title: Monocyte Stimulated 1

status: Public on Jun 22 2010

city: Davis

first: William

last: Hu

address: 451 Health Science Dr.

department: Medical Microbiology & Immunology

institute: UC Davis

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: After scanning, fluorescence data were processed by the GeneChip operating system (version 1.1, Affymetrix). Background correction, normalization, generation of expression values, and analysis of differential gene expression were performed using dChip analysis software (DNA-Chip analyzer (dChip), version 1.3, Harvard University) in compliance with minimal information about microarray experiment (MIAME) guidelines (www.ncbi.nlm.nih.gov).

source_name: Monocyte

label_protocol: cDNA were synthesized (Superscript Choice System, Invitrogen) utilizing an oligo(dT)24 primer. Biotinylated cRNA was synthesized using a BioArray HighYield RNA transcription labeling kit (ENZO Diagnostics) and purified through RNeasy nucleic acid columns. cRNA quality was evaluated by hybridization to Test3 GeneChips (Affymetrix), and only samples whose 3:5 ratios were less than three were utilized for subsequent hybridization to HuGene U95-AV2 GeneChips (Affymetrix).

extract_protocol: Total cellular RNA was extracted (RNeasy kit, Qiagen)

treatment_protocol: S. Typhimurium Flagellin Stimulated

value: Monocyte

tag: stress

value: stimulated with Flagellin


title: Monocyte No Stim 2

type: RNA

state: CA

country: USA

label: Biotin

molecule: total RNA

organism: Homo sapiens

treatment_protocol: No Treatment

tag: cell type

value: unstimulated


title: Endothelial cells; control; 16h

status: Public on Jul 01 2010

city: Berlin

first: Matthias

last: Futschik

address: Invalidenstrasse 41

country: Germany

institute: Charite

description: Gene expression data from non-stimulated endothelial cells

hyb_protocol: Arrays were hybridized at 45°C, washed and stained using GeneChip Fluidics.

scan_protocol: Each slide was scanned on the Affymetrix scanner with a resolution of 10µm/slide.

data_processing: Signal intensities of scanned output files were extracted using the Affymetrix software after exclusion of hybridisation artefacts. Intensities for probe sets  were computated using the Bioconductor implementation of MAS5.

label: biotin

source_name: Human umbilical cord

label_protocol: Total RNA was then used to develop targets for microarray analysis. Biotinylated cRNA was produced by in vitro transcription and fragmented.

growth_protocol: Cord blood specimens were collected in heparin-coated syringes and blue caps from full-term deliveries, after informed consent was obtained from the mothers. Thereafter, the mononuclear cell fraction was isolated by Ficol (Biochrom, Berlin, Germany) followed by two wash steps. The number of viable cells was determined by a hemocytometer after trypan blue exclusion. Human umbilical cord EC were harvested by flushing umbilical veins with 0.1% collagenase (Sigma-Aldrich, Steinheim, Germany). These cells were cultured in endothelial cell conditioning medium consisting of M199 (Biochrom, Berlin, Germany) supplemented with 16% fetal bovine serum (FBS, Hyclone, South Logan, UT), 4% human serum from healthy volunteers, 2 mM L-glutamine, 0.15 mg/ml endothelial growth factor supplement (Intracel; Rockville, MD), 0.015 mg/ml heparin, and 1% fungicide.  Cell pellets were dissolved in RNA lysis buffer (Qiagen, Hilden, Germany) supplemented with beta-mercaptoethanol (10µg/ml) and stored at –80°C until further processing.

extract_protocol: Lysed cells were mixed with 0.2 ml of chloroform for 3 minutes at room temperature and then centrifuged at 11.500 rpm for 15 minutes at 4°C. The upper aqueous phase was collected in RNAse-free eppendorf tubes and mixed with 0.5 ml isopropanol for 10 minutes. Supernatants were aspirated after recentrifugation, and pellets were resuspended in 75% ethanol in DEPC-H20 by vortexing. After airdrying, the RNA quantity was measured by spectrophotometry. Following RNA isolation, samples were run through an RNeasy column (Qiagen, Hilden, Germany) to eliminate DNA and protein contamination. Samples were precipitated with ethanol followed by TBE ethidium bromide gel electrophoresis to confirm the presence of highly pure RNA.

treatment_protocol: Confluent endothelial cells passage 2-4 were stimulated with IL-1beta for 4, 8 and 16 hours, and cells were harvested by collagenase (0.1% in PBS). CD34(+) hematopoietic progenitor cells were used directly post isolation.

value: Endothelial cells

tag: treatment

tag: time point


title: Endothelial cells; IL-1beta; 8h

description: Gene expression data from IL1beta-stimulated endothelial cells


title: Endothelial cells; IL-1beta; 4h


title: GM-CSF_IFNr_4

status: Public on Jun 03 2010

city: Boston

first: Wenzhong

last: xiao

state: MA

address: 55 Fruit Street, GRB 1302

institute: Massachusetts General Hospital

description: Gene expression data from Microfluidics isolated human neutrophils, GM-CSF and IFNg stimulated

hyb_protocol: the labeled cDNA was hybridized onto GeneChip™ Human Genome U133 Plus 2.0 Arrays according to standard Affymetrix protocol

scan_protocol: Chips were washed and scanned as recommended by the Ovation System User Guide (version 1.0).

data_processing: Low level analysis was performed using dChip using the perfect match only option.

label_protocol: cDNA was synthesized using Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies) from 20 ng of total RNA as starting material.

growth_protocol: Freshly drawn peripheral blood was anti-coagulated with sodium heparin and was directly processed for cell isolation by microfluidics (designated as unstimulated) or stimulated before cell isolation. In addition to microfluidic processing, leukocytes were isolated using density gradient techniques from both unstimulated and stimulated whole blood.

extract_protocol: RNA extraction followed a modified commercial protocol (QIAGEN RNeasy Plus). To remove genomic DNA, 350 l of guanadinium isothiocyanate with detergent (Qiagen RLT Plus Buffer) was added to the thawed, original lysate along with 2 mercaptoethaol (Sigma) at 20 l/ml. This combined lysate was then processed according to manufacturer protocols (Qiagen RNeasy Plus Kit) yielding purified total RNA analyzed on an Agilent Bioanalyzer 2100 system.

treatment_protocol: Stimulated cells were treated with LPS (50 ng/ml) or GM-CSF (20 ng/ml) + IFN-g(100 IU/ml) (abbreviated as GM+I) for 16 hours on a rocker at 37 °C in 5% CO2 atmosphere before cell isolation.

value: human neutrophils

tag: isolation

value: Microfluidics isolated

tag: condition

value: GM-CSF and IFNg stimulated

tag: subject


title: Endothelial cells; IL-1beta; 16h


title: GM-CSF_IFNr_1

source_name: Microfluidics isolated human neutrophils, GM-CSF and IFNg stimulated


title: Endothelial cells; control; 0h


title: GM-CSF_IFNr_2


title: LPS_1

description: Gene expression data from Microfluidics isolated human neutrophils, LPS stimulated

value: LPS stimulated


title: GM-CSF_IFNr_3


title: Monocyte No Stim 1


title: HUVEC_Unstimulated

status: Public on Jun 05 2010

city: London

first: Yiannis

last: Ioannou

address: Centre For Rheumatology, Rm 331, Windeyer Building 46 Cleveland Street

country: United Kingdom

institute: University College London

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Biotinylated cRNA targets were hybridised to two 'HG-U133 Plus 2.0' GeneChips according to protocol (defined by Clive and Vera Ramaciotti Centre for Gene Function Analysis, University of New South Wales, Sydney, Australia).

scan_protocol: GeneChips were scanned using the Agilent microarray scanner.

data_processing: The data were analyzed with GeneSpring analysis platform (Silicon genetics) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Unstimulated HUVEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Defined by Clive and Vera Ramaciotti Centre for Gene Function Analysis, University of New South Wales, Sydney, Australia).

growth_protocol: HUVEC were harvested and grown under optimal conditions in M199/10% fetal calf serum.

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

treatment_protocol: After passage 2, at 90% confluence cells RNA extracted with the cells unstimulated.

tag: tissue

value: Human umbilical vein endothelial cell


title: LPS_4

source_name: Microfluidics isolated human neutrophils, LPS stimulated


title: BGO1 hESC (mTESR)

status: Public on Apr 22 2010

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data of cell lineBGO1 hESC (mTESR)

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Affy and limma package (MAS5)

source_name: BGO1 hESC (mTESR)

label_protocol: 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010

treatment_protocol: RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.

value: Human embryonic stem cells (hESC)

tag: cell subtype

value: BGO1 hESC (mTESR)


title: WIBR2 hESC

description: Gene expression data of cell lineWIBR2 hESC

source_name: WIBR2 hESC

value: WIBR2 hESC


title: WIBR1 hESC

description: Gene expression data of cell lineWIBR1 hESC

source_name: WIBR1 hESC

value: WIBR1 hESC


title: LPS_3


title: BGO1-Nanog transgenic hESC line

description: Gene expression data of cell lineBGO1-Nanog transgenic hESC line

source_name: BGO1-Nanog transgenic hESC line

value: BGO1-Nanog transgenic hESC line


title: Mesodermal progenitor population, 2

status: Public on May 06 2010

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

description: Gene expression data from day 3.5 CD326negCD56+ cells

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

scan_protocol: The acquisition of each array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC)

data_processing: raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Thresholds for selecting significant genes were set at a relative difference >= 2-fold, absolute difference >100 signal intensity units and p<0.05.

