title: Comparative Genome Hybridization of Porphyromonas gingivalis strains W83 and AJW4

city: New York

first: Emil

last: Kozarov

state: NY

institute: Columbia University

hyb_protocol: The pellet was resuspended in 60 µl of hybridization buffer containing 50% formamide/5XSSC/1%SDS/50 µl/ml sheared salmon sperm DNA. Before hybridization the labeled DNA was heated twice at 95oC for 5 min. Independently labeled genomic DNA was used for each slide. Microarray prehybridization, hybridization and severity washes were performed according to JCVI/TIGR protocol http://pfgrc.jcvi.org/index.php/microarray/protocols.html.

scan_protocol: Hybridized, washed slides were scanned for Cy3 and Cy5 fluorescence intensities using Agilent microarray scanner.  The TIF format images were analyzed using GenePix 6.0 software (Molecular Devices Corporation, Sunnyvale, CA) producing GPR format image files. Data was assembled from four independent array experiments. Data were log2-transformed and normalized using GINGKO 1.0 software (LOWESS and Histogram Mode Centering from JCVI, PFGRC). Additionally, background correction and the within-array (LOWESS) and between arrays (Aquantile) image data normalization resulting in a table with numerical values were carried out using SAOPMD (Significance Analysis for Oral Pathogen Microarray Data) software tool at http://www.brop.org/saopm.

data_processing: Value column data were generated analyzing GPR and MEV files of 16-bit format images in BROP and GINKGO software packages. Background correction, normalization, within-microarray normalization, statistical adjustment and between-array normalization were done using BROP and GINKGO.

organism: Porphyromonas gingivalis

source_name: Porphyromonas gingivalis AJW4 genomic DNA

label_protocol: Microbial genomic DNA’s labeling, prehybridization and hybridization was performed using protocols utilized by The Institute for Genomic Research (TIGR). In short, genomic DNA was digested with BfuCI (New England Biolabs, Ipswich, Mass.), 1 unit/1µg of DNA for 5 min. on ice to average fragment sizes of 2-5 Kb. For a 39 µl reaction, 4 µg of DNA was combined with 3 µg of random hexamers (Invitrogen, Carlsbad, Calif.), incubated at 100 o C for 10 min and chilled on ice. The volume of reaction was adjusted to 50 µl by adding the components to final concentration as follows: 1X Eco Pol (Klenow) buffer, 0.2 mM dNTP/aa-UTP labeling mix (Invitrogen/Sigma) and 20 units of the Klenow fragment (NEB). After overnight incubation in 37oC water bath, Klenow fragment was inactivated by adding 5 µl of 0.5M EDTA. Unincorporated aa-dUTP and free amines were removed using PCR purification kit (Qiagen). Labeled DNA was eluted with 60 µl of 0.1M KPO4 buffer, pH 8.5 and dried in a Speed Vac for 1h. The dried DNA pellet was dissolved in 4.5 µl of 0.1M sodium carbonate buffer, pH 9.3 and 4.5 µl of the appropriate Cy dye (Amersham, Piscataway, NJ) was added.  After incubation in dark for 1h at room temperature dye-coupled DNA samples were purified with a PCR purification kit (Qiagen), eluted with 60 µl of PE buffer and dried in a Speed Vac for 1h.

growth_protocol: Porphyromonas gingivalis strains were grown anaerobically at 37o C on blood agar plates (BAP) and in Tryptic Soy Broth (Difco/BD, Franklin Lakes, NJ) supplemented with 0.5% yeast extract, 0.0.5% L-cysteine, 0.05 mg/ml hemin and 0.1mg/ml vitamin K1.

extract_protocol: P. gingivalis genomic DNA was extracted from strains using the DNeasy Tissue Kit (Qiagen, Germantown, Maryland) according to the manufacturer’s instructions.

treatment_protocol: DNA extraction and labeling

tag: strain

value: tester

source_name: Porphyromonas gingivalis W83 genomic DNA

value: control


title: Universal human reference RNA non-amplified EM8XT17

status: Public on Jul 28 2011

type: RNA

city: Kamakura

first: Hiroko

last: Sudo

state: Kanagawa

address: 6-10-1 Tebiro

department: New Frontiers Research Laboratories

country: Japan

institute: Toray Industries, Inc.

description: Used in Fig. 1 and 2

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.. The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: ScanArray Lite (Perkin Elmer) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments). Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing:
F635 Median column as Red signal. The raw data of each spot was globally normalized by adjusting the median signal intensity for each DNA chip. To be equal.
The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

molecule: total RNA

organism: Homo sapiens

source_name: Universal human reference RNA

label_protocol:
Biotinylated UTP was incorporated into cDNA during reverse transcription. After hybridization, the microarrays were post-labled using nucleic acid dendrimers attached with Oyster650 dye (Genisphere).
For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol: Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

tag: method

tag: sample type

value: Mixture of ten human cell lines


title: Chinese hamster ovary (CHO) cell culture_8

city: Dublin

first: Colin

last: Clarke

address: Collin's Av.

department: NICB

country: Ireland

institute: Dublin City University

description: CHO gene expression data

hyb_protocol: A pre-qualified standard curve reagent consisting of fragmented biotinylated cRNA (Hill AA, Brown EL, Whitley MZ, Tucker-Kellogg G, Hunter CP, Slonim DK. 2001. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biology 2, 12, Research 0055.1-0055.13) was included in all hybridization reactions. Hybridisation solution (1 mol/L NaCl, 20 mmol/L EDTA, 100 mmol/L 2-(N-morpholino)ethanesulfonic acid, and 0.01% Tween 20) was used to pre-hybridise custom WyeHamster2a oligonucleotide microarrays for 10 min at 45oC and 60 rpm. The prehybridisation solution was removed and replaced with 200 ul hybridisation solution containing 0.025 ug/ul fragmented cRNA. The arrays were hybridised for 16 hrs at 45oC and 60 rpm in a Hybridization Oven 640 (Affymetrix). Arrays were subsequently washed and stained with streptavidin-phycoerythrin solution (2 mg/ml acetylated BSA and 10 ug/ml streptavidin R-phycoerythrin; Molecular Probes) in a Fluidics Station 450 (Affymetrix) as per manufacturer's instructions.

scan_protocol: WyeHamster2a arrays were scanned on an GCS GeneChip GeneArray scanner (Affymetrix) as per manufacturer's instructions.

data_processing: All microarray data were pre-processed using the RMA algorithm

label: biotin

organism: Cricetulus griseus

source_name: Cell lysate

label_protocol: 5 ug of Total RNA from each sample underwent cDNA synthesis, followed by cleanup and overnight IVT amplification, labeling and subsequent cleanup using the GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents (#900493, Affymetrix) according to manufacturer's instructions (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf).

growth_protocol: All samples were from production cell lines and were grown in replicate suspension cultures using proprietary chemically-defined culture media at both shake flask and benchtop bioreactor scale. Cultures were maintained at 37oC (Pre-temperature shift (Ts) or at either 31oC or 29.5oC (Post-Ts).

extract_protocol: Total RNA was isolated using the RNeasy kit according to the manufacturer's instructions. RNA quantity and purity were assessed at 260 nm and 280 nm using a Nanodrop (Labtech Int.) and Spectramax Spectrophotometer (Molecular Devices). A Bioanalyser 2100 (Agilent Technologies) was used to qualitatively assess RNA after isolation, biotin-labeling and fragmentation.

treatment_protocol: Samples were taken down at discrete time (day) intervals that ranged between 3-14 days of culture. Typically, cell pellets of 5x10^6 cells were lysed in 1ml RLT lysis buffer containing beta-mercaptethanol (RNeasy Mini Prep kit, Qiagen), and stored at -80oC until required.

tag: growth rate

tag: temperature

tag: qammonia

tag: qlactate

tag: cell viability

tag: seeding density

tag: cell density

tag: titre

tag: qproductivity


title: Chinese hamster ovary (CHO) cell culture_9

description: CHO gene expression data


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-4, rep 3

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

country: USA

institute: University of Michigan

description: Biological replicate 3 of 3.

hyb_protocol: 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 Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: LNCaP prostate cancer stem cells, PCAT1 siRNA-4

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Cells were grown in RPMI 1640 (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer’s instructions.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and transfected with 20uM experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating.  Knockdowns were performed with Oligofectamine and Optimem.  Knockdown efficiency was determined by qPCR.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer

tag: treatment

source_name: LNCaP prostate cancer stem cells, control siRNA

tag: tissue

value: siRNA-control


title: Universal human reference RNA non-amplified EM8XT01

description: Used in Fig. 1 and 2


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-4, rep 1

description: Biological replicate 1 of 3.


title: Chinese hamster ovary (CHO) cell culture_6

description: CHO gene expression data


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-4, rep 2

description: Biological replicate 2 of 3.


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-3, rep 3

description: Biological replicate 3 of 3.

source_name: LNCaP prostate cancer stem cells, PCAT1 siRNA-3


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 3

description: Biological replicate 3 of 3.

source_name: LNCaP prostate cancer stem cells, PCAT1 siRNA-2


title: C. elegans: Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 4

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 4 of 4.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the “normexp” method (Ritchie et al., 2007). The arrays were lowess normalized individually (“normalizeWithinArrays option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans dauer-exit-12hours

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Mixed stage worms were grown on 10 cm NGM plates seeded with 10-15 young adults, and harvested on day 5 for RNA extraction. Dauer larvae were grown in liquid culture in S-medium at 22 C and were harvested on day 12. For dauer-exit time-course, about 200 purified dauers were seeded onto 10cm NGM plates spotted with 2ml of OP50 and allowed to recover at 20C. These worms were washed off at the 12hour time-point and used for RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: N2 Bristol

source_name: C. elegans mix-stage

value: mix-stage


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 2

description: Biological replicate 2 of 3.


title: C. elegans: Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 3

description: Biological replicate 3 of 4.

tag: strain


title: Chinese hamster ovary (CHO) cell culture_5

description: CHO gene expression data


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-3, rep 1

description: Biological replicate 1 of 3.


