title: Liver-high dose-rep2

description: no additional information


title: BM_HSC_BM_NBM1483

status: Public on Dec 22 2010

type: RNA

city: Stanford

first: Ash

middle: A

last: Alizadeh

state: CA

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

country: USA

institute: Stanford University School of Medicine

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were normalized using MAS5

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

extract_protocol: Total RNA was extracted using TRIzol reagent containing either glycogen or linear acrylamide according to the manufacturer's protocol, and then treated with DNaseI (Ambion).

tag: patient

tag: age group

value: adult

tag: disease state

value: normal

tag: cell source

value: bone marrow

tag: cell type (purified cell subset)


title: BM_HSC_BM_NBM1481


title: Liver-control-rep4

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description: no additional information

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added to 750 ng labeled experimental and reference samples.  Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers; 17 hrs overnight at 65 degrees C. After hybridization, slides were washed and dipped into acetonitrile.

scan_protocol: Scanned on an Agilent  scanner at ICBR, UF; Feature Extraction Software (version 9.1.3.1).

data_processing: GeneSpring version 9.0.3; two-color technology; threshold = 5, baseline to median, LOWESS

organism: Pimephales promelas

source_name: Adult male - 96 hr (experimental sample)

label_protocol: Agilent Low-RNA Input Linear Amplification Kit (LRILAK)

extract_protocol: Total RNA extracted using Qiagen RNEasy Plus columns following manufacturer's instructions

treatment_protocol: Aqueous static renewal.  Nominal concentrations of 0 (control), 1 mg/L (low dose) and 10 mg/L (high dose) of TiO2.

tag: agent

value: control

tag: nominal dose

value: 0 mg/L

source_name: Reference sample

tag: reference composition

value: Male & Female, Liver, gonad, brain


title: Liver-control-rep3

description: no additional information


title: Liver-high dose-rep1

description: no additional information

value: 10 mg/L


title: monocytes_+LPS_3

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

country: Germany

institute: Christian-Albrechts-University Kiel

description: 24h medium, 4h LPS stimulation

hyb_protocol: 20 µg of fragmented cRNA was hybridized to a Human Genome U133 Plus 2.0 array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

scan_protocol: Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix) using GCOS software.

data_processing: Expression data was normalized with GC-RMA algorithm.

source_name: blood, +LPS

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (IVT Labeling Kit, Affymetrix).

growth_protocol: THP-1 cells were cultivated in RPMI medium 1640 (Invitrogen, Karlsruhe, Germany) supplemented with 10% FCS and 1% antibiotics (penicillin/ streptomycin) in a humidified incubator containing 5% CO2 at 37°C. Twenty four hours before pre-incubation, cells were plated at a density of 3 x 106 per well in a 6-well plate.

extract_protocol: Cells were collected in Qiazol-lysis buffer (Qiagen, Hilden, Germany) and stored at -80 °C until isolation of total RNA.

treatment_protocol: In 6-well plates, cells were pre-incubated with 10 µM oxidized ubiquinone (Q10), or the respective vehicle controls (KANEKA Corporation, Japan). After 24 hours, cell culture medium was removed and fresh lipopolysaccharide (LPS, E. coli, O55:B5, Sigma Aldrich, Taufkirchen, Germany) containing medium (1 µg/ ml) was added for 4 hours, except in the negative control wells (-LPS).

tag: cell type

value: myeloid monocytic cells

tag: protocol

value: 24h medium, 4h LPS stimulation


title: monocytes_Q10_1

description: 24h Q10 preincubation, 4h LPS stimulation

source_name: blood, +Q10, +LPS


title: RWPE 266 vs. RWPE ni 24h

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description:
Human RWPE cells were infected with Propionibacterium acnes strain 266 and samples were isolated 24h post infection. Uninfected cells isolated at 24h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

hyb_protocol: After precipitation, purification and quantification, 1.25 µg of each labeled cRNA was fragmented and subsequent hybridized to whole human genome 44k microarrays (AMADID-014850) according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Hybridized microarrays were washed using the SSC washing protocol (Agilent Technologies). Scanning of microarrays was performed with extended mode (100% and 10%) at 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: The extracted MAGE-ML files were further analyzed with the Rosetta Resolver Biosoftware, Build 7.2 (Rosetta Biosoftware, Seattle, WA, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: RWPE 266 24h

label_protocol: RNA labeling was performed with the Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled with either Cyanine 3-CTP or Cyanine 5-CTP according the suppliers instructions

extract_protocol: total RNA was extracted with Trizol (invitrogen) according the suppliers instructions using Glycogen as carrier

tag: cell line

value: prostate epithelial

tag: infection

value: Propionibacterium acnes strain 266

tag: time

source_name: RWPE ni 24h


title: RWPE ni vs. RWPE P6 24h

description:
Human RWPE cells were infected with Propionibacterium acnes strain P6 and samples were isolated 24h post infection. Uninfected cells isolated at 24h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

source_name: RWPE P6 24h

value: Propionibacterium acnes strain P6


title: BM_HSC_BM_NBM1440


title: A549 H3K9K14ac_0 h

type: genomic

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Chip-chip A549 cells_0 h H3K19K14ac

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

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

molecule: genomic DNA

source_name: H3K9K14ac ChIP DNA from A549 cells_0 h

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: A549 cells were cultured in the Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum and 1% penicillin-streptomycin  and incubated at 37°C in a 5% CO2 humidified incubator.

extract_protocol: 4 x 10E6 cells seeded on 100-mm culture dishes in DMEM medium containing 10% FBS were grown to approximately 80–90% confluency and treated with DMSO or 2.5 μM OSU-HDAC-44 for 2 h, and then cross-linked with 1% formaldehyde. Lysate was sonicated to shear DNA and ChIP was as described above. Immunoprecipitation was performed with anti-acetylated lysine 9 and lysine 14 of histone H3 (H3K9K14Ac) for 16 h at 4C.

treatment_protocol: A549 cells were left untreated with OSU-HDAC-44.

tag: chip antibody

source_name: Input DNA from A549 cells_0 h

value: none, input DNA


title: monocytes_+LPS_2

description: 24h medium, 4h LPS stimulation


title: RWPE P6 vs. RWPE ni 96h

description:
Human RWPE cells were infected with Propionibacterium acnes strain P6 and samples were isolated 96h post infection. Uninfected cells isolated at 96h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

source_name: RWPE P6 96h

source_name: RWPE ni 96h


title: BM_HSC_BM_NBM1444


title: RWPE ni vs. RWPE P6 96h


title: CB_HSC_CB_CB023

source_name: umbilical cord blood

value: fetus

value: umbilical cord blood


title: Liver-control-rep2

description: no additional information


title: Liver-control-rep1

description: no additional information


title: Gill-low dose-rep3

description: no additional information

value: 1 mg/L


title: CB_HSC_CB_CB008


title: monocytes_+LPS_1

description: 24h medium, 4h LPS stimulation


title: Liver-high dose-rep4

description: no additional information


title: Gill-low dose-rep4

description: no additional information


title: HepG2_HNF4a&HNF4g_knockdown_control_rep3

city: Meguro

first: Kenji

last: Daigo

state: Tokyo

department: Research Center for Advanced Science and Technology

country: Japan

institute: University of Tokyo

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 with target intensity=100

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: hepatocellular carcinoma


title: Gill-low dose-rep2

description: no additional information


title: Gill-low dose-rep1

description: no additional information


title: BM_GMP_BM_NBM1483

value: adult


title: HepG2_HNF4a&HNF4g_knockdown1_rep3


title: BM_GMP_BM_NBM1481

value: normal


title: HepG2_HNF4a&HNF4g_knockdown2_rep3


title: CB_HSC_CB_CB020


title: Gill-high dose-rep4

description: no additional information


title: BM_GMP_BM_NBM1444

value: bone marrow


title: Gill-high dose-rep3

description: no additional information


title: HepG2_HNF4a&HNF4g_knockdown2_rep2


title: Gill-high dose-rep2

description: no additional information


title: HepG2_HNF4a&HNF4g_knockdown_control_rep2


title: HepG2_HNF4a&HNF4g_knockdown2_rep1


title: HepG2_HNF4a&HNF4g_knockdown_control_rep1


title: BM_CMP_BM_NBM1483


title: HepG2_HNF4a&HNF4g_knockdown1_rep2


title: BM_GMP_BM_NBM07


title: RWPE P6 vs. RWPE ni 24h


title: RWPE ni vs. RWPE KPA 24h

description:
Human RWPE cells were infected with Propionibacterium acnes strain KPA and samples were isolated 24h post infection. Uninfected cells isolated at 24h were used as a control.
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies) using default settings and the GE2_105_Dec08 protocol.

source_name: RWPE KPA 24h

value: Propionibacterium acnes strain KPA


title: Gill-high dose-rep1

description: no additional information


title: Profiling neuroblastoma SH-SY5Y ctrl 17

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: Transcription profiling of neuroblastoma SH-SY5Y treated with Paraquat (PQ) were compared with untreated cells

hyb_protocol: Standard Affymetrix washing and staining protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Probeset summarization was done with RMA and normalization with sketch quantile.

source_name: ctrl

label_protocol: Standard Affymetrix labelling protocol  with rRNA depletion for GeneChip® Exon 1.0 ST.

extract_protocol: Total RNA was extracted using TRIzol® Reagent (Invitrogen), and subsequently purified using silica membrane spin columns from RNeasy Mini kit (Qiagen). RNA quantity and purity were assessed using a NanoDrop® instrument (Thermo Fisher Scientific Inc.). Total RNA integrity was assessed by using a 2100 Bioanalyzer (Agilent Technologies) and the RNA Integrity Number (RIN) was calculated.

treatment_protocol: Paraquat treatment on cell lines derived from human neuroblastoma SH-SY5Y was done as described by Maracchioni, A., Totaro, A., Angelini, D.F., Di Penta, A., Bernardi, G., Carri, M.T., and Achsel, T. (2007). Mitochondrial damage modulates alternative splicing in neuronal cells: implications for neurodegeneration. J Neurochem 100, 142-153.