source_name: Human Embryonic Stem Cells (hESC H9)

label_protocol: Biotinylated cRNA were prepared by using MessageAmp™ Premier RNA Amplification Kit (Ambion) according to the instructions

growth_protocol: Mesoderm induction using activin a, BMP4, FGF2 and VEGF in Stemline II media

extract_protocol: mRNA extraction from undiffentiated hESC and CD326negCD56+ mesodermal progenitors weas carried out using Rneasy Qiagen micro kit

treatment_protocol: CD326negCD56+progenitors were sorted by FACS at day 3.5 of culture

tag: cell line

value: Human Embryonic Stem Cells (hESC H9)

tag: cell population

value: CD326negCD56+ cells


title: Mesodermal progenitor population, 3


title: Mesodermal progenitor population, 1


title: WIBR3 hESC

description: Gene expression data of cell lineWIBR3 hESC

source_name: WIBR3 hESC

value: WIBR3 hESC


title: WIBR3

description: Gene expression data of cell lineWIBR3


title: WIBR3 hESC (5%pO2)

description: Gene expression data of cell lineWIBR3 hESC (5%pO2)

source_name: WIBR3 hESC (5%pO2)

value: WIBR3 hESC (5%pO2)


title: BGO1 hESC

description: Gene expression data of cell lineBGO1 hESC

source_name: BGO1 hESC

value: BGO1 hESC


title: Bone Marrow_1

status: Public on Mar 01 2010

city: Stockholm

first: Cecilia

last: Götherström

address: Karolinska University Hospital Huddinge

department: Department for Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description:
Human mesenchymal stem cells circulate in 1st and early 2nd trimester fetal blood, but not in adults. Like other fetal cell types they cross the placenta, and can be found in maternal organs decades later.
To determine potential ligands in human fetal mesenchymal stem cells not present in maternal blood, the gene expression of 1st trimester human fetal bone marrow, liver and blood derived mesenchymal stem cells will be compared to blood mononuclear cells from pregnant women using a Affymetrix human gene array system.

hyb_protocol: Hybridization was performed at the Microarray Centre, MRC at Imperial College, London, UK according to the manufacturers protocols.

scan_protocol: Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.

data_processing:
Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).

Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.

source_name: Human fetal material, 9-14 weeks, from legal abortions.

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol:
Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.

Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in  80ºC.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Kit. Isolated RNA was analysed with Agilent 2100 Bioanalyzer to verify sample integrity and quantify total RNA yield.

tag: developmental stage

value: 9-14 week old fetus

value: mesenchymal stem cells

value: bone marrow


title: Liver_3

value: liver


title: Blood_2

value: blood


title: Liver_2


title: Bone Marrow_3


title: CXCL4_A

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

institute: Rottal-Inn Kliniken KU

scan_protocol: Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0).

data_processing: Microarray gene expression intensities were normalized to ensure that all chips have the same interquartile ranges (IQR). In addition, they were log-transformed with base 2, which transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.r-project.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering and heat-map analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix web site (www.affymetrix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyze. We eliminated nonexpressed (within 2 SD from zero in all conditions) and housekeeping genes [not significantly regulated with false discovery rate (FDR) <0.05]. We analyzed the regulated genes in two approaches; candidate gene analysis using LPE, HEM, and heat-map analysis, and unbiased analysis of all regulated genes without prior knowledge such using hierarchical clustering analysis.

source_name: primary human monocyte-derived macrophages

label_protocol: Standard Affymetrix protocol.

growth_protocol: With approval from the institutional review board, peripheral blood mononuclear cells were isolated from human peripheral blood using Histopaque (Sigma, St.Louis, MO) followed by negative isolation with magnetic beads (Stem cell, Vancouver, Canada). Monocyte purity was 96.2 ± 0.2 % as assessed by CD14 expression. After red blood cell lysis and several wash steps with 1 mM EDTA, monocytes were essentially free from platelet contamination as demonstrated by virtual absence of CD41 positivity in flow cytometry (data not shown). Monocytes were cultured in macrophage serum-free medium (Gibco, Carlsbard, CA) supplemented with Nutridoma SP (Roche, Indianapolis, IN) and penicillin/streptomycin (Sigma, St. Louis, MO) for six days in the presence of 100 ng/ml rhMCSF (Peprotech, Rocky Hill, NJ) or 1 µM rhCXCL4 (Peprotech). The concentration of 1 µM rhCXCL4 was chosen because this concentration was previously demonstrated to be sufficient to induce macrophage differentiation from monocytes (13). Furthermore, our own preliminary experiments confirmed that after six days, this concentration induced expression of typical macrophage markers like CD11b or CD68 to a similar extent as MCSF (Fig. 1 and data not shown).

extract_protocol: For each condition RNA was isolated from macrophages derived from two donors using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen, Valencia, CA).

treatment_protocol: Please see growth protocol.

tag: differentiation factor


title: Bone Marrow_2


title: Blood_3


title: Blood_1

data_processing:
Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS).
Data were further analysed as follows: (i) the mean expression ratio and p value was calculated for each transcript, (ii) all transcripts that scored as present in all fetal mesenchymal stem cells absent in all maternal peripheral blood lymphocytes were selected, (iii) these transcripts were then filtered for molecules involved in cell surface linked signal transduction and antigen presentation and (iv) transcripts with a mean expression ratio of >300 were further analysed.

growth_protocol:
Human fetal mesenchymal stem cells were isolated from 3 sources (fetal blood, bone marrow and liver, from 9-14 week old fetuses), all from different individuals at legal abortion after informed consent from the patients. Procedures were approved by Hammersmith and Queen Charlotte’s Research Ethics Committee.
Fetal liver was disintegrated by passage through a 100 μm nylon filter and fetal bone marrow was prepared by flushing long bones with 25-gauge needles. Single cells were suspended in DMEM-High Glucose supplemented with 10% fetal calf serum and 2 mmol/l L-glutamine and 50 IU/ml penicillin/streptomycin. Cells were plated at 1.8x104 cells/cm2 in 10 cm Petri dishes and maintained at 37oC in a humidified environment containing 5% CO2. After 3 days, the non-adherent cells were removed and the medium replaced. The medium was changed every three to four days thereafter. At sub-confluence (70%), cells were detached using 0.05% trypsin and 0.53 mM EDTA and replated at a density of 4x103 cells/cm2. Cells were counted and thereafter snap frozen in  80ºC.


title: LPS_2

value: human neutrophils

value: Microfluidics isolated

value: LPS stimulated


title: Liver_1


title: hASC-derived iPS cells using lentiviral factors replicate 3

status: Public on Feb 01 2010

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

hyb_protocol: Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.

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

data_processing:
The data were analyzed with AGCC (Affymetrix Genechip Command Console).
Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.

source_name: iPSC derived from hASC using lentiviral reprogramming vector

label_protocol: Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.

growth_protocol: Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes  with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen)

value: undifferentiated


title: human adipose stem cell replicate 1

source_name: adipose stem cells derived from adult human donor


title: JT-iPSC_GSM378833

source_name: iPS cells from episomal vectors (Defined Factor)

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).


title: hASC-derived iPS cells using lentiviral factors replicate 2

value: iPSC derived from hASC using lentiviral reprogramming vector


title: JT-iPSC_GSM378837

source_name: iPS cells from episomal vectors (Defined Factor sub-clone)


title: hASC-derived iPS cells using lentiviral factors replicate 1


title: Foreskin_GSM378832

source_name: Foreskin Cells Parental

value: Foreskin Cells Parental

value: adult


title: human adipose stem cell replicate 3

value: adipose stem cells derived from adult human donor


title: normal fibroblast_case6

status: Public on Jan 29 2010

city: Madison

first: Andreas

last: Friedl

state: WI

address: 1111 Highland Avenue

department: Pathology

institute: University of Wisconsin

hyb_protocol: After fragmentation, 10 µg of cRNA were hybridized at 45 °C for 16 h to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to >47 000 transcripts.  After inhibition of endogenous peroxidase and blocking, the slides were incubated with primary antibody for 60 min. The following primary antibodies were used: Goat anti-WISP1/CCN4 (1:50; R&D Systems, Minneapolis, MN, USA), mouse anti-TGF?2 (1:500; Abcam) and goat anti-KLF4 (1:100; R&D Systems). This was followed by incubation with an appropriate horseradish peroxidase-based detection reagent (Biocare, Concord, CA, USA) and DAB+ chromogenic substrate (Dako). The slides were counterstained with hematoxylin and coverslipped.

data_processing: The data were analyzed with R language and environment using Affymetrix default analysis settings and RMA as normalization method.  The expression levels were compared using empirical Bayes methods and a lognormal-normal model.

source_name: Fibroblast isolated from adjacent normal breast tissue

label_protocol: Ambion MessageAmp II-Biotin Enhanced kit

growth_protocol: CAF and NF were routinely maintained in DMEM and 10% fetal bovine serum at 37 °C in a humidified atmosphere containing 5% CO2. RNA was extracted from confluent cultures as soon as epithelial cells had disappeared. This criterion was met typically after one to three passages. The purity of the fibroblasts was assessed in parallel cultures by immunolabeling for the epithelial cell marker pan-cytokeratin (mouse monoclonal antibody, dilution 1:100; Lab Vision, Fremont, CA, USA) and the endothelial cell marker von Willebrand factor (rabbit polyclonal antibody, dilution 1:1000; Dako, Carpinteria, CA, USA) and the mesenchymal marker vimentin (mouse monoclonal antibody, dilution 1:100; Lab Vision). For further characterization, the fibroblast cultures were labeled with antibodies to ?-SMA (mouse monoclonal antibody ?SMA, dilution 1:100, Sigma) and fibroblast-specific protein FSP1/S100A4 (rabbit polyclonal, dilution 1:50, Abcam, Cambridge, MA, USA).

extract_protocol: Total RNA from CAF and NF was isolated using the RNeasy Micro kit according to the manufacturer's instructions (Qiagen, Alameda, CA, USA).