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-3, rep 2

description: Biological replicate 2 of 3.


title: Chinese hamster ovary (CHO) cell culture_2

description: CHO gene expression data


title: Chinese hamster ovary (CHO) cell culture_1

description: CHO gene expression data


title: LNCaP Cell Line, Control siRNA versus PCAT1-siRNA-2, rep 1

description: Biological replicate 1 of 3.


title: C. elegans: Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 2

description: Biological replicate 2 of 4.


title: MC3T3 cell line siTwist1 2

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

description: Samples used for hybridization consisted of  RNA extracts from MC3T3-E1 cells treated with siScr or siTwist1.

hyb_protocol: standard Affymetrix protocol

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing: Affymetrix murine MOE 430 2.0 gene chips were utilized. GeneChip .CEL files were subjected to RMA normalization using the GeneSpring GX 7.3. Standard Affymetrix internal control genes were used to check the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control gene, GAPDH. Acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine if hybridization of target RNA to the array occurred properly. GeneSpring Gx 7.3 (Agilent technologies) was used for normalization, clustering, and filtering. Individual clusters were then analyzed for functional relatedness using PANTHER classification.

organism: Mus musculus

source_name: MC3T3 cell line siTwist1

label_protocol: The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

growth_protocol: MEM-alpha medium/10% FBS/1%Pen-Strep for 24 hours then treated according to treatment protocol.

extract_protocol: RNA collection with Trizol Reagent.  Isolated RNA was subjected to additional purification using RNeasy Mini Kit (Qiagen). RNA integrity testing of all six samples was performed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA 6000 Nano Assay.

treatment_protocol: 5.0 ul Lipofectamine 2000 and 500 ul OPTI-MEM were mixed and incubated for 5 minutes at room temperature.  8 ul siRNA was mixed with 500 ul OPTI-MEM, followed by mixing of Lipofectamine/OPTI-MEM and siRNA/OPTI-MEM and incubation at room temperature for 20 minutes. The siRNA mixture was added to cells and incubated for 4-6 hours.   Then siRNA mixture was removed, MEM-alpha media/10%FBS/1%Pen-Strep was added, and cells were incubated for an additional 48 hours before RNA collection with Trizol Reagent.

tag: sirna


title: C. elegans: Dauers vs Mix-Stage, Biological replicate 3

description: Biological replicate 3 of 4.

source_name: C. elegans dauers

value: dauers


title: Chinese hamster ovary (CHO) cell culture_4

description: CHO gene expression data


title: MC3T3 cell line siTwist1 1


title: MC3T3 cell line siScrambled 3

source_name: MC3T3 cell line siScrambled

value: siScrambled


title: MC3T3 cell line siScrambled 2


title: C. elegans: Dauer-Exit (12hrs) vs Mix-Stage, Biological replicate 1

description: Biological replicate 1 of 4.


title: MC3T3 cell line siTwist1 3


title: C. elegans: Dauers vs Mix-Stage, Biological replicate 2

description: Biological replicate 2 of 4.


title: MC3T3 cell line siScrambled 1


title: C. elegans: Dauers vs Mix-Stage, Biological replicate 1

description: Biological replicate 1 of 4.


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-q-7

status: Public on Jul 27 2011

city: Dummerstorf

first: Bodo

last: Brand

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute of Farm Animal Biology

description: Gene expression data from S.aureus inoculated cells

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hours at 42°C on Affymetrix GeneChip Bovine Genome Arrays (Affymetrix, St. Clara, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 (Affymetrix, St. Clara, USA)

data_processing: Data were analysed with Affymetrix Expression Console 1.1 software using global scaling to a target signal of 500

organism: Bos taurus

source_name: primary bovine mammary gland epithelial cells

label_protocol: 2µg of total RNA were used for preparation of antisense biotinylated RNA using the GeneChip 3’IVT Express kit (Affymetrix, St. Clara, USA)

growth_protocol: On day 42 of their first lactation all selected heifers were slaughtered. Two samples of about 1.5 x 1.5 x 1.5 cm were taken aseptically from the parenchyma immediately after the animal was slaughtered and were transferred in 200 ml of room-temperate Hank’s balanced salt solution (HBSS; Sigma-Aldrich, Munich, Germany) containing 200 μg/ml penicillin, 200μg/ml streptomycin, 200μg/ml gentamicin and 10μg/ml amphotericin B (Sigma-Aldrich, Munich, Germany). After the tissue was minced and blood as well as milk residues were flushed away with HBSS, the samples were transferred to a digestion mix consisting of 200ml HBSS, 0.5mg/ml collagenase IA, 0.4 mg/ml DNAse type I, 0.5 mg/ml hyaluronidase (enzymes from Sigma-Aldrich, Munich, Germany) and the same antibiotics mentioned above. The cells were placed in a shaking incubator at 37°C for 165 minutes and were separated from connective tissue and non-epithelial cell conglomerates by filtration and centrifugation (500 U; 4min). This procedure was repeated two times each with a decreased pore size of the strainer (smallest one: 100μm, BD Biosciences, Erembodegem, Belgium). After washing and separation, the cells were resuspended in Dulbecco’s modified eagle’s medium nutrient mixture F-12 Ham (DMEM/F12, Sigma-Aldrich, Munich, Germany) containing penicillin, streptomycin, gentamicin, and amphotericin B in the same concentrations as described above, as well as 10% FBS and 10 μl/ml ITS (0.5 mg/ml bovine Insulin, 0.5 mg/ml apo-transferrin, 0.5μg/ml sodium selenite; Sigma-Aldrich, Munich, Germany). The cells were incubated in a 75 cm² tissue culture flask (Greiner bio-one, Frickenhausen, Germany) for 40 min at 37°C, 5% CO2, and 90% humidity. Thereafter the fibroblasts had attached and epithelial cells could be isolated by decanting. Epithelial cells were seeded in 25 cm² tissue culture flasks (Greiner bio-one, Frickenhausen, Germany) and cultured until they reached about 80% confluence. Cells were cryopreserved at -80°C in 1 ml freezing medium containing DMEM/F12, 20%FBS, and 10% DMSO. An immunocytochemical staining was conducted to verify the epithelial origin of the cells. Approximately 90 to 95% off the cells were represented by epithelial cells.

extract_protocol: Cells were harvested after 1, 6 and 24 hours and total RNA was extracted with the TriFast reagent as indicated in the manufacturer’s instructions (PEQLAB Biotechnology GmbH, Erlangen, Germany)

treatment_protocol: Heat inactivated S. aureus M60 and E. coli isolates deriving from a milk sample of an udder with bovine mastitis were used for inoculation. Epithelial cells were thawed and cultured under cultivation conditions (37°C, 5% CO2, and 90% humidity) in DMEM/F12 medium containing 100 μg/ml penicillin, 100 μg/ml streptomycin, 100 μg/ml gentamicin, 5 μg/ml amphotericin, 10% FBS and 10 μl/ml ITS for 2 further passages. For pathogen challenge they were seeded in 3 six-well tissue culture plates (Greiner bio-one, Frickenhausen, Germany), one plate for each time point (1, 6 and 24 hours), in a concentration of 300,000 cells/well. Two wells in each plate were prepared for control and two each for S. aureus and E. coli treatment. The medium was replaced by DMEM/F12 supplemented with ITS on the following day. At a confluence of about 70% on the second day after seeding, the medium was refreshed. 100 μl of bacterial-solution representing a multiplicity of infection of 10, was added. 100 μl PBS were used as control treatment of the uninoculated control cells.

tag: genotype

value: Staphylococcus aureus

tag: time point

value: 6 hours

tag: sample type

value: heifer with unfavorable QTL allele


title: C. elegans: Dauers vs Mix-Stage, Biological replicate 4

description: Biological replicate 4 of 4.


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-q-9


title: dNeurog1_neuraltube_rep2

city: Dallas

first: Helen

middle: C

last: Lai

state: TX

address: 6000 Harry Hines Blvd, NA4.146

institute: UT Southwestern Medical Center

description: GFP sorted cells from the dNeurog1-GFP Transgenic line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Preprocessing with MAS 5.0 to generate normalized signal intensity data.
Two biological samples per transgenic mouse type were processed/analyzed using GeneSpring Agilent GX 7.3 Expression Analysis software. Signals <0.01 were set to 0.01 and each chip was normalized to the 50th percentile and analyzed for probes with over two-fold change in signal where the Affymetrix probes had to be present or marginal in at least one of the Atoh1BAC-GFP or dNeurog1-GFP samples. The first arrays performed for Atoh1BAC-GFP+ cells versus the dNeurog1-GFP+ cells were compared to each other and the second arrays were compared to each other.

label: GFP

source_name: neural tube, E10.5

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Whole mouse embryos from Atoh1BAC-GFP or dNeurog1-GFP mice were dissected at E10.5 where E0 was timed as halfway through the dark cycle of the morning that the vaginal plug was detected.

extract_protocol: RNA was extracted from GFP cell sorted E10.5 neural tubes using the Mini RNA Isolation II Kit (Zymo Research).

treatment_protocol: Atoh1BAC-GFP and dNeurog1-GFP transgenic mouse E10.5 neural tubes from forelimb to hindlimb were dissected in DMEM/F12 (Gibco) and dissociated with 0.25% Trypsin-EDTA (Gibco).  Fluorescence activated cell sorting (FACS) was performed by the UT Southwestern Flow Cytometry Core Facility.  Cells were sorted into GFP – and + cells with a MoFlo (Dako/Beckman Coulter, 100 μm nozzle) or a FACSAria (BD Biosciences) cell sorter directly into ZR RNA buffer (Zymo Research).

value: mixed B6SJLF1 and ICR strains

tag: transgenic mouse line

value: neural tube

tag: age


title: Chinese hamster ovary (CHO) cell culture_3

description: CHO gene expression data

tag: growth rate

tag: temperature

tag: qammonia

tag: qlactate

tag: cell viability


title: Atoh1_neuraltube_rep2

description: GFP sorted cells from the Atoh1BAC-GFP Transgenic line


title: dNeurog1_neuraltube_rep1


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-q-11


title: Atoh1_neuraltube_rep1


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-q-10

value: 24 hours


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-q-9


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-q-7


title: Universal human reference RNA 2x amplified EH92A22

description: Used in Fig. 1 and 2

tag: method


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-q-11


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-q-10


title: pbMEC inoculated with S. aureus Time point 1h, SCS-BTA18-q-9

value: 1 hour


title: pbMEC inoculated with S. aureus Time point 1h, SCS-BTA18-q-10


title: pbMEC inoculated with S. aureus Time point 1h, SCS-BTA18-q-7


title: pbMEC inoculated with S. aureus Time point 1h, SCS-BTA18-q-11


title: DNA replication origins in mouse P19 cells genome

type: mixed

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description: four independent samples

hyb_protocol: Performed according to NimbleGen protocols

data_processing:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals),
for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). Four independent samples for P19 cells were used. Normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932). Thus, one probe was denoted as significant if the combined p-value was lower than 5% (level of significance).

