout compund E for4 hours

source_name: CUTLL1 MigR1 GSIwash4h


title: CUTLL1 DNMAML1 GSIwash2h-rep3


title: CUTLL1 DNMAML1 GSIwash2h-rep1


title: CUTLL1 MigR1 GSIwash4h-rep2


title: CUTLL1 MigR1 GSI-rep1

description: Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days

source_name: CUTLL1 MigR1 GSI


title: CUTLL1 MigR1 GSIwash2h-rep1

description: Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 2 hours

source_name: CUTLL1 MigR1 GSIwash2h


title: CUTLL1 MigR1 GSIwash4h-rep1


title: CUTLL1 GSI-mockwash-CHX4h-rep2

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and mockwash with medium containing compound E and cycloheximide for 4 hours

source_name: CUTLL1 GSI-mockwash-CHX4h


title: CUTLL1 GSI-mockwash-CHX4h-rep3


title: CUTLL1 MigR1 GSI-rep2


title: CUTLL1 MigR1 GSIwash2h-rep3


title: CUTLL1 MigR1 GSI-rep3


title: CUTLL1 MigR1 GSIwash2h-rep2


title: CUTLL1 GSI-mockwash-CHX4h-rep1


title: CUTLL1 GSI-mockwash-CHX2h-rep3

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and mockwash with medium containing compound E and cycloheximide for 2hours

source_name: CUTLL1 GSI-mockwash-CHX2h


title: CUTLL1 GSI-mockwash-CHX2h-rep2


title: Iliac artery biopsy_large atherosclerotic plaque_rep3

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Approval for all animal procedures was obtained from the Institutional Animal Care and Use Committee.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

organism: Macaca fascicularis

source_name: large atherosclerotic plaque

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 0.275 micrograms total RNA starting material.

extract_protocol: The iliac artery samples were obtained at biopsy.  The artery samples were placed in RNAlater (Ambion) in the surgical suite.  For processing, RNAlater was blotted off and the artery sample was minced with scalpels, and homogenized in TRI reagent (MRC) with a Polytron (Brinkmann).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Cynomolgous monkey

tag: age

value: greater than 20 years

tag: gender

value: female

tag: high fat diet

value: 8 years

tag: ovariectomized

value: 4 years

value: iliac artery biopsy

tag: treatment

tag: atherosclerotic plaque size

tag: animal id


title: CUTLL1 GSI-rep3

description: Gene expression data from CUTLL1 cells treated with compound E for 3days

source_name: CUTLL1 GSI

tag: cell line


title: CUTLL1 GSI-rep2


title: Iliac artery biopsy_medium atherosclerotic plaque_rep4

source_name: medium atherosclerotic plaque

tag: tissue


title: Iliac artery biopsy_medium atherosclerotic plaque_rep5


title: Iliac artery biopsy_small atherosclerotic plaque_rep3

source_name: small atherosclerotic plaque


title: CUTLL1 wash4h+CHX_rep2

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E and treated with cycloheximide for 4 hours

source_name: CUTLL1 wash4h+CHX


title: CUTLL1 wash4h+CHX_rep3


title: CUTLL1 wash4h-CHX_rep3

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E for 4 hours

source_name: CUTLL1 wash4h-CHX


title: far-red vs dark in hypocotyl with 18kB array replicate 3

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: replicate 3 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kB array, with dye swap

hyb_protocol: 3DNA Array Detection Array Kit manual was followed to hybridize samples on cDNA micrarrays.

scan_protocol: Packard ScanArray Express scanner was used to scan the microarrays.

data_processing: Raw data was first normalized with GLOWESS and then differential expressed genes were computed using rank product method.

organism: Glycine max

source_name: hypocotyl dissected from seedlings exposed to 1h far-red light

label_protocol: 3DNA Array Detection Array Kit was used to synthesize cDNA from total RNA samples and to label the probes following the manufacturer's protocol.