value: normal breast

value: normal fibroblast


title: normal fibroblast_case5


title: JT-iPSC_GSM378834

value: iPS cells from episomal vectors (Defined Factor sub-clone)


title: normal fibroblast_case1


title: JT-iPSC_GSM378838

value: iPS cells from episomal vectors (Defined Factor)


title: normal fibroblast_case2


title: normal fibroblast_case8


title: human adipose stem cell replicate 2


title: JT-iPSC_GSM378836


title: normal fibroblast_case7


title: HUVECs Non intoxicated Rep1

status: Public on Jan 26 2010

city: Nice

first: emmanuel

last: lemichez

address: 151 route Saint Antoine de Ginestière

department: Microbiology

country: France

institute: INSERM

description: Experiments performed by AROS Applied biotechnology

hyb_protocol: standard affymetrix protocol

scan_protocol: The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Hewlett Packard GeneArray Scanner G2500A). The readings from the quantitative scanning were analysed by the Affymetrix Gene Expression Analysis Software 5.0 (MAS 5.0).

data_processing: Data from the individual samples was subjected to Pairwise comparison analyses in the Software MAS 5.0, based on empirical algorithms as described in Affymetrix's statistical reference guide. standard affymetrix protocol. Briefly, the Change Algorithm indicated a change in transcript level between a baseline and an experiment array, further indicating an increase, marginal increase, decrease, marginal decrease or no change in gene expression. On the other hand, the Signal Log Ratio (SLR) Algorithm estimated the magnitude and direction of change of a transcript when two arrays were compared (experiment versus baseline), expressed as the log2 ratio.

source_name: HUVEC control monolayer

label_protocol: standard affymetrix protocol

growth_protocol: HUVECs (PromoCell, Heidelberg, Germany) were cultured in human endothelial SFM supplemented with 20 % FBS, 20 ng/ml bFGF, 10 ng/ml EGF (Invitrogen) and 1 microg/ml heparin (Sigma).

extract_protocol: RNeasy MiniKit (Qiagen, Valencia, CA). Both integrity and purity of RNA were checked using the Bioanalyzer 2100 and RNA 6000 LabChip kit from Agilent Technologies (Palo Alto, CA)

treatment_protocol: control condition

value: primary human umbilical vein endothelial cells (HUVECs)


title: HUVECs Intoxicated by LT 8h

source_name: LT-intoxicated HUVEC monolayer, 8h

treatment_protocol: HUVEC monolayers were treated with the letal toxin LT of Bacillus anthracis (PA+LF, 3+1 microg/ml), 8 hours


title: FPV-infected HUVEC_V2

status: Public on Dec 31 2009

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

description: FPV-infected HUVEC

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Fluorescent signals were detected by the GeneChip Scanner 3000 and recorded and computed by GeneChip Operating Software (GCOS) version 1.4 (Affymetrix).

data_processing: GCOS version 1.4 (Affymetrix)

source_name: FPV-infected HUVEC

tag: FPV-infected

tag: HUVEC monolayer


title: HUVEC control_V3

description: HUVEC control

source_name: HUVEC control

label_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

tag: untreated


title: HUVECs Intoxicated by LT _4h

source_name: LT-intoxicated HUVEC monolayer, 4h

treatment_protocol: HUVEC monolayers were treated with LT (PA+LF, 3+1 microg/ml), 4 hours


title: H5N1-infected HUVEC_V2

description: H5N1-infected HUVEC

source_name: H5N1-infected HUVEC

extract_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).


title: FPV-infected HUVEC_V3

description: FPV-infected HUVEC


title: H5N1-infected HUVEC_V3

description: H5N1-infected HUVEC


title: HUVEC control_V2

description: HUVEC control


title: PR8-infected HUVEC_V2

description: PR8-infected HUVEC

source_name: PR8-infected HUVEC


title: BEC KSHV 72h, rep3

status: Public on Sep 30 2009

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

institute: UCL

description: Biological replicate 3 of 6.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm  ('RMA') .

source_name: blood vessel endothelial cells, KSHV-infected, 72h

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)

growth_protocol: Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV-infected LEC and BEC were grown under the same conditions. All cells were mycoplasma free.

extract_protocol: TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.

value: blood vessel endothelial cell

tag: infection

value: KSHV


title: BEC KSHV 72h, rep4

description: Biological replicate 4 of 6.


title: EPN_195, recurrent

status: Public on Oct 01 2009

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: Gene expression data from surgical tumor sample of ependymoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 18,624 genes.

source_name: EPN_195, recurrent

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol and ENZO biotin-labelling kit protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen immediated after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500)
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (ependymoma)

tag: genotype


title: PR8-infected HUVEC_V1

description: PR8-infected HUVEC


title: HUVEC control_V1

description: HUVEC control


title: PR8-infected HUVEC_V3

description: PR8-infected HUVEC


title: BEC control, rep3

description: Biological replicate 3 of 6.

source_name: blood vessel endothelial cells

tag: cell type


title: BEC KSHV 72h, rep2

description: Biological replicate 2 of 6.


title: H5N1-infected HUVEC_V1

description: H5N1-infected HUVEC


title: human age 39 months

city: Oslo

first: Kristin

last: Jensen

address: Kirkeveien 166

department: Department of Clinical Chemistry

country: Norway

institute: Ullevål University Hospital

description: Gene expression data from whole bone marrow stabilized on PAXgene medium

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 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 Affymetrix Gene Chip® Scanner 3000.

data_processing: Robust Multichip Average (RMA) was used to convert the intensity values to normalized expression values. Signal values were scaled by global methods to a target value of 100.

source_name: Human composite bone marrow, 39 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

tag: Female


title: FPV-infected HUVEC_V1

description: FPV-infected HUVEC


title: human age 2 months

source_name: Human composite bone marrow, 2 months

tag: Male


title: BEC control, rep4

description: Biological replicate 4 of 6.


title: human age 9 months

source_name: Human composite bone marrow, 9 months


title: human age 23 months

source_name: Human composite bone marrow, 23 months


title: human age 32 months

source_name: Human composite bone marrow, 32 months


title: human age 20 months

source_name: Human composite bone marrow, 20 months


title: BEC KSHV 72h, rep1

description: Biological replicate 1 of 6.


title: Primary hepatocyte, biological replicate 2

status: Public on Dec 29 2009

city: Kansas City

first: Steven

last: Hart

state: KS

address: 3901 Rainbow Blvd

department: Pharmacology, Toxicology & Therapeutics

institute: University of Kansas Medical Center

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan

data_processing: R/Bioconductor

source_name: Primary hepatocyte

label_protocol: In-vitro Transcription using the GeneChip 3` IVT Express Kit

extract_protocol: Trizol

value: primary hepatocyte

tag: gender

value: female


title: human age 3 months

source_name: Human composite bone marrow, 3 months


title: BEC control, rep2

description: Biological replicate 2 of 6.


title: Primary hepatocyte, biological replicate 1


title: LEC KSHV 72h, rep3

description: Biological replicate 3 of 6.

source_name: lymphatic endothelial cells, KSHV-infected, 72h

value: lymphatic endothelial cell


title: LEC KSHV 72h, rep4

description: Biological replicate 4 of 6.


title: HUVECs Non intoxicated Rep2

source_name: HUVEC control monolayer


title: BEC control, rep1

description: Biological replicate 1 of 6.


title: LEC KSHV 72h, rep1

description: Biological replicate 1 of 6.


title: Primary hepatocyte, biological replicate 3


title: BM-MSC culture osteogenic induction for 3 days rep 2

status: Public on Sep 10 2009

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 3 days.
BM-MSC of a male 72-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 3 day for osteogenic differentiation.

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

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

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database SiPaGene (www.bioretis.de).

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 3 days from normal donor 2

label_protocol: 2µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix).

growth_protocol: Human BM cells obtained from iliac crest aspirates were amplified by cultivation in alpha-MEM with 10 % fetal calf serum (FCS), 1 ng/mL fibroblast growth factor 2 (FGF2), 20 µmol/L L-glutamine and 100 units/mL penicillin G.

extract_protocol: RNA was collected using the RNeasy mini kit (Qiagen).

treatment_protocol: After expansion for 1 passage, cells were stimulated with 10E-7 M dexamethasone for osteogenic induction for 1, 3 and 7 days.

value: male

tag: age

value: 72 years

tag: treatment

value: dexamethasone

tag: treatment time

value: 3 days


title: BM-MSC culture osteogenic induction for 7 days rep 2

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 7 days.
BM-MSC of a male 72-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 7 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 7 days from normal donor 2

value: 7 days


title: BM-MSC culture osteogenic induction for 7 days rep 3

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 7 days.
BM-MSC of a female 74-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 7 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 7 days from normal donor 3

value: 74 years


title: LM6, biological rep1

status: Public on Sep 08 2009

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from LM6 cells and AM1cells were quantitatively determined.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring software version 7.2 GC-RMA preprocessor to use on the CEL files

source_name: Human  lipoma-derived mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: LM6 cells and AM3 cells were cultured in the K-NAC medium that is a modified MCDB 153 medium (Keratinocyte-SFM, GIBCO-Invitrogen) supplemented with N-acetyl-L-cysteine (NAC; Sigma A8199) (2 mM) and L-ascorbic acid 2-phosphate (Asc 2P; sigma A8960) (0.2 mM).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

tag: Gender


title: BM-MSC culture osteogenic induction for 3 days rep 3

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 3 days.
BM-MSC of a female 74-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 3 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 3 days from normal donor 3


title: LEC KSHV 72h, rep2

description: Biological replicate 2 of 6.


title: AM3, biological rep1

source_name: Human  adipose-derived mesenchymal stem cells

growth_protocol: LM6 cells  and AM3 cells were cultured in the K-NAC medium that is a modified MCDB 153 medium (Keratinocyte-SFM, GIBCO-Invitrogen) supplemented with N-acetyl-L-cysteine (NAC; Sigma A8199) (2 mM) and L-ascorbic acid 2-phosphate (Asc 2P; sigma A8960) (0.2 mM).


title: BM-MSC culture osteogenic induction for 3 days rep 1

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 3 days.
BM-MSC of a male 67-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 3 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 3 days from normal donor 1

value: 67 years


title: BM-MSC culture osteogenic induction for 1 day rep 3

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 1 day.
BM-MSC of a female 74-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 1 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 1 day from normal donor 3

value: 1 day


title: BM-MSC culture osteogenic induction for 1 day rep 2

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 1 day.
BM-MSC of a male 72-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 1 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 1 day from normal donor 2


title: BM-MSC culture osteogenic induction for 1 day rep 1

description:
Gene expression data of human bone marrow-derived mesenchymal stem cells after osteogenic induction for 1 day.
BM-MSC of a male 67-years old cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage and induced with 10E-7 M dexamethasone for 1 day for osteogenic differentiation.