molecule: other

source_name: P19 cells nascent strands

extract_protocol:
Nascent strand (NS) preparation
DNA purification
Dividing cells (2.5-5 ×108) were washed in PBS, harvested and lysed in 15 ml DNAzol (Invitrogen) at room temperature (RT) for 5 min. Samples were digested with 200 μg/ml proteinase K at 37°C for 2 hours. We found that combining the proteinase K treatment with DNAzol significantly improved the yield of NS. Insoluble material was discarded by centrifugation at 3000 g at 4°C for 15 min and genomic DNA was precipitated with 15 ml 100% ethanol at RT for 5 min. DNA was transferred to a new tube and washed with 5 ml 70% ethanol at RT for 5 min and air-dried. DNA was resuspended in 2 ml TEN20 (10 mM Tris-Cl pH 7.9, 2 mM EDTA, 20 mM NaCl, 0.1% SDS, 1000 U RNasin) at 70°C, boiled for 10-15 min and chilled on ice.
NS purification by sucrose gradient
1 ml of denatured genomic DNA was loaded onto a 30 ml neutral 5 to 30% sucrose gradient prepared in TEN300 (10 mM Tris pH 7.9, 2mM EDTA, 300 mM NaCl) and centrifuged in a Beckman SW28 rotor at 24000 RPM, 4°C, for 20 h. 1 ml fractions were withdrawn from the top of the gradient using a wide-bore pipette tip. 50 μl of each fraction was run with appropriate size markers on a 2% alkaline agarose gel at 40-50 volts, overnight at 4°C. The gel was neutralized with 1x TBE and stained with Gel Red (Interchim). Fractions corresponding to 0.5-2.5 kb were pooled and precipitated with 2.5 volumes ethanol at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water with 100 U RNasin (NEB).
Lambda exonuclease treatment
After addition of 2 μl T4 polynucleotide kinase (PNK) 10X buffer (NEB), fractions were boiled for 5 min and chilled on ice. Phosphorylation with T4 PNK was performed in 1X PNK buffer containing 0.2 U/μl PNK in a volume of 100 μl at 37°C for 1 hour. After heat inactivation at 75°C for 15 min, DNA was precipitated with 2.5 volumes ethanol-0.3 M sodium acetate (Na-acetate) at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 50 μl water with 100 U RNasin. Digestion with 100 U lambda exonuclease was in exo buffer (67 mM Glycine-KOH pH 9.4, 2.5 mM MgCl2, 50 μg/ml BSA) in 100 μl total volume at 37°C overnight. We found that the quality of the lambda exonuclease is crucial, and deserves to be always  tested before use. For the experiments described here, we used a custom-made preparation by Fermentas (20U/μl). NS were extracted once with phenol/chloroform/isoamylalcohol and once with chloroform/isoamylalcohol, then precipitated with 2.5 volumes ethanol-0.3M Na-acetate at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water. NS were subjected to one or two further cycles of T4 PNK phosphorylation and exonuclease digestion. We observed that the second round of exonuclease treatment significantly improves the NS preparation. Aliquots of digested and undigested DNA were run on a 2% agarose gel to confirm the efficiency of the exonuclease treatment. Finally, NS were purified using the CyScribe GFX Purification Kit (GE Healthcare) and eluted in 60 μl water.

tag: cell type

value: P19 teratocarcinoma cells

value: pluripostent embryonic cells

molecule: genomic DNA

source_name: Genomic DNA

extract_protocol: Genomic DNA were extracted using DNAzol

treatment_protocol: Genomic DNA were extracted using DNAzol (Invitrogen)


title: DNA replication origins in mouse ES cells genome

description: three independent samples

scan_protocol: Performed according to NimbleGen protocols

data_processing:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals),
for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). Three independent samples from ES and three for MEF cells were used. Normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932). Thus, one probe was denoted as significant if the combined p-value was lower than 5% (level of significance).

source_name: Es cells nascent strands

extract_protocol:
Nascent strand (NS) preparation
DNA purification
Dividing cells (2.5-5 ×108) were washed in PBS, harvested and lysed in 15 ml DNAzol (Invitrogen) at room temperature (RT) for 5 min. Samples were digested with 200 μg/ml proteinase K at 37°C for 2 hours. We found that combining the proteinase K treatment with DNAzol significantly improved the yield of NS. Insoluble material was discarded by centrifugation at 3000 g at 4°C for 15 min and genomic DNA was precipitated with 15 ml 100% ethanol at RT for 5 min. DNA was transferred to a new tube and washed with 5 ml 70% ethanol at RT for 5 min and air-dried. DNA was resuspended in 2 ml TEN20 (10 mM Tris-Cl pH 7.9, 2 mM EDTA, 20 mM NaCl, 0.1% SDS, 1000 U RNasin) at 70°C, boiled for 10-15 min and chilled on ice.
NS purification by sucrose gradient
1 ml of denatured genomic DNA was loaded onto a 30 ml neutral 5 to 30% sucrose gradient prepared in TEN300 (10 mM Tris pH 7.9, 2mM EDTA, 300 mM NaCl) and centrifuged in a Beckman SW28 rotor at 24000 RPM, 4°C, for 20 h. 1 ml fractions were withdrawn from the top of the gradient using a wide-bore pipette tip. 50 μl of each fraction was run with appropriate size markers on a 2% alkaline agarose gel at 40-50 volts, overnight at 4°C. The gel was neutralized with 1x TBE and stained with Gel Red (Interchim). Fractions corresponding to 0.5-2.5 kb were pooled and precipitated with 2.5 volumes ethanol at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water with 100 U RNasin (NEB).
Lambda exonuclease treatment
After addition of 2 μl T4 polynucleotide kinase (PNK) 10X buffer (NEB), fractions were boiled for 5 min and chilled on ice. Phosphorylation with T4 PNK was performed in 1X PNK buffer containing 0.2 U/μl PNK in a volume of 100 μl at 37°C for 1 hour. After heat inactivation at 75°C for 15 min, DNA was precipitated with 2.5 volumes ethanol-0.3 M sodium acetate (Na-acetate) at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 50 μl water with 100 U RNasin. Digestion with 100 U lambda exonuclease was in exo buffer (67 mM Glycine-KOH pH 9.4, 2.5 mM MgCl2, 50 μg/ml BSA) in 100 μl total volume at 37°C overnight. We found that the quality of the lambda exonuclease is crucial, and deserves to be always tested before use. For the experiments described here, we used a custom-made preparation by Fermentas (20U/μl). NS were extracted once with phenol/chloroform/isoamylalcohol and once with chloroform/isoamylalcohol, then precipitated with 2.5 volumes ethanol-0.3M Na-acetate at -80°C for 15 min. Pellets were washed with 1 ml 70% ethanol and suspended in 20 μl water. NS were subjected to one or two further cycles of T4 PNK phosphorylation and exonuclease digestion. We observed that the second round of exonuclease treatment significantly improves the NS preparation. Aliquots of digested and undigested DNA were run on a 2% agarose gel to confirm the efficiency of the exonuclease treatment. Finally, NS were purified using the CyScribe GFX Purification Kit (GE Healthcare) and eluted in 60 μl water.

tag: cell line

extract_protocol: Genomic DNA were extracted using DNAzol (Invitrogen)


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-5

tag: treatment

value: heifer with favorable QTL allele


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-5


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-1


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-2


title: pbMEC inoculated with  S. aureus Time point 1h, SCS-BTA18-Q-6


title: DNA replication origins in mouse MEF cells genome

description: three independent samples

data_processing:
Experimental (Cy5) and control (Cy3) signal intensities quantified and provided by Nimblegen were converted into log2 ratios (log2 (Cy5/Cy3)). The Lowess normalization method was applied to eliminate intensity-dependent variations in dye bias (Yang et al. 2002). A sliding median window with a length of 5 oligonucleotide probes was used to smooth the signal. Mode (m) and s (median absolute deviation) of normalized log2 ratios were computed. Assuming that the normal distribution (specified by m and s) covered the entire background noise (non-significant signals),
for each probe, one p-value was computed by applying the false discovery rate (FDR) correction (Benjamin and Hochberg 1995). Three for MEF cells were used. Normalized log2 ratios of replicate samples were combined by averaging the values at the corresponding genomic positions and the corrected p-values were combined using a Chi-Square distribution (Fisher 1932). Thus, one probe was denoted as significant if the combined p-value was lower than 5% (level of significance).

source_name: MEF cells nascent strands

label_protocol: Performed according to NimbleGen protocols

value: MEF cells

tag: tissue

value: embryos

source_name: genomic DNA


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-6


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-6


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-4


title: pbMEC inoculated with  S. aureus Time point 1h, SCS-BTA18-Q-5


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-1


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-2


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-3


title: pbMEC inoculated with  S. aureus Time point 1h, SCS-BTA18-Q-3


title: pbMEC inoculated with S. aureus Time point 24h, SCS-BTA18-Q-4


title: pbMEC inoculated with  S. aureus Time point 1h, SCS-BTA18-Q-2


title: pbMEC inoculated with  S. aureus Time point 1h, SCS-BTA18-Q-4


title: pbMEC inoculated with S. aureus Time point 1h, SCS-BTA18-Q-1


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-q-8

description: Gene expression data from E. coli inoculated cells

value: Escherichia coli


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-q-11


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-q-9


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-q-7


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-q-9


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-q-10


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-q-11


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-q-9


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-q-7


title: pbMEC cultivated 24h, SCS-BTA18-q-7

description: Gene expression data from uninoculated control cells treated with PBS

value: control


title: pbMEC cultivated 24h, SCS-BTA18-q-11


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-q-10


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-q-7


title: pbMEC cultivated 24h, SCS-BTA18-q-10


title: pbMEC cultivated 6h, SCS-BTA18-q-7


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-q-11


title: pbMEC cultivated 24h, SCS-BTA18-q-9


title: pbMEC cultivated 1h, SCS-BTA18-q-9


title: pbMEC cultivated 1h, SCS-BTA18-q-7


title: infection with PCV2 for 48h Replicate 2

city: Wuhan

first: Tao

middle: Wen

last: Li

state: Hubei

address: No.1, Shizi_shan street, Hongshan district

department: Division of Animal Infectious Disease

country: China

institute: Huazhong agricultural university, State Key Laboratory of Agricultural Microbiology

description: Biological replicate 2 of 3. PAMs infected by PCV2 for 48 hours, PAMs cultured for 48 hours but untreated.

hyb_protocol: Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.  Raw data .LSR files linked below were gotten from LuxScan 3.0 software (CapitalBio Corp. Beijing, China).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal, representing test/reference (infected/uninfected). Agilent software was used.

organism: Sus scrofa

source_name: Total RNA from control PAMs after infected with PCV2 for 48h

label_protocol: 10 µg of total RNA from PCV2-infection PAMs were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label,  and the total RNA from control PAMs were labelled by 25 µM Cy5-label with the same procudure as the total RNA from PCV2 infection PAMs.

growth_protocol: PAMs were collected by bronchoalveolar lavage, and PAMs thawed and cultured for 48 h before treatment. The cells were maintained with RPMI1640 containing 10% fetal bovine serum (FBS).