growth_protocol: Soybean seeds were first surface sterilized in a solution of 5% Clorox and 0.1% Tween 20 for 10 minutes, and then grown hydroponically in water, with sterile glass beads as the solid matrix, in transparent boxes at 20˚C in darkness for 8 days

extract_protocol: CTAB RNA extraction protocol was used to extract total RNA.

treatment_protocol: Seedlings were irradiated with FRc (peak 733nm) generated by Snap-Lite Light Emitting Diode arrays (Quantum Devices, Inc, Barneveld, WI). The FRc irradiation was given at 24.7 μmol m-2 s-2 for one hour.

tag: organ

value: hypocotyl

tag: Stage

value: 8 days old seedlings

tag: cultivar

value: Williams 82

value: 1h far-red light

source_name: hypocotyl dissected from dark-grown seedlings

value: dark-grown


title: CUTLL1 wash4h+CHX_rep1


title: Iliac artery biopsy_small atherosclerotic plaque_rep4


title: far-red vs dark in hypocotyl with 18kB array replicate 4

description: replicate 4 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kB array, with dye swap


title: far-red vs dark in hypocotyl with 18kB array replicate 2

description: replicate 2 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kB array


title: CUTLL1 wash4h-CHX_rep2


title: Iliac artery biopsy_medium atherosclerotic plaque_rep2


title: Iliac artery biopsy_medium atherosclerotic plaque_rep3


title: far-red vs dark in hypocotyl with 18kB array replicate 1

description: replicate 1 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kB array


title: CUTLL1 GSI-rep1


title: CUTLL1 GSI-mockwash-CHX2h-rep1


title: far-red vs dark in hook with 18kB array replicate 3

description: replicate 3 of 4, compare far-red light treated hook with dark grown hook with 18kB array, with dye swap

source_name: hook dissected from seedlings exposed to 1h far-red light

value: apical hook

source_name: hook dissected from dark-grown seedlings


title: Iliac artery biopsy_small atherosclerotic plaque_rep2


title: CUTLL1 wash4h-CHX_rep1


title: Iliac artery biopsy_small atherosclerotic plaque_rep1


title: Iliac artery biopsy_large atherosclerotic plaque_rep2


title: Iliac artery biopsy_large atherosclerotic plaque_rep1


title: far-red vs dark in hook with 18kB array replicate 4

description: replicate 4 of 4, compare far-red light treated hook with dark grown hook with 18kB array, with dye swap


title: Iliac artery biopsy_medium atherosclerotic plaque_rep1


title: far-red vs dark in hook with 18kB array replicate 2

description: replicate 2 of 4, compare far-red light treated hook with dark grown hook with 18kB array


title: CUTLL1 wash2h+CHX_rep2

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E and treated with cycloheximide for 2 hours

source_name: CUTLL1 wash2h+CHX


title: far-red vs dark in cotyleodn with 18kB array replicate 4

description: replicate 4 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kB array, with dye swap

source_name: cotyledons dissected from seedlings exposed to 1h far-red light

value: cotyledon

source_name: cotyledons dissected from dark-grown seedlings


title: CUTLL1 wash2h+CHX_rep3


title: Mesentery_Raloxifene_rep3

description: Protocol for dissecting the mesenteric arterial tree is detailed in Rodrigo MC et al., J Pharmacol Toxicol Methods 2002;47(2):87-92.

source_name: Mesenteric arteries, treated with raloxifene

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 2 micrograms total RNA starting material.