value: neuroblastoma SH-SY5Y


title: Profiling neuroblastoma SH-SY5Y ctrl 19


title: AML_34neg_TLA_SU032

source_name: therapeutic leukapheresis

value: AML

value: therapeutic leukapheresis


title: BM_CMP_BM_NBM07


title: Gill-control-rep2

description: no additional information

value: control

value: 0 mg/L

value: Male & Female, Liver, gonad, brain


title: Profiling neuroblastoma SH-SY5Y with Paraquat sample 18

source_name: Paraquat


title: Profiling neuroblastoma SH-SY5Y with Paraquat sample 20


title: Gill-control-rep4

description: no additional information


title: AML_34neg_TLA_SU028


title: HepG2_HNF4a&HNF4g_knockdown1_rep1


title: BM_CMP_BM_NBM1444

source_name: bone marrow


title: Gill-control-rep3

description: no additional information

source_name: Adult male - 96 hr (experimental sample)


title: Gill-control-rep1

description: no additional information

source_name: Reference sample


title: Brain-high dose-rep1

description: no additional information

value: 10 mg/L


title: Brain-low dose-pooled

description: no additional information


title: AML_34neg_TLA_SU018


title: Brain-high dose-rep2

description: no additional information


title: Profiling neuroblastoma SH-SY5Y ctrl 13


title: 900 ng Cy3- and 300 ng Cy5 target RNA

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

description: Competitive hybridization of Cy3- and Cy5 labeled RNA mixed at a 3:1 ratio (900 ng and 300 ng, 18 h hybridization)

hyb_protocol: Labeled RNA was added to hybridization buffer (6X saline-sodium citrate (SSC) buffer, 10% Denhardt’s reagent, 0.1% sodium dodecyl sulfate (SDS), 15% formamide) and incubated at 65°C for 5-15 min. Microarrays were sealed with the HybriWell Hybridization Sealing System (HBW2222-FL, Grace BioLabs), which have a well depth of 0.25 mm. Static microarray hybridizations, i.e.without active mixing of the hybridization solution,were performedin a custom-made hybridization chamber at 42°C for 18 h, except for experiments testing the effect of hybridization time. After hybridization, microarrays were washed by shaking at RT for 5 min sequentially in a 2X SSC, 0.1% SDS buffer and a 0.1X SSC buffer, followed by 20 s in ice-cold MQ water. Slides were dried by centrifugation (3 min, 300 x g) and stored in the dark at RT until scanning on the same day.

scan_protocol: Fluorescence images were recorded by scanning the slides at 10-μm resolution with a GenePix Personal 4100A array scanner (Axon Instruments, Molecular Devices Corporation, Sunnyvale, CA, USA). Each pixel line of the selected area was scanned three times and the obtained signals were averaged to generate the fluorescence image. Gain of the photo multiplier tube was adjusted to record images with signal intensities just below the saturation level. Scanned images were saved as multilayer tiff images and analyzed with the GenePix Pro 6.0 software (Axon Instruments). Low quality hybridizations were repeated.

data_processing:
Cy3- and Cy5-labeled RNA mixed at a 3:1 ratio (900 ng and 300 ng). We analyzed the co-hybridization of Cy3 and Cy5 labeled RNA separately (without displaying the ratio).
Scanned images were analyzed with GenePix Pro 6.0 software (Axon Instruments) and signal intensity surface plots of microarrays were generated using ImageJ with the Interactive 3D Surface Plot plug-in. Signal intensities were analyzed according to the spot position, and mean relative signal intensities for each spot position were either compared directly or in some cases normalized to either the maximum or minimum mean signal intensity to facilitate comparison. Poor quality spots were removed from the analysis . Statistical testing was performed with the Student’s t-test using Microsoft Excel.

organism: Pseudodesulfovibrio halophilus

source_name: D. halophilus 16S rRNA gene, clone

label_protocol: A 1.5 kB-fragment of the 16S rRNA gene of Desulfovibrio halophilus (DSM 5663) was amplified using the PCR primer set 616V-630R. The 616V primer contained a T3 promoter site tag at the 5â€™ end to allow T3 RNA polymerase-based reverse transcription labeling of PCR products. The target was labeled via an in vitro transcription reaction and template DNA was digested. RNA concentration and dye incorporation rates were measured spectrophotometrically, and labeled 16S rRNA was fragmented via incubation with 10 mM ZnCl2 at 60Â°C for 30 min and was then stored in the dark at -20°C.

extract_protocol: Plasmids were used as template. Plasmid DNA was extracted using the Qiaprep Spin Miniprep Kit (QIAgen, Hilden, Germany) according to manufacturer instructions.

tag: strain

tag: amount of labeled rna used for hybridization

tag: hybridization time

value: 18 hours

tag: assayed gene

value: 16S rRNA gene


title: AML_34neg_PB_SU031

source_name: peripheral blood

tag: patient

tag: age group

value: peripheral blood


title: Brain-control-pooled

description: no additional information


title: Profiling neuroblastoma SH-SY5Y with Paraquat sample 12


title: AML_34neg_TLA_SU014

tag: disease state

tag: cell source


title: 140 hour hybridization_a

description: Hybridization of 300 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 140 hours

data_processing: Scanned images were analyzed with GenePix Pro 6.0 software (Axon Instruments) and signal intensity surface plots of microarrays were generated using ImageJ with the Interactive 3D Surface Plot plug-in. Signal intensities were analyzed according to the spot position, and mean relative signal intensities for each spot position were either compared directly or in some cases normalized to either the maximum or minimum mean signal intensity to facilitate comparison. Poor quality spots were removed from the analysis . Statistical testing was performed with the Student’s t-test using Microsoft Excel.

label_protocol: A 1.5 kB-fragment of the 16S rRNA gene of Desulfovibrio halophilus (DSM 5663) was amplified using the PCR primer set 616V-630R. The 616V primer contained a T3 promoter site tag at the 5’ end to allow T3 RNA polymerase-based reverse transcription labeling of PCR products. The target was labeled via an in vitro transcription reaction and template DNA was digested. RNA concentration and dye incorporation rates were measured spectrophotometrically, and labeled 16S rRNA was fragmented via incubation with 10 mM ZnCl2 at 60°C for 30 min and was then stored in the dark at -20 °C.

value: 140 hours


title: 140 hour hybridization_b


title: 65 hour hybridization_c

description: Hybridization of 300 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 65 hours

value: 65 hours


title: AML_34neg_TLA_SU008

tag: cell type (purified cell subset)


title: Profiling neuroblastoma SH-SY5Y with Paraquat sample 14


title: AML_34neg_PB_SU004


title: 140 hour hybridization_c


title: Profiling wt SOD1 sample 17

description: The CEL files resulting from the hybridization were analyzed using oneChannelGUI 1.6.5 . To assess differential expression at gene-level, we used an empirical Bayes method  together with a false discovery rate (FDR) correction of the p-value.  Thus, the list of differentially expressed genes was generated using an FDR ≤ 0.05 together with an absolute log2(fold-change) threshold of 1.

hyb_protocol: Standard Affymetrix hybridization protocol for GeneChip® Exon 1.0 ST arrays

scan_protocol: Standard Affymetrix scanning protocol for GeneChip® Exon 1.0 ST arrays

data_processing: Probeset summarization was done by RMA and normalization by sketch quantile method (Affymetrix APT tools)

label: Biotin

source_name: wild type SOD1

label_protocol: Whole transcriptome Affymetrix protocol with rRNA depletion.

growth_protocol: cell lines were cultured  in D-MEM/F-12 media  with GlutaMAX™ (Gibco, Invitrogen, UK), 10% FBS,  100 Units/ml penicillin G, 100µg/ml streptomycin/ penicillin (Euroclone, Milano, Italy). Stably transfected cells were maintained in the presence of 400µg/ml Geneticin (G418 sulphate, Euroclone).


title: Profiling ALS SOD1(G93A) mutant sample 18

source_name: ALS SOD1(G93A) mutant


title: Profiling ALS SOD1(G93A) mutant sample 15


title: 65 hour hybridization_a


title: 300 ng Cy5 labeled target RNA_c

description: Hybridization of 300 ng Cy5 labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours


title: DrosSalivaryGland_+-cohesin_1.2

city: Cambridge

first: Andrea

last: Pauli

state: MA

address: 16 Divinity Street

institute: Harvard University

description: see above

hyb_protocol: Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package

organism: Drosophila melanogaster

source_name: Total RNA from hs-TEV_genomicRad21 salivary glands (genotype: w1118; hs-TEV/+; genomic Rad21/Rad21ex3)

label_protocol: Klenow Labelling: Between 3 to 5µg total RNA are reverse transcribed to cDNA [anchored oligo (dT)23 (Sigma), Superscript III (Invitrogen)] and second strand synthesis is then performed [Second strand buffer (Invitrogen), DNA Polymerase I (Invitrogen), RNaseH (New England Biolabs), E. coli DNA ligase (GE Healthcare)] to obtain double stranded DNA. Random primers are annealed to this denatured DNA template and extended by Klenow fragment using the Bioprime DNA Labeling System (Invitrogen) while fluorescent dyes Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated. (http://www.flychip.org.uk/protocols/gene_expression/)

extract_protocol: Small scale RNA extraction using TRIzol (http://www.flychip.org.uk/protocols/gene_expression/)

treatment_protocol: salivary glands were heat-shocked for 45 minutes at 37C, then kept for 10-12 hours at RT before total RNA was isolated

value: w1118; hs-TEV/+; genomic Rad21/Rad21ex3

tag: developmental stage

value: Drosophila melanogaster crawling third instar salivary glands

tag: tissue

value: salivary gland

source_name: Total RNA from hs-TEV_TEV-cleavableRad21 (Rad21TEV) salivary glands (genotype: w1118; hs-TEV/+; Rad21ex15 Rad21(TEV)/Rad21ex3)


title: DrosSalivaryGland_-+cohesin_1.3

description: see above

value: w1118; hs-TEV/+; Rad21ex15 Rad21(TEV)/Rad21ex3


title: DrosSalivaryGland_+-cohesin_2.2

description: see above

source_name: Total RNA from hs-TEV_transgenicRad21 salivary glands (genotype: w1118; hs-TEV/+; Rad21ex3 tgRad21/Rad21ex3)


title: DrosSalivaryGland_+-cohesin_1.1

description: see above


title: DrosSalivaryGland_+-cohesin_2.1

description: see above

value: w1118; hs-TEV/+; Rad21ex3 tgRad21/Rad21ex3


title: 300 ng Cy5 labeled target RNA_b


title: Profiling neuroblastoma SH-SY5Y with Paraquat sample 8

value: neuroblastoma SH-SY5Y


title: 4500 ng target RNA_b

description: Hybridization of 4500 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours


title: 4500 ng target RNA_c


title: 4500 ng target RNA_a


title: DrosSalivaryGland_-+cohesin_2.3

description: see above


title: 300 ng Cy5 labeled target RNA_a


title: 65 hour hybridization_b


title: Profiling wt SOD1 sample 11


title: DrosSalivaryGland_-+cohesin_2.4

description: see above


title: 1800 ng target RNA_c

description: Hybridization of 1800 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours


title: Profiling neuroblastoma SH-SY5Y ctrl 7


title: 1800 ng target RNA_b


title: Profiling ALS SOD1(G93A) mutant sample 9


title: Profiling wt SOD1 sample 14


title: Profiling ALS SOD1(G93A) mutant sample 12


title: Profiling wt SOD1 sample 8


title: Profiling ALS SOD1(G93A) mutant sample 3


title: 1800 ng target RNA_a


title: 600 ng target RNA_c

description: Hybridization of 600 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours


title: tI-3_Zn_rep2

city: Watertown

first: James

last: Sherley

address: 64 Grove St.