source_name: bone marrow MSC in culture, stimulated for osteogenic induction for 1 day from normal donor 1


title: LM6, biological rep2


title: AM3, biological rep2


title: spore transfected, array 3

status: Public on Sep 07 2009

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

description: OUHSC-Metcalf, Human alveolar macrophages spore transfected, array 3

hyb_protocol: per Affymetrix instructions using their GeneChip® 450 fluidics station

scan_protocol: using the Affymetrix GeneChip® 3000 7G scanner

data_processing: HG-U133Plus 2.0 array data for each experimental condition were exported from the Affymetrix Suite Software for further analysis. The data were normalized as described in Dozmorov et al., Nucleic Acid Research, 2004. 32(19): p. e147, using the variability of low expressed genes as a reference point. In order to find genes expressed above the level of technical noise, frequency histogram of raw expression values was examined for each array. The histogram yielded a right-skewed unimodal distribution curve with the mode around 2 (Figure 1). A normal distribution curve representing the variability of the data around zero was then fitted around the mode, mirroring the Gaussian profile of the left part of the histogram. Its parameters were than defined (mean, SD) and the data were normalized to the standard deviation of the noise after subtraction of the zero point. The arrays were than adjusted to each other by robust linear regression under the assumption that the expression of most genes does not change. The data was then filtered to remove genes with expression value less than 3.0. This is equivalent to setting a threshold at 3 SD above the noise level. Genes expressed below the noise level under all experimental conditions (about 1,600) were excluded from consideration, as their expression cannot be reliably assessed.

source_name: Human alveolar macrophages infected by B. antracis spore

label_protocol: per Affymetrix instructions

extract_protocol: RNA was prepared using the TRIzolTM RNA extraction method according to the manufacturer’s instructions (Invitrogen). An RNA cleanup step was performed using Qiagen’s RNeasy kit. First- and second- strand cDNA synthesis was carried out with 5μg total RNA as starting material (SuperScriptTM cDNA Synthesis kit, Invitrogen). Biotin-labelled cRNA was prepared using the Affymetrix RNA Transcript Labelling kit, and fragmented in Fragmentation Buffer (Affymetrix). Labelled, fragmented cRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix), which were then washed, stained and scanned as described in Dyrskjot et al, Nat.Genet., 2003. 33(1): p. 90-96. The HG-U133 Plus 2.0 arrays comprised >54,000 probe sets representing >47,000 transcripts and variants, including 38,500 well-annotated genes.

treatment_protocol: Human alveolar macrophages were plated into six well culture plates at 1 x 106 cells/ml in RPMI with 2% FCS containing 50 g/ml of gentamicin and, following overnight attachment, were stimulated with B. anthracis spores (1 MOI) for 6 h. Unstimulated control wells were prepared by exposing cells to equal volumes of spore diluent. Cells were harvested by addition of TRIzol reagent (Invitrogen), and total RNA was isolated according to the manufacturer’s protocol using glycogen (20 mg/ml) as the carrier. Cells yielded 8-10 g total RNA/well, 4 g of which were used for a single RPA reaction.

tag: Preparation of Bacillus anthracis spores

tag: B. anthracis, Sterne strain 7702 (pX01+, pX02-), was kindly provided by Dr. Jimmy Ballard (University of Oklahoma Health Sciences Center, Oklahoma City).  Bacteria were grown overnight at 37C with continuous shaking in LB media and were then streaked onto AK Agar sporulating slants.  Bacteria were incubated for three weeks at 30C.  The slants were washed with 10ml of chilled, sterile, deionized water and spun at 10,000 x g for 10 minutes and resuspended in 10ml chilled water.  The spore suspension was heated at 65C degrees for 30 minutes to kill vegetative bacteria.  After heat treatment the spores were centrifuged for 10 minutes at 10,000 x g.  The supernatant and the very top layer of the pellet were aspirated and then the spores were resuspended in chilled sterile deionized water and centrifuged for 10 minutes.  The pellet was washed 5 times to remove contaminating cell debris.  The titer of the spore preparation was determined by plate counts.  The spores were diluted to 1 X 109 spores/ml and stored at 4C. Titers were reconfirmed by plate counts before each use.  There was no detectable endotoxin in the final spore dilutions used in the experiments as determined by limulus amebocyte lysate assay (Cambrex, Walkersville, MD).

tag: Collection of human alveolar macrophages

tag: Macrophages were obtained by bronchoscopy with the consent of human subjects following a protocol approved by the Oklahoma University Health Sciences Center Institutional Review Board and the Institutional Biosafety Committee.  These volunteers were healthy subjects with no smoking history or history of pulmonary disease.  Cells were collected in sterile saline solution from human subjects and centrifuged at 500 x g for five minutes.  The supernatant was removed and the pellets were washed in 10ml of RPMI-1640 containing 50µg/ml gentamicin and resuspended in 10ml RPMI + 2% fetal calf serum (FCS) with 50µg/ml gentamicin.  Cell counts were determined by a hemocytometer; cell type was determined by morphology using Diff-Quick staining (Baxter, Miami, FL); and cells were resuspended to a concentration of 1 X 106 macrophages/ml.  There were >95% macrophages in each cell preparation. One ml of cells per well was plated into 24 well plates and allowed to incubate for 2 to 4 h to facilitate attachment.  Subsequently, the media was removed and fresh media containing 2% FCS and gentamicin was added.  The cells were incubated overnight at 37C with 5% CO2.


title: spore transfected, array 2

description: OUHSC-Metcalf, Human alveolar macrophages spore transfected, array 2


title: mock transfected, array 4

description: OUHSC-Metcalf, Human alveolar macrophages mock transfected, array 4

source_name: Human alveolar macrophages


title: mock transfected, array 2

description: OUHSC-Metcalf, Human alveolar macrophages mock transfected, array 2


title: spore transfected, array 1

description: OUHSC-Metcalf, Human alveolar macrophages spore transfected, array 1


title: 3D-cultured chondrocytes from normal donor 1

status: Public on Sep 02 2009

first: Tilo

last: Dehne

state: Berlin

address: Tucholskystraße 2

department: Rheumatology and Clinical Immunology

institute: Charité - University Medicine Berlin

description:
ND_1_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage,  undergoing ACT treatment)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 1

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de).

source_name: human subcultured chondrocytes (passage 2) from normal donors maintained for 14 days in scaffold culture

label_protocol: 2 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Human chondrocytes obtained from non-weight bearing area of 3 donors undergoing ACT treatment (normal donor) and from biopsies of 3 donors undergoing total knee replacement (OA donors) were expanded by cultivation in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages,  3D cultured in Hyaff-11 scaffolds for 14 days in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin

extract_protocol: Total RNA from chondrocytes cultured in monolayer (passage 2) was isolated applying protocols for animal tissues of the RNeasy Mini Kit (Qiagen, Hilden, Germany). For scaffold cultures, an 8 mm punch was prepared, snap-frozen in liquid nitrogen, and stored at -80°C until further use. Frozen samples were transferred to 1 ml TriReagent (Sigma-Aldrich) and mechanically homogenized. Subsequently, 133 µl 1-Bromo-3-chloro-propane (Sigma-Aldrich) was admixed followed by centrifugation for 45 min at 13000xg. The aqueous phase was collected and nucleic acids were precipitated by addition of an equal volume ice-cold isopropanol. After 30 min incubation the precipitated nucleic acids were pelletized and resolved in 350 µl RLT buffer (Qiagen). Further purification was performed according to protocols for animal tissues of the RNeasy Mini Kit (Qiagen). RNA from each donor was separately handled; no pooling was done at any stage.

treatment_protocol: Human chondrocytes were isolated by enzymatic digestion. Minced cartilage was digested for 16 hours in a spinner bottle in 10 ml of culture medium containing clostridial collagenase (1 mg per milliliter [150 U per liter]) and deoxyribonuclease I (0.1 mg per milliliter [25,000 U per liter]). . For scaffold culture, 2x106 chondrocytes of passage 2 were per cm2 were seeded in Hyaff-11 and were maintained under serum-free chondotions in presence of TGFbeta 1.

tag: disease group

value: normal

value: chondrocytes

tag: cell culture


title: 3D-cultured chondrocytes from normal donor 2

description:
ND_2_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage,  undergoing ACT treatment)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 2


title: mock transfected, array 3

description: OUHSC-Metcalf, Human alveolar macrophages mock transfected, array 3


title: monolayer chondrocytes from normal donor 3

description:
ND_3_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage, undergoing ACT treatment)
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 3

source_name: human subcultured chondrocytes (passage 2) from normal donors

value: monolayer


title: mock transfected, array 1

description: OUHSC-Metcalf, Human alveolar macrophages mock transfected, array 1

extract_protocol: RNA was prepared using the TRIzolTM RNA extraction method according to the manufacturer’s instructions (Invitrogen). An RNA cleanup step was performed using Qiagen’s RNeasy kit. First- and second- strand cDNA synthesis was carried out with 5μg total RNA as starting material (SuperScriptTM cDNA Synthesis kit, Invitrogen). Biotin-labelled cRNA was prepared using the Affymetrix RNA Transcript Labelling kit, and fragmented in Fragmentation Buffer (Affymetrix). Labelled, fragmented cRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix), which were then washed, stained and scanned as described in Dyrskjot et al., Nat.Genet., 2003. 33(1): p. 90-96. The HG-U133 Plus 2.0 arrays comprised >54,000 probe sets representing >47,000 transcripts and variants, including 38,500 well-annotated genes.


title: monolayer chondrocytes from normal donor 1

description:
ND_1_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage, undergoing ACT treatment)
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 1


title: 3D-cultured chondrocytes from normal donor 3

description:
ND_3_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage,  undergoing ACT treatment)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 3


title: L1_CBP_3_of_3_rep_2

status: Public on Aug 22 2009

type: genomic

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

hyb_protocol: The hybridization solution is composed of 5 ug each of Cy3- and Cy5-labeled DNA, 50 ug of salmon sperm DNA, Agilent Blocking Agent and Agilent Hyb Buffer. The mixture is heated to 95*C for 3 min and then 37*C for 30 minutes immediately prior to hybridization. Samples are hybridized for 40 hours at 65*C. After hybridization the slides are washed in Agilent Wash Buffer 1 for 5 minutes at room temperature and then in Agilent Wash Buffer 2 for 5 minutes at 31*C.

scan_protocol: Channel 1 & 2 are for the Agilent arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1.

data_processing: We preprocessed microarray data to normalize it and reduce experimental noise as described in Qi et al. (Qi et al., Nature biotechnology 2006). In short, the raw intensities from each channel was divided by the median intensity from that channel before computing a ratio to arrive at a median adjusted ratio. We further subtracted average value of negative control probes on the array and then added one as a regularization parameter.