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

treatment_protocol: Cells were collected at 24 HPI and 48 HPI. In TRIzol for RNA extraction and supernatant was collected and frozen at -80 ℃ for protein analysis.

value: primary porcine alveolar macrophages (PAMs)

source_name: Total RNA from control PAMs after cultured for 48h


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-q-10


title: infection with PCV2 for 48h Replicate 3


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-5


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-q-8


title: pbMEC cultivated 1h, SCS-BTA18-q-10


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-4


title: infection with PCV2 for 48h Replicate 1

description: Biological replicate 1 of 3. PAMs infected by PCV2 for 48 hours, PAMs cultured for 48 hours but untreated.


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-3


title: PAO1, NGM Pi <0.1 mM_9

city: Chicago

first: Olga

middle: Y

last: ZABORINA

state: IL

address: 5841 S Maryland

department: Surgery

institute: University of Chicago

description:
gene expression data from lawns at low phosphate concentration (<0.1 mM)
9 Cor Pao1 acute

hyb_protocol: 1.5 µg of fragmented  and biotin labeled targets was hybridized to array for 16 h at 50°C and 60 rpm in an Affymetrix Hybridization Oven 640.

scan_protocol: After hybridization, arrays were washed and stained with Streptavidin Phycoerythrin. The fluorescent signals were amplified using a biotinylated antistreptavidin antibody in a Affymetrix GeneChip Fluidics Station (Affymetrix, Inc.) and the signals were detected in a GeneChip Scanner 3000 7G. The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix).

data_processing:
Data were normalized data using dChip.
The cel file were used for data analysis using ANOVA  to identify  differentially expressed genes [P-value <0.01 , Fold change >1.2.].

organism: Pseudomonas aeruginosa PAO1

source_name: lawn_20 hrs_low Pi

label_protocol: Ten μg of each total RNA was processed  for biotin labeled target preparation for hybridization to Pseudomonas aeruginosa expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).

growth_protocol: P. aeruginosa PAO1 grew on agarized Nematode growth media at different phosphate concentration for 20 hrs, 37C

extract_protocol: Cells were suspended in RNA protector solution (Bio-Rad), centrifuged 5,000 rpm, 10 min, 4C, lyzed in lysozyme TE solution followed by TRIzol. Total RNA was separated using PLG Phase lock gel followed by precipitation with isopropanol. DNA was removed with DNA-free kit

treatment_protocol: no additional treatment

tag: cells

value: P. aeruginosa lawns


title: PAO1, NGM Pi 25 mM_6

description:
gene expression data from lawns at high phosphate concentration (25 mM)
6 Cor Pao1 control

source_name: lawn_20 hrs_high Pi


title: infection with PCV2 for 24h Replicate 2

description: Biological replicate 3 of 3. PAMs infected by PCV2 for 24 hours, PAMs cultured for 24 hours but untreated.

source_name: Total RNA from control PAMs after infected with PCV2 for 24h

source_name: Total RNA from control PAMs after cultured for 24h


title: pbMEC cultivated 6h, SCS-BTA18-q-10


title: PAO1, NGM Pi <0.1 mM_7

description:
gene expression data from lawns at low phosphate concentration (<0.1 mM)
7 Cor Pao1 acute


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-Q-4


title: PAO1, NGM Pi <0.1 mM_8

description:
gene expression data from lawns at low phosphate concentration (<0.1 mM)
8 Cor Pao1 acute


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-1


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-Q-5


title: infection with PCV2 for 24h Replicate 3


title: pbMEC cultivated 6h, SCS-BTA18-q-11


title: PAO1, NGM Pi 25 mM_4

description:
gene expression data from lawns at high phosphate concentration (25 mM)
4 Cor Pao1 control


title: infection with PCV2 for 24h Replicate 1

description: Biological replicate 1 of 3. PAMs infected by PCV2 for 24 hours, PAMs cultured for 24 hours but untreated.


title: PAO1, NGM Pi 25 mM_5

description:
gene expression data from lawns at high phosphate concentration (25 mM)
5 Cor Pao1 control


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-Q-1


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-2


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-6


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-Q-3


title: pbMEC inoculated with E. coli Time point 24h, SCS-BTA18-Q-2


title: pbMEC inoculated with S. aureus Time point 6h, SCS-BTA18-Q-3


title: DP21

city: London

first: Damien

last: Portevin

address: The Ridgeway

country: United Kingdom

institute: NIMR-MRC

description: K2 IL-2 + H37Rv

hyb_protocol: Fragmented labeled cRNA samples (Affymetrix Fragmentation Buffer) were hybridized at 45oC for 16 hours

scan_protocol: Affymetrix Genechip Scanner with 7G upgrade

data_processing: GeneSpring 11, RMA summarized

source_name: Natural Killer cell isolated from human blood

label_protocol: Ambion MegaScript T7 Kit

growth_protocol: Complete RPMI FCS1% for 24h at 37degrees celsius

extract_protocol: Trizol

treatment_protocol: IL-2(100U/ml) or IL-12(10ng/ml) +/- M.bovis BCG or M.tuberculosis (1:1 ratio)

value: Natural Killer cell

tag: donor

value: IL-2 + H37Rv


title: DP20

description: K2 IL-2 + BCG

value: IL-2 + BCG


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-5

tag: genotype


title: Neg-A/p53-KD d7 2nd biological rep (Day 7-2 ds2)

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

description:
Day 7-2 ds2.
Agilent Feature Extraction File:
US45103064_251485035218_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: Because we were interested to accurately determine differences in gene expression between p53-KD and control cells of the same time-point, we employed a pairwise comparison of each p53-KD and control sample at each time-point. Dye-swap replicates were performed for all comparisons to account for dye incorporation bias. Fragmentation of the mixture of Cy3- and Cy5-labeled cRNA material to be compared was performed per Agilent’s protocol in order to reduce the size and complexity of the transcripts, thus improving their specificity to oligo- arrays and raising the average feature signal intensity. Following fragmentation, the transcript mixture was hybridized on 4x44K human microarrays (Agilent) for 17 hours at 65°C inside a DNA Microarray Hybridization Oven (Agilent) under constant rotation to ensure thorough mixing.

scan_protocol: Following hybridization, the slides were washed with Gene Expression wash buffers 1 and 2 (Agilent), followed by acetonitrile and followed by a wash in stabilization and drying solution (Agilent), which is designed to miminize ozone-mediated degradation of Cy5 per Agilent’s protocol. Next, slides were scanned (Agilent Microarray Scanner).

data_processing:
Agilent’s Feature Extraction Software (version 9.5.1, protocol: GE2-v5_95_Feb07) was used to identify spots and feature outliers. The feature extraction processextracts gene expression data from each probe measured on the microarray. In order to normalize signal intensity ratios for both Cy3 and Cy5, we employed the SNNLERM algorithm developed in the Papoutsakis lab, which averages the log-transformed expression ratios for technical and biological replicates (Yang et al. Proc. Natl. Acad. Sci. USA. 2003).
Probes from which >50% of measurements were missing were discarded and not included in the analysis of differential expression. Differentially expressed genes were identified using the significance analysis of microarrays (SAM) with a false discovery rate (FDR) of less than 5%, as implemented in the MultiExperiment Viewer (MeV) tool.

source_name: Neg-A CHRF d7 PMA replicate 2

label_protocol: We employed the Quick Amp Labeling Kit (Agilent) to generate fluorescently-labeled complimentary RNA (cRNA) starting from 500 ng total input RNA. Using this protocol, an oligo-dT primer that contains a T7 promoter is annealed to the poly-A tail of the mRNA. Next, mRNA is reversed transcribed into a first and second strand cDNA. Using T7 RNA polymerase, which simultaneously amplifies the target template and incorporates fluorescent dyes, cRNA labeled with Cy3 or Cy5 was generated. Labeled cRNA was purified using the RNeasy Mini Spin Columns (Qiagen; Germantown, MD); its yield and the degree of fluorescent labeling were quantified using the Nanodrop spectrophotometer.

growth_protocol: For induction of Mk differentiation, cells from the p53-KD CHRF and the control (Neg-A) CHRF cell line were seeded at 50,000–75,000 cells/ml and treated with 10 ng/ml PMA in DMSO on day 0. Protocol was similar to Fuhrken et al. J. Biol. Chem. 2008.

extract_protocol: RNA was isolated from cell pellets using the Total RNA Isolation Mini Kit (Agilent; Wilmington, DE). RNA purity and yield were estimated using a Nanodrop spectrophotometer (Model: ND-1000, Nanodrop; Wilmington, DE). The integrity of the isolated RNA was assessed by running the RNA 6000 Nano Assay (Agilent) on the Bioanalyzer (Model: 2100, Agilent).

treatment_protocol: As previously reported (Fuhrken et al. Exp. Hematol. 2007), cells ceased expanding and rapidly adhered to the tissue culture flask upon PMA treatment. At the designated time points, cells were washed with PBS and harvested using 1× trypsin-EDTA. Adherent and nonadherent fractions were combined for all analyses. Cell samples taken from CHRF cell cultures (p53-KD) and control cells) on days 1, 3, 5 and 7 following stimulation with PMA (10 ng/ml) and unstimulated cells (day 0) were flash-frozen in liquid nitrogen to be used later for microarray and Q-RT-PCR analysis.

value: megakaryocytic

source_name: p53-KD CHRF d7 PMA replicate 2


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-3

tag: time point


title: p53-KD/Neg-A d7 2nd biological rep (Day 7-2 ds1)

description:
Day 7-2 ds1.
Agilent Feature Extraction File:
US45103064_251485035218_S01_GE2-v5_95_Feb07_1_3.txt


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-2

tag: sample type


title: p53-KD/Neg-A d5 2nd biological rep (Day 5-2 ds1)

description:
Day 5-2 ds1.
Agilent Feature Extraction File:
US45103064_251485035218_S01_GE2-v5_95_Feb07_1_1.txt

source_name: p53-KD CHRF d5 PMA replicate 2

source_name: Neg-A CHRF d5 PMA replicate 2


title: DP19

description: K2 IL-2 alone

value: IL-2 alone


title: Neg-A/p53-KD d5 2nd biological rep (Day 5-2 ds2)

description:
Day 5-2 ds2.
Agilent Feature Extraction File:
US45103064_251485035218_S01_GE2-v5_95_Feb07_1_2.txt