extract_protocol: The mesenteric arterial tree was dissected free from veins and adipose tissue under RNAlater (Ambion). The RNAlater was blotted off and the tissue was minced, then homogenized in TRI reagent (MRC).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Sprague Dawley

value: 9 weeks

value: mesenteric artery

tag: agent

value: raloxifene


title: Mesentery_Raloxifene_rep1


title: far-red vs dark in cotyleodn with 18kB array replicate 3

description: replicate 3 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kB array, with dye swap


title: far-red vs dark in cotyleodn with 18kB array replicate 2

description: replicate 2 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kB array


title: CUTLL1 wash2h-CHX_rep3

description: Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E for 2 hours

source_name: CUTLL1 wash2h-CHX

value: CUTLL1 (T lymphoblastic leukemia / lymphoma)


title: far-red vs dark in cotyleodn with 18kB array replicate 1

description: replicate 1 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kB array


title: CUTLL1 wash2h-CHX_rep1


title: CUTLL1 GSId3_rep3

description: Gene expression data from CUTLL1 cells treated with compound E

source_name: CUTLL1 GSId3


title: CUTLL1 wash2h-CHX_rep2


title: Mesentery_Raloxifene_rep2


title: CUTLL1 wash2h+CHX_rep1


title: CUTLL1 GSId3_rep2


title: Mesentery_Equilin_rep2

source_name: Mesenteric arteries, treated with equilin

value: equilin


title: far-red vs dark in hook with 18kB array replicate 1

description: replicate 1 of 4, compare far-red light treated hook with dark grown hook with 18kB array


title: Mesentery_Equilin_rep1

value: female


title: Mesentery_Tamoxifen_rep3

source_name: Mesenteric arteries, treated with tamoxifen

value: tamoxifen


title: CUTLL1 DMSO_rep3

description: Gene expression data from CUTLL1 cells treated with vehicle

source_name: CUTLL1 DMSO


title: CUTLL1 GSId3_rep1


title: Mesentery_Tamoxifen_rep1


title: Mesentery_Tamoxifen_rep2


title: Mesentery_Tamoxifen_rep4


title: BrdU-labeled DNA in late S phase

type: genomic

city: Raleigh

first: Pete

middle: E

last: Pascuzzi

state: NC

address: 851 Main Campus Drive

institute: North Carolina State University

hyb_protocol: The Cy dye-labeled target and reference samples were co-hybridized on a custom-printed tiling array with a dye-swap experimental design. After the overnight hybridization, DyeSaver2 was used to minimize oxidation of Cy dyes.

scan_protocol: Hybridized arrays were scanned using a PerkinElmer ScanArray Express scanner and quantified using GenePix Pro software (version 6.01).

data_processing: Arrays were loess and quantile normalized using the limma package in R to obtain log2 ratios.  The variance between biological replicates and technical replicates was similar so biological replicates were then treated as technical replicates.

molecule: genomic DNA

source_name: late S phase nuclei of cultured cells - BrdU IP

label_protocol: Amplified target and reference DNA samples were labeled with either Cy3 or Cy5 and purified using a BioPrime Array CGH Genomic Labeling System (Invitrogen).

growth_protocol: At (Col-0) cells were grown in Gamborg's B5 basal medium with minor salt, maintained on a rotary shaker at 160 rpm under constant light at 23C, and subcultured weekly.

extract_protocol: Genomic DNA was extracted from the sorted nuclei after reversing the crosslinks. The extracted gDNA was purified using a phase lock gel (Sigma), precipitated by ethanol, and resuspended in RT-grade water.

treatment_protocol: A 7-d split culture was grown for 16 hrs and then labeled for 1 hr with 100 uM BrdU.

tag: ecotype

value: Columbia 0

source_name: late S phase nuclei of cultured cells - Input

treatment_protocol: no treatment (input DNA)


title: CUTLL1 DMSO_rep1


title: CUTLL1 DMSO_rep2


title: BrdU-labeled DNA in early S phase

source_name: early S phase nuclei of cultured cells - BrdU IP

source_name: early S phase nuclei of cultured cells - Input


title: Mesentery_Equilin_rep3

tag: strain


title: BrdU-labeled DNA in mid S phase

source_name: mid S phase nuclei of cultured cells - BrdU IP

source_name: mid S phase nuclei of cultured cells - Input


title: Mesentery_Estradiol benzoate_rep2

source_name: Mesenteric arteries, treated with estradiol benzoate

value: estradiol benzoate


title: Mesentery_Ethinyl estradiol_rep2

source_name: Mesenteric arteries, treated with ethinyl estradiol

value: ethinyl estradiol


title: 13852133 - WT vs A311

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Fonctionnal caracterization of the transcription factor VvMYB82 wich is a regulator of the different phenolic compound biosynthesis.