department: Programs in Regenerative Biology and Cancer Biology

institute: Boston Biomedical Research Institute

description: Line tI-3  is a congenic derivative of Ind-8 cells that expresses an IMPDH II transgene constitutively.

hyb_protocol: cRNA was fragmented and hybridized onto the Affymetrix mouse whole genome GeneChip® 430 2.0 array. The arrays were washed and quantified with a fluorescence array scanner.

scan_protocol: Quantification and statistics were performed using model-based expression and the perfect match (PM) minus mismatch (MM) method in the G-COS® software (version 1.0) and/or the dChip software version 2005. Data across 8 arrays were originally normalized by setting target intensity at 500 in the G-COS.

data_processing: Additional analysis of the data was performed in R/Bioconductor, using .CEL files and the affy() package. Background correction, normalization, and summarization was carried out using RMA. A custom chip description file (Mouse4302_Mm_REFSEQ) which organizes the probes based on RefSeq was used. The ID_REF values in the attached matrix are the probeset names from the custom CDF, and except for control probesets consist of a refseq ID with an _at suffix.

organism: Mus musculus

source_name: tI-3 cells grown in ZnCl2 supplemented medium

label_protocol: Five micrograms of total RNA was used to make cDNA, and the cDNA was used to make biotinylated cRNA.

growth_protocol: Cells were grown for 3 days in Zn-free medium to about 50% confluency, trypsinized, and plated in Zn-free medium (DMEM, 10% dialyzed fetal bovine serum, 5 ug/ml puromycin, with the addition of 1 ug/ml G418 for tI-3 cells) at a cell number:plating area:medium volume ratio of 100,000 cells:75 cm2:20 ml.

extract_protocol: Total RNA was extracted using Trizol, followed by Qiagen Rneasy.  Only cultures meeting strict quality control standards (population division cycles = 1.8-2.2) for ideal symmetric self-renewal versus asymmetric self-renewal, respectively, were used.

treatment_protocol: 16 - 24 hrs later, the culture medium was replaced with media containing 65 uM ZnCl2. Cells were harvested by trypsinization 48 hours later (i.e., two cell cycles).


title: 600 ng target RNA_b


title: tI-3_Zn_rep1


title: 600 ng target RNA_a


title: Con-3_Zn_rep3

description: Con-3 is a p53-null cell line that is the congenic parent of line Ind-8.

source_name: Con-3 cells grown in ZnCl2 supplemented medium


title: 300 ng target RNA_c

description: Hybridization of 300 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours


title: 300 ng target RNA_b


title: Con-3_Zn_rep2


title: Ind-8_Zn_rep2

description: Ind-8 is a p53-inducible cell line that expresses physiological levels of wild-type mouse p53 in response to Zn.

source_name: Ind-8 cells grown in ZnCl2 supplemented medium


title: Ind-8_Zn_rep3


title: GIS2_delta vs. wt (2)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86209.gif

hyb_protocol: not provided

scan_protocol: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: BY4741 total RNA (WT)

label_protocol: not provided

extract_protocol: not provided

tag: cell line/genotype

source_name: delta Gis2 total RNA

value: delta Gis2


title: GIS2_delta vs. wt (3)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86210.gif


title: GIS2_delta vs. wt (1)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86208.gif


title: Con-3_Zn_rep1


title: BM_CMP_BM_NBM1481

value: adult

value: normal

value: bone marrow


title: Gis2 IP (3) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72831.gif

source_name: Extract tot. RNA Gis2-TAP (3)

tag: test

value: Extract total RNA Gis2-TAP (3)

source_name: Affinity isolated RNA, Gis2-TAP (3)

tag: control

value: Affinity isolated RNA, Gis2-TAP (3)


title: 150 ng target RNA_c

description: Hybridization of 150 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours

value: 18 hours


title: 300 ng target RNA_a

value: 16S rRNA gene


title: 150 ng target RNA_b


title: Gis2 IP (2) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72830.gif

source_name: Extract tot. RNA Gis2-TAP (2)

value: Extract total RNA Gis2-TAP (2)

source_name: Affinity isolated RNA, Gis2-TAP (2)

value: Affinity isolated RNA, Gis2-TAP (2)


title: Gis2 Overexpression (3a)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/82096.gif

source_name: BY4741 pBG1805 empty vector

tag: cell line

tag: transfection

value: pBG1805 empty vector


title: 150 ng target RNA_a

source_name: D. halophilus 16S rRNA gene, clone


title: Gis2 IP (1) A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72320.gif

source_name: Extract tot. RNA Gis2-TAP (1)

value: Extract total RNA Gis2-TAP (1)

source_name: Affinity isolated RNA, Gis2-TAP (1)

value: Affinity isolated RNA, Gis2-TAP (1)


title: Susceptible vs Resistant Angus 3

city: Beltsville

first: George

last: Liu

state: MD

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

description: Hybridization of susceptible Angus sample against resistant Angus sample

hyb_protocol: Performed by NimbleGen standard protocol

data_processing: Normalized by standard NimbleGen methods

organism: Bos taurus

source_name: Whole blood from susceptible Angus 3

label_protocol: Labeled by NimbleGen

extract_protocol: Gentra Puregene Blood Kit

tag: genetic background

value: Angus

tag: gender

value: Male

value: Whole blood

tag: phenotype

value: parasite susceptible

source_name: Whole blood from resistant Angus 3

value: parasite resistant


title: Gis2 Overexpression (3b)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82576.gif


title: Jurkat vs Jurkat P12

description: Quantification of RNA and quality control was done using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA) and a Nan drop photometer (Kisker, Steinfurt, Germany).

hyb_protocol: Dual color hybridizations with 0.25-1 µg RNA per Cy-dye were performed for 16 h at 60°C with hybridization buffer (Exiqon) and LifterSlips (Erie Scientific).

scan_protocol: After hybridization and washing, arrays were scanned with a DNA Microarray Scanner BA (Agilent Technologies) at 5 µm resolution.

data_processing: Raw microarray images were analyzed with the Image Analysis/Feature Extraction software G2567AA (Version A.7.5, Agilent Technologies) using almost default settings for miRNA microarrays loaded with a grid file or standard setting. Non-uniformity outlier flagging was done with a 5x default value of the constant coefficient of variation for features ((CV)2 Term(A) = 0.55) and background ((CV)2 Term(A) = 0.45). Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

source_name: Jurkat

label_protocol: RNA samples were labeled with the miRCURY LNA microRNA Power Labeling Kit (Exiqon A/S) according the supplier’s instructions.

extract_protocol: Total RNA was harvested by using TRIzol Reagent (Invitrogen). For small RNAs (< 200 nt) isolation, cells were resuspended in TRIzol (Invitrogen). After addition of chloroform and centrifugation, the upper aqueous phase was column purified according to Qiagen´s instructions (RNeasy MinElute Cleanup kit). Quality control of the RNA preparations and quantification of total RNA amount was done using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

tag: environmental factor

value: uninfected (control)

value: Jurkat

source_name: Jurkat P12

value: infected with Helicobacter pylori for 3 hours at an MOI of 100


title: J774a Hp76 vs J774a

value: infected with the mouse-adapted strain Helicobacter pylori 76 for 3 hours at an MOI of 100

label_protocol: RNA samples were labeled with the miRCURY LNA microRNA Power Labeling Kit (Exiqon A/S) according the supplier’s instructions


title: Susceptible vs Resistant Angus 2

scan_protocol: Performed by NimbleGen standard protocol

source_name: Whole blood from susceptible Angus 2

value: whole blood

source_name: Whole blood from resistant Angus 2


title: WT Hippocampus - 3

city: Illkirch

first: André

last: Hanauer

address: 1, rue laurent Fries

department: Neurobiology and Genetics

country: France

institute: IGBMC

description: gene expression data from pools of 2 hippocampi of WT littermate males

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner 3000 (Affymetrix Inc. Santa Clara, CA 95051, USA).

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

source_name: Hippocampus of 2 months old WT males

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

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

treatment_protocol:
Male Rsk2-KO and WT mice with a C57Bl/6J genetic background were killed by cervical dislocation.
Brains were rapidly dissected and the hippocampus isolated using a standard dissection procedure. Tissue samples were immediately frozen in liquid nitogen and kept at - 80 °C until use.

tag: strain

tag: genotype/variation

value: wild type


title: WT Hippocampus - 1


title: WT Hippocampus - 2


title: J774a vs J774a Hp76


title: 75 ng target RNA_b

description: Hybridization of 75 ng labeled RNA (by in vitro transcription) from a clone carrying the D. halophilus 16S rRNA gene. Microarray was hybridized for 18 hours

tag: amount of labeled rna used for hybridization

value: 75 ng

tag: hybridization time

value: 18 hours

tag: assayed gene

value: 16S rRNA gene


title: Jurkat P12 vs Jurkat


title: 75 ng target RNA_a


title: Profiling wt SOD1 sample 2

description: The CEL files resulting from the hybridization were analyzed using oneChannelGUI 1.6.5 . To assess differential expression at gene-level, we used an empirical Bayes method  together with a false discovery rate (FDR) correction of the p-value.  Thus, the list of differentially expressed genes was generated using an FDR ≤ 0.05 together with an absolute log2(fold-change) threshold of 1.

source_name: wild type SOD1

value: neuroblastoma SH-SY5Y


title: 75 ng target RNA_c


title: Ind-8_Zn_rep1

source_name: Ind-8 cells grown in ZnCl2 supplemented medium


title: MKN vs. MKN P12

source_name: MKN

value: MKN

source_name: MKN P12


title: Gis2 Overexpression (2b)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82575.gif

value: pBG1805 empty vector


title: Susceptible vs Resistant Angus 1

source_name: Whole blood from susceptible Angus 1

value: Angus

value: Female

source_name: Whole blood from resistant Angus 1


title: Rsk2-KO Hippocampus - 3

description: gene expression data from pools of 2 hippocampi of Rsk2-KO males

source_name: Hippocampus of 2 months old Rsk2-KO males


title: Gis2 Overexpression (2a)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/82095.gif

source_name: BY4741 pBG1805 empty vector


title: AGS vs AGS P12

source_name: AGS

value: AGS

source_name: AGS P12


title: Profiling neuroblastoma SH-SY5Y ctrl 11

description: Transcription profiling of neuroblastoma SH-SY5Y treated with Paraquat (PQ) were compared with untreated cells

source_name: ctrl


title: NO_KIDNEY_8 [GSM278788]

status: Public on Dec 21 2010

city: Grand Rapids

first: Jeff

last: Klomp

state: MI

address: 333 Bostwick Ave, NE

institute: Van Andel Research Institute

description: Gene expression ratios were obtained from human BHD renal tumors and normal kidney tissues.

