title: wild type dendritic cells stimulated with LPS for 6 hours

description:
Total RNA extraction and Quality Controls
Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy clean-up procedure. RNA purity was assessed by spectrophotometer (Nanodrop): 260/280 and 260/230 ratios were evaluated. If the 260/280 and 260/230 ratios were < of 1.9, RNA samples were ethanol precipitated. Total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated. Only high quality RNAs, with RIN greater than 7 were used in the experiment. In this case the RIN was 10.
cRNA Synthesis:
GeneChip® One-Cycle Target Labeling and Control Reagents Kit (Affymetrix®). Biotinylated cRNA was prepared and fragmented according to the Affymetrix protocol. Very strict quality control measures were applied during the target preparation procedures. cRNA before and following fragmentation was analysed by Agilent Bioanalyzer. Typical cRNA products examined on an Agilent 2100 Bioanalyzer have a size range from 500nt to 2500nt with a peak around 1500nt, The expected amount of cRNA obtained should be above 10 times more than the amount of starting total RNA material. Starting RNA material was 3 μg and the obtained cRNA material was 124 μg.

treatment_protocol: Dendritic cells were resuspended in complete IMDM, plated in 10 ml plates (5 million cells/plate), and treated with smooth LPS (1μg/ml). After 6 hours cells were harvested, washed in PBS and processed


title: ChIP H3K4 Cerebellum biological replicate 2

status: Public on Jun 16 2009

type: genomic

city: College Station

first: Scott

last: Dindot

state: TX

address: Texas Veterinary Medical Center, 4467 TAMU

department: Veterinary Pathobiology

country: USA

institute: Texas A&M University

description: ChIP biological replicate 2

hyb_protocol: Labeled MeDIP and ChIP DNA products were processed using the Agilents instructions for two color hybridizations.

scan_protocol: Arrays were scanned on an Axon GenePix 4000A scanner.

data_processing: Images were quantified using the Agilent Feature Extraction Software.

molecule: genomic DNA

organism: Mus musculus

source_name: Cerebellum

label_protocol: 300-500 ng of DNA was diluted to a final volume of 48 ul and 40 ul of random primers was added.  Samples were denatured at 100 C for 10 min.  Ten ul of 10X CTP Nucleotide Mix, 4 ul of Cy3 or Cy5 labeled CTP, and 2 ul of exo Klenow fragment were added to each sample and incubated at 37 C overnight.

extract_protocol: DNA was extracted by Proteinase K digestion followed by phenol chloroform extraction and ethanol precipitation.  Chromatin was isolated using Douncing buffer with homogenization.

tag: tissue

value: Cerebellum

tag: strain

tag: antibody

tag: type

value: input


title: MCF_10A cytoplasm and nucleus small RNAs

type: RNA

city: Beijing

first: Tao

middle: Paul

last: Wu

address: Datun Road 15#

department: Systems Biology

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: Hybridization was performed overnight on a uParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

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

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: mcf10a cytoplasmic small RNAs

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3£§-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Subcellular fractioning was executed according to the Subcellular fractionation protocol provided by Abcam (http://www.abcam.com/index.html?pageconfig=resource&rid=11473). Total RNA was extracted from the subcellular fractions with Trizol (Invitrogen).

tag: cell line

molecule: nuclear RNA

source_name: mcf10a nuclear smallRNAs


title: ChIP H3K9 Heart biological replicate 2

description: ChIP biological replicate 2

source_name: Heart

value: Heart


title: MeDIP Sperm biological replicate 2

description: MeDIP biological replicate 2

source_name: Sperm

value: Sperm

value: Methylated DNA Immunoprecipitation


title: MeDIP Cerebellum biological replicate 1

description: MeDIP biological replicate 1


title: MeDIP Cerebellum biological replicate 2

description: MeDIP biological replicate 2


title: MeDIP Heart biological replicate 2

description: MeDIP biological replicate 2


title: MeDIP Sperm biological replicate 1

description: MeDIP biological replicate 1


title: MeDIP Cerebellum technical replicate 1

description: MeDIP technical replicate 1


title: MDA-MB-231 cytoplasm and nucleus small RNAs

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics). Axon GenePix 4000B Microarray Scanner 10um 385_and_500

source_name: mda231 cytoplasm_small RNA

source_name: mda231 nucleus small RNAs


title: ChIP H3K9 Cerebellum biological replicate 1

description: ChIP biological replicate 1


title: MeDIP Heart biological replicate 1

description: MeDIP biological replicate 1


title: Aspergillus fumigatus 17oC vs 32oC replicate 3

city: New Haven

first: Swee Yang

last: Low

state: CT

address: 9 Hillhouse Avenue, Mason Laboratory Room 320

department: Environmental Engineering

institute: Yale University

hyb_protocol: The resulting dye-coupled cDNA was hybridized using a BioMicro (Salt Lake City, UT) MAUI hybridization station at the W. M. Keck Microarray Resource Facility at Yale University.

scan_protocol: The microarray slides were scanned at the W. M. Keck Microarray Resource Facility at Yale University using an Axon GenePix 4200 laser confocal scanner.

data_processing: The generated 16-bit .tiff images were analyzed by TIGR Spotfinder (version 3.1.2) for raw intensity values by the Otsu method, which were subsequently imported into TIGR MIDAS (version 2.20). Intensity values less than 10000 were removed with the low intensity filter, and data normalization was carried out using the LOWESS (Locfit) algorithm. Standard deviation regularization was also performed to address print-tip bias.

molecule: total RNA

organism: Aspergillus fumigatus

source_name: sporulating culture at 17oC biological replicate 3

label_protocol: Aminoallyl-labeled first strand cDNA synthesis and indirect Cy dye incorporation of purified RNA from 17oC and 32oC conidiating cultures were performed using the standard TIGR protocol (SOP #: M007), except that a 3:1 aminoallyl-dUTP to dTTP ratio was used.

growth_protocol: Liquid potato dextrose medium was inoculated with 1 × 106 resting conidia/ml and grown in a shaking (200 rpm) culture at 37oC overnight. At the end of the overnight incubation, the culture was filtered under vacuum, and the harvested mycelia was divided and plated onto potato dextrose agar. One set of plates was incubated at 17oC, and the other at 32oC, for 48 h. At the end of the 2-day incubation, the cultures were harvested with a sterile, moistened cotton swab, resuspended in sterile water, and collected under vacuum filtration. The extracted culture was subsequently ground under liquid nitrogen using a mortar and pestle.

extract_protocol: Total RNA was isolated from the ground culture using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.

source_name: sporulating culture at 32oC biological replicate 3


title: ChIP H3K9 Cerebellum biological replicate 2

description: ChIP biological replicate 2


title: Aspergillus fumigatus 17oC vs 32oC replicate 2

source_name: sporulating culture at 17oC biological replicate 2

source_name: sporulating culture at 32oC biological replicate 2


title: MeDIP Cerebellum technical replicate 2

description: MeDIP technical replicate 2


title: MeDIP Heart biological replicate 3

description: MeDIP biological replicate 3


title: ChIP H3K4 Cerebellum biological replicate 1

description: ChIP biological replicate 1


title: Aspergillus fumigatus 17oC vs 32oC replicate 1

source_name: sporulating culture at 17oC biological replicate 1

source_name: sporulating culture at 32oC biological replicate 1


title: MCF_7 cytoplasm and nuclear small RNAs

source_name: MCF_7 cytoplasm small RNAs

source_name: MCF_7_nucleus small RNAs


title: Pulmonary hypertension from CHF rep2

city: Turku

first: Ilana

last: Saarikko

address: Linnankatu 55

country: Finland

institute: Genolyze Ltd

hyb_protocol: Each sample was hybridized at +45°C overnight (16 h) according to GeneChip® Expression Analysis Technical Manual. GeneChip® Fluidics Station 450 was used to wash and stain the arrays.

scan_protocol: GeneChip® Scanner 3000 with AutoLoader was used to scan the arrays. GeneChip® Operating Software (GCOS) was used to control GeneChip® Fluidics Stations and Scanner.

data_processing: Raw data was processed using R/Bioconductor and normalised with GC-RMA

label: biotin

organism: Rattus norvegicus

source_name: lung

label_protocol: Samples were processed according to One-Cycle Target Labeling protocol from GeneChip® Expression Analysis Technical Manual. 3 ug of total RNA was used as a starting material for sample preparation.

growth_protocol: control and aortic banding rats were kept for 9 weeks for the disease to establish

extract_protocol: RNA was extracted 9 weeks after aortic banding operation

value: lung

tag: disease state

value: pulmonary hypertension, CHF


title: Control rep2

value: control


title: Pulmonary hypertension from CHF rep3


title: Pulmonary hypertension from CHF rep1


title: wild-type with osmotic stress vs atfA mutant with osmotic stress (Exp.8) Dye-swapped

city: Sendai

first: Daisuke

last: Hagiwara

state: Miyagi

address: 6-6-10 Aoba Aramaki

department: New Industry Creation Hatchery Center

country: Japan

institute: Tohoku university

description: Gene expression was considered to be significantly higher or lower whenever the spot intensity changed by at least 2-fold in all four replicates.