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-4

source_name: primary bovine mammary gland epithelial cells


title: DP18

description: J2 IL-2 + H37Rv


title: pbMEC inoculated with E. coli Time point 1h, SCS-BTA18-Q-1


title: pbMEC cultivated 6h, SCS-BTA18-Q-6

value: 6 hours


title: pbMEC cultivated 6h, SCS-BTA18-Q-5


title: DP17-2

description: J2 IL-2 + BCG


title: DP16

description: J2 IL-2 alone


title: pbMEC cultivated 6h, SCS-BTA18-Q-2


title: p53-KD/Neg-A d3 2nd biological rep (Day 3-2 ds1)

description:
Day 3-2 ds1.
Agilent Feature Extraction File:
US45103064_251485035216_S01_GE2-v5_95_Feb07_1_3.txt

source_name: p53-KD CHRF d3 PMA replicate 2

source_name: Neg-A CHRF d3 PMA replicate 2


title: p53-KD/Neg-A d1 2nd biological rep (Day 1-2 ds1)

description:
Day 1-2 ds1.
Agilent Feature Extraction File:
US45103064_251485035216_S01_GE2-v5_95_Feb07_1_1.txt

source_name: p53-KD CHRF d1 PMA replicate 2

source_name: Neg-A CHRF d1 PMA replicate 2


title: DP15

description: I2 IL-12 + H37Rv


title: pbMEC cultivated 6h, SCS-BTA18-Q-3

description: Gene expression data from uninoculated control cells treated with PBS


title: pbMEC cultivated 6h, SCS-BTA18-Q-4


title: Neg-A/p53-KD d3 2nd biological rep (Day 3-2 ds2b)

description:
Day 3-2 ds2b.
Agilent Feature Extraction File:
US45103064_251485035216_S01_GE2-v5_95_Feb07_1_4.txt


title: DP14

description: I2 IL-12 + BCG

value: IL-12 + BCG


title: DP13

description: I2 IL-12 alone

value: IL-12 alone


title: Neg-A/p53-KD d1 2nd biological rep (Day 1-2 ds2)

description:
Day 1-2 ds2.
Agilent Feature Extraction File:
US45103064_251485035216_S01_GE2-v5_95_Feb07_1_2.txt


title: Neg-A/p53-KD d3 2nd biological rep (Day 3-2 ds2a)

description:
Day 3-2 ds2a.
Agilent Feature Extraction File:
US45103064_251485036022_S01_GE2-v5_95_Feb07_1_3.txt


description:
Day 7-2 ds1.
Agilent Feature Extraction File:
US45103064_251485036022_S01_GE2-v5_95_Feb07_1_4.txt


title: pbMEC cultivated 24h, SCS-BTA18-Q-6

value: 24 hours


title: DP10

description: H2 IL-12 alone


title: DP11

description: H2 IL-12 + BCG


title: pbMEC cultivated 24h, SCS-BTA18-Q-3


title: DP8

description: G2 IL-12 + BCG


title: pbMEC cultivated 24h, SCS-BTA18-Q-4


title: Neg-A/p53-KD d5 1st biological rep (Day 5-1 ds2b)

description:
Day 5-1 ds2b.
Agilent Feature Extraction File:
US45103064_251485036065_S01_GE2-v5_95_Feb07_1_3.txt

source_name: Neg-A CHRF d5 PMA replicate 1

source_name: p53-KD CHRF d5 PMA replicate 1


title: pbMEC cultivated 24h, SCS-BTA18-Q-2


title: DP12

description: H2 IL-12 + H37Rv


title: p53-KD/Neg-A d1 1st biological rep (Day 1-1 ds1)

description:
Day 1-1 ds1.
Agilent Feature Extraction File:
US45103064_251485036063_S01_GE2-v5_95_Feb07_1_2.txt

source_name: p53-KD CHRF d1 PMA replicate 1

source_name: Neg-A CHRF d1 PMA replicate 1


title: Neg-A/p53-KD d7 1st biological rep (Day 7-1 ds2)

description:
Day 7-1 ds2.
Agilent Feature Extraction File:
US45103064_251485036065_S01_GE2-v5_95_Feb07_1_2.txt

source_name: Neg-A CHRF d7 PMA replicate 1

source_name: p53-KD CHRF d7 PMA replicate 1


title: pbMEC cultivated 1h, SCS-BTA18-Q-6

value: 1 hour


title: DP6

description: F2 IL-12 + H37Rv


title: DP9

description: G2 IL-12 + H37Rv


title: Neg-A/p53-KD d1 1st biological rep (Day 1-1 ds2)

description:
Day 1-1 ds2.
Agilent Feature Extraction File:
US45103064_251485036063_S01_GE2-v5_95_Feb07_1_4.txt


title: p53-KD/Neg-A d3 1st biological rep (Day 3-1 ds1)

description:
Day 3-1 ds1.
Agilent Feature Extraction File:
US45103064_251485036062_S01_GE2-v5_95_Feb07_1_4.txt

source_name: p53-KD CHRF d3 PMA replicate 1

source_name: Neg-A CHRF d3 PMA replicate 1


title: pbMEC cultivated 24h, SCS-BTA18-Q-1

value: heifer with favorable QTL allele


title: DP7

description: G2 IL-12 alone

source_name: Natural Killer cell isolated from human blood


title: p53-KD/Neg-A d5 1st biological rep (Day 5-1 ds1)

description:
Day 5-1 ds1.
Agilent Feature Extraction File:
US45103064_251485036062_S01_GE2-v5_95_Feb07_1_3.txt


title: p53-KD/Neg-A d7 1st biological rep (Day 7-1 ds1)

description:
Day 7-1 ds1.
Agilent Feature Extraction File:
US45103064_251485036065_S01_GE2-v5_95_Feb07_1_1.txt


title: Neg-A/p53-KD d3 1st biological rep (Day 3-1 ds2)

description:
Day 3-1 ds2.
Agilent Feature Extraction File:
US45103064_251485036062_S01_GE2-v5_95_Feb07_1_2.txt


title: pbMEC inoculated with E. coli Time point 6h, SCS-BTA18-Q-6

description: Gene expression data from E. coli inoculated cells


title: pbMEC cultivated 24h, SCS-BTA18-Q-5


title: pbMEC cultivated 1h, SCS-BTA18-Q-4


title: DP5

description: F2 IL-12 + BCG


title: Neg-A/p53-KD d5 1st biological rep (Day 5-1 ds2a)

description:
Day 5-1 ds2a.
Agilent Feature Extraction File:
US45103064_251485036062_S01_GE2-v5_95_Feb07_1_1.txt


title: pbMEC cultivated 1h, SCS-BTA18-Q-5


title: DP4

description: F2 IL-12 alone


title: pbMEC cultivated 1h, SCS-BTA18-Q-3


title: GC B cell_pCDNA3_LMP1_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

description: Amplified total RNA from transfected and FACS sorted GC B cells

hyb_protocol: Affymetrix hybridization protocol onto Human Genome U133 Plus 2.0 Array

scan_protocol: Affymetrix Standard protocol

data_processing: GCOS

source_name: GC B cell transfected with pcDNA3.1-LMP1, rep2

label_protocol: Affymetrix labelling protocol

growth_protocol: GC B cells were cultivated overnight post-transfection in RPMI supplemented with 20% FCS and antibiotics.

extract_protocol: Total cellular RNA was isolated using RNeasy Micro Kit, Qiagen, and RNA was amplified with ExpressArt mRNA Amplification kit protocol (Amptech).

treatment_protocol: 1 x E6 CD10+ GC B cells were co-transfected with pcDNA3.1-LMP1 vector together with pMACS LNGFR vector (Miltenyi Biotec Ltd., Surrey, UK) at ratio 7:3. Transfection was performed by Nucleofection using the B Cell Nucleofector Kit B (Amaxa, Cologne, Germany) for the Nucleofector II 6 Device (Amaxa) using U-15 program. Cells were cultivated overnight, stained with α-LNGFR-allophycocyanin (APC) (Miltenyi Biotec) and propidium iodide (PI). APC-labelled and PI-negative cells were collected by FACS on a MoFlo sorter (Dako Cytomation, Colorado, USA).

tag: transfection

value: GC B cells sorted using CD10 MACS from reactive human tonsils


title: pbMEC cultivated 1h, SCS-BTA18-Q-1


title: Neg-A/p53-KD d0 2nd biological rep (Day 0-2 ds2c)

description:
Day 0-2 ds2c.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485035270_S01_GE2-v5_95_Feb07_1_4.txt

source_name: Neg-A CHRF no PMA replicate 2

source_name: p53-KD CHRF no PMA replicate 2


title: Neg-A/p53-KD d0 1st biological rep (Day 0-1 ds2c)

description:
Day 0-1 ds2c.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485035270_S01_GE2-v5_95_Feb07_1_2.txt

source_name: Neg-A CHRF no PMA replicate 1

source_name: p53-KD CHRF no PMA replicate 1


title: p53-KD/Neg-A d0 1st biological rep (Day 0-1 ds1c)

description:
Day 0-1 ds1c.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485035270_S01_GE2-v5_95_Feb07_1_1.txt


title: control animal 2

city: Stockholm

first: Emma

last: Lindahl

address: Scheeles väg 2

country: Sweden

institute: Karolinska Institutet

hyb_protocol: From non-degraded high-quality total RNA, we prepared and hybridized biotinylated complementary ssDNA to Rat Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standard protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used a GeneChip Scanner 3000 and standard Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.

organism: Rattus norvegicus

source_name: proximal tubular cells, untreated

label_protocol: Total RNA were amplified and converted to cDNA and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

extract_protocol: Total RNA was extracted from rat proximal tubular cells stored in RNA later using Rneasy (QIAGEN, Valencia, CA, USA).

treatment_protocol: Isolated proximal tubular cells from diabetic rats were treated with or without C-peptide for 2 hrs.

tag: strain

value: Sprague-Dawley

value: kidney

value: proximal tubular cells

tag: phenotype

value: type I diabetes

value: untreated


title: p53-KD/Neg-A d0 2nd biological rep (Day 0-2 ds1c)

description:
Day 0-2 ds1c.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485035270_S01_GE2-v5_95_Feb07_1_3.txt


title: control animal 1


title: 5FU_07

city: Tokushima-city

first: Toshihito

last: Tanahashi

address: Kuramoto-cho 3-18-15

institute: Tokushima University

hyb_protocol: Hybridization were performed in accordance with the manufacturer’s procedure.

scan_protocol: The array was scanned with a laser scanner (G2565BA; Agilent).

data_processing: Feature Extraction 9.5 software (Agilent) was used to obtain the microarray raw data.

label_protocol: One-color microRNA labeling with Cy3 fluorescence were performed in accordance with the manufacturer’s procedure.

