title: Pre-eclampsia_3

status: Public on Sep 15 2010

city: Toyoake

first: Haruki

last: Nishizawa

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Obstetrics and Gynecology

institute: Fujita Health University

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 26 hour collection.

hyb_protocol: Samples were hybridized to Affymetrix Human Exon 1.0 ST Array kit.

scan_protocol: Signal intensities were amplified using a second staining with a biotin-labeled anti-streptavidin antibody followed by phycoerythrin-streptavidin staining. Array fluorescent images were obtained using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
Microarray experiment data analyses were performed using Microsoft Excel (Microsof t, Redmond, WA), Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) and Genespring GX11 (Silicon Genetics, Redwood City, CA). All data were subjected to per chip and per gene normalization, intensity dependent normalization and quality control.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0st-v2.r2.dt.hg18.core.mps

source_name: Human placenta (Pla25)

label_protocol: After fragmentation into ~200 bp with uracil DNA glycosylase, , synthesized sense-strand cDNAs were end-labeled with biotin.

growth_protocol: All of the placental biopsies both from pre-eclampsia and normal normotensive pregnancies with or without FGR pregnancy were obtained after Caesarean sections. To avoid the effect of labor to the expression profile further, only placental samples that were obtained from the women who had not undergone labor were included to the study

extract_protocol: Total RNA was extracted from the chorionic villous tissues with an RNeasy mini-kit (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions. The quality of the RNA samples was determined by electrophoresis through denaturing agarose gels and staining with ethidium bromide. The RNA was quantified and evaluated for purity by UV spectrophotometry. Approximately 1 ug of each total RNA sample was used for double strand cDNA synthesis. Then cRNA was synthesized with in vitro transcription followed by sense-strand cDNA synthesis using the Ambion Whole Transcript Expression Kit (Applied Biosystems, Foster City, CA).

treatment_protocol: not applicable

value: Placenta

tag: disease state

value: Pre-eclampsia


title: Gene expression profile of P. aeruginosa PA14 grown to early log phase in MOPS-Glucose(replicateA)

status: Public on May 31 2010

type: RNA

city: Sydney

first: Jim

last: Manos

state: NSW

address: Camperdown

country: Australia

institute: University of Sydney

description: Microarrays were performed in biological duplicate for each sample in each condition tested (same isolate; with different culture, RNA extraction, and microarray) to assess biological variability at the culture level. Substitution of different biological (culture) replicates had little or no effect on the prediction of differentially expressed genes

hyb_protocol: A ‘test3’ array (Affymetrix-100 housekeeping genes) was used to determine cDNA suitability for the full array. Hybridizations were conducted at 50oC and 60 rpm for 16h, followed by washing and scanning of the chip.

scan_protocol: Affymetrix GeneChip Scanner 3000 at 532nm for excitation/570nm for emission

data_processing: Microarray data were analysed using BIOCONDUCTOR. The robust multi-array average (RMA) method was used for data normalization, incorporating probe level background-correction, quantile normalization, and linear extraction of a final expression measure for each gene per array. The empirical Bayes method was used to determine differential gene expression. The false discovery rate method was controlled to reduce false positives and a positive B-statistic (B>0) was used as a guide for statistically significant differential expression

label: Biotin

molecule: total RNA

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: Gram negative bacterium

label_protocol: Fragments were 3’-end-labeled using GeneChip® DNA Labelling Reagent (Affymetrix) for hybridisation to the Affymetrix PAO1 GeneChip® (Affymetrix).

growth_protocol: MOPS minimal medium containing 20mM glucose, for use as a comparison to logarithmic-growth gene expression in ASMDM, was inoculated with a starting culture of OD600 0.003 McFarland 0.5 Standard (bioMerieux). Cultures were incubated with shaking at 37oC with uninoculated medium used as a blank. Cell density was monitored using optical density at OD600. Cells were harvested during exponential growth at an OD600 = 0.2±0.02. Cells were pelleted (5 min, 5000 x g, 4°C), resuspended in 1× PBS, and treated with RNAprotect™ (Qiagen).

extract_protocol: Total RNA was isolated using the RNeasy Mini Purification kit (Qiagen) and RNA concentration determined at A260/280nm. RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (2). cDNA was synthesized, fragmented and labelled as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA). cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen), and fragmented with DNase I (GE Healthcare Bio-Sciences, Australia).The overall quality of fragmented DNA was assessed using a Bioanalyser 2100 (Agilent GmbH, Germany)

tag: growth phase/media

value: early log phase in MOPS-Glucose

tag: strain

tag: isolate

value: clinical burns wound isolate


title: CTRL_A

status: Public on Nov 27 2010

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

description: Gene expression data from fibrobast activated with PBS

hyb_protocol: Following fragmentation, human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained  and washed according to the Affymetrix protocol.