hyb_protocol: DNA microarray slides were hybridized in a Slide Booster (Advalytix) at 42ºC overnight (16-18 h). Then, the slides were washed twice in wash buffers (first in a buffer containing 2×SSC and 0.1 % SDS for 15 min, then in a buffer containing 1×SSC and 0.1% SDS for 5 min at room temperature. Finally, the slides were rinsed with 0.2×SSC at room temperature for 5 min and dried by centrifugation.

scan_protocol: The slides were scanned using GenePix4000B scanner (Molecular Devices).

data_processing: The resulting TIFF images were imported into GenePix Pro and fluorescent intensity of spots were calculated for each of the Cy3 and Cy5 channels. Global normalization was applied to  analysis. Following normalization, spots whose Cy3 or Cy5 intensity was less than 0 were removed from the data set (the exceptional case was that intensity of the other channel was more than 100). The dye-swap replicates and in-slide replicates were subjected to all analyses. Finally, gene expression ratios (channel 2/channel 1) were calculated for each replicates.

molecule: polyA RNA

organism: Aspergillus nidulans

source_name: wild-type with osmotic shock

label_protocol: Cy3- and Cy5-labeled cDNA probes were prepared using the Amersham CyScribe Post-Labelling Kit (GE Healthcare). Initially, amino allyl-dUTP (AA-dUTP) was incorporated into cDNA in a reverse transcriptase reaction, in which 1 μg mRNA was used as the template for each sample. The AAdUTP-modified cDNA samples were labeled with Cy3 or Cy5 using CyDye NHS-esters, resulting in Cy3- or Cy5-labeled cDNA probes. The Cy3 and Cy5 probes were purified using the CyScribe GFX Purification Kit (GE Healthcare) and evaporator-dried. Samples were then dissolved in 28 μL of hybridization buffer (50% formamide, 5×SSC, 0.1% SDS, 0.6 μg/μL Salmon Sperm DNA).

growth_protocol: 10 8 conidia of each strain were added into 100 ml of standard A. nidulans minimal media, Czapek-Dox (CD) medium (adjusted pH 6.5 with KOH) containing 2% glucose and appropriate requirements, and were cultured for 18 hours in a rotated shaker (160 rpm) at 37ºC. After this, 50 ml of 3 M sorbitol was added (final concentration, 1 M). After 15min, mycelia were harvested, frozen in liquid nitrogen, ground to powder, and used for RNA preparation.

extract_protocol: Total RNA was purified using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions (QIAGEN).

tag: genotype

value: (biA1, pyrG89, wA3, argB2, pyroA4, argB+)

source_name: atfA mutant with osmotic stress

value: atfA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, atfA::argB)


title: wild-type with osmotic stress vs atfA mutant with osmotic stress (Exp.8)

source_name: wild-type with osmotic stress


title: CHIPnull_240m_Baseline_rep3

status: Public on Jun 15 2009

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

hyb_protocol: Labeled cRNA was co-hybridized to Agilent G4122F Whole Mouse Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UMRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner.

data_processing: The data were processed using Feature Extraction software and normalized using per-chip and per-spot intensity-dependent LOWESS normalization with a threshold of 0.01.  The data at the two heat shock time-points, 30 and 240 minutes, were normalized by their respective un-shocked controls.

source_name: CHIP(-/-) MEF, control, 240 min

label_protocol: 500 ng of total RNA from three biological replicates from each condition were used for amplification and labeled with Cy5 using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

growth_protocol: MEFs (mouse embryonic fibroblasts) isolated from day 13.5 embryos of C57BL6 CHIP (+/-) crosses were grown under similar conditions with the addition of β-mercaptoethanol at 37° C, 5% CO2.

extract_protocol: Total RNA was purified using the RNeasy microkit (Qiagen)  in accordance with the manufacturer’s instructions which included DNase treatment to eliminate genomic contamination. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer.

treatment_protocol: MEF cultures were either maintained at 37° C or heat shocked at  43° C for the indicated time points prior to RNA harvesting.

tag: embryonic fibroblast

source_name: Stratagene UMRR

tag: pool of mouse reference RNA


title: Control rep1


title: wild-type with osmotic stress vs hogA mutant with osmotic stress (Exp.7) Dye-swapped

source_name: hogA mutant with osmotic stress

value: hogA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, hogA::argB)


title: Control rep3


title: wild-type with osmotic shock vs wild-type with control treatment (Exp.6)

source_name: wild-type with control treatment

growth_protocol: 10 8 conidia of each strain were added into 100 ml of standard A. nidulans minimal media, Czapek-Dox (CD) medium (adjusted pH 6.5 with KOH) containing 2% glucose and appropriate requirements, and were cultured for 18 hours in a rotated shaker (160 rpm) at 37ºC. After this, 50 ml of water was added (as a control). After 15min, mycelia were harvested, frozen in liquid nitrogen, ground to powder, and used for RNA preparation.


title: MeDIP Cerebellum biological replicate 3

description: MeDIP biological replicate 3

source_name: Cerebellum


title: CHIPnull_240m_Heatshock_rep1

source_name: CHIP(-/-) MEF, heat shock, 240 min


title: Wildtype_240m_Heatshock_rep2

source_name: CHIP(+/+) MEF, heat shock, 240 min


title: CHIPnull_240m_Heatshock_rep3


title: Wildtype_240m_Heatshock_rep3


title: Wildtype_240m_Baseline_rep1

source_name: CHIP(+/+) MEF, control, 240 min


title: CHIPnull_240m_Baseline_rep1


title: CHIPnull_240m_Baseline_rep2


title: Wildtype_240m_Baseline_rep2


title: wild-type with osmotic stress vs hogA mutant with osmotic stress (Exp.7)


title: CHIPnull_240m_Heatshock_rep2


title: Wildtype_240m_Heatshock_rep1


title: CHIPnull_30m_Heatshock_rep1

source_name: CHIP(-/-) MEF, heat shock, 30 min


title: Wildtype_240m_Baseline_rep3


title: CHIPnull_30m_Baseline_rep3

source_name: CHIP(-/-) MEF, control, 30 min


title: CHIPnull_30m_Heatshock_rep2


title: CHIPnull_30m_Baseline_rep1


title: wild-type with osmotic shock vs wild-type with control treatment (Exp.6) Dye-swapped


title: CHIPnull_30m_Heatshock_rep3


title: CHIPnull_30m_Baseline_rep2


title: InputSpermD4 and MeDIPSpermD4, Replica 3, Slide 2

city: Salt Lake City

first: Bradley

middle: R.

last: Cairns

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: HHMI and Huntsman Cancer Institute

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 3

hyb_protocol: Fluorescently labeled DNA samples were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization Oven and were incubated at 65ºC for 40 hours with a rotational speed of 20 rpm.  Following incubation, the microarray slide was washed for 5 minute in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC).  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing:
The Tiling Microarray Analysis Tools 2 package (http://timat2.sourceforge.net) was used to quantile normalize both treatment and control samples, median scale, and window scan (150bp) the tiled gene promoters.  Rank lists (best to worst) of enriched regions/ intervals were generated by setting log2 ratio thresholds that generated the top 100, 200, 400, 800, 1600, 3200, and 6400 regions.

The enriched regions are listed in the '*EnrichedRegions.xls' files, available from the GSE15701 record.

The files containing oligo ratio data (log2(AveTreatment/AveControl)) are in the '*OligoRatioData.zip' folders, also available from the GSE15701 record.

All coordinates are relative to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006.

source_name: Sperm Patient D4

label_protocol: PCR-amplified DNA samples (2-3 µg) derived from chromatin immunoprecipitation reactions were labeled using the Agilent Genomic DNA Labeling Kit PLUS.  The labeling kit uses random primers and the exo-Klenow fragment to label DNA through incorporation of fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP).  Following termination of the labeling reaction, fluorescently labeled DNA molecules were purified by isopropanol precipitation.  Precipitated pellets were dried and then rehydrated in distilled water.  The concentration of purified samples was determined using a NanoDrop ND-1000 spectrophotometer.  A fraction of the labeled DNA (100 ng) was run on an Agilent BioAnalyzer to validate the size distribution of the labeled DNA molecules.

growth_protocol: Sperm samples were obtained from three known fertile donors attending the University of Utah Andrology laboratory, consented for research. Primary human fibroblast cells were obtained from Lonza (CC2511) and were cultured in DMEM containing 10% FBS and supplemented with penicillin and streptomyocin (37°C and 5% CO2).

extract_protocol: Sperm samples were collected after 2-5 days abstinence and subjected to an ISolate density gradient (to purify viable, motile, mature sperm) and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 20 min on ice to eliminate white blood cell contamination. Samples were centrifuged at 10,000 G for 3 min and the sperm pellet was resuspended in 1X PBS and used immediately for chromatin preparation. Chromatin was prepared as previously described by Zalenskaya et al Biochem Biophys Res Commun 279, 213-8 (2000) in the absence of crosslinking reagent. Sperm was treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were used for chromatin immunopreciptation (below), or the DNA extracted and gel purified (~140-155bp) for  array analysis. All Chromatin IPs (ChIPs) were performed as previously described by Gordon et al Mol Cell Biol 27, 4058-69 (2007). All Data for CHIP modifications and histone variants were normalized to the three Histone replicates as input. Fibroblast chromatin was processed according to Zalenskaya et al 2000 and ChIPed according to Gordon et al 2007.