hyb_protocol: A311 Cy5 / WT1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: flower - in vitro

extract_protocol: A311:41.9ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: columbia

tag: genotype

source_name: WT

extract_protocol: WT1:47ug. (Qiagen_RNeasy.pdf)

value: wild type


title: 13848395 - WT vs KO62

hyb_protocol: KO62 Cy5 / WT Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: KO62:39ug. (Qiagen_RNeasy.pdf)

extract_protocol: WT:33ug. (Qiagen_RNeasy.pdf)


title: FB1∆rak1_2nd replicate

city: Marburg

first: Regine

last: Kahmann

state: Hesse

address: Karl-von-Frisch Str. 10

department: Organismic Interactions

institute: MPI für terrestrische Mikrobiologie

hyb_protocol: EukGE-WS2 protocol on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

organism: Mycosarcoma maydis

source_name: U. maydis strain FB1∆rak1 grown in CM medium with 1% glucose

label_protocol: Target preparation was performed according to the standard Affymetrix expression analysis technical manual using the GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900493).

growth_protocol:
FB1∆rak1 was grown on a rotary shaker (200 rpm) in liquid Ustilago complete medium (CM,0,25% (w/v) Casaminoacids (Difco)
0,1% (w/v) Yeast-extract (Difco)
1,0% (v/v) Vitamin solution (Holliday 1974)
6,25% (v/v) Salt solution (Holliday 1974)
0,05% (w/v) DNA degr. Free Acid (Sigma, D-3159)
0,15% (w/v) NH4NO3
1,0% (w/w) 1M Tris-Cl pH 8,0) with 1% glucose at 28°C to an OD600 of 0.5.

extract_protocol: The cell pellets from 50 ml of liquid culture were harvested by centrifugation for 5 min at 3500 rpm. Following resuspension of the cells in Trizol (Invitrogen) and addition of glass beads (200µl) cells were cracked on a IKA shaker. Total RNA was prepared following the Trizol reagent protocol (Invitrogen)

value: FB1∆rak1 deleted for the gene um10146 (http://mips.helmholtz-muenchen.de/genre/proj/ustilago) termed rak1 by replacement of the complete ORF with a Hygromycin resistance cassette (Kamper et al., 2004, Mol Genet Genomics), exponential growth phase


title: 13852129 - KO62 vs WT

hyb_protocol: WT Cy5 / KO62 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852132 - A311 vs WT

hyb_protocol: WT1 Cy5 / A311 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotye


title: far-red vs dark in hypocotyl with 18kA array replicate 4

description: replicate 4 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kA array, with dye swap

source_name: hypocotyl dissected from seedlings exposed to 1h far-red light

value: hypocotyl

value: 8 days old seedlings

value: Williams 82

value: 1h far-red light

source_name: hypocotyl dissected from dark-grown seedlings

value: dark-grown


title: Mesentery_Ethinyl estradiol_rep1

value: Sprague Dawley

tag: age

value: 9 weeks

value: mesenteric artery


title: Mesentery_Ethinyl estradiol_rep3

tag: gender


title: Mesentery_control_rep3

source_name: Mesenteric arteries, vehicle treated control

value: vehicle


title: Mesentery_control_rep4

value: female


title: far-red vs dark in hypocotyl with 18kA array replicate 1

description: replicate 1 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kA array


title: Mesentery_control_rep2


title: FB1∆rak1_1st replicate


title: far-red vs dark in hook with 18kA array replicate 3

description: replicate 3 of 4, compare far-red light treated hook with dark grown hook with 18kA array, with dye swap