extract_protocol: The miRNeasy mini kit (Qiagen, Valencia, CA) was used to extract total RNA including microRNA.

tag: status

value: 5-FU sensitive

tag: time


title: 5FU_08

value: 5-FU resistant


title: Neg-A/p53-KD d0 2nd biological rep (Day 0-2 ds2b)

description:
Day 0-2 ds2b.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037375_S01_GE2-v5_95_Feb07_1_4.txt


title: 5FU_06


title: pbMEC cultivated 1h, SCS-BTA18-Q-2

description: Gene expression data from uninoculated control cells treated with PBS

source_name: primary bovine mammary gland epithelial cells

value: control


title: treated animal 2

source_name: proximal tubular cells, C-peptide treatment

value: C-peptide


title: GC B cell_pCDNA3_LMP1_rep1

source_name: GC B cell transfected with pcDNA3.1-LMP1, rep1


title: GC B cell_PRDM1α_rep1

source_name: GC B cell transfected with pcDNA3.1-PRDM1α, rep1

treatment_protocol: 1 x E6 CD10+ GC B cells were co-transfected with pcDNA3.1-BLIMP1α  vector together with pMACS LNGFR vector (Miltenyi Biotec Ltd., Surrey, UK) at ratio 7:3. Transfection was performed by Nucleofection using the B Cell Nucleofector Kit B (Amaxa, Cologne, Germany) for the Nucleofector II 6 Device (Amaxa) using U-15 program. Cells were cultivated overnight, stained with α-LNGFR-allophycocyanin (APC) (Miltenyi Biotec) and propidium iodide (PI). APC-labelled and PI-negative cells were collected by FACS on a MoFlo sorter (Dako Cytomation, Colorado, USA).


title: 5FU_05


title: treated animal 1


title: 5FU_04

value: 5-FU resistance


title: GC B cell_pCDNA3_rep1

source_name: GC B cell transfected with empty vector (pCDNA3.1), rep1

treatment_protocol: 1 x E6  CD10+ GC B cells were co-transfected with pcDNA3.1 vector together with pMACS LNGFR vector (Miltenyi Biotec Ltd., Surrey, UK) at ratio 7:3. Transfection was performed by Nucleofection using the B Cell Nucleofector Kit B (Amaxa, Cologne, Germany) for the Nucleofector II 6 Device (Amaxa) using U-15 program. Cells were cultivated overnight, stained with α-LNGFR-allophycocyanin (APC) (Miltenyi Biotec) and propidium iodide (PI). APC-labelled and PI-negative cells were collected by FACS on a MoFlo sorter (Dako Cytomation, Colorado, USA).

value: empty vector (pCDNA3.1)


title: GC B cell_pCDNA3_rep2

source_name: GC B cell transfected with empty vector (pCDNA3.1), rep2

treatment_protocol: 1 x E6 CD10+ GC B cells were co-transfected with pcDNA3.1 vector together with pMACS LNGFR vector (Miltenyi Biotec Ltd., Surrey, UK) at ratio 7:3. Transfection was performed by Nucleofection using the B Cell Nucleofector Kit B (Amaxa, Cologne, Germany) for the Nucleofector II 6 Device (Amaxa) using U-15 program. Cells were cultivated overnight, stained with α-LNGFR-allophycocyanin (APC) (Miltenyi Biotec) and propidium iodide (PI). APC-labelled and PI-negative cells were collected by FACS on a MoFlo sorter (Dako Cytomation, Colorado, USA).


title: Neg-A/p53-KD d0 1st biological rep (Day 0-1 ds2b)

description:
Day 0-1 ds2b.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037375_S01_GE2-v5_95_Feb07_1_2.txt

value: megakaryocytic


title: p53-KD/Neg-A d0 2nd biological rep (Day 0-2 ds1b)

description:
Day 0-2 ds1b.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037375_S01_GE2-v5_95_Feb07_1_3.txt


title: treated animal 3


title: HBEC3 3D culture sample 3

first: Lianghao

last: Ding

address: 5323 Harry Hines Blvd

description: replicate 3

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction and quantile normalization using MBCB algorithm

source_name: Bronchial Epithelial Cells

label_protocol: Illumina TotalPrep Kit

extract_protocol: Rneasy Mini Kit from Qiagen

tag: culture condition


title: 5FU_03


title: p53-KD/Neg-A d0 1st biological rep (Day 0-1 ds1b)

description:
Day 0-1 ds1b.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037375_S01_GE2-v5_95_Feb07_1_1.txt


title: GC B cell_KDM6B_rep2

description: Total RNA from MACS-sorted GC B cells.

hyb_protocol: 10ug of fragmented cRNA was hybridized onto Human Genome U133 Plus 2.0 Array using Affymetrix hybridization protocol.

source_name: GC B cell, KDM6B

growth_protocol: Cells were snap frozen after isolation.

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

treatment_protocol: Mononuclear cells were isolated by Ficoll-Isopaque centrifugation of tonsils from pediatric patients under informed consent and with ethical approval. Briefly, CD10+ GC B cells were isolated by magnetic separation at 4oC with anti-CD10-Phycoerythrin (PE) and anti-PE microbeads with LS columns (Miltenyi Biotec).

value: tonsils

value: CD10+ GC B cells

tag: developmental stage

value: pediatric


title: 5FU_02


title: GC B cell_KDM6B_rep3

description: Total RNA from MACS-sorted GC B cells.


title: HBEC3 3D culture sample 2

description: replicate 2


title: HBEC3 2D culture sample 3

description: replicate 3


title: GC B cell_PRDM1α_rep2

source_name: GC B cell transfected with pcDNA3.1-PRDM1α, rep2

treatment_protocol: 1 x E6 CD10+ GC B cells were co-transfected with pcDNA3.1-BLIMP1α vector together with pMACS LNGFR vector (Miltenyi Biotec Ltd., Surrey, UK) at ratio 7:3. Transfection was performed by Nucleofection using the B Cell Nucleofector Kit B (Amaxa, Cologne, Germany) for the Nucleofector II 6 Device (Amaxa) using U-15 program. Cells were cultivated overnight, stained with α-LNGFR-allophycocyanin (APC) (Miltenyi Biotec) and propidium iodide (PI). APC-labelled and PI-negative cells were collected by FACS on a MoFlo sorter (Dako Cytomation, Colorado, USA).


title: Neg-A/p53-KD d0 2nd biological rep (Day 0-2 ds2a)

description:
Day 0-2 ds2a.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037374_S01_GE2-v5_95_Feb07_1_4.txt


title: 5FU_01


title: HBEC3 2D culture sample 2

description: replicate 2


title: p53-KD/Neg-A d0 2nd biological rep (Day 0-2 ds1a)

description:
Day 0-2 ds1a.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037374_S01_GE2-v5_95_Feb07_1_3.txt


title: Neg-A/p53-KD d0 1st biological rep (Day 0-1 ds2a)

description:
Day 0-1 ds2a.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037374_S01_GE2-v5_95_Feb07_1_2.txt


title: HBEC3 3D culture sample 1

description: replicate 1


title: HBEC3 2D culture sample 1

description: replicate 1


title: GC B cell_PCMV_rep3

description: Total RNA from MACS-sorted GC B cells.

source_name: GC B cell, control vector

value: vector


title: GC B cell_PCMV_rep2

description: Total RNA from MACS-sorted GC B cells.


title: GC B cell_KDM6B_rep1

description: Total RNA from MACS-sorted GC B cells.


title: GC B cell_PCMV_rep1

description: Total RNA from MACS-sorted GC B cells.


title: 4p_e

status: Public on Jul 26 2011

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: RNA extracted from PMBCs

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization using R (version 2.10.1), Bioconductor (version 2.6).

label: Biotin

source_name: PBMCs from peripheral blood

label_protocol: Biotin

growth_protocol: Peripheral blood was collected in 4 ml Vacutainer tubes. PBMCs were extracted using the Ficoll-Paque Plus kit (Amersham Biosciences) and incubated in RPMI (15% FBS, Pen/Strep/Fung., and 1x HEPES) overnight.

extract_protocol: Ficoll Extraction (PBMCs from peripheral blood); Qiagen RNAeasy kiy (total RNA from PBMCs)

treatment_protocol: Three compounds were used (24h treatment): 1) Compound 106 (N1-(2-aminophenyl)-N7-p-tolylheptanediamide); 2) Compound 4b (N1-(2-aminophenyl)-N7-phenylheptanediamide); and 3) Compound 9b (N1-(2-Methoxyphenyl)-N7-phenylheptanediamide) (Herman et al., 2006). Concentration was 10 μM in DMSO. Control samples received no treatment (‘empty’) or vehicle alone (DMSO).

tag: disease status

value: FRDA

value: empty

tag: barcode


title: 5p_e

description: RNA extracted from PMBCs


title: 2p_C

description: RNA extracted from PMBCs


title: 1n_C

description: RNA extracted from PMBCs

value: Normal


title: 5n_e

description: RNA extracted from PMBCs


title: 3n_e

description: RNA extracted from PMBCs


title: 6n_e

description: RNA extracted from PMBCs


title: 2n_C

description: RNA extracted from PMBCs


title: 4n_C

description: RNA extracted from PMBCs


title: 3n_C

description: RNA extracted from PMBCs


title: 1p_C

description: RNA extracted from PMBCs


title: p53-KD/Neg-A d0 1st biological rep (Day 0-1 ds1a)

description:
Day 0-1 ds1a.
Agilent Feature Extraction File:
10-20-09 hybridization Pani_251485037374_S01_GE2-v5_95_Feb07_1_1.txt