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

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

data_processing:
The data were analyzed with custom CDF environments created by the MBNI - The version 12 entrez gene ID CDF was used. Normalization algorithm: RMA.
Gene expression ratios were obtained as the ratio from human BHD renal tumor/normal kidney tissues. The (BHD/normal) ratio data was derived by first log2-transforming all data, then subtracting the average (median) of the 12 normal samples from each of the gene expression values for the BHD sample.  This was carried out for each of the 6 BHD samples in the analysis to produce a ratio of expression for a given sample (BHD) to median expression across all normals. The (BHD/normal) ratio data can be found at the foot of GSE21816.

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA, R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  (we use 6 ul per reaction)

tag: disease state

value: control (normal kidney)


title: NO_KIDNEY_7 [GSM278787]


title: Rsk2-KO Hippocampus - 2


title: NO_KIDNEY_3 [GSM278783]


title: NO_KIDNEY_9 [GSM278789]


title: NO_KIDNEY_11 [GSM278791]


title: NO_KIDNEY_10 [GSM278790]


title: Rsk2-KO Hippocampus - 1


title: NO_KIDNEY_1 [GSM278781]


title: NO_KIDNEY_2 [GSM278782]


title: AGS P12 vs AGS


title: BHD_004

value: BHD renal tumor

tag: subtype

value: Hybrid


title: MKN P12 vs. MKN

value: uninfected (control)


title: BHD_006


title: BHD_001

value: Chromophobe


title: NO_KIDNEY_12 [GSM162194]


title: NO_KIDNEY_4 [GSM278784]


title: NO_KIDNEY_5 [GSM278785]


title: BHD_003

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 12 entrez gene ID CDF was used. Normalization algorithm: RMA.


title: NO_KIDNEY_6 [GSM278786]


title: BHD_005


title: BHD_002


title: CAL1_Ig_chip2

city: New York

first: Boris

last: Reizis

state: NY

department: Microbiology and Immunology

institute: Columbia University Medical Center

hyb_protocol: Labeled IP and WCE DNA were hybridized symultaneously following the manufacturer’s instructions (Agilent Mammalian ChIP-on-chip protocol, version 10.0, December 2007)

scan_protocol: Fluorescent images were obtained at the HICCC Genomics Facility (Columbia University Medical Center) using an Agilent Microarray scanner and quantified through the Feature Extraction software (Agilent Technology)

data_processing: Data analysis was performed using DNA Analytics v4.0.81 software (Agilent Technology)

source_name: control Ig-bound genomic DNA

label_protocol: After crosslink reversal, the isolated chromatin was amplified and labeled using Agilent Genomic DNA Labeling Kit

extract_protocol: CAL-1 cells grown in culture (Maeda et al., Int J Hematol 2005) were crosslinked with formaldehyde, sonicated, and subjected to immunoprecipitation with anti-E2-2 mAb or mouse IgG control as described (Cisse et al., Cell 2008).

tag: cell type

value: plasmacytoid dendritic cell neoplasm

tag: isolation

value: chromatin immunoprecipitation (ChIP)

tag: antibody

value: control mouse IgG (Sigma)

source_name: input genomic DNA

label_protocol: The isolated chromatin was amplified and labeled using Agilent Genomic DNA Labeling Kit

extract_protocol: CAL-1 cells grown in culture (Maeda et al., Int J Hematol 2005) were crosslinked with formaldehyde, sonicated, and total genomic DNA was isolated as described (Cisse et al., Cell 2008).

value: whole cell extract (WCE)


title: PE_no_treatment_PEt12_tech-rep2_Cy5

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: uPE-series_Array-CSK3_061:Cy3-PEPEt0|Cy5-PEPEt12

hyb_protocol: Slides were pre-hybridized (5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 1% (w/v) bovine serum albumin, fraction V (Sigma)) for 45 minutes at 42°C to block the remaining reactive epoxide groups and reduce background signal. Cy3 and Cy5 labelled RNA samples were combined as described in the experimental design and mixed with 2x hybridization mixture to a final concentration of 5x SSC, 25% (v/v) formamide, 0.1% (w/v) SDS, 0.2 \mug/\muL herring sperm DNA (Invitrogen). Target-RNA mix was denatured for 5 minutes at 70°C and incubated at 42°C for 30 minutes. Hybridization was done in a GeneTAC hybridization station (Genomic Solutions) for 16 hours at 42°C with agitation. The arrays were washed at room temperature in 5 successive buffers, i.e., 1x SSC + 0.2% SDS, 0.1x SSC + 0.2% SDS, 1x SSC, 0.1x SSC and 0.001x SSC, each step lasting 4 minutes. The slides were finally pressure-air dried and stored in the dark.

scan_protocol: Slides were scanned using an Agilent G2565BA microarray scanner on a 10 micro m resolution. The resulting images were split into the red and green channels prior to feature extraction with the GenePix Pro 6.1.0.2 (Axon Instruments Inc.) software.

data_processing: Median spot intensities were imported from the genepix results files using the Limma package. Flagged spots were assigned a weight of 0.1, control spots were removed and the remaining data were normalized with lowess (parameters: span = 0.25, iterations = 2) and aquantile transformations using the R/Limma package in Bioconductor

organism: Gallus gallus

source_name: PE, no_treatment, PEt12

label_protocol: 1500 ng amplified RNA ( Ambion MessageAmp-II ) wasd labelled with either Cy3 or Cy5 as decribed by 't Hoen PA ( Nucleic Acids Res. 2003 Mar 1;31(5):e20 )

growth_protocol: Embryonic Proepicardia and Epicardium were isolated and grown as described by van den Hoff MJ et al ( Dev Biol. 2001 Dec 1;240(1):61-76 ) and Boudewijn P T et al ( Dev Biol. 2006 Jul 15;295(2):507-22 )

extract_protocol: Total RNA was isolated using Macherey-Nagel nucleospin columns and DnaseI treated. Quantified with the Nanodrop ND1000 and QC with an Agilent nanoChip.

treatment_protocol: PE explant cultures were treated with either U0126+Bmp2, Fgf2 or Fgf2+Vegf as described by Boudewijn P T et al ( Dev Biol. 2006 Jul 15;295(2):507-22 )


title: PE_no_treatment_PEt36_tech-rep4_Cy5

description: uPE-series_Array-CSK3_066:Cy3-PEPEt48|Cy5-PEPEt36

source_name: PE, no_treatment, PEt36


title: PE_no_treatment_PEt48_tech-rep7_Cy3

source_name: PE, no_treatment, PEt48


title: PE_no_treatment_PEt36_tech-rep2_Cy3

description: uPE-series_Array-CSK3_064:Cy3-PEPEt36|Cy5-PEPEt24


title: PE_no_treatment_PEt24_tech-rep3_Cy3

description: uPE-series_Array-CSK3_063:Cy3-PEPEt24|Cy5-PEPEt12

source_name: PE, no_treatment, PEt24


title: PE_no_treatment_PEt60_tech-rep4_Cy3

description: uPE-series_Array-CSK3_067:Cy3-PEPEt60|Cy5-PEPEt48

source_name: PE, no_treatment, PEt60


title: PE_no_treatment_PEt0_tech-rep4_Cy3

description: uPE-series_Array-CSK3_068:Cy3-PEPEt0|Cy5-PEPEt120

source_name: PE, no_treatment, PEt0


title: PE_no_treatment_PEt12_tech-rep3_Cy3

description: uPE-series_Array-CSK3_062:Cy3-PEPEt12|Cy5-PEPEt0


title: PE_no_treatment_PEt120_tech-rep4_Cy5

source_name: PE, no_treatment, PEt120


title: PE_no_treatment_PEt12_tech-rep4_Cy5


title: PE_no_treatment_PEt0_tech-rep3_Cy5


title: PE_no_treatment_PEt24_tech-rep4_Cy5


title: PE_no_treatment_PEt48_tech-rep8_Cy5


title: PE_no_treatment_PEt72_tech-rep4_Cy3

description: uPE-series_Array-CSK3_056:Cy3-PEPEt72|Cy5-PEPEt60

source_name: PE, no_treatment, PEt72


title: PE_no_treatment_PEt72_tech-rep2_Cy5

description: uPE-series_Array-CSK3_053:Cy3-PEPEt120|Cy5-PEPEt72


title: PE_no_treatment_PEt120_tech-rep3_Cy3


title: PE_no_treatment_PEt36_tech-rep3_Cy3

description: uPE-series_Array-CSK3_065:Cy3-PEPEt36|Cy5-PEPEt48


title: CAL1_E2-2_chip2

source_name: E2-2-bound genomic DNA

tag: chip antibody

value: monoclonal anti-human E2-2 (Bain et al., Mol Cell Biol 1993)


title: PE_no_treatment_PEt60_tech-rep2_Cy3

description: uPE-series_Array-CSK3_054:Cy3-PEPEt60|Cy5-PEPEt72


title: PE_no_treatment_PEt120_tech-rep2_Cy5

description: uPE-series_Array-CSK3_052:Cy3-PEPEt72|Cy5-PEPEt120


title: PE_no_treatment_PEt72_tech-rep3_Cy5


title: PE_no_treatment_PEt0_tech-rep2_Cy3


title: PE_no_treatment_PEt60_tech-rep3_Cy5


title: PE_no_treatment_PEt72_tech-rep1_Cy3


title: PE_no_treatment_PEt48_tech-rep6_Cy5


title: PE_no_treatment_PEt60_tech-rep1_Cy5

description: uPE-series_Array-CSK3_048:Cy3-PEPEt48|Cy5-PEPEt60


title: PE_no_treatment_PEt48_tech-rep1_Cy3


title: PE_no_treatment_PEt120_tech-rep1_Cy3

description: uPE-series_Array-CSK3_051:Cy3-PEPEt120|Cy5-PEPEt0


title: PE_no_treatment_PEt0_tech-rep1_Cy5


title: PE_no_treatment_PEt48_tech-rep5_Cy5

description: Epi-2-PE-series_Array-CSK3_060:Cy3-PEHH29|Cy5-PEPEt48


title: PE_no_treatment_PEt24_tech-rep1_Cy5

description: uPE-series_Array-CSK3_042:Cy3-PEPEt12|Cy5-PEPEt24


title: PE_no_treatment_PEt12_tech-rep1_Cy3


title: PE_no_treatment_PEt48_tech-rep3_Cy5

description: Epi-2-PE-series_Array-CSK3_058:Cy3-PEHH25|Cy5-PEPEt48


title: Epi_no_treatment_PEt48_HH25_tech-rep8_Cy3

description: Epi-2-PE-series_Array-CSK3_058:Cy3-EpiHH25|Cy5-EpiPEt48

source_name: Epi, no_treatment, PEt48_HH25


title: Epi_no_treatment_HH32_tech-rep6_Cy5

description: Epi-series_Array-CSK3_038:Cy3-EpiHH25|Cy5-EpiHH32

source_name: Epi, no_treatment, HH32


title: PE_no_treatment_PEt24_tech-rep2_Cy3

description: uPE-series_Array-CSK3_044:Cy3-PEPEt24|Cy5-PEPEt36


title: Epi_no_treatment_PEt48_HH29_tech-rep7_Cy5

description: Epi-2-PE-series_Array-CSK3_059:Cy3-EpiPEt48|Cy5-EpiHH29

source_name: Epi, no_treatment, PEt48_HH29


title: PE_no_treatment_PEt48_tech-rep4_Cy3

description: Epi-2-PE-series_Array-CSK3_059:Cy3-PEPEt48|Cy5-PEHH29


title: Epi_no_treatment_PEt48_HH29_tech-rep8_Cy3

description: Epi-2-PE-series_Array-CSK3_060:Cy3-EpiHH29|Cy5-EpiPEt48


title: Epi_no_treatment_HH25_tech-rep6_Cy3

source_name: Epi, no_treatment, HH25


title: PE_no_treatment_PEt36_tech-rep1_Cy5


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137053R

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

description: Gene expression analysis.