source_name: hook dissected from seedlings exposed to 1h far-red light

value: apical hook

source_name: hook dissected from dark-grown seedlings


title: FB1∆rak1_3rd replicate


title: far-red vs dark in hook with 18kA array replicate 4

description: replicate 4 of 4, compare far-red light treated hook with dark grown hook with 18kA array, with dye swap


title: ExVivoDT40cell_4hr_2ug/ml_rep1

city: Nanjing

first: Pu

middle: Yan

last: Chen

address: No. 1, Weigang

institute: Nanjing Agriculture University

description: Gene expression after 4hr in 2ug/ml BSP-II-treated DT40 cell

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >20.0 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 Chicken (V2) Gene Expression Microarray (Agilent, G2519F-015068) for 17 hours at 65℃ 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℃ 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 (part number G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization)

organism: Gallus gallus

source_name: DT40 cell, 4hr, 2ug/ml, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop® ND-1000 Spectrophotometer.

growth_protocol: DT40 cells were cultured with RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen),5% avian serum and 1% 0.05mM Thioglycol, at 37℃ with 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA quality was assessed by Nanodrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: DT40 cells were treated by BP5 and BSP-II in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen),5% avian serum and 1% 0.05mM Thioglycol, respectively. The cultures were incubated for 4 hours at 37 ºC in a humidified incubator with 5% CO2.


title: Mesentery_Estradiol benzoate_rep3


title: far-red vs dark in hypocotyl with 18kA array replicate 3

description: replicate 3 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kA array, with dye swap


title: far-red vs dark in hypocotyl with 18kA array replicate 2

description: replicate 2 of 4, compare far-red light treated hypocotyl with dark grown hypocotyl with 18kA array


title: FB1_3rd replicate

source_name: U. maydis strain FB1 grown in CM medium with 1% glucose

growth_protocol:
FB1 was grown on a rotary shaker (200 rpm) in liquid Ustilago complete medium (CM,0,25% (w/v) Casaminoacids (Difco)
0,1% (w/v) Yeast-extract (Difco)
1,0% (v/v) Vitamin solution (Holliday 1974)
6,25% (v/v) Salt solution (Holliday 1974)
0,05% (w/v) DNA degr. Free Acid (Sigma, D-3159)
0,15% (w/v) NH4NO3
1,0% (w/w) 1M Tris-Cl pH 8,0) with 1% glucose at 28°C to an OD600 of 0.5.

value: FB1, exponential growth phase


title: ExVivoDT40cell_4hr_0.02ug/ml_rep1

description: Gene expression after 4hr in 0.02ug/ml BP5-treated DT40 cell

source_name: DT40 cell, 4hr, 0.02ug/ml, replicate 1


title: ExVivoDT40cell_4hr_0ug/ml_rep1

description: Gene expression after 4hr in 0ug/ml BP5 or BSP-II-treated DT40 cell

source_name: DT40 cell, 4hr, 0ug/ml, replicate 1


title: Mesentery_control_rep1

description: Protocol for dissecting the mesenteric arterial tree is detailed in Rodrigo MC et al., J Pharmacol Toxicol Methods 2002;47(2):87-92.


title: FB1_1st replicate


title: FB1_2nd replicate


title: Early Tumor Regression 2

city: San Francisco

first: Andrei

last: Goga

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol (Agilent).