value: sperm

tag: chip antibody


title: InputSpermD2 and MeDIPSpermD2, Replica 3, Slide 2

source_name: Sperm Patient D2


title: Wildtype_30m_Heatshock_rep3

source_name: CHIP(+/+) MEF, heat shock, 30 min


title: Wildtype_30m_Heatshock_rep1


title: InputSpermD2 and MeDIPSpermD2, Replica 1, Slide 2

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 1


title: Wildtype_30m_Baseline_rep3

source_name: CHIP(+/+) MEF, control, 30 min


title: Wildtype_30m_Baseline_rep2


title: InputSpermD2 and MeDIPSpermD2, Replica 2, Slide 2

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 2


title: Lung_CBA OVA v Lung CBA PBS rep3

city: Brisbane

first: Ashley

last: Connolly

address: St Lucia

country: Australia

institute: University of Queensland

hyb_protocol: Labeled cDNA, yeast tRNA, poly A and Cot-1 DNA were mixed with 16uL of formamide and 16uL of 6.25 X SSC. The mixture was heated to 100C for 3min. and applied to the centre of the microarray. Hybridisation occurred at 42C overnight in a humidified chamber. The array was then washed in 0.5 X SSC containing 0.01% SDS for 5 min., 0.5 X SSC for 5 min then 0.2 X SSC for 3 min. then dried by centrifugation (detailed protocols can be obtained from www.microarray.adelaide.edu.au).

scan_protocol: Microarrays were scanned using an Axon 4000B microarray scanner.

data_processing: Single channel .tif images of microarray slides were analysed using SPOT software. The data was normalised and anlaysed using Lima GUI.

source_name: CBA PBS treatment

label_protocol: cDNA was made from total RNA (>20μg) using Superscript II, anchored polyT(V)N (2μg/μL) and an aminoallyl dNTP mix. The RNA was hydrolysed, the cDNA purified then coupled to Cy3 or Cy5 NHS esters (detailed protocols can be obtained from www.microarray.adelaide.edu.au)

growth_protocol: Mice were immunized by intraperitoneal injection of 10 ug OVA mixed with 1 mg of aluminium hydroxide gel in 50 uL of endotoxin-free (ef) PBS, on each of days 0 and 12. Using a clinical nebulizer, mice were then challenged with aerosols of 1% OVA in efPBS or with efPBS alone, for either 20 min on each of days 28 and 29. Mice were euthanized by CO2 inhalation on day 30 or 32.

extract_protocol: RNA was extracted using Trizol according to the manufacturer’s instructions. The extracted RNA was purified using an RNEasy column (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Lung tissue was recovered 72 h after OVA or PBS challenge. Both lungs were placed in 2 ml of Trizol and homogenized. RNA was extracted according to the manufacturer’s instructions.

value: CBA

tag: treatment

value: saline

source_name: CBA OVA treatment

value: ovalbumin


title: Wildtype_30m_Baseline_rep1


title: Lung_CBA OVA v Lung CBA PBS rep4


title: Wildtype_30m_Heatshock_rep2


title: Lung_CBA OVA v Lung CBA PBS rep2


title: SYNW0948_mutant_bsy89255c0072_rep5

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

institute: Macquarie University

description: This slide measures gene expression of a synw0948 mutant as compared to wild type.

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each.  The sequences are:  At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGGACAA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG). Dry using a speed vac. Make pre-hybridization buffer by combining: 0.5 g BSA; 37 mL DEPC water; 12.5 mL 20X SSC; 0.5 mL 10% SDS. Incubate pre-hybridization buffer for 20 minutes at 42 degrees C. Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar. Incubate for 20 minutes at 42 degrees C. Make hybridization buffer by combining: 500 microliters fomamide; 250 microliters 20X SSC; 10 microliters 10% SDS; 240 microliters DEPC water. Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter. Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer. Add 60 microliters hybridization buffer to speed vac-dried probes. Put slide into pre-hybridization buffer in coplin jar. Incubate for 45 minutes at 42 degrees C. Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand. Dry slide by spinning. Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature. Dip in 100% EtOH and dry with a Chem Wipe. Heat probes for 15 minutes at 95 degrees C with occassional "flicking" to resuspend probes. Remove probes from heat block and centrifuge for 2 minutes at 15,000g. Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip. Hybridize overnight at 42 degrees C. Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C. Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature. Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature. Dry slide by spinning.

scan_protocol: Slide were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15, and applying the default quality control filter options.  The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software).

organism: Parasynechococcus marenigrum WH 8102

source_name: SYNW0948 mutant in SOW medium RH32r

label_protocol:
Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
4.7 microliters 13.279 ng/microliter ltp6 RNA;
11.8 microliters 21.313 ng/microliter rcp1 RNA;
40.7 microliters 23.23 ng/microliter nac RNA;
4.6 microliters 18.177 ng/microliter xcp2 RNA;
14.7 microliters 11.436 ng/microliter prk RNA;
18.9 microliters 11.084 ng/microliter tim RNA;
826.5 microliters water.
And for Cy3 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
1.6 microliters 13.279 ng/microliter ltp6 RNA;
3.9 microliters 21.313 ng/microliter rcp1 RNA;
13.6 microliters 23.23 ng/microliter nac RNA;
13.9 microliters 18.177 ng/microliter xcp2 RNA;
44.1 microliters 11.436 ng/microliter prk RNA;
56.8 microliters 11.084 ng/microliter tim RNA;
788.1 microliters water.
To label Synechococcus sp. WH 8102 RNA sample combine:
4 micrograms RNA;
2 microliters 3 mg/mL random hexamers (Invitrogen);
2 microliters arabidopsis spike-in control RNA;
DEPC water to a final volume to 17.5 microliters.
Mix and incubated at 70 degrees C for 10 minutes.
Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.
Add:
6 microliters 5X Superscript II buffer (Invitrogen);
3 microliters 0.1 M dithiothreitol;
1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;
2 microliters SuperScript II (Invitrogen).
Mix and incubated overnight at 42 degrees C.
Add:
10 microliters 1 M NaOH;
10 microliters 0.5 M EDTA.
Incubate for 15 minutes at 65 degrees C.
Add:
25 microliters 1 M Tris pH 7.4;
400 microliters PB buffer (Qiagen).
Apply sample to QIAquick column (Qiagen).
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Dry sample using a speed vac.
Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).
Allow the sample to resuspend for 15 minutes at room temperature.
Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.
Incubate for 1 hour at room temperature in the dark.
Add 4.5 microliters 4 M hydroxylamine.
Incubate for 15 minutes at room temperature in the dark.
Add:
35 microliters 100 mM NaOAc pH 5.2;
500 microliters PB buffer.
Apply to Qiaquick column.
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters PE buffer (Qiagen).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters EB buffer (Qiagen).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Check quality of probes spectrophotometrically from 200nm to 700nm.
Store at -80 degrees C.

growth_protocol: Synechococcus sp. WH 8102 cells were grown in 1 liter of artificial seawater (SOW) containing 87 micromolar phosphate medium to late-log phase.

extract_protocol: Cells were harvested by centrifugation for 10 minutes at 9000g at room temperature.  RNA was extracted using Trizol (Invitrogen) according to the manufacturer's recommendation.  RNA was resuspended in 100 microliters DEPC-treated water.  RNA was digested twice with DNase I (Qiagen) using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.  RNA yield and purity were determined by measuring optical density spectrophotometrically at 260 and 280 nm.  RNA was stored at -80 degrees C.

tag: Axenic Synechococcus sp. WH 8102

tag: synw0948 mutant

source_name: wild type in SOW medium RH35r

tag: wild type


title: Lung_CBA OVA v Lung CBA PBS rep1


title: Lung_BALB/c OVA v Lung BALB/c PBS rep4

source_name: BALB/c PBS treatment

value: BALB/c

source_name: BALB/c OVA treatment


title: InputSpermD1 and ProtamineSpermD1, Replica 1, Slide 2

description: protamine bound DNA enrichment, replica 1

source_name: Sperm Patient D1


title: InputSpermD1 and ProtamineSpermD1, Replica 2, Slide 2

description: protamine bound DNA enrichment, replica 2


title: Lung_BALB/c OVA v Lung BALB/c PBS rep2


title: Lung_BALB/c OVA v Lung BALB/c PBS rep3


title: Lung_BALB/c OVA v Lung BALB/c PBS rep1


title: SYNW0948_mutant_bsy89255c0073_rep6


title: SYNW0947_mutant_bsy89255c0071_rep4

description: This slide measures gene expression of a synw0947 mutant as compared to wild type.

source_name: SYNW0947 mutant in SOW medium RH30r

tag: synw0947 mutant


title: SYNW0947_mutant_bsy89255c0068_rep1

source_name: SYNW0947 mutant in SOW medium RH26r


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 3, Slide 2

description: histone bound DNA enrichment via MNase digestion and nucleosome isolation, replica 3


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 2, Slide 2

description: histone bound DNA enrichment via MNase digestion and nucleosome isolation, replica 2


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 1, Slide 2

description: histone bound DNA enrichment via MNase digestion and nucleosome isolation, replica 1


title: Lung_BALB/c OVA v Lung CBA OVA rep4


title: InputFibroblast and MeDIPFibroblast, Replica 2, Slide 2

source_name: Primary fibroblasts

value: Primary fibroblasts, Lonza CC2511


title: SYNW0948_mutant_bsy89255c0064_rep1

source_name: SYNW0948 mutant in SOW medium RH25r

source_name: wild type in SOW medium RH5r


title: InputFibroblast and MeDIPFibroblast, Replica 1, Slide 2


title: TH2B, Replica 2, Slide 2

description: chIP-chip, Upstate Biotechnology Inc TH2B antibody 07-680, replica 3


title: Lung_BALB/c OVA v Lung CBA OVA rep3


title: HaCaT_TiO2(T-200)_24h

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Label, hybridization, and scan protocols were performed according to the Agilent manufacturer’s instructions.