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a  solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul.  Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the  microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed  once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were  shrinked? in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing:
Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. R scripts (PMID 16755501) were used to normalize the data. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the test condition time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((Cy3+Cy5)/2)].

Filtering low intensity spots, LOWESS normalization.

organism: Xylella fastidiosa

source_name: J1a12 in XDM0 for 12h

label_protocol: 20ug of total RNA was reverse transcribed and labeled using the CyScribe Post-labelling kit (GE Healthcare). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH  4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in a speed vac.

growth_protocol: The citrus strain J1a12 of Xylella fastidiosa (Monteiro et al., 2001) was cultivated in PW medium (Davis et al., 1981) without bovine serum albumin and phenol red and supplemented with 0.5% glucose (w/v) (PWG) at 25°C with no agitation.

extract_protocol: Total RNA was isolated from X. fastidiosa wild type and rpoN mutant cells, grown under nitrogen excess or nitrogen starvation conditions as described above, using the TRIZOL reagent (Invitrogen), according to the manufacturer's instructions. DNA was removed using RQ1 DNase I (Promega). RNA samples were evaluated by electrophoresis on formaldehyde-agarose gels and stored at -80°C.

treatment_protocol: Wild type strain cells were grown during 12 days in the XDM2 medium (mid-log phase) and harvested by centrifugation. Cells were washed with XDM2 medium and cultivated in a medium lacking all nitrogen sources (XDM0). The cultivation was continued for 12 h.

tag: treatment

tag: time

source_name: J1a12 in XDM2

treatment_protocol: Wild type strain cells were grown during 12 days in the XDM2 medium (mid-log phase) and harvested by centrifugation. Cells were washed with XDM2 medium.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137052L

description: Gene expression analysis.

source_name: J1a12 in XDM0 for 8h

treatment_protocol: Wild type strain cells were grown during 12 days in the XDM2 medium (mid-log phase) and harvested by centrifugation. Cells were washed with XDM2 medium and cultivated in a medium lacking all nitrogen sources (XDM0). The cultivation was continued for 8 h.

extract_protocol: Total RNA was isolated from X. fastidiosa wild type and rpoN mutant cells, grown under nitrogen excess or nitrogen starvation conditions as described above, using the TRIZOL reagent (Invitrogen), according to the manufacturer's instructions. DNA was removed using RQ1 DNase I (Promega). RNA samples were evaluated by electrophoresis on  formaldehyde-agarose gels and stored at -80°C.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137049R

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137048L

description: Gene expression analysis.

source_name: J1a12 in XDM0 for 2h

treatment_protocol: Wild type strain cells were grown during 12 days in the XDM2 medium (mid-log phase) and harvested by centrifugation. Cells were washed with XDM2 medium and cultivated in a medium lacking all nitrogen sources (XDM0). The cultivation was continued for 2 h.


title: Epi_no_treatment_HH37_tech-rep6_Cy3

description: Epi-series_Array-CSK3_036:Cy3-EpiHH37|Cy5-EpiHH25

source_name: Epi, no_treatment, HH37


title: Epi_no_treatment_HH37_tech-rep5_Cy5

description: Epi-series_Array-CSK3_035:Cy3-EpiHH29|Cy5-EpiHH37


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137050R

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137048R

description: Gene expression analysis.


title: Epi_no_treatment_HH25_tech-rep7_Cy5

description: Epi-2-PE-series_Array-CSK3_057:Cy3-EpiPEt48|Cy5-EpiHH25


title: Epi_no_treatment_HH29_tech-rep6_Cy3

source_name: Epi, no_treatment, HH29


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137047R

description: Gene expression analysis.


title: PE_no_treatment_PEt48_tech-rep2_Cy3

description: Epi-2-PE-series_Array-CSK3_057:Cy3-PEPEt48|Cy5-PEHH25

source_name: PE, no_treatment, PEt48


title: Epi_no_treatment_HH25_tech-rep5_Cy5


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137052R

description: Gene expression analysis.


title: Epi_no_treatment_HH37_tech-rep2_Cy5

description: Epi-series_Array-CSK3_032:Cy3-EpiHH32|Cy5-EpiHH37


title: Epi_no_treatment_HH37_tech-rep4_Cy5

description: Epi-series_Array-CSK3_034:Cy3-EpiHH25|Cy5-EpiHH37


title: Epi_no_treatment_HH37_tech-rep3_Cy3

description: Epi-series_Array-CSK3_033:Cy3-EpiHH37|Cy5-EpiHH32


title: Epi_no_treatment_HH32_tech-rep4_Cy3


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137053L

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137047L

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137049L

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 12h - 3000137050L

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137045R

description: Gene expression analysis.


title: Epi_no_treatment_HH25_tech-rep4_Cy3


title: Epi_no_treatment_HH32_tech-rep3_Cy5

description: Epi-series_Array-CSK3_031:Cy3-EpiHH29|Cy5-EpiHH32


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137046L

description: Gene expression analysis.


title: J1a12 vs rpoN mutant - 3000137043L

description: Gene expression analysis.

source_name: rpoN mutant

growth_protocol: The rpoN mutant strain (da Silva Neto et al., 2008), was cultivated in PW medium (Davis et al., 1981) without bovine serum albumin and phenol red and supplemented with 0.5% glucose (w/v) (PWG) and 10 µg ampicillin ml-1 at 25°C with no agitation.

value: rpoN mutant


title: Epi_no_treatment_HH29_tech-rep4_Cy5

description: Epi-series_Array-CSK3_030:Cy3-EpiHH25|Cy5-EpiHH29


title: Epi_no_treatment_HH25_tech-rep3_Cy3


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137045L

description: Gene expression analysis.


title: J1a12 vs rpoN mutant - 3000137043R

description: Gene expression analysis.


title: Epi_no_treatment_HH32_tech-rep5_Cy5


title: J1a12 vs rpoN mutant - 3000137042R

description: Gene expression analysis.


title: J1a12 vs rpoN mutant - 3000137042L

description: Gene expression analysis.


title: Epi_no_treatment_HH25_tech-rep2_Cy5

description: Epi-series_Array-CSK3_028:Cy3-EpiHH32|Cy5-EpiHH25


title: Epi_no_treatment_HH29_tech-rep3_Cy5

description: Epi-series_Array-CSK3_029:Cy3-EpiHH37|Cy5-EpiHH29


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137044R

description: Gene expression analysis.

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked? in water for 10s and dried with nitrogen gas.

label_protocol: 20ug of total RNA was reverse transcribed and labeled using the CyScribe Post-labelling kit (GE Healthcare). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in a speed vac.

extract_protocol: Total RNA was isolated from X. fastidiosa wild type and rpoN mutant cells, grown under nitrogen excess or nitrogen starvation conditions as described above, using the TRIZOL reagent (Invitrogen), according to the manufacturer's instructions. DNA was removed using RQ1 DNase I (Promega). RNA samples were evaluated by electrophoresis onformaldehyde-agarose gels and stored at -80°C.


title: Epi_no_treatment_HH32_tech-rep2_Cy3


title: Epi_no_treatment_HH37_tech-rep1_Cy3


title: J1a12 vs rpoN mutant - 3000137041R

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 2h - 3000137044L

description: Gene expression analysis.


title: Epi_no_treatment_HH29_tech-rep5_Cy3


title: Epi_no_treatment_HH29_tech-rep2_Cy5

description: Epi-series_Array-CSK3_025:Cy3-EpiHH32|Cy5-EpiHH29


title: Epi_no_treatment_HH32_tech-rep1_Cy3


title: Epi_no_treatment_HH25_tech-rep1_Cy5

description: Epi-series_Array-CSK3_024:Cy3-EpiHH29|Cy5-EpiHH25


title: J1a12 vs rpoN mutant - 3000137041L

description: Gene expression analysis.


title: J1a12 in XDM2 vs J1a12 in XDM0 for 8h - 3000137046R

description: Gene expression analysis.


title: Epi_no_treatment_HH29_tech-rep1_Cy3


title: brain 13week vs. brain 14week, replicate 2

city: Beijing

first: Shunmin

last: He

address: 15 Datun Road, Chaoyang District

department: National Laboratory of Biomacromolecules

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: brain 13week vs. brain 14week rep2

hyb_protocol: The microarray slides were prehybridized at 42℃ for 1 h and hybridized at 42℃ for 16 h.

scan_protocol: Scanned using the GenePix 4000B (Axon) scanner.

data_processing: Data were normalized using standard global media normalization implemented by marray and limma packages in R.

source_name: fetal brain-13week

label_protocol: Total RNA was dephosphorylated and ligated to the same 3’ adapter oligonucleotide. One µg ligated RNA of each sample was used to create cRNA:the ligated ncRNAs were reverse transcribed using an oligonucleotide complementary to the 3’ adapter  and extended with a 5’ end T7 promoter sequence extension. The cRNA was purified and labeled with Cy3 (or Cy5) using the CyDye mono-reactive NHS Esters kit (Amersham Biosciences), and then was purified using the Qiagen Rneasy mini kit .