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

data_processing:
Primary normalization and data extraction were done by the UCSF Microarray Core Facility. Briefly, raw log-intensities were normalized using the quantile normalization method (Bolstad et al., 2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
Normalized Log-intensities for each sample as well as the mean for the samples in each sample group are shown in the GSE28198_normalized_matrix.txt file.  For example, 'Cntrl.1' column heading represents an individual sample.  While 'meanCntrl' indicates the mean of all three CTRL samples.

source_name: LAP-tTA x TRE-MYC Transgenic Mouse 8-9 weeks off Doxy, placed on doxy for 72 hrs, liver tumor tissue

label_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com). RNA was amplified using the Sigma whole transcriptome amplification kit (Sigma-Aldrich), and subsequent Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc.). The labeled DNA was assessed using Nanodrop 8000, and equal amounts of Cy3 labeled target were hybridized to Agilent mouse whole genome 4x44K Ink-jet arrays.

growth_protocol: Mice were fed Doxycycline chow 200 mg/kg until >8 weeks of age and then doxy-chow was removed for the indicated time.  In the Early Tumor Regression Cohort doxy-chow was re-introduced into the mouse diet for 72 hrs.

extract_protocol: Liver and liver tumor tissues were frozen using liquid nitrogen and RNA was subsequently extracted (mirVanaTM mirna isolation kit, Ambion).  RNA quality was assessed using the Nanodrop ND-8000 (Nanodrop Technologies, Inc.) and a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies) and run on Agilent mouse whole genome 4x44K Ink-jet arrays.

value: FVB/N

tag: genotype/variation

value: LAP-tTA x TRE-MYC Transgenic Mouse


title: Early Tumor Regression 3


title: far-red vs dark in hook with 18kA array replicate 1

description: replicate 1 of 4, compare far-red light treated hook with dark grown hook with 18kA array


title: Early Tumor Regression 4


title: c-Maf KO fetal liver macrophage

city: Tsukuba

first: Manabu

last: Kusakabe

state: IBARAKI

address: 1-1-1, Tennodai,

department: Department of Anatomy and Embryology

institute: University of Tsukuba

description: Fetal liver cells from E15.5 c-Maf+/+ and c-Maf-/- embryos were incubated with APC-conjugated anti-Mac-1 antibody (eBioscience) and PE-conjugated anti-F4/80 antibody (Serotec). Mac-1+F4/80+ cells were sorted by a FACSAria cell sorter (Becton Dickinson) as fetal liver macrophages.

hyb_protocol: Biotin-labeled cRNA was synthesized from 4 to 6 μg RNA and hybridized to a GeneChip Mouse Genome 430 2.0 Array (Affymetrix).

scan_protocol: After washing, arrays were stained with streptavidin-phycoethrin and analysed on a scanner.

data_processing: The data processing has been performed according to the manufacture's protocol (Affymetrix). Affymetrix Algorithm: ExpressionStat 5.0

source_name: fetal liver macrophage

label_protocol: The microarray procedure was performed as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix).

growth_protocol: None.

extract_protocol: Total RNA was extracted from fetal liver macrophages using a QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: None.

tag: cell type

value: Fetal liver cells

value: c-Maf KO


title: far-red vs dark in cotyleodn with 18kA array replicate 3

description: replicate 3 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kA array, with dye swap

source_name: cotyledons dissected from seedlings exposed to 1h far-red light

value: cotyledon

tag: treatment

source_name: cotyledons dissected from dark-grown seedlings


title: Wild type fetal liver macrophage

value: wild type


title: far-red vs dark in hook with 18kA array replicate 2

description: replicate 2 of 4, compare far-red light treated hook with dark grown hook with 18kA array

value: 8 days old seedlings


title: Tumor Nodule 4

source_name: LAP-tTA x TRE-MYC Transgenic Mouse 8-9 weeks off Doxy, liver tumor tissue


title: far-red vs dark in cotyleodn with 18kA array replicate 4

description: replicate 4 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kA array, with dye swap

value: Williams 82


title: far-red vs dark in cotyleodn with 18kA array replicate 2

description: replicate 2 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kA array

value: 1h far-red light


title: far-red vs dark in cotyleodn with 18kA array replicate 1

description: replicate 1 of 4, compare far-red light treated cotyledon with dark grown cotyledon with 18kA array

value: dark-grown


title: Tumor Nodule 2


title: Early Tumor Regression 1


title: Tumor Nodule 1


title: Tumor Nodule 3