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: 2 ug of amplified IP DNA are used for random primer labeling reaction (invitrogen). Cy3-dCTP is incorporated for the ChIP samples while Cy5-dCTP is incorporated for the Input chromatin sample. After washing of the labeled material on Centricon columns, 5ug of labeled DNA is used for hybridization.

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of first instar larvae, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours.  3. L1 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

extract_protocol: Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IP'd material is extracted and purified. Amplification of the DNA is done by linker-mediated PCR and used for labeling.

treatment_protocol: No treatment

tag: development stage

tag: antibody

value: CBP

tag: antibody provider

value: Dr. Mattias Mannervik in Stockholm University

tag: test

value: ChIP

tag: reference

value: Input


title: L1_CBP_3_of_3_rep_3


title: E16-20_8wg16_3_of_3_rep_3

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a 16-20 hours egg laying, new plates are added after a 2hours pre-egglaying at 1 pm and flies are allowed to lay eggs for 4 hours.  3. Embryos are collected at 8.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

value: PolII (8wg16)

tag: antibody manufacturer

value: Covance

tag: antibody catalog number

tag: antibody lot number


title: E16-20_8wg16_3_of_3_rep_1


title: E16-20_8wg16_3_of_3_rep_2


title: L3_PolII_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of third instar larvae (L3), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 48 hours.  3. L3 larvae are collected at 8.45 am using a filter mesh and a brush. L3 larvae are the larvae not going through the first mesh. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

value: PolII


title: L3_H3K9Me3_3_of_3_rep_1

value: Abcam


title: E0-4_CBP_3_of_3_rep_3

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 0-4 hours egg laying, new plates are added after a 2hours pre-egglaying at 10 am and flies are allowed to lay eggs for 4 hours.   3. Embryos are collected at 1.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 2 pm in 1.8% formaldehyde at room temperature for 15 min.


title: E0-4_CBP_3_of_3_rep_2


title: L2_PolII_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of second instar larvae (L2), new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Plates are then kept at 25C for another 24 hours.  3. L2 larvae are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: Pupae_H3K9Me3_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of pupae at 1-2 days APF (after puparium formation), new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles.  3. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.

value: Pupae


title: L2_PolII_3_of_3_rep_3


title: L3_H3K9Me3_3_of_3_rep_3


title: E4-8_8wg16-Set2_3_of_3_rep_3

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 4-8 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 4.45 pm using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 5 pm in 1.8% formaldehyde at room temperature for 15 min.


title: L1_CBP_3_of_3_rep_1


title: E0-4_CBP_3_of_3_rep_1


title: Pupae_H3K9Me3_3_of_3_rep_3


title: L3_PolII_3_of_3_rep_3


title: E4-8_8wg16-Set2_3_of_3_rep_2


title: E0-4_H3K9Ac_3_of_3_rep_2


title: L2_PolII_3_of_3_rep_1


title: E0-4_H3K9Ac_3_of_3_rep_3


title: L3_PolII_3_of_3_rep_1


title: E4-8_H3K9Ac_3_of_3_rep_3


title: E0-4_H3K9Ac_3_of_3_rep_1


title: E4-8_8wg16-Set2_3_of_3_rep_1


title: Pupae_H3K9Me3_3_of_3_rep_1


title: AdultMale_H3K9Me3-Set2_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of Drosophila Adult Male 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles.  3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultMale


title: L3_H3K9Me3_3_of_3_rep_2


title: AdultMale_H3K9Me3-Set2_3_of_3_rep_1


title: E4-8_H3K9Ac_3_of_3_rep_1


title: E4-8_H3K9Ac_3_of_3_rep_2


title: AdultMale_H3K9Me3-Set2_3_of_3_rep_3


title: Pupae_H3K9Ac_3_of_3_rep_3


title: E20-24_H3K9Ac_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a 20-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours.  3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.


title: E20-24_H3K9Ac_3_of_3_rep_3


title: L3_H3K9Ac_3_of_3_rep_2


title: Pupae_H3K9Ac_3_of_3_rep_1


title: E20-24_H3K9Ac_3_of_3_rep_1


title: AdultMale_H3K9Ac-Set2_3_of_3_rep_3


title: AdultMale_H3K9Ac-Set2_3_of_3_rep_2


title: AdultMale_H3K9Ac-Set2_3_of_3_rep_1


title: E8-12_H3K9Ac_3_of_3_rep_1

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a 8-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 8 pm and flies are allowed to lay eggs for 4 hours.  3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8 am in 1.8% formaldehyde at room temperature for 15 min.


title: L3_H3K9Ac_3_of_3_rep_1


title: AdultFemale_H3K4Me3_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.  2. For a collection of Drosophila Adult Female 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles.  3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

value: AdultFemale


title: L3_H3K4Me3_3_of_3_rep_1


title: E8-12_H3K9Ac_3_of_3_rep_2


title: AdultFemale_H3K4Me1_3_of_3_rep_3


title: Pupae_H3K4Me3_3_of_3_rep_3


title: AdultFemale_H3K4Me1_3_of_3_rep_1


title: L3_H3K4Me3_3_of_3_rep_3


title: AdultFemale_H3K4Me3_3_of_3_rep_3


title: Pupae_H3K4Me3_3_of_3_rep_2


title: AdultFemale_H3K4Me1_3_of_3_rep_2


title: AdultMale_H3K4Me1-Set2_3_of_3_rep_2


title: L1_H3K4Me1_3_of_3_rep_3


title: AdultFemale_H3K4Me3_3_of_3_rep_1


title: L2_H3K4Me1_3_of_3_rep_2


title: L2_H3K4Me1_3_of_3_rep_3


title: AdultMale_H3K4Me1-Set2_3_of_3_rep_1


title: L3_H3K4Me1_3_of_3_rep_3


title: L3_H3K9Ac_3_of_3_rep_3


title: L1_H3K4Me1_3_of_3_rep_2


title: L3_H3K4Me1_3_of_3_rep_1


title: Pupae_H3K4Me1_3_of_3_rep_3


title: Pupae_H3K9Ac_3_of_3_rep_2


title: L3_H3K4Me1_3_of_3_rep_2


title: E0-4_H3K4Me1_3_of_3_rep_3


title: Pupae_H3K4Me1_3_of_3_rep_2


title: L1_H3K4Me1_3_of_3_rep_1


title: AdultMale_H3K4Me1-Set2_3_of_3_rep_3


title: L2_H3K4Me1_3_of_3_rep_1


title: Pupae_H3K27Ac_3_of_3_rep_1


title: E0-4_H3K4Me1_3_of_3_rep_1


title: Pupae_H3K27Ac_3_of_3_rep_2


title: AdultFemale_H3K27Me3_3_of_3_rep_2

value: Upstate

value: input


title: Pupae_H3K27Ac_3_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_3_of_3_rep_3