hyb_protocol: The hybridaization was performed according to the Agilent manufacturer's instructions.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions, and were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution. The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1.

data_processing:
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold raw signals to 1.0
Normalization algorithm: Percentile Shift
Normalization: Shift to 50 percentile

source_name: HaCaT, TiO2 (T-200) exposure for 24h (n=3)

label_protocol: cRNA labeled with fluorescent Cyanine 3-CTP was hybridized onto the Whole Human Genome Oligo Multiplex Microarray slides (#G4112F, Agilent Technologies, Santa Clara, CA) containing approximately 41,000 oligonucleotide probes.

extract_protocol: After incubations with the DMEM-FBS medium in the presence or absence of TiO2 particles, the cells were collected by trypsinization, and total RNA was extracted with the RNeasy Mini kit (Qiagen, Tokyo, Japan) following the manufacturer’s instructions. RNA quality and the concentration were determined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

value: human keratinocytes cell line (HaCaT)

tag: agent

tag: time


title: Early_log_phase_phosphate_stress_bsy89255d0022_rep4

description: This slide measures gene expression during early log phase growth under phosphate stress as compared to expression without phosphate stress.

source_name: wild type in 5 micromolar phosphate SOW medium, early log phase CD43r

source_name: wild type in 87 micromolar phosphate SOW medium, early log phase CD44r


title: Early_log_phase_phosphate_stress_bsy89255d0021_rep1

source_name: wild type in 5 micromolar phosphate SOW medium, early log phase CD39r

source_name: wild type in 87 micromolar phosphate SOW medium, early log phase CD40r


title: Lung_BALB/c OVA v Lung CBA OVA rep2

tag: tissue


title: HaCaT_TiO2(T-20)_24h

source_name: HaCaT, TiO2 (T-20) exposure for 24h (n=3)


title: TH2B, Replica 1, Slide 2

description: chIP-chip, Upstate Biotechnology Inc TH2B antibody 07-680, replica 1


title: SYNW0947_mutant_bsy89280d0003_rep5


title: HaCaT_TiO2(T-20)_6h

source_name: HaCaT, TiO2 (T-20) exposure for 6h (n=3)


title: Lung C57 OVA v Lung  CBA OVA rep4

source_name: CBA OVA treatment

tag: strain

source_name: C57 OVA treatment


title: H3K4Me3, Replica 2, Slide 2

description: chIP-chip, Abcam H3K4Me3 antibody 8580, replica 2


title: Lung C57 OVA v Lung  CBA OVA rep3


title: HaCaT_TiO2(T-200)_2h

source_name: HaCaT, TiO2 (T-200) exposure for 2h (n=3)


title: HaCaT_TiO2(T-20)_2h

source_name: HaCaT, TiO2 (T-20) exposure for 2h (n=3)


title: SYNW0947_mutant_bsy89280d0097_rep2

source_name: wild type in SOW medium RH35r


title: H3K4Me3, Replica 3 and 1, Slide 2

description: chIP-chip, Abcam H3K4Me3 antibody 8580, replica 1 and 3

source_name: Sperm Patient D1


title: HaCaT_TiO2(T-200)_6h

source_name: HaCaT, TiO2 (T-200) exposure for 6h (n=3)


title: Lung_BALB/c OVA v Lung CBA OVA rep1

source_name: BALB/c OVA treatment


title: SYNW0947_mutant_bsy89280d0098_rep3

source_name: SYNW0947 mutant in SOW medium RH26r


title: HaCaT_TiO2(T-7)_24h

source_name: HaCaT, TiO2 (T-7) exposure for 24h (n=3)


title: SYNW0948_mutant_bsy89280d0091_rep3

source_name: wild type in SOW medium RH5r

source_name: SYNW0948 mutant in SOW medium RH25r


title: SYNW0948_mutant_bsy89280d0006_rep4

source_name: SYNW0948 mutant in SOW medium RH32r


title: Lung C57 OVA v Lung  CBA OVA rep2


status: Public on Aug 07 2009

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 260 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: Gene expression data from PD18-PD21 chase Bu (1-2 Division) cells, mouse 2

hyb_protocol: Labelled cDNA are hybridized to Gene Chip MOE 430 2.0 according to manufactuer's manual (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneArray 3000 scanner.

data_processing: The data were analyzed with GCOS software using Affymetrix default analysis settings and global scaling as normalization method to generate present calls and signal values (Affymetrix).

label: GeneChip IVT labelling

source_name: Tet-off H2BGFP mouse skin after PD18-PD21 Doxycycline chase

label_protocol: 5 ng of high quality RNA (Bioanalyzer, Agilent) were amplified (Ovation Amplification; Nugene) in the Cornell Microarray Core Facility. GeneChip IVT labelling was performed according to manufacturer's instructions (Affymetrix).

growth_protocol: Mice are housed in the Biotechnology Building mouse facility of Cornell University approved by Cornell IACUC.

extract_protocol: Total RNA was extracted using Absolutely RNA kit (Stratagene) according to the manufacturer's instructions.

treatment_protocol: K5tTA (FvB) x pTREH2B-GFP (CD1) mice were fed doxy at 1g/KG of food (Bio-serv) to repress H2BGFP expression.

value: skin

tag: cell type

value: bulge

value: K5tTA x pTRE-H2B-GFP

tag: age

tag: protocol

value: Doxycycline chase

tag: cell division

value: 1-2 Division


title: SYNW0947_mutant_bsy89280d0004_rep6

source_name: SYNW0947 mutant in SOW medium RH30r


title: HaCaT_TiO2(T-7)_6h

source_name: HaCaT, TiO2 (T-7) exposure for 6h (n=3)

tag: cell line


title: Lung C57 OVA v Lung  CBA OVA rep1

value: lung


title: Lung C57 OVA v Lung  C57 PBS rep4

source_name: C57 PBS treatment


title: H3K4Me2, Replica 1 and 2, Slide 2

description: chIP-chip, Abcam H3K4Me2 antibody 32356, replica 1 and 2


title: InputSpermD4 and MeDIPSpermD4, Replica 3, Slide 1

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 3

source_name: Sperm Patient D4


title: SYNW0948_mutant_bsy89280d0090_rep2


title: InputSpermD4 and MeDIPSpermD4, Replica 2, Slide 1

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 2


title: HaCaT_TiO2(T-7)_2h

source_name: HaCaT, TiO2 (T-7) exposure for 2h (n=3)


title: Early_log_phase_phosphate_stress_bsy89280d0051_rep6

source_name: wild type in 87 micromolar phosphate SOW medium, early log phase CD44r

source_name: wild type in 5 micromolar phosphate SOW medium, early log phase CD43r


title: Early_log_phase_phosphate_stress_bsy89280d0050_rep5


title: HaCaT_Control_6h

source_name: HaCaT, Untreated control for 6h (n=3)

value: Untreated


title: InputSpermD4 and MeDIPSpermD4, Replica 1, Slide 1

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 1


title: HaCaT_Control_24h

source_name: HaCaT, Untreated control for 24h (n=3)


title: Lung C57 OVA v Lung  C57 PBS rep3

source_name: C57 OVA treatment


title: InputSpermD2 and MeDIPSpermD2, Replica 2, Slide 1

source_name: Sperm Patient D2


title: Lung C57 OVA v Lung  C57 PBS rep2


title: InputSpermD2 and MeDIPSpermD2, Replica 3, Slide 1


title: Early_log_phase_phosphate_stress_bsy89280d0049_rep3

source_name: wild type in 87 micromolar phosphate SOW medium, early log phase CD40r

source_name: wild type in 5 micromolar phosphate SOW medium, early log phase CD39r


title: Early_log_phase_phosphate_stress_bsy89280d0048_rep2


title: InputSpermD2 and MeDIPSpermD2, Replica 1, Slide 1


title: HaCaT_Control_2h

source_name: HaCaT, Untreated control for 2h (n=3)


title: InputSpermD1 and ProtamineSpermD1, Replica 2, Slide 1

source_name: Sperm Patient D1


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)1B

city: Fujisawa

first: Tsukasa

last: Mori

state: kanagawa

address: Kameino 1866

department: Nihon University College of Bioresource Sciences

institute: Nihon University

description: Replicate 1 of 3 (8day-out)

hyb_protocol: Each Cy3 and Cy5 labeled antisense RNA (15 μl) solutions was mixed together, and was supplemented with 12.5 μl of 20× SSC (3 M NaCl, 0.3 M C6H5Na3O7•2H2O), 2.5 μl of 10% SDS. After heating (95°C) this hybridization solution for 2 min, then incubated on ice for 30 seconds. Formamide (5 μl) was added to the mixtures and used as hybridization solution, and incubated the hybridization solution at 42°C for 5 min. The pre-warmed hybridization solution was dropped onto DNA chip slides, and cover glass was placed over the solution without forming bubbles. These DNA chips were incubated in ArrayIt Hybridization Casette (Telechem International, Inc.), and hybridized 65°C for 16 hours. After hybridization, DNA chips were soaked in 2× SSC, 0.1% SDS solution at room temperature, and cover glasses were removed by gently rocking of the slides. DNA chips were washed by soaking the solution for 20 min, with occasionally gentle shaking. Chips were subsequently soaked in low stringency wash buffers (0.2× SSC, 0.1% SDS solution) and (0.05× SSC, 0.1% SDS solution) for 20 min each.