tag: cell line


title: 5p_C

description: RNA extracted from PMBCs

tag: treatment


title: 7n_e

description: RNA extracted from PMBCs


title: 4n_e

description: RNA extracted from PMBCs


title: 2p_e

description: RNA extracted from PMBCs


title: 3p_e

description: RNA extracted from PMBCs


title: 1c_C

description: RNA extracted from PMBCs

value: Carrier


title: 3p_C

description: RNA extracted from PMBCs


title: 5c_C

description: RNA extracted from PMBCs


title: 3c_C

description: RNA extracted from PMBCs


title: 3c_e

description: RNA extracted from PMBCs


title: 4p_C

description: RNA extracted from PMBCs


title: 2c_e

description: RNA extracted from PMBCs


title: 5c_e

description: RNA extracted from PMBCs


title: 1p_e

description: RNA extracted from PMBCs


title: 2c_C

description: RNA extracted from PMBCs


title: 4n_D

description: RNA extracted from PMBCs

value: DMSO


title: 5p_D

description: RNA extracted from PMBCs


title: 1p_D

description: RNA extracted from PMBCs


title: 6n_D

description: RNA extracted from PMBCs


title: 3n_D

description: RNA extracted from PMBCs


title: 7n_9b

description: RNA extracted from PMBCs


title: 1n_9b

description: RNA extracted from PMBCs


title: 2n_D

description: RNA extracted from PMBCs


title: 1n_D

description: RNA extracted from PMBCs


title: 4c_e

description: RNA extracted from PMBCs


title: 1c_D

description: RNA extracted from PMBCs


title: 4n_9b

description: RNA extracted from PMBCs


title: 6n_9b

description: RNA extracted from PMBCs


title: 4c_C

description: RNA extracted from PMBCs


title: 4p_D

description: RNA extracted from PMBCs


title: 1c_e

description: RNA extracted from PMBCs


title: 5c_D

description: RNA extracted from PMBCs


title: 7n_D

description: RNA extracted from PMBCs


title: 4c_D

description: RNA extracted from PMBCs


title: 3p_D

description: RNA extracted from PMBCs


title: 3c_D

description: RNA extracted from PMBCs


title: 2n_9b

description: RNA extracted from PMBCs


title: 5n_9b

description: RNA extracted from PMBCs


title: 3n_9b

description: RNA extracted from PMBCs


title: 5p_9b

description: RNA extracted from PMBCs


title: 4p_9b

description: RNA extracted from PMBCs


title: 3c_9b

description: RNA extracted from PMBCs


title: 2p_9b

description: RNA extracted from PMBCs


title: 1p_9b

description: RNA extracted from PMBCs


title: 6n_4b

description: RNA extracted from PMBCs


title: 2n_4b

description: RNA extracted from PMBCs


title: 3p_4b

description: RNA extracted from PMBCs


title: 5c_9b

description: RNA extracted from PMBCs


title: 1n_4b

description: RNA extracted from PMBCs


title: 2p_4b

description: RNA extracted from PMBCs


title: 3p_9b

description: RNA extracted from PMBCs


title: 4n_4b

description: RNA extracted from PMBCs


title: 5n_4b

description: RNA extracted from PMBCs


title: 2c_4b

description: RNA extracted from PMBCs


title: 4c_4b

description: RNA extracted from PMBCs


title: 1c_9b

description: RNA extracted from PMBCs


title: 2c_9b

description: RNA extracted from PMBCs


title: 5p_4b

description: RNA extracted from PMBCs


title: 1p_4b

description: RNA extracted from PMBCs


title: 4p_4b

description: RNA extracted from PMBCs


title: 1c_4b

description: RNA extracted from PMBCs


title: 3c_4b

description: RNA extracted from PMBCs


title: 7n_4b

description: RNA extracted from PMBCs


title: 5c_4b

description: RNA extracted from PMBCs


title: 9p_106

description: RNA extracted from PMBCs


title: 7c_106

description: RNA extracted from PMBCs


title: 10p_106

description: RNA extracted from PMBCs


title: 9c_106

description: RNA extracted from PMBCs


title: 11n_106

description: RNA extracted from PMBCs


title: 10n_106

description: RNA extracted from PMBCs


title: 3n_106

description: RNA extracted from PMBCs


title: 9n_106

description: RNA extracted from PMBCs


title: 1n_106

description: RNA extracted from PMBCs


title: 10c_106

description: RNA extracted from PMBCs


title: 8n_106

description: RNA extracted from PMBCs


title: 6c_106

description: RNA extracted from PMBCs


title: 4c_9b

description: RNA extracted from PMBCs


title: 8c_106

description: RNA extracted from PMBCs


title: 6n_106

description: RNA extracted from PMBCs


title: 8p_106

description: RNA extracted from PMBCs


title: 7p_106

description: RNA extracted from PMBCs


title: 3n_4b

description: RNA extracted from PMBCs


title: 3p_106

description: RNA extracted from PMBCs


title: 6p_106

description: RNA extracted from PMBCs


title: 5n_106

description: RNA extracted from PMBCs


title: 2n_106

description: RNA extracted from PMBCs


title: 4n_106

description: RNA extracted from PMBCs


title: 2c_106

description: RNA extracted from PMBCs


title: 7n_106

description: RNA extracted from PMBCs


title: 5p_106

description: RNA extracted from PMBCs


title: 3c_106

description: RNA extracted from PMBCs


title: 1c_106

description: RNA extracted from PMBCs


title: 1p_106

description: RNA extracted from PMBCs


title: 5c_106

description: RNA extracted from PMBCs


title: PB-6

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

description:
251485036540_4_PB-6
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the 'Gene Expression Hybridization Kit' (Agilent, 5188-5242). After posthybridization washes ('Wash Buffers 1 and 2 Kit', Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: After processing, microarray slides were scanned at 535 nm and 5um/pixel resolution using a GenePix 4000B scanner and the software 'GenePix Pro 6.0' (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Images were analyzed with the software 'Agilent Feature Extraction 8.5' and extracted expression values (gProcessedSignal) were further normalized to the 75 percentile expression value, considering all non-control features (ControlType=0). Following normalization, replicate probes were averaged, resulting in the final set of 41,000 unique probes.

source_name: CLL cells_peripheral blood

label_protocol: Cy3-labelled cRNA was generated using the 'Quick Amp Labeling Kit, one-color' (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA ('One Color RNA Spike-In Kit', Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

extract_protocol: Total RNA was extracted using TRIZOL-LS (Invitrogen), treated with DNase and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA). RNA quality was assessed by agarose gel electrophoresis and quantified using a NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).

tag: gender

value: female

tag: tissue source

value: peripheral blood

tag: cell type

value: Chronic lymphocytic leukemia (CLL) B-cells


title: BM-5

description:
251485036540_1_BM-5
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).

source_name: CLL cells_bone marrow

value: bone marrow


title: PB-3

description:
251485036486_2_PB-3
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: PB-5

description:
251485036540_2_PB-5
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: 2p_106

description: RNA extracted from PMBCs


title: 4c_106

description: RNA extracted from PMBCs


title: heart atherogenic diet with OPP rep2

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized with the rank invariant normalization in the Illumina BeadStudio 1.5.1.3 software

source_name: heart, treatment

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

growth_protocol: Mice were given an atherogenic diet for six weeks

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given distilled water while treatment group was given OPP (1500 ppm GAE) as drinks ad libitum

value: BALB/c

tag: age

value: 12 weeks

value: male

value: atherogenic diet with OPP

tag: tissue

value: heart


title: heart atherogenic diet with OPP rep1

description: replicate 1


title: 3-172-10, biological rep1

city: Kawasaki

first: Yoko

last: Asakura

address: 1-1 Suzuki-cho Kawasaki-ku

department: Institule of Life Sciences

institute: Ajinomoto

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip E.coli antisense genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner.

data_processing: The data were analyzed with GeneChip Operation Software 1.0 (GCOS 1.0) using Affymetrix default analysis settings, and normalized to scaling factor 500 using GCOS 1.0.

organism: Escherichia coli

source_name: clone 3-172-10, isolated from an evolved population of YA027 at the 172th passage (about 1000 generations)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microgram of total RNA.

growth_protocol: The cells were cultured at 37 ℃ in Davis's MM medium containig 20 kinds of amino acids (200 mg / l each) with Cm and Km selection, until the optical density (OD) at 660nm reached to 0.1.

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

treatment_protocol: The cells were harvested by centrifugation, and stabilized using RNA Protect Bacteria Reagent (Qiagen) in accordance with the manufacturer's protocols (see http://www.qiagen.com).

value: evolved from YA027

tag: genotype/variation

tag: evolved passage

value: 172 (about 1000 generatios)


title: BM-4

description:
251485036486_3_BM-4
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: BM-6

description:
251485036540_3_BM-6
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: spleen atherogenic diet with OPP rep1

description: replicate 1

source_name: spleen, treatment

tag: strain

value: spleen


title: heart atherogenic diet with OPP rep3

description: replicate 3


title: 3-172-10, biological rep2


title: spleen atherogenic diet with distilled water rep3

description: replicate 3

source_name: spleen, control

value: atherogenic diet with distilled water


title: spleen atherogenic diet with OPP rep2

description: replicate 2


title: PB-4

description:
251485036486_4_PB-4
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: heart atherogenic diet with distilled water rep2

description: replicate 2

source_name: heart, control


title: Y38placenta_rep1

city: New York

first: Le

last: Jiang

address: 1130 St. Nicholas Ave

institute: Columbia University

hyb_protocol: The microarray slides were cleaned and placed in prehybridization buffer (5XSSC, 0.1%SDS and 1%BSA) for 1 hr at 45°C. The probe mixture was combined with 40 µl 2X hybridization buffer (50% Formamide, 10XSSC and 0.2% SDS) and then applied to the microarray slides in a hybridization chamber (Corning, Corning, NY) before incubating in a dark, 45°C water bath for approximately 42 hr.

scan_protocol: Scanned on an GenePix 4000B scanner. Scanned images were examined thoroughly and analyzed by GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA)

data_processing: Median normalization was carried out for each microarray slide, and background-subtracted data were imported into GeneSpring 7.3.1 (Agilent Technologies, Palo Alto, CA). LOESS normalization was applied to all microarray data.

source_name: in vitro placenta 180 days

label_protocol: Ten µg of total RNA was mixed with 2 µl random hexamers (3 µg/µl, Invitrogen, Carlsbad, CA), heated at 70°C for 5 min, snap-cooled on ice, and added to the following reaction mix: 6 µl 5X first strand buffer (Invitrogen), 3 µl 0.1 M DTT, 0.6 µl 25 mM dNTP (except for dTTP: 15 mM), 0.12 µl 50 mM aminoallyl-dUTP, 2 µl SuperScript III reverse transcriptase (200 U/µl, Invitrogen) and 0.5 µl RNase inhibitor (20 U/µl, Ambion, Austin, TX). The 30 µl reaction was then incubated at 25 °C for 10 min, followed by further incubation at 46 °C overnight.

extract_protocol: Total RNA from dissected tissues was extracted using the RNeasy mini/midi kit according to manufacture's instructions (Qiagen, Valencia, CA)

value: placenta

tag: in vitro or in vivo

value: in vitro

tag: gestation day

value: 180 days

source_name: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney

tag: reference


title: BM-3

description:
251485036486_1_BM-3
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: heart atherogenic diet with distilled water rep1

description: replicate 1


title: heart atherogenic diet with distilled water rep3

description: replicate 3


title: BM-1

description:
251485036484_1_BM-1
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: PB-2

description:
251485036484_4_PB-2
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: BM-2

description:
251485036484_3_BM-2
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).