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: Samples were collected and frozen in liquid nitrogen.

tag: tissue

value: fetal brain

tag: developmental stage

value: 13-week gestation stage

source_name: fetal brain-14week

value: 14-week gestation stage


title: U251 vs. brain mix, replicate 2

description: U251 vs. brain rep2

tag: cell line

value: glioblastoma

source_name: brain mix

value: mix from 4 different gestational stages (13w, 14w, 20w, 24w)


title: SHSY-5Y vs. brain mix, replicate 2

description: SHSY-5Y vs. brain rep2

value: neuroblastoma


title: brain 14week vs. brain 24week, replicate 1

description: brain 14week vs. brain 24week rep1

source_name: fetal brain-24week

value: 24-week gestation stage


title: brain 14week vs. brain 24week, replicate 2

description: brain 14week vs. brain 24week rep2


title: SHSY-5Y vs. brain mix, replicate 1

description: SHSY-5Y vs. brain rep1


title: U251 vs. brain mix, replicate 1

description: U251 vs. brain rep1


title: AtT-20-DS9837-DEX-4-hrs

city: SEATTLE

first: John

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: The AtT‐20 cell line is an anterior pituitary corticotroph of murine origin. Dexamethasone treated, 4 hours.

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol.

scan_protocol: Affymterix Gene Chip Scanner 3000

data_processing:
Probe-level CEL files were processed through Affymetrix Expression Console using RMA summarization and median normalization methods.
MoEx-1_0-st-v1.r2.pgf

source_name: mouse pituitary corticotroph, dexamethasone 4 hours

label_protocol: RNA from untreated and dex treated cells were labeled with biotin-CTP using manufacturer's recommendations (Affymetrix, Santa Clara, Ca)

growth_protocol: Cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gemini, Woodland, California), 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 5 mg/ml penicillin-streptomycin (Invitrogen, Carlsbad, CA) and kept at 37ºC incubator with 5% CO2. Cells were transferred to 10% charcoal-dextran-treated, heat-inactivated fetal bovine serum for 48 hrs prior to hormone treatment.

extract_protocol: RNA was extracted from cells either vehicle treated or treated with 100 nM hormone (dexamethasone, Dex) for 0h, 2h, 4h or 8h. 3134 and AtT-20 RNA for microarray analysis was prepared via standard manufacturer protocols (Qiagen, Valencia, Ca) using cells resuspended in Trizol reagent (Invitrogen, Carlsbad, Ca)

treatment_protocol: Dex treated: treatment_hour with 100 nM dexamethasone. Control, untreated 0 hour.

tag: term

value: mouse pituitary corticotroph

tag: gender

value: male

value: Dex 4 hours hour


title: 3134-DS8970-DEX-4-hrs

description: The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. Dexamethasone treated, 4 hours.

source_name: mouse mammary adenocacinoma tumor, dexamethasone 4 hours

tag: strain

value: RIII

value: mouse mammary adenocacinoma tumor


title: brain 20week vs. brain 13week, replicate 2

description: brain 20week vs. brain 13week rep2

source_name: fetal brain-20week

value: 20-week gestation stage


title: AtT-20-DS9833-DEX-0-ctrl

description: The AtT‐20 cell line is an anterior pituitary corticotroph of murine origin. Dexamethasone untreated, 0 hour control.

source_name: mouse pituitary corticotroph, dexamethasone 0 hour control

value: control 0 hour hour


title: brain 13week vs. brain 14week, replicate 1

description: brain 13week vs. brain 14week rep1


title: 3134-DS8797-DEX-0-ctrl

description: The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. Dexamethasone untreated, 0 hour control.

source_name: mouse mammary adenocacinoma tumor, dexamethasone 0 hour control


title: 3134-DS8966-DEX-0-ctrl


title: pDCs-NYVAC-C-dB19R-rep5

city: port st-lucie

first: Ali

last: Filali

state: Florida

address: 11350 SW Village Parkway, 3rd Floor

institute: Vaccine & Gene Therapy Institute of Florida

description: pDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes lacking  the gene, B19R, coding for a soluble protein preventing binding of type-I IFN

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Human RefSeq-8 BeadChips V2 and V3  at 58oC for 20 hrs

scan_protocol: Fluoresent array images were collected using Illumina BeadStation 500GX scanner and image intensity data were extracted using  Illumina BeadStudio v3.

data_processing: Illumina probe data were exported from BeadStudio as raw data and were screened for quality. Samples failing chip visual inspection and control examination were removed. Probeset from the two Illumina platforms were mapped to a common probeset Id using a mapping file provided by Illumina.  One dataset containing probeset common to both platforms was then used for pre-processing and subsequent  analysis steps. The R software was used to quantile-normalized the probe intensities, and to minimun replace (surrogate-replacement policy) values below backround using the mean backround value of the built-in Illumina probe controls as an alternative to background substraction (which may introduce negative values) to reduce ‘over inflated’ expression ratios in subsequent steps.

source_name: Plasmacytoid Dendritic Cells (pDCs)

label_protocol: Total RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol.

growth_protocol: cDCs and pDCs were obtained by MACS cell sorting from freshly isolated peripheral blood mononuclear cells (PBMC). Cells were used directly after isolation.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad).

treatment_protocol: cDCs and pDCs were infected for 1 hour and after washing left in medium for 6 hours before RNA extraction.

value: Plasmacytoid Dendritic Cells (pDCs)

tag: viral infection


title: pDCs-NYVAC-C-dB19R-rep3


title: pDCs-NYVAC-C-dB19R-rep4


title: AtT-20-DS9836-DEX-2-hrs

description: The AtT‐20 cell line is an anterior pituitary corticotroph of murine origin. Dexamethasone treated, 2 hours.

source_name: mouse pituitary corticotroph, dexamethasone 2 hours

value: Dex 2 hours hour


title: pDCs-NYVAC-C-KC-dB19R-rep6

description: pDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes ,lacking  the gene, B19R, coding for a soluble protein preventing binding of type-I IFN , whose  replication capacity  was restored by inserting two viral host range genes, K1L and C7L


title: pDCs-NYVAC-C-KC-dB19R-rep4


title: 3134-DS8971-DEX-8-hrs

description: The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. Dexamethasone treated, 8 hours.

source_name: mouse mammary adenocacinoma tumor, dexamethasone 8 hours

value: Dex 8 hours hour


title: 3134-DS8969-DEX-2-hrs

description: The 3134 cell line was derived by transformation of C127, originally isolated from a mammary adenocacinoma tumor of the RIII mouse. Dexamethasone treated, 2 hours.

source_name: mouse mammary adenocacinoma tumor, dexamethasone 2 hours


title: pDCs-NYVAC-C-KC-rep1

description: pDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes whose  replication capacity  was restored by inserting two viral host range genes, K1L and C7L

value: NYVAC-C-KC


title: pDCs-NYVAC-C-KC-dB19R-rep5


title: 3134-DS8801-DEX-4-hrs


title: pDCs-NYVAC-C-dB19R-rep6


title: pDCs-NYVAC-C-dB19R-rep7


title: brain 20week vs. brain 13week, replicate 1

description: brain 20week vs. brain 13week rep1

value: fetal brain

value: 13-week gestation stage


title: brain 24week vs. brain 20week, replicate 2

description: brain 24week vs. brain 20week rep2


title: brain 24week vs. brain 20week, replicate 1

description: brain 24week vs. brain 20week rep1


title: pDCs-NYVAC-C-KC-dB19R-rep3


title: pDCs-NYVAC-C-rep12

description: pDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes

value: NYVAC-C


title: pDCs-NYVAC-C-rep10


title: pDCs-NYVAC-C-dB19R-rep2


title: pDCs-NYVAC-C-KC-rep10


title: pDCs-NYVAC-C-KC-rep12


title: pDCs-NYVAC-C-rep9


title: pDCs-NYVAC-C-KC-dB19R-rep2


title: CAL1_Ig_chip1

source_name: control Ig-bound genomic DNA

value: plasmacytoid dendritic cell neoplasm

value: chromatin immunoprecipitation (ChIP)

value: control mouse IgG (Sigma)

source_name: input genomic DNA

value: whole cell extract (WCE)


title: heart  24week vs. brain 24week, replicate 1

description: heart vs. brain rep1

source_name: fetal heart-24week

value: fetal heart

value: 24-week gestation stage


title: CAL1_E2-2_chip1

source_name: E2-2-bound genomic DNA

value: monoclonal anti-human E2-2 (Bain et al., Mol Cell Biol 1993)


title: pDCs-NYVAC-C-KC-rep11


title: AtT-20-DS8794-DEX-8-hrs

description: The AtT‐20 cell line is an anterior pituitary corticotroph of murine origin. Dexamethasone treated, 8 hours.

source_name: mouse pituitary corticotroph, dexamethasone 8 hours

value: mouse pituitary corticotroph

value: male


title: pDCs-NYVAC-C-rep11


title: pDCs-NYVAC-C-KC-rep9


title: 3134-DS8802-DEX-8-hrs

value: RIII

value: mouse mammary adenocacinoma tumor


title: lung 24week vs. heart 24week, replicate 2

description: lung  vs. heart rep2

source_name: fetal lung-24week

value: fetal lung


title: heart  24week vs. brain 24week, replicate 2

description: heart vs. brain rep2


title: pDCs-NYVAC-C-dB19R-rep1

value: Plasmacytoid Dendritic Cells (pDCs)


title: AtT-20-DS8792-DEX-2-hrs

value: Dex 2 hours hour


title: AtT-20-DS8789-DEX-0-ctrl

value: control 0 hour hour


title: AtT-20-DS8793-DEX-4-hrs

value: Dex 4 hours hour


title: lung 24week vs. heart 24week, replicate 1

description: lung  vs. heart rep1


title: pDCs-NYVAC-C-KC-rep6

value: NYVAC-C-KC


title: pDCs-NYVAC-C-rep8

value: NYVAC-C


title: pDCs-NYVAC-C-KC-rep7


title: spleen 24week vs. lung 24week, replicate 1

description: spleen vs. lung rep1

source_name: fetal spleen-24week

value: fetal spleen


title: pDCs-NYVAC-C-KC-rep8


title: pDCs-NYVAC-C-rep4


title: pDCs-NYVAC-C-rep7


title: pDCs-NYVAC-C-rep6


title: pDCs-NYVAC-C-KC-rep4


title: brain 24week vs. liver 24week, replicate 2

description: brain vs. liver rep2

source_name: fetal brain-24week

value: fetal brain

source_name: fetal liver-24week

value: fetal liver


title: liver 24week vs. spleen 24week, replicate 2

description: liver vs. spleen rep2


title: pDCs-NYVAC-C-rep5


title: pDCs-NYVAC-C-KC-rep5


title: pDCs-NYVAC-C-KC-rep3


title: pDCs-NYVAC-C-rep3


title: pDCs-NYVAC-C-rep2


title: pDCs-NYVAC-C-rep1


title: brain 24week vs. liver 24week, replicate 1

description: brain vs. liver rep1


title: cDCs-NYVAC-C-KC-dB19R-rep8

description: cDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes ,lacking  the gene, B19R, coding for a soluble protein preventing binding of type-I IFN , whose  replication capacity  was restored by inserting two viral host range genes, K1L and C7L

source_name: Circulating conventional Dendritic Cells(cDCs)


title: cDCs-NYVAC-C-KC-dB19R-rep7

value: Circulating conventional Dendritic Cells(cDCs)


title: cDCs-NYVAC-C-dB19R-rep2


title: pDCs-NYVAC-C-KC-rep2


title: cDCs-NYVAC-C-KC-dB19R-rep6


title: cDCs-NYVAC-C-dB19R-rep1


title: cDCs-NYVAC-C-rep15

description: cDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes


title: cDCs-NYVAC-C-KC-dB19R-rep5


title: Control Rat1, T90'

city: Roma

first: Sergio

last: Nasi

state: Italia

address: P.le A. Moro 5

department: IBPM - Sapienza Università di Roma

institute: CNR - Consiglio Nazionale delle Ricerche

description: Gene expression data from Control Rat1 cells, 90' after serum re-addition

hyb_protocol: Each biotin-labeled and fragmented cRNA sample was hybridized onto a GeneChip® Probe Array RG-U34A for 16 h at 45°C in a GeneChip Hybridization Oven - according to the manufacturer's recommendation.