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protocol

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

organism: Homo sapiens

source_name: fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Normal human mamary fibroblasts were cultured with DMEM medium containing 10% calf serum and 10% fetal bovine serum

extract_protocol: Total RNA was extracted from fibroblasts using RNA extraction kits according to the manufacturer’s instructions (Qiagen)

treatment_protocol: Cells were cultured for 6 days in presence of 1ug/ml recombinant human granulin protein or PBS control

tag: clinical status

value: Normal mamary human

tag: cell type

value: mammary fibroblast

tag: treatment

value: control


title: CTRL_C


title: Pre-eclampsia_5

country: Japan

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 28 hour collection.

label: biotin

source_name: Human placenta (Pla85b)

tag: tissue


title: Pre-eclampsia_2

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 25 hour collection.

source_name: Human placenta (Pla24)


title: Gene expression profile of P. aeruginosa PA14 grown to early log phase in MOPS-Glucose(replicateB)


title: Pre-eclampsia_8

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 31 hour collection.

source_name: Human placenta (Pla88a)


title: Pre-eclampsia_6

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 29 hour collection.

source_name: Human placenta (Pla83b)


title: Pre-eclampsia_7

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 30 hour collection.

source_name: Human placenta (Pla89)


title: CTRL_B


title: Stationary phase gene expression profile of P. aeruginosa PA14 grown in ASMDM (replicateA)

description: Microarrays were performed in biological duplicate for each sample in each condition tested (same isolate; with different culture, RNA extraction, and microarray) to assess biological variability at the culture level. Substitution of different biological (culture) replicates had little or no effect on the prediction of differentially expressed genes.

hyb_protocol: The overall quality of fragmented DNA was assessed using a Bioanalyser 2100 (Agilent GmbH, Germany) and hybridized to the P. aeruginosa PAO1 GeneChip microarray as suggested by the manufacturer (Affymetrix). A ‘test3’ array (Affymetrix-100 housekeeping genes) was used to determine cDNA suitability for the full array on the Affymetrix PAO1 GeneChip® (Affymetrix). Hybridizations were conducted at 50oC and 60 rpm for 16h, followed by washing of the chip.

scan_protocol: Scanning of the chip was conducted on an Affymetrix GeneChip Scanner 3000 at 532nm for excitation/570nm for emission. CEL and CHP files were generated using the scanner program GCOS (Affymetrix).

data_processing: Microarray data were analysed using BIOCONDUCTOR. The robust multi-array average (RMA) method was used for data normalization, incorporating probe level background-correction, quantile normalization, and linear extraction of a final expression measure for each gene per array. The empirical Bayes method was used to determine differential gene expression. The false discovery rate method was controlled to reduce false positives and a positive B-statistic (B>0) was used as a guide for statistically significant differential expression.

label_protocol: Fragments 3’-end-labeled using GeneChip® DNA Labelling Reagent (Affymetrix).

growth_protocol: Ten ml ASMDM in McCartney bottles was inoculated with 50 μl of the diluted culture just under the surface of the media. Bottles were incubated statically with a loose lid to permit gas exchange at 37°C, and checked for growth every 24 h. A negative control containing no bacterial inoculum was included to detect media contamination.

extract_protocol: Cells were harvested at 72 h by removal of biofilm material from the thick surface growth and the deep anaerobic projections, followed by washing in ice-cold 1× PBS to increase cell yield and remove debris. Briefly, suspensions (~10 ml) were transferred to a 50 ml Falcon tube and washed 5× or until the pellet was cleared of non-cellular debris with an equal amount of 1× PBS by pelleting (5 min/5000 x g/4°C), and re-suspension in fresh ice-cold 1× PBS. All steps were performed on ice or at 4oC to avoid cell and RNA degradation. Cells were extracted for RNA  as per the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix Inc. USA), and the Rneasy® Midi spin column with a larger membrane and therefore a greater surface area, was used to increase RNA yield. RNA quality and the presence of residual DNA were checked by formaldehyde agarose gel electrophoresis. cDNA was synthesized, fragmented and labelled as per the technical manual, and cDNA was purified using the MinEluteTM PCR Purification kit (Qiagen) and fragmented with DNase I (GE Healthcare Bio-Sciences, Australia).

treatment_protocol: An overnight culture of P. aeruginosa UCBPP-PA14 was diluted in 1× Phosphate Buffered Saline (PBS) to an optical density equivalent to a MacFarland 0.5 Standard (bioMerieux), corresponding to ca. 1×108 CFU/ml.

value: stationary phase grown in ASMDM


title: Pre-eclampsia_4

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 27 hour collection.

source_name: Human placenta (Pla84a)


title: Pseudomonas aeruginosa planktonic culture 11 - AES-2

status: Public on Feb 05 2009

description: No further information.