title: Y38placenta_rep2

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: 45placenta_rep2


title: 4p_106

description: RNA extracted from PMBCs

value: Carrier


title: spleen atherogenic diet with OPP rep3

description: replicate 3


title: 3-84-6, biological rep1

source_name: clone 3-84-6, isolated from an evolved population of YA027 at the 84th passage (about 500 generations)

value: 84 (about 500 generatios)


title: spleen atherogenic diet with distilled water rep2

description: replicate 2


title: 3-84-6, biological rep2


title: 45placenta_rep1


title: 3-172-1, biological rep2

source_name: clone 3-172-1, isolated from an evolved population of YA027 at the 172th passage (about 1000 generations)


title: 3-172-1, biological rep3


title: 3-172-9, biological rep2

source_name: clone 3-172-9, isolated from an evolved population of YA027 at the 172th passage (about 1000 generations)


title: liver atherogenic diet with distilled water rep3

description: replicate 3

source_name: liver, control

value: liver


title: 3-172-1, biological rep1


title: liver atherogenic diet with OPP rep1

description: replicate 1

source_name: liver, treatment


title: 3-84-2, biological rep2

source_name: clone 3-84-2, isolated from an evolved population of YA027 at the 84th passage (about 500 generations)


title: spleen atherogenic diet with distilled water rep1

description: replicate 1


title: 3-172-9, biological rep1


title: liver atherogenic diet with OPP rep3

description: replicate 3


title: 3-84-4, biological rep1

source_name: clone 3-84-4, isolated from an evolved population of YA027 at the 84th passage (about 500 generations)


title: 3-84-4, biological rep3


title: PB-1

description:
251485036484_2_PB-1
All CLL cell samples were obtained by negative selection (using the RosetteSep human B cell–enrichment cocktail, from StemCell Technologies) to purities above 95% (% of CD19+CD5+ cells, determined by flow cytometry).

value: female

value: peripheral blood

value: Chronic lymphocytic leukemia (CLL) B-cells


title: liver atherogenic diet with distilled water rep4

description: replicate 4

value: BALB/c

value: 12 weeks

value: male


title: 711placenta_rep2


title: 3-84-10, biological rep2

source_name: clone 3-84-10, isolated from an evolved population of YA027 at the 84th passage (about 500 generations)

value: evolved from YA027


title: 373placenta_rep2


title: 3-84-4, biological rep2


title: liver atherogenic diet with OPP rep2

description: replicate 2

value: atherogenic diet with OPP


title: 3234placenta_rep1


title: 711placenta_rep1


title: 3234placenta_rep2


title: 3-84-10, biological rep1


title: 3-84-2, biological rep1


title: 3-11-10, biological rep2

source_name: clone 3-11-10, isolated from an evolved population of YA027 at the 11th passage (about 70 generations)

value: 11 (about 70 generatios)


title: 3-11-10, biological rep1


title: 3-11-9, biological rep2

source_name: clone 3-11-9, isolated from an evolved population of YA027 at the 11th passage (about 70 generations)


title: 3-11-4, biological rep2

source_name: clone 3-11-4, isolated from an evolved population of YA027 at the 11th passage (about 70 generations)


title: 3-11-9, biological rep1


title: liver atherogenic diet with distilled water rep1

description: replicate 1

value: atherogenic diet with distilled water


title: 373placenta_rep1

value: placenta


title: 51231placenta_rep2

source_name: in vivo placenta 180 days

value: in vivo


title: 3-11-2, biological rep2

source_name: clone 3-11-2, isolated from an evolved population of YA027 at the 11th passage (about 70 generations)


title: liver atherogenic diet with distilled water rep2

description: replicate 2


title: 51231placenta_rep1

value: 180 days


title: YA105, biological rep3

value: as MG1655, but lacZ::PaeR7Ir- KmR, lacZ::CmR


title: 3-11-2, biological rep1


title: 4409placenta_rep1

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: 4409placenta_rep2


title: YA105, biological rep2


title: A15placenta_rep2


title: heart atherogenic diet rep2

description: replicate 2

source_name: heart, treatment

growth_protocol: Mice were given distilled water for six weeks

treatment_protocol: Control group was given normal diet while treatment group was given atherogenic diet ad libitum

value: atherogenic diet

value: heart


title: heart atherogenic diet rep1

description: replicate 1


title: YA074, biological rep2

value: as MG1655, but lacZ::PaeR7Ir-m+ KmR, lacZ::CmR


title: YA105, biological rep1


title: YA074, biological rep3


title: 3-11-4, biological rep1


title: spleen atherogenic diet rep3

description: replicate 3

source_name: spleen, treatment

value: spleen


title: heart atherogenic diet rep3

description: replicate 3


title: YA074, biological rep1


title: A15placenta_rep1


title: spleen atherogenic diet rep1

description: replicate 1


title: YA027, biological rep2

source_name: YA027 (parent)

value: as MG1655, but lacZ::PaeR7Ir+m+ KmR, lacZ::CmR

value: 0 (parent)


title: YA027, biological rep3


title: liver atherogenic diet rep4

description: replicate 4

value: BALB/c

value: 12 weeks

value: liver


title: YA027, biological rep1


title: 6396placenta_rep1

source_name: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: 322Hplacenta_rep2

source_name: in vitro placenta 90 days

value: in vitro

value: 90 days


title: WT#2

city: Huddinge

first: Peter

last: Swoboda

state: Stockholm

address: Hälsovägen 7

department: Department of Biosciences and Nutrition

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization

source_name: 3-fold stage embryos

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: genotype

value: N2 Bristol

value: 3-fold stage embryo

value: whole embryo


title: WT#3


title: WT#1


title: daf-12#4


title: 322Hplacenta_rep1

value: placenta


title: WT#4


title: liver atherogenic diet rep2

description: replicate 2

value: male


title: daf-19,daf-12#4


title: daf-12#2


title: 4709placenta_rep1

value: Total RNA of pooled RNA from bovine control fetal liver, placental and kidney


title: daf-12#1


title: 4709placenta_rep2


title: daf-19,daf-12#3


title: Control.Cy5_Msi1.Cy3_4

city: san antonio

first: raquel

last: abreu

address: 8403 Floyd Curl Drive

institute: CCRI

description: Biological Replicate 2, duplicate dye swap 2

hyb_protocol: Samples were hybridized using Agilent's Gene Expression Hybridization Kit.

scan_protocol: Scanned with Agilent G2565BA Scanner, 10 µm resolution.

data_processing: TIFF images were quantified using Agilent Feature Extraction Software 8.5.

source_name: Daoy medulloblastoma cells

label_protocol: cRNA synthesis was carried out using Agilent's Low RNA Linear Amplification Kit Plus, two-color.

growth_protocol: Grown at 37°C in 5% CO2

extract_protocol: Phenol/chloroform extraction and isopropanol precipitation.

treatment_protocol: The cell lysate and antibody coated sepharose beads were incubated at room temperature while tumbling end over end. Following incubation, the beads were spun down and washed 4 times with ice cold NT2 buffer. Subsequently, the material was digested with proteinase K, extracted with phenol/chloroform, and precipitated with isopropanol.

tag: transient transfection with

value: RIP with Msi1 Antibody

tag: treatment time

value: 48 hours

value: RIP with Prebleed Antibody


title: daf-19,daf-12#2

source_name: 3-fold stage embryo


title: Y52placenta_rep2


title: spleen atherogenic diet rep2

description: replicate 2

value: atherogenic diet

value: spleen


title: liver atherogenic diet rep3

description: replicate 3

source_name: liver, treatment


title: daf-12#3


title: Y52placenta_rep1


title: liver atherogenic diet rep1

description: replicate 1


title: Control.Cy5_Msi1.Cy3_3

description: Biological Replicate 2, dye swap 2


title: daf-19,daf-12#1


title: A105Hplacenta_rep2


title: Control.Cy3_Msi1.Cy5_3

description: Biological Replicate 2, dye swap 1


title: ID6 B cell CD20 2

city: Oxford

first: Josine

last: Min

address: Roosevelt Drive

institute: The Wellcome Trust Centre for Human Genetics

description:
1718911527_F
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

hyb_protocol: Arrays were hybridised with labelled cRNA material and scanned according to manufacturer’s instructions.

scan_protocol: Manufacturer’s instructions

data_processing: The resultant data was parsed with the software package BeadStudio to produce raw intensity values for all probes. Signal was checked for quality using hybridisation and labelling controls internal to each array and subtracted for background within the statistical scripting environment, R v2.4.1. Signal was transformed and normalised using the variance stabilization algorithm as implemented in the vsn2 Bioconductor package.

label_protocol: Manufacturer’s instructions

extract_protocol: For the isolation of CD19 and CD20 B-cells, 40ml whole blood from EDTA tubes was collected and PBMCs were isolated by using a Ficoll-Paque™ gradient (Amersham). CD19 and CD20 B-cells were prepared by positive selection from the PBMCs by incubation with magnetic anti-CD19 or CD20 mAb-coated microbeads (MACS, Miltenyi Biotec). For the isolation of PBMCs from whole blood, BD Vacutainer® CPT Mononuclear Cell Preparation Tubes (Becton and Dickinson) were used. Total RNA was isolated from 5 ml of whole blood samples with the PAXGene Blood RNA system (Qiagen) and samples were left at room temperature for 24 hours before processing according to manufacturer’s instructions.Only two people at a time were sampled on any one day for logistical reasons. After blood draw standard protocols were followed for cell isolation, transformation or RNA extraction. With the exception of the PAXgene samples all RNA was isolated using TRI™ reagent (SIGMA) and resuspended in RNase free water.

treatment_protocol: For each individual, five different post venipuncture methods were performed. B Lymphocytes from 10ml of blood were isolated by tubes with sodium citrate. LCLs were generated by EBV-mediated transformation and cells were grown for eight weeks.

tag: method

tag: individual (indiv.id)

tag: visit

tag: ChIP

tag: yield

tag: rin

value: B cell-CD20


title: 6396placenta_rep2

value: in vivo

value: 180 days


title: Control.Cy3_Msi1.Cy5_4

description: Biological Replicate 2, duplicate dye swap 1


title: 4429placenta_rep2


title: 4429placenta_rep1


title: ID6 B cell CD19 2

description:
1718911527_E
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

tag: cell type

value: B cell-CD19


title: ID6 PBMC 1

description:
1718911527_A
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number

source_name: PBMC

value: PBMC

tag: tissue


title: Control.Cy5_Msi1.Cy3_2

description: Biological Replicate 1, duplicate dye swap 2


title: ID6 B cell CD19 1

description:
1718911527_C
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number


title: ID6 PBMC 2

description:
1718911527_B
source name = post venipuncture method; Indiv.id = Individual Identifier; Visit: Visit number