title: E0-4_H3K4Me1_3_of_3_rep_2


title: Pupae_H3K4Me1_3_of_3_rep_1


title: AdultMale_H3K27Ac-Set2_3_of_3_rep_2


title: AdultMale_H3K27Ac-Set2_3_of_3_rep_1


title: AdultFemale_H3K27Me3_3_of_3_rep_3


title: L3_H3K27Ac_3_of_3_rep_2


title: L3_H3K4Me3_3_of_3_rep_2


title: AdultFemale_H3K27Me3_3_of_3_rep_1


title: L3_H3K27Ac_3_of_3_rep_3


title: L1_H3K27Ac_3_of_3_rep_2


title: L1_H3K27Ac_3_of_3_rep_1


title: L1_H3K27Ac_3_of_3_rep_3


title: E20-24_H3K27Ac_3_of_3_rep_3


title: L3_H3K27Ac_3_of_3_rep_1


title: E20-24_H3K27Ac_3_of_3_rep_2


title: L2_H3K27Ac_3_of_3_rep_2


title: E16-20_H3K27Ac_3_of_3_rep_2


title: L1_CBP_2_of_3_rep_1


title: E8-12_H3K27Ac_3_of_3_rep_2


title: L2_H3K27Ac_3_of_3_rep_1


title: E16-20_H3K27Ac_3_of_3_rep_1


title: L1_CBP_2_of_3_rep_3


title: E12-16_H3K27Ac_3_of_3_rep_3


title: E20-24_H3K27Ac_3_of_3_rep_1


title: L2_H3K27Ac_3_of_3_rep_3


title: E8-12_H3K27Ac_3_of_3_rep_1


title: E16-20_8wg16_2_of_3_rep_2


title: E12-16_H3K27Ac_3_of_3_rep_1


title: L1_CBP_2_of_3_rep_2


title: E12-16_H3K27Ac_3_of_3_rep_2


title: E4-8_8wg16-Set2_2_of_3_rep_2


title: E4-8_8wg16-Set2_2_of_3_rep_3


title: E0-4_CBP_2_of_3_rep_3


title: E16-20_8wg16_2_of_3_rep_3


title: E16-20_8wg16_2_of_3_rep_1


title: E0-4_CBP_2_of_3_rep_2


title: L3_PolII_2_of_3_rep_2


title: L2_PolII_2_of_3_rep_3


title: E16-20_H3K27Ac_3_of_3_rep_3


title: L2_PolII_2_of_3_rep_1


title: L3_H3K9Me3_2_of_3_rep_2


title: L3_H3K9Me3_2_of_3_rep_1


title: AdultMale_H3K9Me3-Set2_2_of_3_rep_3


title: AdultMale_H3K9Me3-Set2_2_of_3_rep_2


title: E0-4_H3K9Ac_2_of_3_rep_2


title: L3_H3K9Me3_2_of_3_rep_3


title: E0-4_H3K9Ac_2_of_3_rep_3


title: AdultMale_H3K9Me3-Set2_2_of_3_rep_1


title: L3_H3K9Ac_2_of_3_rep_3


title: E0-4_H3K9Ac_2_of_3_rep_1


title: E4-8_H3K9Ac_2_of_3_rep_2


title: E4-8_H3K9Ac_2_of_3_rep_1


title: E20-24_H3K9Ac_2_of_3_rep_3


title: L3_H3K9Ac_2_of_3_rep_1


title: Pupae_H3K9Me3_2_of_3_rep_1


title: E4-8_H3K9Ac_2_of_3_rep_3


title: L3_PolII_2_of_3_rep_1


title: Pupae_H3K9Me3_2_of_3_rep_2


title: Pupae_H3K9Ac_2_of_3_rep_3


title: E0-4_CBP_2_of_3_rep_1


title: L3_H3K9Ac_2_of_3_rep_2


title: E8-12_H3K9Ac_2_of_3_rep_1


title: L2_PolII_2_of_3_rep_2


title: L3_H3K4Me3_2_of_3_rep_2


title: L3_PolII_2_of_3_rep_3


title: Pupae_H3K9Ac_2_of_3_rep_1


title: E8-12_H3K9Ac_2_of_3_rep_2


title: Pupae_H3K9Ac_2_of_3_rep_2


title: Pupae_H3K9Me3_2_of_3_rep_3


title: E20-24_H3K9Ac_2_of_3_rep_2


title: E4-8_8wg16-Set2_2_of_3_rep_1


title: AdultMale_H3K9Ac-Set2_2_of_3_rep_2


title: Pupae_H3K4Me3_2_of_3_rep_3


title: AdultFemale_H3K4Me1_2_of_3_rep_2


title: AdultMale_H3K9Ac-Set2_2_of_3_rep_3


title: L1_H3K4Me1_2_of_3_rep_3


title: L2_H3K4Me1_2_of_3_rep_3


title: L1_H3K4Me1_2_of_3_rep_2


title: L3_H3K4Me3_2_of_3_rep_3


title: L3_H3K4Me3_2_of_3_rep_1


title: L3_H3K4Me1_2_of_3_rep_3


title: AdultFemale_H3K4Me3_2_of_3_rep_3


title: L1_H3K4Me1_2_of_3_rep_1


title: L2_H3K4Me1_2_of_3_rep_1


title: AdultMale_H3K4Me1-Set2_2_of_3_rep_1


title: L3_H3K4Me1_2_of_3_rep_2


title: E20-24_H3K9Ac_2_of_3_rep_1


title: L3_H3K4Me1_2_of_3_rep_1


title: AdultMale_H3K9Ac-Set2_2_of_3_rep_1


title: AdultFemale_H3K4Me3_2_of_3_rep_2


title: AdultFemale_H3K4Me3_2_of_3_rep_1


title: AdultFemale_H3K4Me1_2_of_3_rep_3


title: AdultFemale_H3K4Me1_2_of_3_rep_1


title: AdultMale_H3K4Me1-Set2_2_of_3_rep_3


title: Pupae_H3K4Me1_2_of_3_rep_2


title: E0-4_H3K4Me1_2_of_3_rep_2


title: L2_H3K4Me1_2_of_3_rep_2


title: AdultMale_H3K4Me1-Set2_2_of_3_rep_2


title: Pupae_H3K4Me3_2_of_3_rep_2


title: AdultFemale_H3K27Me3_2_of_3_rep_3


title: AdultFemale_H3K27Me3_2_of_3_rep_2


title: Pupae_H3K4Me1_2_of_3_rep_1


title: Pupae_H3K27Ac_2_of_3_rep_2


title: Pupae_H3K27Ac_2_of_3_rep_3


title: Pupae_H3K27Ac_2_of_3_rep_1


title: E0-4_H3K4Me1_2_of_3_rep_3


title: L3_H3K27Ac_2_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_2_of_3_rep_1


title: L3_H3K27Ac_2_of_3_rep_1


title: L2_H3K27Ac_2_of_3_rep_3


title: L3_H3K27Ac_2_of_3_rep_2


title: Pupae_H3K4Me1_2_of_3_rep_3


title: L2_H3K27Ac_2_of_3_rep_1


title: E20-24_H3K27Ac_2_of_3_rep_2


title: E16-20_H3K27Ac_2_of_3_rep_1


title: L1_H3K27Ac_2_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_2_of_3_rep_3


title: E16-20_H3K27Ac_2_of_3_rep_3


title: L1_H3K27Ac_2_of_3_rep_1


title: AdultFemale_H3K27Me3_2_of_3_rep_1


title: E20-24_H3K27Ac_2_of_3_rep_3


title: E20-24_H3K27Ac_2_of_3_rep_1


title: E12-16_H3K27Ac_2_of_3_rep_2


title: L2_H3K27Ac_2_of_3_rep_2


title: E0-4_H3K4Me1_2_of_3_rep_1


title: L1_H3K27Ac_2_of_3_rep_2


title: L1_CBP_1_of_3_rep_3


title: L1_CBP_1_of_3_rep_2


title: E8-12_H3K27Ac_2_of_3_rep_2


title: E16-20_H3K27Ac_2_of_3_rep_2


title: E8-12_H3K27Ac_2_of_3_rep_1


title: E12-16_H3K27Ac_2_of_3_rep_1


title: L1_CBP


title: E12-16_H3K27Ac_2_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_2_of_3_rep_2


title: E4-8_8wg16-Set2_1_of_3_rep_2


title: E0-4_CBP_1_of_3_rep_3


title: E16-20_8wg16_1_of_3_rep_3


title: L3_PolII_1_of_3_rep_1


title: E16-20_8wg16_1_of_3_rep_1


title: E0-4_CBP


title: E4-8_8wg16-Set2_1_of_3_rep_1


title: L3_PolII_1_of_3_rep_2


title: L3_PolII_1_of_3_rep_3


title: E4-8_8wg16-Set2_1_of_3_rep_3


title: E0-4_CBP_1_of_3_rep_2


title: L3_H3K9Me3_1_of_3_rep_1


title: L2_PolII_1_of_3_rep_3


title: L3_H3K9Me3_1_of_3_rep_3


title: AdultMale_H3K9Me3-Set2_1_of_3_rep_1


title: L2_PolII_1_of_3_rep_2


title: Pupae_H3K9Me3_1_of_3_rep_3


title: E0-4_H3K9Ac_1_of_3_rep_1


title: L3_H3K9Me3_1_of_3_rep_2


title: Pupae_H3K9Me3_1_of_3_rep_1


title: E4-8_H3K9Ac_1_of_3_rep_2


title: E4-8_H3K9Ac_1_of_3_rep_3


title: AdultMale_H3K9Me3-Set2_1_of_3_rep_2


title: AdultMale_H3K9Me3-Set2_1_of_3_rep_3


title: L2_PolII_1_of_3_rep_1


title: E0-4_H3K9Ac_1_of_3_rep_2


title: Pupae_H3K9Me3_1_of_3_rep_2


title: E0-4_H3K9Ac_1_of_3_rep_3


title: E20-24_H3K9Ac_1_of_3_rep_2


title: L3_H3K9Ac_1_of_3_rep_3


title: E20-24_H3K9Ac_1_of_3_rep_3


title: AdultMale_H3K9Ac-Set2_1_of_3_rep_2


title: L3_H3K9Ac_1_of_3_rep_1


title: E4-8_H3K9Ac_1_of_3_rep_1


title: L3_H3K9Ac_1_of_3_rep_2


title: AdultFemale_H3K4Me3_1_of_3_rep_3


title: AdultMale_H3K9Ac-Set2_1_of_3_rep_3


title: E8-12_H3K9Ac_1_of_3_rep_2


title: L3_H3K4Me3_1_of_3_rep_1


title: E8-12_H3K9Ac_1_of_3_rep_1


title: E16-20_8wg16_1_of_3_rep_2


title: L3_H3K4Me3_1_of_3_rep_3


title: AdultMale_H3K9Ac-Set2_1_of_3_rep_1


title: Pupae_H3K9Ac_1_of_3_rep_2


title: Pupae_H3K4Me3_1_of_3_rep_3


title: Pupae_H3K9Ac_1_of_3_rep_1


title: AdultMale_H3K4Me1-Set2_1_of_3_rep_3


title: AdultFemale_H3K4Me3_1_of_3_rep_2


title: L1_H3K4Me1_1_of_3_rep_1


title: AdultFemale_H3K4Me1_1_of_3_rep_1


title: AdultMale_H3K4Me1-Set2_1_of_3_rep_2


title: L2_H3K4Me1_1_of_3_rep_3


title: L1_H3K4Me1_1_of_3_rep_2


title: L2_H3K4Me1_1_of_3_rep_2


title: AdultFemale_H3K4Me1_1_of_3_rep_3


title: L3_H3K4Me1_1_of_3_rep_2


title: AdultMale_H3K4Me1-Set2_1_of_3_rep_1


title: AdultFemale_H3K4Me1_1_of_3_rep_2


title: L2_H3K4Me1_1_of_3_rep_1


title: L3_H3K4Me1_1_of_3_rep_3


title: L1_H3K4Me1_1_of_3_rep_3


title: L3_H3K4Me1_1_of_3_rep_1


title: Pupae_H3K4Me1_1_of_3_rep_1


title: AdultFemale_H3K27Me3_1_of_3_rep_3


title: E0-4_H3K4Me1_1_of_3_rep_2


title: Pupae_H3K4Me1_1_of_3_rep_2


title: Pupae_H3K9Ac_1_of_3_rep_3


title: E0-4_H3K4Me1_1_of_3_rep_1


title: AdultFemale_H3K27Me3_1_of_3_rep_2


title: E0-4_H3K4Me1_1_of_3_rep_3


title: Pupae_H3K27Ac_1_of_3_rep_2


title: Pupae_H3K27Ac_1_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_1_of_3_rep_2