scan_protocol: Scanned on GenePix 4100A, and data was analyzed using GenePix Pro 6.0 software (Axon Instruments)

data_processing: Back ground signals were subtracted from raw data, and the raw data were performed Lowess normalization between Cy5 and Cy3. Data were transformed into Cy3/Cy5 ratios. These ratios were further transformed into Log2 ratio.

organism: Rana pirica

source_name: mRNA extracted from face part of tadpoles placed with the predator for full 8 days, labelled with Cy5

label_protocol: Total RNAs (5μg) were extracted from facial parts of tadpoles placed with the predator for full 8 days according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

extract_protocol: mRNA isolated using Invitrogen's FastTrack 2.0 kit.

tag: One group of tadpoles was placed with predator for 4 days to induce formation of the bulgy morph phenotype; the predator was then removed and the tadpoles were allowed to revert to the normal phenotype for 4 days. This group is termed 8 day out tadpoles. A second group of tadpoles was placed with the predator for the full 8 days.

source_name: mRNA extracted from face part of 8 day out tadpoles, labelled with Cy3

label_protocol: Total RNAs (5μg) were extracted from facial parts of 8 day out tadpoles according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

tag: One group of tadpoles was placed with predator for 4 days to induce formation of the bulgy morph phenotype; the predator was then removed and the tadpoles were allowed to revert to the normal phenotype for 4 days. This group is termed “8 day out tadpoles”. A second group of tadpoles was placed with the predator for the full 8 days.


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)3A

description: Replicate 3 of 3 (8day-out)

data_processing: Back ground signals were subtracted from raw data, and the raw data were performed Lowess normalization between Cy5 and Cy3. Data were transformed into Cy5/Cy3 ratios. These ratios were further transformed into Log2 ratio.

source_name: mRNA extracted from face part of 8 day out tadpoles, labelled with Cy5

label_protocol: Total RNAs (5μg) were extracted from facial parts of  8 day out tadpoles according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

source_name: mRNA extracted from face part of tadpoles placed with the predator for full 8 days, labelled with Cy3

label_protocol: Total RNAs (5μg) were extracted from facial parts of tadpoles placed with the predator for full 8 days according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.


title: Late_log_phase_phosphate_stress_bsy89280c0069_rep5

description: This slide measures gene expression during late log phase growth under phosphate stress as compared to expression without phosphate stress.

source_name: wild type in 87 micromolar phosphate SOW medium, late log phase LC17r

source_name: wild type in 10 micromolar phosphate SOW medium, late log phase RH1r


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)2B

description: Replicate 2 of 3 (8day-out)


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)3B

description: Replicate 3 of 3 (8day-out)


title: InputSpermD1 and ProtamineSpermD1, Replica 1, Slide 1

description: protamine bound DNA enrichment, replica 1


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 1, Slide 1


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 3, Slide 1


title: Late_log_phase_phosphate_stress_bsy89280c0039_rep3

source_name: wild type in 10 micromolar phosphate SOW medium, late log phase LC19r


title: InputFibroblast and MeDIPFibroblast, Replica 2, Slide 1

source_name: Primary fibroblasts

tag: chip antibody


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)1A

description: Replicate 1 of 3 (8day-out)

tag: One group of tadpoles was placed with predator for 4 days to induce formation of the bulgy morph phenotype; the predator was then removed and the tadpoles were allowed to revert to the normal phenotype for 4 days.  This group is termed “8 day out tadpoles”.  A second group of tadpoles was placed with the predator for the full 8 days.

tag: One group of tadpoles was placed with predator for 4 days to induce formation of the bulgy morph phenotype; the predator was then removed and the tadpoles were allowed to revert to the normal phenotype for 4 days.  This group is termed 8 day out tadpoles.  A second group of tadpoles was placed with the predator for the full 8 days.


title: InputFibroblast and MeDIPFibroblast, Replica 1, Slide 1


title: Tadpoles with induced bulgy morph phenotype and those reverting to normal from this phenotype (8day-out)2A

description: Replicate 2 of 3 (8day-out)


title: Late_log_phase_phosphate_stress_bsy89280c0047_rep4

tag: Axenic Synechococcus sp. WH 8102


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)3B

description: Replicate 3 of 3 (8day)

source_name: mRNA extracted from face part of control tadpole tissue, labelled with Cy5

label_protocol: Total RNAs (5μg) were extracted from facial parts of control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

tag: Standard tadpole (control), RNA extracted from a pooled sample

source_name: mRNA extracted from face part of bulgy induced tadpole tissue, labelled with Cy3

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

tag: Bulgy induced tadpole (experiment), RNA extracted from a pooled sample


title: Late_log_phase_phosphate_stress_bsy89280c0029_rep2

source_name: wild type in 87 micromolar phosphate SOW medium, late log phase LC16r


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)2B

description: Replicate 2 of 3 (8day)


title: TH2B, Replica 2, Slide 1

description: chIP-chip, Upstate Biotechnology Inc TH2B antibody 07-680, replica 2


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)2A

description: Replicate 2 of 3 (8day)

source_name: mRNA extracted from face part of bulgy induced tadpole tissue, labelled with Cy5

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

source_name: mRNA extracted from face part of control tadpole tissue, labelled with Cy3

label_protocol: Total RNAs (5μg) were extracted from facial parts of control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.


title: TH2B, Replica 1, Slide 1


title: H3K4Me3, Replica 2, Slide 1


title: InputSpermD1 and Histone-MNAseSpermD1, Replica 2, Slide 1


title: H3K4Me3, Replica 3 and 1, Slide 1


title: H3K4Me2, Replica 1 and 2, Slide 1


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)3B

description: Replicate 3 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)2B

description: Replicate 2 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)1A

description: Replicate 1 of 3 (8day)


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)3A

description: Replicate 3 of 3 (8day)


title: Late_log_phase_phosphate_stress_bsy89280c0017_rep1


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)3A

description: Replicate 3 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)1B

description: Replicate 1 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)2A

description: Replicate 2 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)2B

description: Replicate 2 of 3 (0hr)


title: Predator-specific morphological responses of tadpoles of Rana pirica (4day)1A

description: Replicate 1 of 3 (4days)


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)1B

description: Replicate 1 of 3 (0hr)


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)3B

description: Replicate 3 of 3 (0hr)


title: Predator-specific morphological responses of tadpoles of Rana pirica (8day)1B

description: Replicate 1 of 3 (8day)


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)3A

description: Replicate 3 of 3 (0hr)

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles and control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles and control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion). Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion). The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)1A

description: Replicate 1 of 3 (0hr)

hyb_protocol: Each Cy3 and Cy5 labeled antisense RNA (15 μl) solutions was mixed together, and was supplemented with 12.5 μl of 20× SSC (3 M NaCl, 0.3 M C6H5Na3O7•2H2O), 2.5 μl of 10% SDS.  After heating (95°C) this hybridization solution for 2 min, then incubated on ice for 30 seconds.  Formamide (5 μl) was added to the mixtures and used as hybridization solution, and incubated the hybridization solution at 42°C for 5 min.  The pre-warmed hybridization solution was dropped onto DNA chip slides, and cover glass was placed over the solution without forming bubbles.  These DNA chips were incubated in ArrayIt Hybridization Casette (Telechem International, Inc.), and hybridized 65°C for 16 hours.  After hybridization, DNA chips were soaked in 2× SSC, 0.1% SDS solution at room temperature, and cover glasses were removed by gently rocking of the slides.  DNA chips were washed by soaking the solution for 20 min, with occasionally gentle shaking.  Chips were subsequently soaked in low stringency wash buffers (0.2× SSC, 0.1% SDS solution) and (0.05× SSC, 0.1% SDS solution) for 20 min each.