hyb_protocol: Fragmented labelled cDNA was sent to the Australian Genome Research Facility (AGRF), Melbourne, Australia, for microarray analysis, where fragmentation quality was checked using a Bioanalyser 2100 (Agilent GmbH, Waldbronn, Germany) and the NanoChip protocol (Agilent). Samples were prepared for hybridization to the Pseudomonas aeruginosa Genome Array (Affymetrix) by adding 3-7μg DNA to a probe cocktail including 1×Hybridization Buffer (100mM 2-Morpholinoethanesulfonic acid, 1mM NaCl, 20mM EDTA, 0.01% Tween-20), 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml BSA, and 7% Dimethylsulfoxide (Sigma-Aldrich). 90μl of probe cocktail was loaded into a ‘test3’ array (Affymetrix) comprising 100 housekeeping genes to check cDNA quality, followed by 130μl into the full array. The chip was hybridized by rotation at 60rpm (50 degrees C for 16h) and washed using the Pseudomonas fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: The chip was scanned using the Affymetrix GeneChip Scanner 3000 at 532 nm for excitation and 570 nm for emission. CEL and CHP files were generated for analysis using the scanner operating software, GCOS.

data_processing: Microarray data were analysed using the BIOCONDUCTOR software suite. Data normalisation used the multi-array average (RMA) method in the affy package, incorporating probe level background-correction, quantile normalisation, and the use of a linear model to extract a final expression measure for each gene on each array. The resulting expression measures were then used to determine differential expression using an empirical Bayes approach within the limma package. The false discovery rate method of Benjamini and Hochberg was controlled to reduce false positives introduced by multiple simultaneous inference.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa AES-2 planktonic culture

label_protocol: cDNA was synthesised, fragmented and labelled as per the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix Corp., CA. USA). Briefly, cDNA was synthesised by using random hexamers as primers for reverse transcription (Invitrogen Australia Pty Ltd, Victoria, Australia). The primers were annealed (70 degrees C for 10 min; 25 degress C for 10 min) to 10μg total RNA. Polyadenylated control transcripts (130 pM) were added to each sample (Affymetrix) to monitor transcriptional efficiency and array performance. Transcripts were extended with SuperScript II reverse transcriptase (Invitrogen) (25 degrees C for 10 min; 37 degrees C for 60 min; 42 degrees C for 60 min and 70 degrees C for 10 min). Residual RNA was removed by alkaline treatment followed by neutralisation and the cDNA was purified using the MinElute(TM) PCR Purification kit (QIAGEN). Purified cDNA was fragmented using DNaseI (Amersham Biosciences, NSW Australia) and the fragments 3’-end-labelled using GeneChip® DNA Labelling Reagent (Affymetrix).

growth_protocol: Cells were grown to mid-log phase (optical density (OD600) = 0.5±0.05) with shaking (200 rpm) at 35 degrees C.

extract_protocol: Total RNA was stabilized for purification using RNAprotect™ Bacteria Reagent and extracted using the RNeasy Mini Purification kit (QIAGEN Pty Ltd, Victoria, Australia) as per the manufacturer’s protocols. Briefly, 500μl aliquots of cells in RNAprotect™ were lysed using 5 mg/ml lysozyme (L6876, Sigma-Aldrich, MO USA). DNA was removed using the RNase-Free Dnase Set (QIAGEN) and the RNA eluted in 30μl RNase-free water. RNA concentration was measured at A260 nm, with a minimum concentration of ca. 500 ng/µl required to proceed to cDNA synthesis. The quality of the RNA and presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (Ausubel et al., Current protocols in molecular biology, 2003).

tag: Strain

tag: ID

value: clonal isolate 11


title: PGRN_B

description: Gene expression data from fibrobast activated with Granulin

value: granulin


title: Pseudomonas aeruginosa AES-2 (clonal isolate 12) - Biofilm culture

description: No further information

data_processing: Microarray data were analysed using the BIOCONDUCTOR software suite. Data normalisation used the multi-array average (RMA) method in the affy package, incorporating probe level background-correction, quantile normalisation, and the use of a linear model to extract a final expression measure for each gene on each array. The resulting expression measures were then used to determine differential expression using an empirical Bayes approach within the limma package. The false discovery rate method of Benjamini and Hochberg was controlled to reduce false positives introduced by multiple simultaneous inference

label: GeneChip® DNA Labelling Reagent (Affymetrix)

source_name: Pseudomonas aeruginosa AES-2 biofilm culture

growth_protocol: Cells were grown to mid-log phase (optical density (OD600) = 0.5±0.05) with shaking (200 rpm) at 35C. Cells were then inoculated into 800ml Luria Broth in a Bioreactor (CDC Atlanta, GA, USA) at a 1:100 dilution and the reactor incubated in a water bath at 35C for 3 days, with a constant stir rate of 100 rpm.