title: AdultFemale_H3K27Me3_1_of_3_rep_1


title: AdultMale_H3K27Ac-Set2_1_of_3_rep_3


title: Pupae_H3K27Ac_1_of_3_rep_1


title: L2_H3K27Ac_1_of_3_rep_2


title: Pupae_H3K4Me3_1_of_3_rep_2


title: L3_H3K27Ac_1_of_3_rep_2


title: AdultFemale_H3K4Me3_1_of_3_rep_1


title: L3_H3K27Ac_1_of_3_rep_3


title: AdultMale_H3K27Ac-Set2_1_of_3_rep_1


title: E20-24_H3K27Ac_1_of_3_rep_1


title: L3_H3K27Ac_1_of_3_rep_1


title: L3_H3K4Me3_1_of_3_rep_2


title: L1_H3K27Ac_1_of_3_rep_2


title: E16-20_H3K27Ac_1_of_3_rep_3


title: L2_H3K27Ac_1_of_3_rep_1


title: L1_H3K27Ac_1_of_3_rep_3


title: E20-24_H3K27Ac_1_of_3_rep_2


title: E20-24_H3K9Ac_1_of_3_rep_1


title: E16-20_H3K27Ac_1_of_3_rep_2


title: iPS_undifferentiated_3

status: Public on Aug 01 2009

city: Charleston

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Reprogrammed somatic cells offer a valuable source of pluripotent cells that have the potential to differentiate into many cells types and provide a new tool for regenerative medicine. In the present study we differentiated induced pluripotent stem cells (iPS cells) into hepatic cells. We first showed that mouse iPS cells could from a complete liver in mouse embryo (E14.5) including hepatocytes, endothelial cells, sinusoidal cells and resident macrophages. We then designed a highly efficient hepatocyte differentiation protocol using defined factors on human embryonic stem cells (ES cells). This protocol was found to generate more than 80% albumin expressing cells that show hepatic functions and express most of liver genes as shown by microarray analyses. Similar results were obtained when human iPS cells were induced to differentiate following the same procedure.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard Affymetrix protocol, standard GCOS data processing produced the values in the accompanying table

source_name: induced pluripotent stem cells derived from ATCC cell line CRL2097 (human foreskin fibroblasts)

label_protocol: Affymetrix One-Cycle Target Labeling

extract_protocol: Rneasy (Qiagen)

tag: cell line

value: ATCC CRL2097

tag: cell type

value: induced pluripotent stem cells derived from human foreskin fibroblasts


title: E12-16_H3K27Ac_1_of_3_rep_2


title: E16-20_H3K27Ac_1_of_3_rep_1


title: L1_H3K27Ac_1_of_3_rep_1


title: iPS_undifferentiated_1


title: E12-16_H3K27Ac_1_of_3_rep_3


title: iPS_d20_hepatic differentiated_1

value: human foreskin fibroblasts subjected to a hepatic differentiation protocol. samples harvested on d20 of protocol


title: iPS_d20_hepatic differentiated_3


title: E8-12_H3K27Ac_1_of_3_rep_2


title: E8-12_H3K27Ac_1_of_3_rep_1


title: iPS_d20_hepatic differentiated_2


title: fibroblasts_3

source_name: ATCC cell line CRL2097 (human foreskin fibroblast)

value: human foreskin fibroblasts


title: Pupae_H3K4Me1_1_of_3_rep_3


title: fibroblasts_1


title: fibroblasts_2


title: control cell donor 3

status: Public on Jun 29 2009

city: Bethesda

first: Teresa

last: Wild

state: MD

address: 30 Convent Drive

department: NIDCR

institute: NIH

description: RNA from healthy donor

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

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

data_processing: Affymetrix Microarray Suite version 5.0

source_name: primary macrophages, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monocytes plated 6x10^6/well of 6 well plate in DMEM.  10% FCS added after 4 hours and left to differentiate 7 days.

extract_protocol: RNA extraction using Qiagen Rneasy mini-kit.

treatment_protocol: Cells were mock-treated or treated with IFNalpha for 4 hours.

value: monocyte-derived macrophage

tag: agent

value: control


title: IFNa treated donor 3

description: RNA from healthy donor

source_name: primary macrophages, IFNa-treated

value: IFNalpha


title: control cell donor 2

description: RNA from healthy donor


title: control cell donor 1

description: RNA from healthy donor


title: E20-24_H3K27Ac_1_of_3_rep_3

value: ChIP

value: Input


title: E12-16_H3K27Ac_1_of_3_rep_1


title: L2_H3K27Ac_1_of_3_rep_3


title: AdultFemale_8wg16_2_of_3_rep_3

status: Public on Jun 24 2009

scan_protocol: Channel 1 & 2 are for the Agilent arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1. Channel 1 & 2 are for the Agilent arrays are scanned on Agilent's DNA Microarray Scanner G2505B at a resolution of 5 microns. Data is extracted from the images using Agilent's Feature Extraction Software 9.5.3.1.

value: PolII (8wg16)