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles and control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion).  Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion).  The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with Cy5 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.

tag: Bulgy induced tadpole (Experiment), RNA extracted from a pooled sample

label_protocol: Total RNAs (5μg) were extracted from facial parts of bulgy tadpoles and control according to the experiments, and double strand cDNA was synthesized using MessageAmpII aRNA Amplification Kit (Ambion).  Then, in vitro transcription to synthesize aminoallyl-labeled antisense RNA was performed using MessageAmpII aRNA Amplification Kit (Ambion).  The synthesized aminoallyl-labeled antisense RNAs (8μg) were coupled with  Cy3 using Mono-Reactive Dye Pack (GE Healthcare) according to the manufacture’s instructions.


title: Predator-specific morphological responses of tadpoles of Rana pirica (6hr)2A

description: Replicate 2 of 3 (0hr)

extract_protocol: mRNA isolated using Invitrogen's FastTrack 2.0 ki


title: Lb. helveticus DPC5389 replicates 1,2

status: Public on Jun 12 2009

city: Fermoy

first: Pawel

last: Kaleta

state: Co Cork

address: Moorepark

department: Biotechnology

country: Ireland

institute: TEAGASC

description:
raw_file: replicate1_(test) = 5389_1.txt
raw_file: replicate2_(test) = 5389_2.txt
raw_file: replicate1_(reference) = 5389_4571_1.txt
raw_file: replicate2_(reference) = 5389_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571

hyb_protocol: Genomic DNA hybridizations were carried out in metal chamber placed in water bath. Before hybridisation, 40 µl of purified sample was mixed with 10 µl of salmon sperm DNA (1 µg/ µl), 120 µl of pre-heated to 42°C salt-based hybridization buffer and heated for 3 min. at 95°C followed by 1 min. snap on ice. Final volume of 170 µl sample was applied on the OciChip™ array (Ocimum Biosolutions, Hyderabad, India) and hybridized for 24h at 42°C. Microarray slides were washed with pre-warmed washing buffer 1 (2x Salin-Sodium Citrate, 0.1% SDS) at 42°C on orbital shaker for 5 min, buffer 2 (1x SSC) at 30°C and buffer 3 (0.1x SSC) at 30°C. Washed slides were dried in a 50 ml conical-bottom tubes by centrifugation at room temperature for 1 min. at 500 rpm

scan_protocol: Scanned on Agilent 428 Array Scanner

data_processing: background subtracted data obtained from log2 of processed green signal/processed red signal, global normalization. Microprep and Genesis tools used

organism: Lactobacillus helveticus

source_name: Chromosome

label_protocol: Three micrograms of random primers and 10 µg of DNA were dissolved in distilled water up to the total volume of 41 µl was reached. The mixture was then centrifuged briefly, heated at 95°C for 5 min and cooled on ice for 3 min. The labeling process was performed by random-primed reaction (using hexamers) with 1.5 µl of dNTPs (5 mM dA/G/T, 2 mM dC), 1 µl of klenow fragment, exo¯ (5U/µl) and 1.5 µl (2 mM) of Cy3 dCTP (GE Healthcare, Bucks, UK) at 37°C for two hours followed by 15 min. incubation at 75°C to inactivate the enzyme. Purification of the labeling reaction was performed with Qiagen MinElute purification kit (Qiagen, Crawley, United Kingdom) according to manufacturer instructions. Purified labeled DNA (1 µl) was quantified using the NanoDrop ND1000 Spectrophotometer (MASON Technology, Dublin, Ireland) to minimize the amount of sample consumed by the measurement

extract_protocol: Large scale DNA extraction followed by sonication at 2Am for 15min with 30sec intervals

organism: Lactobacillus helveticus DPC 4571


title: Lb. helveticus CNRZ32 replicates 1,2

description:
raw_file: replicate1_(test) = CNRZ32_1.txt
raw_file: replicate2_(test) = CNRZ32_2.txt
raw_file: replicate1_(reference) = CNRZ32_4571_1.txt
raw_file: replicate2_(reference) = CNRZ32_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571

organism: Lactobacillus helveticus CNRZ32


title: Lb. helveticus DPC5367 replicates 1,2

description:
raw_file: replicate1_(test) = 5367_1.txt
raw_file: replicate2_(test) = 5367_2.txt
raw_file: replicate1_(reference) = 5367_4571_1.txt
raw_file: replicate2_(reference) = 5367_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Lb. helveticus DPC5607 replicates 1,2

description:
raw_file: replicate1_(test) = 5607_1.txt
raw_file: replicate2_(test) = 5607_2.txt
raw_file: replicate1_(reference) = 5607_4571_1.txt
raw_file: replicate2_(reference) = 5607_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Lb. helveticus DPC5352 replicates 1,2

description:
raw_file: replicate1_(test) = 5352_1.txt
raw_file: replicate2_(test) = 5352_2.txt
raw_file: replicate1_(reference) = 5352_4571_1.txt
raw_file: replicate2_(reference) = 5352_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Lb. helveticus DPC5364 replicates 1,2

description:
raw_file: replicate1_(test) = 5364_1.txt
raw_file: replicate2_(test) = 5364_2.txt
raw_file: replicate1_(reference) = 5364_4571_1.txt
raw_file: replicate2_(reference) = 5364_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Lb. helveticus DPC5365 replicates 1,2

description:
raw_file: replicate1_(test) = 5365_1.txt
raw_file: replicate2_(test) = 5365_2.txt
raw_file: replicate1_(reference) = 5365_4571_1.txt
raw_file: replicate2_(reference) = 5365_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Lb. helveticus DPC5360 replicates 1,2

description:
raw_file: replicate1_(test) = 5360_1.txt
raw_file: replicate2_(test) = 5360_2.txt
raw_file: replicate1_(reference) = 5360_4571_1.txt
raw_file: replicate2_(reference) = 5360_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571


title: Test array design TA4_2520025_array 2_PMT gain 400

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

description: Testing 244K 60-mer or 40-mer probes designed using eArray

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

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain levels 400 and 500 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix 5 (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 020025_D_20080421_gal to obtain signal intensities. The background-subtracted median signal intensity (SI) was reported. A threshold SI (mean + 2 × standard deviation of the lowest three spike-in RNA concentrations) was set for each array. Any spot with a SI smaller than the threshold was flagged as absent, whereas others were considered present and thus probes deposited on these spots were regarded as positive probes. Negative control spots were also checked to make sure their SI did not exceed those of the lowest spike-in RNAs.

organism: Eisenia fetida

source_name: Pooled RNA isolated from adult, juvenile and cocoon earthworms

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

growth_protocol: Earthworms were kept in moistened sphagnum peat (pH 6.5–7.5, moisture content 50%) and fed ad libitum on a diet of with Magic Worm Food (Carolina Biological Supply).

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adults bearing clitelum, juveniles and cocoons were pulled out of the culture immediately before being used for RNA extraction.

value: whole body or cocoon

value: varied


title: Lung C57 OVA v Lung  C57 PBS rep1

source_name: C57 PBS treatment

label_protocol: cDNA was made from total RNA (>20μg) using Superscript II, anchored polyT(V)N (2μg/μL) and an aminoallyl dNTP mix. The RNA was hydrolysed, the cDNA purified then coupled to Cy3 or Cy5 NHS esters (detailed protocols can be obtained from www.microarray.adelaide.edu.au)

tag: treatment

source_name: C57 OVA treatment


title: Test array design TA4_2520025_array 1_PMT gain 400

tag: tissue


title: Test array design TA4_2520025_array 1_PMT gain 500


title: Lb. helveticus DPC5394 replicates 1,2

description:
raw_file: replicate1_(test) = 5394_1.txt
raw_file: replicate2_(test) = 5394_2.txt
raw_file: replicate1_(reference) = 5394_4571_1.txt
raw_file: replicate2_(reference) = 5394_4571_2.txt
Four replicates of hybridization to the reference fully sequenced genome of Lb. helveticus DPC4571

tag: strain


title: Test array design TA2_2520023_array 2_PMT gain 400

description: Testing 244K 60-mer probes designed using eArray

data_processing: The scanned images were analyzed with GenePix 5 (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 020023_D_20080421_gal to obtain signal intensities. The background-subtracted median signal intensity (SI) was reported. A threshold SI (mean + 2 × standard deviation of the lowest three spike-in RNA concentrations) was set for each array. Any spot with a SI smaller than the threshold was flagged as absent, whereas others were considered present and thus probes deposited on these spots were regarded as positive probes. Negative control spots were also checked to make sure their SI did not exceed those of the lowest spike-in RNAs.


title: Test array design TA4_2520025_array 2_PMT gain 500


title: MSC-HIP_donor5-95yrs_P2

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were hybridized with 15 µg amplified RNA and washed with a fluidics station 450 (Affymetrix).

scan_protocol: GeneChip Human Genome U133_Plus_2.0 (Affymetrix) were scanned with GeneChip scanner 3000 (Affymetrix)

label: Biotin

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor5 (85 years old) - passage 2

label_protocol: Two µg total RNA was amplified with GeneChip one-cycle target labeling kit (Affymetrix, High Wycombe, United Kingdom) according to the manufacturers instructions. Quality of amplified RNA was controlled by LabChip technology.

growth_protocol:
MSC were isolated from the femoral head (caput femoris; HIP) of  elderly patients that received femoral head prosthesis. All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. The bone was flushed with PBS under sterile conditions. Subsequently the mononuclear cell fraction was isolated by ficoll density fractionation and then taken into culture.
The culture conditions have been first described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625) and in our previous work (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use.  MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cells were harvested by trypsination after passage 2

tag: mesenchymal stromal cells from human bone marrow

tag: (alternatively named mesenchymal stem cells)

tag: 85 year old human donor

tag: passage 2


title: Test array design TA2_2520023_array 2_PMT gain 500

tag: age


title: MSC-HIP_donor6-85yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor6 (85 years old) - passage 2


title: Test array design TA3_2520024_array 2_PMT gain 500

data_processing: The scanned images were analyzed with GenePix 5 (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 020024_D_20080421_gal to obtain signal intensities. The background-subtracted median signal intensity (SI) was reported. A threshold SI (mean + 2 × standard deviation of the lowest three spike-in RNA concentrations) was set for each array. Any spot with a SI smaller than the threshold was flagged as absent, whereas others were considered present and thus probes deposited on these spots were regarded as positive probes. Negative control spots were also checked to make sure their SI did not exceed those of the lowest spike-in RNAs.