scan_protocol: The expression probe arrays (RG-U34A) were washed and stained through a GeneChip Fluidics Station 400 according to the Affymetrix GeneChip Expression Analysis manual. The probe arrays were scanned using an HP Gene Array Scanner, controlled by the GeneChip software.

data_processing: Data were processed with the GeneChip Microarray Analysis Suite version 4.0 software (MAS 4, Affymetrix) with default analysis settings. The Rat1_control_T0 sample was taken as reference for calculating relative expression values.

organism: Rattus norvegicus

label_protocol: Biotinylated target RNA was prepared according to the instructions provided in the Affymetrix GeneChip Expression Analysis manual. This involved synthesis and cleanup of double-stranded cDNA followed by synthesis, cleanup and fragmentation of biotin-labeled cRNA.

growth_protocol: Cells were cultured in DMEM, supplemented with 10% foetal calf serum, at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted with the TRIzol reagent (GIBCO-BRL) according to the manufacturer’s protocol. RNA was checked for quantity, purity and integrity by gel electrophoresis and UV spectrophotometric measurements.

treatment_protocol: For  serum induction, cells were grown for 48 h in 0.1% serum (serum-starvation) in the presence of 4-OHT and harvested at the indicated time after switching to media with 10% serum. Total RNA was prepared at the time of serum re-addition and 90' thereafter using the TRIzol reagent (GIBCO-BRL).

value: Fibroblasts

value: 90 min

tag: transfection

value: Omomyc


title: cDCs-NYVAC-C-KC-dB19R-rep4


title: liver 24week vs. spleen 24week, replicate 1

description: liver vs. spleen rep1

value: 24-week gestation stage


title: cDCs-NYVAC-C-rep14


title: Control Rat1, T0

description: Gene expression data from Control Rat1 cells, at the time of serum re-addition

value: 0  min

value: control vector


title: Omomer expressing Rat1, T0'

description: Gene expression data from Rat1 cells expressing Omomer, at the time of serum re-addition

source_name: Omomer expressing Rat1 cells, at the time of serum re-addition


title: Dystrophin siRNA Knockdown 7

city: Egham

last: Dickson

address: Royal Holloway University

department: School of Biological Sciences

country: United Kingdom

institute: Royal Holloway University

description: Dystrophin knockdown replicate 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi R package in bioconductor.

source_name: Limb muscles

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

growth_protocol: Cells homogenates were prepared, cultured and maintained according to standard protocols (Graham IR et. al. J Gene Medicien 2004, Vol 6, p1149).

extract_protocol: PARIS kit (Ambion) used following the protocol recommended by the manufacturer.

treatment_protocol: On days 2 and 4 cells were treated with siRNAs. On day 4 the media changed to differentation media before siRNA treatment. On day 6 total RNA was extracted using PARIS kit (Ambion).

tag: age

value: Neonate (3-5 days old)


title: Dystrophin siRNA Knockdown 5

description: Dystrophin knockdown replicate 5


title: Dystrophin siRNA Knockdown 1

description: Dystrophin knockdown replicate 1


title: Omomer expressing Rat1, T90'

description: Gene expression data from Rat1 cells expressing Omomer, 90' after serum re-addition

source_name: Omomer expressing Rat1 cells, 90' after serum re-addition


title: cDCs-NYVAC-C-KC-dB19R-rep3


title: Dystrophin siRNA Knockdown 3

description: Dystrophin knockdown replicate 3


title: Dystrophin siRNA Knockdown 4

description: Dystrophin knockdown replicate 4


title: cDCs-NYVAC-C-KC-dB19R-rep2


title: Dystrophin siRNA Knockdown 6

description: Dystrophin knockdown replicate 6


title: Dystrophin siRNA Knockdown 2

description: Dystrophin knockdown replicate 2


title: cDCs-NYVAC-C-rep11


title: cDCs-NYVAC-C-rep10


title: Endometrial CD14+ cells animal 3 technical replicate 1

city: Gainesville

first: Peter

middle: J

last: Hansen

email: lijoli@ufl.edu, pjhansen@ufl.edu

address: 1812 Shealy Drive

department: Animal Sciences

institute: University of Florida

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 3, technical replicate 1.

hyb_protocol: 1.5 µg of each labeled sample were co-hybridized to the array for 17 h at 65oC at 10 rpm in a rotating oven in an ozone-free room using sureHyb chambers from Agilent (Agilent Technologies, Santa Clara CA, USA).

scan_protocol: Wash conditions were as outlined in the Agilent processing manual.  Two technical replicates were performed.  For the first replicate, RNA samples from blood were labeled with Cy3 and RNA from endometrium was labeled with Cy5.  For the second technical replication, 3 samples of RNA from blood were labeled with Cy5 and their matching pairs of RNA from endometrial were labeled with Cy3 while the fourth pair used Cy3 for blood and Cy5 for endometrium.

data_processing: The microarray image extraction and data pre-processing were performed using Agilent’s Feature Extraction software v 9.5 (Agilent Technologies, Santa Clara CA, USA).  The intensity of each spot was summarized as the median pixel intensity followed by log transformation. The lowess normalization was done within-array lowess on median of the intensities of the spots.  The JMP® Genomics 3.1 for SAS® 9.1.3 software (SAS Inst., Inc., Cary, NC) was used. The quantile normalization method for data global normalization was performed.  Differentially regulated genes were identified by least-squares analysis of variance (ANOVA) by the PROC ANOVA procedure of JMP® Genomics 3.1 for SAS® 9.1.3.  The model included animal, replicate, and tissue source (blood or endometrium).  Fixed effects included tissue and replicate and random effects included animal.  Tissue x animal was the error term for tissue. Correction for false discovery rate was performed by the Benjamini and Hochberg method (1995) with a maximum false discovery rate (FDR) of 0.01.  Genes with a minimum intensity of 16 were considered to be expressed.  Only genes with at least 2-fold difference and a probability of P≤0.05 for a tissue difference were considered differentially expressed.

source_name: Animal 3: Endometrial CD14+ cells

label_protocol: Four pairs of samples of blood and endometrial CD14+ cells were subjected to transcriptional profiling using the Bovine Oligo Microarray Chip (Bovine 4X44K G2519F) from Agilent (Santa Clara CA, USA).  Prior to microarray hybridization, 10-50 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification Kit (NuGen Technologies, Inc, San Carlos, CA, USA) according to the manufacturer’s protocol.  A total of 2.0 µg of the amplified material was labeled with Cy3 or Cy5 using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara CA, USA)

extract_protocol: RNA was prepared using the the RNeasy Micro kit (Qiagen Inc, Valencia, CA, USA) following the manufacturer's recommendations. Concentration of total cellular RNA was determined using the Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and integrity determined by Agilent 2100 Bioanalyzer with RNA 6000 Pico LabChip kit (Agilent Technologies, Santa Clara CA, USA).  Only samples that showed high RNA integrity (RIN > 7) were used for the microarray hybridization and quantitative PCR analysis. Extracted RNA was stored at -80oC until microarray analysis.

treatment_protocol: samples were collect at a local abatoir. Pregnant uterus and the reminiscent in the heart of 4 pregnant cows were collected and brught to the lab. The CD14+ cells from blood and endometrium were obtained by flow cytometry cell sorting of enzymatically dispersed stromal endometrial cells and peripheral blood mononuclear cells. The final preparation of endometrial CD14+ cells had a purity of 90-95% based on flow cytometry while blood CD14+ cells were 98-99% pure.

value: Endometrial CD14+ cells

tag: day of pregnancy


title: cDCs-NYVAC-C-KC-rep17

description: cDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes whose  replication capacity  was restored by inserting two viral host range genes, K1L and C7L


title: cDCs-NYVAC-C-rep12


title: Endometrial CD14+ cells animal 4 technical replicate 1

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate  4, technical replicate 1.

source_name: Animal 4: Endometrial CD14+ cells


title: cDCs-NYVAC-C-KC-rep18


title: GL2 siRNA treatment control 6

description: Treatment control replicate 6


title: Blood CD14+ cells animal 4 technical replicate 1

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 4, technical replicate 1.

source_name: Animal 4: Peripheral blood CD14+ cells

value: Blood CD14+ cells


title: 3134-DS8800-DEX-2-hrs

source_name: mouse mammary adenocacinoma tumor, dexamethasone 2 hours

value: RIII

value: mouse mammary adenocacinoma tumor

value: male

value: Dex 2 hours hour


title: GL2 siRNA treatment control 5

description: Treatment control replicate 5


title: cDCs-NYVAC-C-rep9

value: NYVAC-C


title: cDCs-NYVAC-C-KC-rep16

value: NYVAC-C-KC


title: cDCs-NYVAC-C-KC-dB19R-rep1


title: cDCs-NYVAC-C-rep8


title: GL2 siRNA treatment control 7

description: Treatment control replicate 7


title: Blood CD14+ cells animal 3 technical replicate 1

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 3, technical replicate 1.

source_name: Animal 3: Peripheral blood CD14+ cells


title: cDCs-NYVAC-C-KC-rep15


title: Blood CD14+ cells animal 1 technical replicate 1

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 1, technical replicate 1.