value: Covance


title: IFNa treated donor 1

description: RNA from healthy donor


title: E0-4_8wg16_2_of_3_rep_3


title: E0-4_8wg16_2_of_3_rep_2


title: Pupae_PolII_2_of_3_rep_3

value: PolII


title: L3_8wg16_2_of_3_rep_3


title: E4-8_8wg16_2_of_3_rep_1


title: E4-8_8wg16_2_of_3_rep_3


title: AdultFemale_8wg16_2_of_3_rep_1


title: E4-8_8wg16_2_of_3_rep_2


title: L3_CBP_2_of_3_rep_3

value: CBP

value: Dr. Mattias Mannervik in Stockholm University


title: E0-4_8wg16_2_of_3_rep_1


title: AdultFemale_8wg16_2_of_3_rep_2


title: L3_8wg16_3_of_3_rep_3


title: L3_8wg16_2_of_3_rep_2


title: Pupae_CBP_2_of_3_rep_1


title: L3_CBP_2_of_3_rep_2


title: L3_8wg16_2_of_3_rep_1


title: AdultMale_H3K27Ac_2_of_3_rep_2

value: Abcam


title: Pupae_PolII_2_of_3_rep_2


title: iPS_undifferentiated_2


title: IFNa treated donor 2

description: RNA from healthy donor


title: Pupae_CBP_2_of_3_rep_2


title: Pupae_CBP_2_of_3_rep_3


title: Pupae_PolII_2_of_3_rep_1


title: AdultMale_H3K27Ac_2_of_3_rep_1


title: AdultFemale_8wg16_3_of_3_rep_2


title: L3_8wg16_3_of_3_rep_1


title: L3_CBP_2_of_3_rep_1


title: AdultMale_H3K27Ac_2_of_3_rep_3


title: E0-4_8wg16_3_of_3_rep_3


title: AdultFemale_8wg16_3_of_3_rep_1


title: AdultFemale_8wg16_3_of_3_rep_3


title: E0-4_8wg16_3_of_3_rep_1


title: L3_8wg16_3_of_3_rep_2


title: E4-8_8wg16_3_of_3_rep_3


title: Pupae_PolII_3_of_3_rep_3


title: Pupae_PolII_3_of_3_rep_1


title: Pupae_PolII_3_of_3_rep_2


title: E4-8_8wg16_3_of_3_rep_2


title: E0-4_8wg16_3_of_3_rep_2


title: L3_CBP_3_of_3_rep_1


title: AdultMale_H3K27Ac_3_of_3_rep_3


title: E16-20_CBP_3_of_3_rep_3


title: AdultMale_CBP_3_of_3_rep_2


title: L3_CBP_3_of_3_rep_2


title: Pupae_CBP_3_of_3_rep_3


title: AdultMale_CBP_3_of_3_rep_3


title: AdultMale_H3K27Ac_3_of_3_rep_2


title: AdultMale_H3K27Ac_3_of_3_rep_1


title: E4-8_8wg16_3_of_3_rep_1


title: E16-20_CBP_3_of_3_rep_1


title: E16-20_CBP_3_of_3_rep_2


title: Pupae_CBP_3_of_3_rep_1


title: Pupae_CBP_3_of_3_rep_2


title: E8-12_H3K4Me1_3_of_3_rep_1


title: E8-12_H3K4Me1_3_of_3_rep_2


title: AdultMale_H3K9Ac-set2_3_of_3_rep_3

tag: tissue

value: adult male


title: E8-12_H3K4Me1_3_of_3_rep_3

value: input


title: AdultMale_CBP_3_of_3_rep_1


title: L3_CBP_3_of_3_rep_3


title: AdultFemale_CBP_3_of_3_rep_2


title: AdultFemale_CBP_3_of_3_rep_1


title: AdultMale_H3K9Ac-set2_3_of_3_rep_1


title: AdultFemale_CBP_3_of_3_rep_3


title: E8-12_H3K4Me3_3_of_3_rep_2


title: E8-12_H3K4Me3_3_of_3_rep_3


title: AdultMale_H3K9Ac-set2_3_of_3_rep_2


title: E8-12_H3K4Me3_3_of_3_rep_1


title: E8-12_H3K27Me3_3_of_3_rep_1

value: Upstate


title: E8-12_H3K9Me3_3_of_3_rep_2


title: E8-12_H3K27Me3_3_of_3_rep_3


title: E8-12_H3K9Me3_3_of_3_rep_3


title: AdultMale_H3K9Me3-set2_3_of_3_rep_3


title: E8-12_H3K9Me3_3_of_3_rep_1


title: E16-20_CBP_2_of_3_rep_1


title: AdultMale_CBP_2_of_3_rep_2


title: E16-20_CBP_2_of_3_rep_2


title: E8-12_H3K27Me3_3_of_3_rep_2


title: AdultMale_CBP_2_of_3_rep_3


title: AdultMale_H3K9Ac-set2_2_of_3_rep_2


title: E8-12_H3K4Me1_2_of_3_rep_3


title: AdultFemale_CBP_2_of_3_rep_3


title: E16-20_CBP_2_of_3_rep_3


title: AdultMale_CBP_2_of_3_rep_1


title: E8-12_H3K4Me3_2_of_3_rep_2


title: AdultMale_H3K9Ac-set2_2_of_3_rep_1


title: AdultMale_H3K9Ac-set2_2_of_3_rep_3


title: E8-12_H3K4Me1_2_of_3_rep_2


title: E8-12_H3K4Me1_2_of_3_rep_1


title: E8-12_H3K4Me3_2_of_3_rep_3


title: E8-12_H3K4Me3_2_of_3_rep_1


title: AdultFemale_CBP_2_of_3_rep_2


title: AdultMale_H3K9Me3-set2_3_of_3_rep_1


title: AdultMale_H3K9Me3-set2_3_of_3_rep_2


title: AdultMale_H3K27Me3-Set2_3_of_3_rep_2


title: AdultFemale_CBP_2_of_3_rep_1


title: E4-8_8wg16_1_of_3_rep_2


title: L3_8wg16_1_of_3_rep_1


title: L3_8wg16_1_of_3_rep_3


title: E4-8_8wg16_1_of_3_rep_3


title: E4-8_8wg16_1_of_3_rep_1


title: AdultMale_H3K27Me3-Set2_3_of_3_rep_1


title: E8-12_H3K27Me3_2_of_3_rep_3


title: E0-4_8wg16_1_of_3_rep_2


title: AdultMale_H3K27Me3-Set2_3_of_3_rep_3


title: L3_8wg16_1_of_3_rep_2


title: E0-4_8wg16_1_of_3_rep_3


title: E8-12_H3K27Me3_2_of_3_rep_2


title: E8-12_H3K9Me3_2_of_3_rep_3


title: AdultMale_H3K9Me3-set2_2_of_3_rep_2


title: E8-12_H3K27Me3_2_of_3_rep_1


title: AdultMale_H3K27Me3-Set2_2_of_3_rep_3


title: E8-12_H3K9Me3_2_of_3_rep_2


title: E8-12_H3K9Me3_2_of_3_rep_1


title: AdultMale_H3K9Me3-set2_2_of_3_rep_3


title: AdultMale_H3K9Me3-set2_2_of_3_rep_1


title: E0-4_8wg16_1_of_3_rep_1


title: AdultMale_H3K27Me3-Set2_2_of_3_rep_2


title: AdultFemale_8wg16_1_of_3_rep_3


title: Pupae_PolII_1_of_3_rep_1


title: AdultFemale_8wg16_1_of_3_rep_2


title: AdultFemale_CBP_1_of_3_rep_2


title: L3_CBP_1_of_3_rep_3


title: AdultMale_H3K27Ac_1_of_3_rep_3


title: Pupae_PolII_1_of_3_rep_3


title: AdultMale_H3K27Me3-Set2_2_of_3_rep_1


title: AdultFemale_8wg16_1_of_3_rep_1


title: E16-20_CBP_1_of_3_rep_1


title: AdultMale_H3K27Ac_1_of_3_rep_2


title: E16-20_CBP_1_of_3_rep_2


title: AdultMale_H3K27Ac_1_of_3_rep_1


title: Pupae_PolII_1_of_3_rep_2


title: E16-20_CBP_1_of_3_rep_3


title: L3_CBP_1_of_3_rep_1


title: Pupae_CBP_1_of_3_rep_3


title: AdultMale_H3K9Ac-set2_1_of_3_rep_2


title: L3_CBP_1_of_3_rep_2


title: AdultMale_CBP_1_of_3_rep_2


title: Pupae_CBP_1_of_3_rep_2


title: E8-12_H3K4Me1_1_of_3_rep_1


title: AdultFemale_CBP_1_of_3_rep_3


title: AdultMale_CBP_1_of_3_rep_3


title: AdultMale_CBP_1_of_3_rep_1


title: AdultMale_H3K9Ac-set2_1_of_3_rep_3


title: AdultFemale_CBP_1_of_3_rep_1


title: Pupae_CBP_1_of_3_rep_1


title: E8-12_H3K4Me3_1_of_3_rep_2


title: E8-12_H3K4Me3_1_of_3_rep_1


title: E8-12_H3K4Me1_1_of_3_rep_3


title: E8-12_H3K4Me3_1_of_3_rep_3


title: E8-12_H3K4Me1_1_of_3_rep_2


title: AdultMale_H3K9Ac-set2_1_of_3_rep_1


title: E8-12_H3K27Me3_1_of_3_rep_1


title: AdultMale_H3K27Me3-Set2_1_of_3_rep_1


title: E8-12_H3K27Me3_1_of_3_rep_2


title: AdultMale_H3K9Me3-set2_1_of_3_rep_2


title: E8-12_H3K27Me3_1_of_3_rep_3


title: AdultMale_H3K9Me3-set2_1_of_3_rep_1


title: E-20-24h_CBP_3_of_3_rep_2

status: Public on Mar 28 2009

description: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_2

source_name: ChIP, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_2

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 20-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.

value: embryos

tag: time point

value: 20-24 hours of development

tag: replicate

source_name: Input, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_2


title: E8-12_H3K9Me3_1_of_3_rep_2


title: E-20-24h_CBP_3_of_3_rep_3

description: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_3

source_name: ChIP, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_3

source_name: Input, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_3


title: E8-12_H3K9Me3_1_of_3_rep_3


title: AdultMale_H3K9Me3-set2_1_of_3_rep_3


title: E8-12_H3K9Me3_1_of_3_rep_1


title: E-0-4h_H3K27AC_3_of_3_rep_3, B

description: ChIP-chip of H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_3

source_name: ChIP, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_3

value: 0-4 hours of development

source_name: Input, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_3


title: E-0-4h_H3K27AC_3_of_3_rep_1, B

description: ChIP-chip of H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_1

source_name: ChIP, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_1

source_name: Input, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_1


title: E-0-4h_H3K27AC_3_of_3_rep_2, B

description: ChIP-chip of H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_2

source_name: ChIP, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_2

source_name: Input, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_2


title: AdultMale_H3K27Me3-Set2_1_of_3_rep_3


title: AdultMale_H3K4Me3_3_of_3_rep_3

description: ChIP-chip of H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_3

source_name: ChIP, H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_3

growth_protocol: 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Male 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.

source_name: Input, H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_3


title: N_CD4_3

status: Public on May 20 2009

city: London

first: Rifca

last: Le Dieu

address: 3rd Floor, John Vane Science Building, Charterhouse Square

department: Institute of Cancer

institute: Queen Mary University of London

description: NS3 CD4

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridised for 16 hours at 45C on Affymetrix U133Plus2 GeneChips. Chips were then washed and stained with SAPE in an Affymetrix GeneChip 450 Fluidics Station.

scan_protocol: GeneChips were scanned using the Ayymetrix GeneChip 3000 scanner

data_processing: Data was normalised using RMA

source_name: CD4 T cells, Negative Selection

label_protocol: Affymetrix Expression GeneChip Protocol one-cycle procedure. Between 2 and 5micrograms of RNA was used as starting material.

extract_protocol: RNA was extracted using Trizol.

tag: age

tag: gender

value: Female


title: P_CD4_10

description: PS10 CD4

source_name: CD4 T cells, Positive Selection


title: AdultMale_H3K4Me3_3_of_3_rep_2

description: ChIP-chip of H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_2

source_name: ChIP, H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_2

source_name: Input, H3K4me3 in adult male Drosophila, AdultMale_H3K4Me3_3_of_3_rep_2


title: E-4-8h_CBP_3_of_3_rep_2

description: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_2

source_name: ChIP, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_2

value: 4-8 hours of development

source_name: Input, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_2


title: AdultMale_H3K27Me3-Set2_1_of_3_rep_2


title: E-4-8h_CBP_3_of_3_rep_3

description: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_3

source_name: ChIP, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_3

source_name: Input, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_3


title: E-4-8h_H3K27AC_3_of_3_rep_3

description: ChIP-chip of H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_3

source_name: ChIP, H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_3

source_name: Input, H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_3


title: E-0-4h_H3K27AC_3_of_3_rep_3

source_name: ChIP, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_3

source_name: Input, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_3


title: E-4-8h_H3K27AC_3_of_3_rep_2

description: ChIP-chip of H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_2

source_name: ChIP, H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_2

source_name: Input, H3K27AC in Drosophila embryos at 4-8 hours of development, E-4-8h_H3K27AC_3_of_3_rep_2


title: E-20-24h_CBP_3_of_3_rep_1

description: ChIP-chip of CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_1

source_name: ChIP, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_1

source_name: Input, CBP in Drosophila embryos at 20-24 hours of development, E-20-24h_CBP_3_of_3_rep_1


title: E-4-8h_CBP_3_of_3_rep_1

description: ChIP-chip of CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_1

source_name: ChIP, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_1

source_name: Input, CBP in Drosophila embryos at 4-8 hours of development, E-4-8h_CBP_3_of_3_rep_1


title: E-0-4h_H3K27AC_3_of_3_rep_2

source_name: ChIP, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_2

source_name: Input, H3K27AC in Drosophila embryos at 0-4 hours of development, E-0-4h_H3K27AC_3_of_3_rep_2