title: Test array design TA2_2520023_array 1_PMT gain 500


title: MSC-HIP_donor1-79yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor1 (79 years old) - passage 2

tag: 79 year old human donor


title: Test array design TA2_2520023_array 1_PMT gain 400


title: Test array design TA3_2520024_array 2_PMT gain 400


title: Test array design TA3_2520024_array 1_PMT gain 500


title: MSC-BM_donor275-50yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor275 (50 years old) - passage 2

growth_protocol:
20ml of bone marrow aspirate were taken from the iliac crest (BM) from healthy donors (healthy donors for allogeneic bone marrow transplantation). All samples were taken after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Heidelberg. The mononuclear cell fraction was isolated by ficoll density fractionation and then taken into culture.
The culture conditions have been first described by M. Reyes and colleagues (Reyes et al., 2001, Blood, 98, 2615-2625) and in our previous work (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). The medium consists of 58% Dulbecco´s Modified Eagles Medium-Low Glucose (DMEM-LG, Cambrex, Apen, Germany) and 40% MCDB201 (Sigma, Deisenhofen, Germany), 2% FCS (HyClone, Bonn, Germany), supplemented with 2 mM L-Glutamine, 100 U/ml Pen/Strep (Cambrex), 1% insulin transferrin selenium, 1% linoleic acid bovine serum albumin, 10 nM dexamethasone, 0.1 mM L-ascorbic-acid-2-phosphate (all from Sigma), PDGF-bb and EGF (10ng/ml each, R&D Systems, Wiesbaden, Germany). Tissue culture flasks were coated with 10 ng/ml fibronectin (Sigma) before use.  MSC were cultured at 37°C in a humidified atmosphere containing 5% carbon dioxide with medium changes twice a week. After 7-10 days initial colonies were replated in a new culture flask (passage 1, P1). Upon subconfluent growth (70%) cells were always replated at a density of 10(4) cells/cm(2).

tag: 50 year old human donor


title: Test array design TA1_2520022_array 2_PMT gain 500

data_processing: The scanned images were analyzed with GenePix 5 (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GAL grid file 020022_D_20080421_gal to obtain signal intensities. The background-subtracted median signal intensity (SI) was reported. A threshold SI (mean + 2 × standard deviation of the lowest three spike-in RNA concentrations) was set for each array. Any spot with a SI smaller than the threshold was flagged as absent, whereas others were considered present and thus probes deposited on these spots were regarded as positive probes. Negative control spots were also checked to make sure their SI did not exceed those of the lowest spike-in RNAs.


title: MSC-HIP_donor8-85yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor8 (85 years old) - passage 2


title: Erythroid AcH4

status: Public on Jun 13 2009

city: London

first: Steve

last: Best

address: 125 Coldharbour Lane

department: The James Black Centre

country: United Kingdom

institute: King's College London

description: Images generated at 635 and 532 nm as per NimbleGen ChIP protocol

hyb_protocol: Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.

scan_protocol: GenePix scanner at 5 micron resolution.

data_processing: Images processed and data generated using NimbleScan v2 exactly as described in NimbleChip Arrays User's Guide. The Scaled Log2-ratio is the ratio of the input signals for the experimental and test samples co-hybridised to the array. The log2-ratio is computed and scaled to centre the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: AcH4 Erythroid d10 ChIP input sample

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. Acetylated Histone H4 ChIP study. Sample precessed as ChIP input.

tag: cell type

value: erythroid cells

source_name: AcH4 Erythroid d10 ChIP test sample

extract_protocol: ChIP material generated from 30 million cells using the NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.


title: Test array design TA3_2520024_array 1_PMT gain 400


title: MSC-HIP_donor7-53yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (caput femoris) of donor7 (53 years old) - passage 2

tag: 53 year old human donor


title: JB1ts_x_JB2ts_5dpi_9h_31C_III

status: Public on Jun 11 2009

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: Experiment to measure effects after temperature-mediated (31 °C) inactivation of the b heterodimer in planta in RAb1ts/RAb2ts. Control Experiment is FB1/FB2 wildtype infection under restrictive conditions. RAb1ts (a1,bW1bE1ts) and RAb2ts (a2,bW2bE2ts) are compatible strains that carry temperature sensitive bE allels, which is active under permissive conditions (22°C) and inactive under restrictive conditions (31°C). The mating types are indicated in brackets. The strains are derivatives of JB1 (a1,∆b) and JB2 (a2,∆b) with integration of bW/bEts into the ip-locus (carboxin resistance).

hyb_protocol: Affymetrix EukGE-2V4 on GeneChip Fluidics Station 400

scan_protocol: Affymetrix GSC3000

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: Tumor material from maize leaves 5 days post RAb1ts/RAb2ts mixed infection at 31°C

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50 °C for first strand cDNA synthesis

growth_protocol:
U. maydis strains were grown at 28°C in YEPS (Tsukuda et al., 1988) medium as pre-culture for plant infections. Plant infections were performed as described by (Brachmann et al., 2001).
- Brachmann, A., Weinzierl, G., Kämper, J., and Kahmann, R. (2001) Mol Microbiol 42(4): 1047-63.
- Tsukuda, T., Carelton, S., Fotheringham, S., and Holloman, W.K. (1988). Mol Cell Biol 8: 3703-09.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer's instructions. RNA samples were further column purified using (Qiagen  RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

treatment_protocol: U. maydis RAb1ts/RAb2ts infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Prior to infection with U. maydis maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. After mixed infection with RAb1ts/RAb2ts the plants were kept at 22 °C. 111 hours post infection plants were shifted for 9 hours to 31 °C, inactivating b function after RAb1ts/RAb2ts but not after FB1/FB2 infection. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period. Sample material from at least 3 independent replicates of RAb1ts/RAb2ts infections at 31°C was directly frozen in liquid nitrogen for RNA-extraction.


title: Test array design TA1_2520022_array 2_PMT gain 400


title: Erythroid AcH3

source_name: AcH3 Erythroid d10 ChIP input sample

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. AcH3 ChIP study. Sample precessed as ChIP input.

extract_protocol: ChIP material generated from 30 million cells using the NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol

source_name: AcH3 Erythroid d10 ChIP testsample

label_protocol: Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol.

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. AcH3 ChIP study. Sample precessed as ChIP test.


title: FB1_x_FB2_5dpi_9h_31C_III

description: Control experiment (base line) to measure effects after temperature-mediated (31 °C) inactivation of the b heterodimer in planta in RAb1ts/RAb2ts. FB1 (a1,bW1bE1) and FB2 (a2,bW2bE2) are compatible wild-type strains. Mating types are indicated in brackets.

source_name: Tumor material from maize leaves 5 days post FB1/FB2 mixed infection at 31°C

treatment_protocol: U. maydis FB1/FB2 infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Prior to infection with U. maydis maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. After mixed infection with FB1/FB2 the plants were kept at 22 °C. 111 hours post infection plants were shifted for 9 hours to 31 °C, inactivating b function after RAb1ts/RAb2ts but not after FB1/FB2 infection. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period. Sample material from at least 3 independent replicates of FB1/FB2 infections at 31°C was directly frozen in liquid nitrogen for RNA-extraction.

value: FB1 (a1,bW1bE1) and FB2 (a2,bW2bE2)


title: JB1ts_x_JB2ts_5dpi_9h_31C_II

value: RAb1ts (a1,bW1bE1ts) and RAb2ts (a2,bW2bE2ts)


title: FB1_x_FB2_5dpi_9h_31C_II


title: Erythroid PolII

source_name: PolII Erythroid d10 ChIP input sample

label_protocol: Followed NimbleGen EZ-ChIP kit exactly as per manufacturer's protocol

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. PolII ChIP study. Sample processed as ChIP input.

source_name: PolII Erythroid d10 ChIP test sample

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. PolII ChIP study. Sample processed as ChIP test.


title: MSC-BM_donor277-21yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor277 (21 years old) - passage 2

tag: 21 year old human donor


title: Test array design TA1_2520022_array 1_PMT gain 400

source_name: Pooled RNA isolated from adult, juvenile and cocoon earthworms


title: FB1_x_FB2_5dpi_9h_31C_I


title: MSC-BM_donor300-24yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor300 (24 years old) - passage 2

tag: 24 year old human donor


title: JB1ts_x_JB2ts_5dpi_22C_I

description: Control experiment to test if in planta development of U. maydis strains RAb1ts/RAb2ts (this sample), which express temperature sensitive b heterodimers, is comparable to wild-type FB1/FB2 crossings at permissive conditions (22°C). RAb1ts (a1,bW1bE1ts) and RAb2ts (a2,bW2bE2ts) are compatible strains that carry temperature sensitive bE allels, which is active under permissive conditions (22°C) and inactive under restrictive conditions (31°C). The mating types are indicated in brackets. The strains are derivatives of JB1 (a1,∆b) and JB2 (a2,∆b) with integration of bW/bEts into the ip-locus (carboxin resistance).

source_name: Tumor material from maize leaves 5 days post RAb1ts/RAb2ts mixed infection at 22°C

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50 °C for first strand cDNA synthesis.

treatment_protocol: U. maydis RAb1ts/RAb2ts infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Prior to infection with U. maydis maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. After mixed infection with RAb1ts/RAb2ts the plants were kept at 22 °C. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction.


title: FB1_x_FB2_5dpi_22C_I

description: Control experiment to test if in planta development of U. maydis strains RAb1ts/RAb2ts, which express temperature sensitive b heterodimers, is comparable to wild-type FB1/FB2 (this sample) crossings at permissive conditions (22°C). FB1 (a1,bW1bE1) and FB2 (a2,bW2bE2) are compatible wild-type strains. Mating types are indicated in brackets.