source_name: Animal 1: Peripheral blood CD14+ cells


title: cDCs-NYVAC-C-KC-rep14


title: cDCs-NYVAC-C-rep13


title: GL2 siRNA treatment control 1

description: Treatment control replicate 1


title: GL2 siRNA treatment control 2

description: Treatment control replicate 2


title: Endometrial CD14+ cells animal 1 technical replicate 1

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 1, technical replicate 1.

source_name: Animal 1: Endometrial CD14+ cells


title: GL2 siRNA treatment control 3

description: Treatment control replicate 3


title: cDCs-NYVAC-C-rep5


title: cDCs-NYVAC-C-KC-rep13


title: GL2 siRNA treatment control 4

description: Treatment control replicate 4


title: cDCs-NYVAC-C-rep4


title: cDCs-NYVAC-C-rep7


title: cDCs-NYVAC-C-rep6


title: cDCs-NYVAC-C-KC-rep12


title: Blood CD14+ cells animal 4 technical replicate 2

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 4, technical replicate 2.


title: Untreated Control 4

description: Untreated Replicate 4


title: Endometrial CD14+ cells animal 3 technical replicate 2

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 3, technical replicate 2.


title: Blood CD14+ cells animal 2 technical replicate 1

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 2, technical replicate 1.

source_name: Animal 2: Peripheral blood CD14+ cells


title: Endometrial CD14+ cells animal 2 technical replicate 1

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 2, technical replicate 1.

source_name: Animal 2: Endometrial CD14+ cells


title: spleen 24week vs. lung 24week, replicate 2

description: spleen vs. lung rep2

value: fetal spleen

source_name: fetal lung-24week

value: fetal lung


title: cDCs-NYVAC-C-KC-rep11

value: Circulating conventional Dendritic Cells(cDCs)


title: Endometrial CD14+ cells animal 4 technical replicate 2

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 4, technical replicate 2.


title: cDCs-NYVAC-C-rep3

description: cDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes


title: cDCs-NYVAC-C-KC-rep9


title: Untreated Control 1

description: Untreated Replicate 1


title: Blood CD14+ cells animal 3 technical replicate 2

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 3, technical replicate 2.


title: pDCs-NYVAC-C-KC-dB19R-rep1

description: pDCs infected by restricted poxvirus NYVAC containing HIV clade C gag, pol, nef and env genes ,lacking  the gene, B19R, coding for a soluble protein preventing binding of type-I IFN , whose  replication capacity  was restored by inserting two viral host range genes, K1L and C7L

source_name: Plasmacytoid Dendritic Cells (pDCs)

value: Plasmacytoid Dendritic Cells (pDCs)


title: Untreated Control 2

description: Untreated Replicate 2


title: Untreated Control 3

description: Untreated Replicate 3


title: cDCs-NYVAC-C-rep2


title: cDCs-NYVAC-C-KC-rep10


title: cDCs-NYVAC-C-KC-rep7


title: Endometrial CD14+ cells animal 2 technical replicate 2

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 2, technical replicate 2.


title: cDCs-NYVAC-C-rep1


title: cDCs-NYVAC-C-KC-rep6


title: cDCs-NYVAC-C-KC-rep8


title: Blood CD14+ cells animal 2 technical replicate 2

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 2, technical replicate 2.


title: cDCs-NYVAC-C-KC-rep5


title: Femur bone_HLS_24hr_rep4

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

source_name: Femur bone, muscle unloaded by hind-limb suspension, 24hr, animal #4

label_protocol: 600 ng RNA and 3 µl Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows:  1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC).  The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum. At 1 wk after arrival, the animals were separated into individual cages for a 3-day acclimation period then were randomly assigned to either of two experimental groups: freely ambulating controls and hindlimb-unloaded animals.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit Qiagen.  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: Hindlimb muscles were unloaded using methods described previously (Matuszczak, Arbogast, Reid 2004). Briefly, Elastoplast tape (Beiersdorf-Jobst, Rutherford College, NC) was used to wrap the tail of each animal. A metal clip on the tape was attached to a nylon monofilament line via a stainless steel swivel. The distal end of the nylon line was attached to an overhead support and shortened to suspend the animal in a 45° head-down tilt position. The swivel enabled the animal to explore the cage (360° range of motion) and obtain food and water freely. Animals were observed daily for changes in appearance and activity. Each animal was weighed and the angle of hindlimb suspension was adjusted if necessary. After 24hr, each animal was deeply anesthetized in the hindlimb-unloaded condition. The animal was removed from the unloading device, the femur bones were excised with the animal under surgical anesthesia, and the animal was euthanized.  Bone was immediately placed in RNAlater (Ambion, Foster City, CA) and stored until RNA extraction.

tag: Strain

value: ICR

tag: Gender

value: Male

tag: Age

value: 6 months

tag: Body weight

tag: Tissue

value: Bone


title: cDCs-NYVAC-C-KC-rep2

tag: cell type


title: Femur bone_HLS_24hr_rep2

source_name: Femur bone, muscle unloaded by hind-limb suspension, 24hr, animal #2


title: cDCs-NYVAC-C-KC-rep1

source_name: Circulating conventional Dendritic Cells(cDCs)


title: Femur bone_HLS_24hr_rep1

source_name: Femur bone, muscle unloaded by hind-limb suspension, 24hr, animal #1


title: Femur bone_HLS_24hr_rep3

source_name: Femur bone, muscle unloaded by hind-limb suspension, 24hr, animal #3


title: cDCs-NYVAC-C-KC-rep4


title: Femur bone_HLS_24hr_rep5

source_name: Femur bone, muscle unloaded by hind-limb suspension, 24hr, animal #5


title: cDCs-NYVAC-C-KC-rep3


title: Blood CD14+ cells animal 1 technical replicate 2

description: Gene expression CD14+ cells from pregnant cow blood, biological replicate 1, technical replicate 2.


title: Endometrial CD14+ cells animal 1 technical replicate 2

description: Gene expression CD14+ cells from the endometrium of pregnant cow , biological replicate 1, technical replicate 2.


title: Femur bone_Control_24hr_rep1

source_name: Femur bone, freely ambulating control, 24hr, animal #1


title: Endometrium-prog C (07B13462-3)

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner.

data_processing: Affymetrix GeneChip Operating (GCOS) 1.4 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval, prog group C

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix).

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: GnRH-antagonist/rec-FSH stimulated IVF cycle

value: Endometrial biopsy tissue

value: Endometrial dating d3

tag: pregnancy status

value: biochemical pregnancy

tag: progesterone serum level

value: group C (> 1.5ng/ml)


title: Femur bone_Control_24hr_rep4

source_name: Femur bone, freely ambulating control, 24hr, animal #4


title: Endometrium-prog C (BS-3)

tag: tissue

tag: developmental stage

value: Endometrial dating late proliferative

value: not pregnant


title: Femur bone_Control_24hr_rep3

source_name: Femur bone, freely ambulating control, 24hr, animal #3


title: Femur bone_Control_24hr_rep5

source_name: Femur bone, freely ambulating control, 24hr, animal #5


title: Endometrium-prog A (01B05313-1)

source_name: Endometrium on day of oocyte retrieval, prog group A

value: Endometrial dating d2-3

value: pregnant

value: group A (<=0.9ng/ml)


title: Endometrium-prog C (08B9935)

value: Endometrial dating d2

value: non-pregnant


title: Femur bone_Control_24hr_rep2

source_name: Femur bone, freely ambulating control, 24hr, animal #2


title: Endometrium-prog B (01B06037)

source_name: Endometrium on day of oocyte retrieval, prog group B

value: group B (1-1.5 ng/ml)


title: PDC_null_day6_rep1

hyb_protocol: Labeled RNA samples (10 ug/array) were hybridized at the HICCC Genomics Facility of the Columbia University according to the manufacturer's instructions.

scan_protocol: Array scanning and raw data processing were done using GCOS 1.4 software (Affymetrix).

source_name: Ex vivo sorted plasmacytoid dendritic cells (PDC)

label_protocol: The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP and Biotin-11-CTP in the second round. Labeled aRNA was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).

treatment_protocol: Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Six days later total splenocytes were isolated, pooled from 2-3 mice and enriched for lineage (CD3/CD19)-negative cells by magnetic selection. PDC (CD11b- B220+ CD11clow Bst2+) were isolated using BD FACSAria II flow sorter directly into Trizol reagent.

tag: genotype/varation

value: E2-2-deficient (null)

tag: time point

value: spleen

value: PDC

tag: agent

value: tamoxifen


title: PDC_null_day6_rep2

tag: strain


title: Endometrium-prog B (01B08073)


title: PDC_control_day6_rep2

value: control


title: Endometrium-prog A (01B04869)

value: Endometrial biopsy tissue


title: PDC_null_day4_rep1


title: Endometrium-prog A (01B05559)


title: Endometrium-prog B (01B04871-3)


title: PDC_control_day4_rep2

treatment_protocol: Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Four days later total splenocytes were isolated, pooled from 2-3 mice and enriched for lineage (CD3/CD19)-negative cells by magnetic selection. PDC (CD11b- B220+ CD11clow Bst2+) were isolated using BD FACSAria II flow sorter directly into Trizol reagent.


title: Endometrium-prog B (01B03997)


title: PDC_control_day6_rep1


title: Endometrium-prog B (01b5848-1)

value: Endometrial dating d4


title: Endometrium-prog C (01b7079-3)


title: Metastatic lymph node 2

city: Chuo-ku

first: Satoshi

last: Yamashita

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

description: Replicate 2 of 3. MeDIP-CGI microarray analysis of metastatic lymph node from esophageal squamous cell carcinoma patient.

hyb_protocol: Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.

scan_protocol: Arrays were washed and scanned immediately with Agilent microarray scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Arrays were processed using Agilent Feature Extraction software and normalized (Background subtraction) using Agilent Chip Analytics software with default settings.

source_name: MeDIP of Metastatic lymph node 2

label_protocol: Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).

growth_protocol: Esophageal squamous cell carcinoma and metastatic lymph node were obtained from patients who underwent esophagectomy with informed consents.  Samples were stored at -80 ˚C.

extract_protocol: High molecular weight DNA was extracted by the phenol/chloroform method.

treatment_protocol: Five µg of genomic DNA fragmented by sonication was immunoprecipitated with five µg of anti-5-methyl cytidine antibody (Diagnode, Liége, Belgium) in 1 x IP buffer [10 mM Na-phosphate, pH 7.0, 140 mM NaCl, 0.05 % (w/v) Triton X-100]. (Yamashita et al. DNA Res 2009;16:275-86.)

value: Metastatic lymph node

tag: disease status

value: ESCC with metastasis

tag: dna treatment

value: Sonicated and immunoprecipitated with anti-5-methyl cytidine antibody (Diagnode, Liége, Belgium)

source_name: Metastatic lymph node 2

value: Sonicated