source_name: Tumor material from maize leaves 5 days post FB1/FB2 mixed infection at 22°C

treatment_protocol: U. maydis FB1/FB2 infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Prior to infection with U. maydis maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. After infection the plants were kept at 22 °C. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction.


title: pmel-1 cd8+ t cells, naive (CD44-), stimulated, biological replicate 3

status: Public on Jun 10 2009

city: Bethesda

first: Zachary

last: Borman

state: MD

address: National Institutes of Health, 9000 Rockville Pike, Building 10 CRC 3W-5816

department: Surgery Branch

institute: National Cancer Institute

hyb_protocol: Hybridization cocktail containing 10 mg of fragmented biotinylated cRNA and oligo B2 and EHC as internal controls, was hybridized to Affymetrix Mouse 430 2.0 microarrays for 16 hours at 45ºC according to the manufacturer’s protocol. Microarrays were washed and stained with streptavidin-phycoerythrin (SAPE) and anti-streptavidin antibody using the Affymetrix Fluidics Station 450.

scan_protocol: Laser detection (Affymetrix Scanner 3000 7G) was performed and signal intensities quantified (Affymetrix Genechip Command Console).

data_processing:
Gene expression was quantitated with the Affymetrix Expression Console (Affymetrix). Affymetrix signal values from the Expression Console software were normalized with an adaptive variance-stabilizing, quantile-normalizing transformation (P. J. Munson, GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html). The transform, termed S10, is scaled to match the logarithm transform (base 10).
Differential gene expression was assessed by analysis of variance (ANOVA). A one-factor ANOVA of four treatment levels was performed, followed by post hoc tests comparing naïve to memory cell populations in the unstimulated and stimulated states. A fold change (FC) of at least 2 and a false discovery rate (FDR) of 2% (53) was required to declare a probeset differentially expressed.

label_protocol: Total RNA was processed using Expression 3’ amplification One-cycle Target Labeling and Control Reagents kit according to the manufacturer’s directions (Affymetrix). Briefly, 1.5 mg of total RNA was reverse transcribed employing T7-(dT). Primer yielding cDNA, followed by cleanup. Biotinylated cRNA was synthesized by in vitro transcription, cleaned, and fragmented. Total RNA, cRNA and fragmented cRNA were visualized using RNA Flash gel (Lonza).

growth_protocol: Pmel-1 CD8+ T cells were grown in RPMI w/antibiotics and 10 cetus units of IL2 in a 37 degree Celsius incubator with 5% carbon dioxide. Cells were grown for two weeks.

extract_protocol: Cells were lysed using RLT buffer and applied to Qiashredder columns treated with DNAase (Qiagen). Total RNA was isolated using RNeasy Mini kits (Qiagen).

treatment_protocol: Pmel-1 CD8+ T cells were enriched for naïve (CD44-) or central memory (CD44+) populations. Cells were stimulated with plate-bound CD3/CD28 and grown for one week and restimulated with allogeneic feeders pulsed with hgp100(25-33) peptide. Cells received either a final 4-hour CD3/CD28 stimulation or no stimulation after the two weeks, and total RNA was then extracted.

tag: genotype

value: Pmel-1 transgenic mouse

value: Naïve (CD44-) CD8 T cells


title: target strand labeled: Sense - rep1

type: other

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Mixed RNA form 5 tissue types of Chinese Spring wheat cultivar.  Tissue types were; i.Germinated seed (germinated on wetted filter paper in a petri-dish in the dark for two days), ii.Shoot (Feekes 1.2, emergence with second leaf unfolded), iii.Flag leaf (Feekes 9.0, flag leaf stage with ligule emerged), iv.Spike pre-anthesis (Feekes 10.5, heading complete), and v.Spike post-anthesis (Feekes 10.5.3, flowering complete to base of spike).

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

molecule: other

organism: Triticum aestivum

source_name: whole plant (target strand labeled: Sense)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  For each tissue type except ‘Germinated seed’, six seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate). Seedlings were grown to the appropriate growth stages for tissue collection in a greenhouse with a stable temperature of  25±2ºC and a 16 h light/8 h dark cycle.

extract_protocol: Trizol Plus RNA Purification (Invitrogen)

tag: Chinese Spring (Germplasm Name); PO:0000003 whole plant, (Organism Part); PO:0007033 whole plant growth stages (Development Stage); peat/perlite/soil (Growth Media).


title: pmel-1 cd8+ t cells, naive (CD44-), unstimulated biological replicate 2


title: Sir4 wild type

status: Public on Aug 01 2009

city: Los Angles

first: Adam

middle: Samuel

last: Sperling

state: CA

address: 332 Boyer Hall

department: Biological Chemistry

institute: UCLA

description: Sir4 ChIP in wild type yeast

hyb_protocol: Done according to Affymetrix 500K protocol

data_processing:
Data were quantile normalized to 13 input samples in the Affymetrix Tiling Analysis Software using the following parameters: PM only; Bandwidth = 50. Log2 (IP/input) is reported in bar files.
.bar files were generated by quantile normalization of 2 sample files and 13 control files.

organism: Saccharomyces cerevisiae

source_name: Sir4 ChIP

growth_protocol: Grown to log phase in YPD

extract_protocol: Done as in Hecht et al., Nature 1996.

value: Wild Type

tag: antibody

source_name: input DNA

tag: sample type

value: input DNA


title: pmel-1 cd8+ t cells, memory (CD44+), stimulated biological replicate 3

value: central memory (CD44+) CD8 T cells


title: pmel-1 cd8+ t cells, memory (CD44+), unstimulated, biological replicate 3


title: Test array design TA1_2520022_array 1_PMT gain 500

tag: tissue


title: pmel-1 cd8+ t cells, naive (CD44-), stimulated, biological replicate 1


title: 6 hours no HGF n7 h6hgf0n7 experiment TR5

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.

hyb_protocol: arrays were hybridized as suggested by manufacturer

scan_protocol: arrays were scanned as suggested by manufacturer

data_processing:
Two of the time-course experiments, done independently, were analyzed. From digitized image data
files of raw data, background-normalized image data (CEL
files) were generated. Microarray quality control and
statistical validation was done using Bioconductor.
The presence of hybridization/construction artifacts was
evaluated with the fitPLM function (Bioconductor package
affyPLM). The probes (PM) intensity distribution was
evaluated using hist function (Bioconductor package affy).
Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
in TR7 experiment were discarded due to low quality. TR5
and TR7 experiments were then analyzed separately. Probe
set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
method. Probe sets in TR5 and
TR7 were filtered separately to have an interquantile range
for each probe set greater than 0.4.
TR5 and TR7, represented as ratio with
respect to probe sets mean across the experiments, were
combined in a unique exprSet object. The identification of
differentially expressed genes associated to the HGF effect
was addressed using linear modeling approach. For
assessing differential expression, an empirical Bayes
method was used to moderate the SE of the estimated
log-fold changes together with the BH correction of the
false discovery rate.

source_name: SK-OV-3 ovarian carcinoma cells

label_protocol: cRNAs were generated as suggested by Affymetrix

extract_protocol:
Total RNA was extracted and purified from SK-OV-3 cell
lines at each time point using the Concert Cytoplasmic
RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
suggested by the manufacturer

treatment_protocol:
Exponentially growing cells were cultured for 48 hours in
the presence of pure recombinant HGF (R&D Systems,
Minneapolis, MN) at the concentration of 50 ng/mL or
control medium. Apoptosis was then induced by adding
fresh medium, with or without HGF, supplemented with
10 Amol/L CDDP.

tag: cell line


title: pmel-1 cd8+ t cells, memory (CD44+), stimulated, biological replicate 1


title: pmel-1 cd8+ t cells, memory (CD44+), stimulated biological replicate 2


title: 6 hours with HGF n9 h6hgf1n9 experiment TR5


title: target strand labeled: Antisense - rep1

source_name: whole plant (target strand labeled: Antisense)

label_protocol: Affy- Whole transcript target preparation


title: pmel-1 cd8+ t cells, naive (CD44-), stimulated biological replicate 2


title: 24 hours no HGF n16 h24hgf0n16 experiment TR7


title: JB1ts_x_JB2ts_5dpi_9h_31C_I

tag: strain


title: pmel-1 cd8+ t cells, memory (CD44+), unstimulated biological replicate 2


title: 6 hours no HGF n8bis h6hgf0n8bis experiment TR7


title: pmel-1 cd8+ t cells, memory (CD44+), unstimulated, biological replicate 1


title: 6 hours with HGF n10 h6hgf1n10 experiment TR7


title: pmel-1 cd8+ t cells, naive (CD44-), unstimulated, biological replicate 1


title: 24 hours with HGF n17 h24hgf1n17 experiment TR5


title: 24 hours with HGF n18 h24hgf1n18 experiment TR7


title: MSC-BM_donor279-25yrs_P2

source_name: Mesenchymal stromal cells from human bone marrow (iliac crest) of donor279 (25 years old) - passage 2

tag: mesenchymal stromal cells from human bone marrow

tag: (alternatively named mesenchymal stem cells)

tag: 25 year old human donor


title: 24 hours no HGF n15 h24hgf0n15 experiment TR5