extract_protocol: Glass slides containing attached biofilm were washed with ice-cold 1xPBS to remove biofilm. Cells were pelleted and washed again in ice-cold 1xPBS before resuspension in RNAprotect™ Bacteria Reagent. RNA was extracted using the RNeasy Mini Purification kit (QIAGEN Pty Ltd, Victoria, Australia) as per the manufacturer’s protocols. Briefly, 500μl aliquots of cells in RNAprotect™ were lysed using 5 mg/ml lysozyme (L6876, Sigma-Aldrich, MO USA). DNA was removed using the RNase-Free Dnase Set (QIAGEN) and the RNA eluted in 30μl RNase-free water. RNA concentration was measured at A260 nm, with a minimum concentration of ca. 500 ng/µl required to proceed to cDNA synthesis. The quality of the RNA and presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (Ausubel et al., Current protocols in molecular biology, 2003).

treatment_protocol: Total RNA was stabilized for purification using RNAprotect™ Bacteria Reagent and extracted using the RNeasy Mini Purification kit (QIAGEN Pty Ltd, Victoria, Australia) as per the manufacturer’s protocols. Briefly, 500μl aliquots of cells in RNAprotect™ were lysed using 5 mg/ml lysozyme (L6876, Sigma-Aldrich, MO USA). DNA was removed using the RNase-Free Dnase Set (QIAGEN) and the RNA eluted in 30μl RNase-free water. RNA concentration was measured at A260 nm, with a minimum concentration of ca. 500 ng/µl required to proceed to cDNA synthesis. The quality of the RNA and presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (Ausubel et al., Current protocols in molecular biology, 2003).

value: clonal isolate 12


title: Pseudomonas aeruginosa planktonic culture 12 - AES-2

description: No further information.


title: Pseudomonas aeruginosa planktonic culture 10 -AES-2

description: No further information.

value: clonal isolate 10


title: Pseudomonas aeruginosa planktonic culture 9- AES-2

description: No further information.

value: Clonal isolate 9


title: Pseudomonas aeruginosa AES-2 (clonal isolate 9) biofilm culture

description: No further information


title: Pseudomonas aeruginosa AES-2 (clonal isolate 10) - Biofilm culture

description: No further information


title: Pre-eclampsia_1

description: Pre-eclampsia was defined as a blood pressure of higher than 160/110 mmHg, with proteinuria of more than 2g in a 24 hour collection.

source_name: Human placenta (Pla20c)


title: Pseudomonas aeruginosa AES-2 (clonal isolate 11) Biofilm culture

description: No further information

growth_protocol: Cells were grown to mid-log phase (optical density (OD600) = 0.5±0.05) with shaking (200 rpm) at 35C. Cells were then inoculated into 800ml Luria Broth in a Bioreactor (CDC Atlanta, GA, USA) at a 1:100 dilution and the reactor incubated in a water bath at 35C for 3 days, with a constant stir rate of 100 rpm


title: Pseudomonas aeruginosa (non-clonal isolate 5) planktonic culture

status: Public on Dec 05 2008

description: No further information.

source_name: Pseudomonas aeruginosa non-clonal planktonic culture

value: non-clonal

value: Isolate 5


title: Pseudomonas aeruginosa AES-1 (clonal isolate 4) biofilm culture

description: No further information.

source_name: Pseudomonas aeruginosa AES-1 biofilm culture

extract_protocol: Glass slides containing attached biofilm were washed with ice-cold 1xPBS to remove biofilm. Cells were pelleted and washed again in ice-cold 1xPBS before resuspension in RNAprotect™ Bacteria Reagent to stabilize the RNA. The RNA was extracted using the RNeasy Mini Purification kit (QIAGEN Pty Ltd, Victoria, Australia) as per the manufacturer’s protocols. Briefly, 500μl aliquots of cells in RNAprotect™ were lysed using 5 mg/ml lysozyme (L6876, Sigma-Aldrich, MO USA). DNA was removed using the RNase-Free Dnase Set (QIAGEN) and the RNA eluted in 30μl RNase-free water. RNA concentration was measured at A260 nm, with a minimum concentration of ca. 500 ng/µl required to proceed to cDNA synthesis. The quality of the RNA and presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (Ausubel et al., Current protocols in molecular biology, 2003).

tag: id

value: clonal isolate 4


title: Pseudomonas aeruginosa AES-1 (clonal isolate 1) planktonic culture

description: No further information.

source_name: Pseudomonas aeruginosa planktonic culture

value: Australian Epidemic Strain-1 (AES-1)

value: Clonal isolate 1


title: Pseudomonas aeruginosa AES-1 (clonal isolate 4) planktonic culture

description: No further information.

value: Isolate 4


title: Pseudomonas aeruginosa (non-clonal isolate 5) biofilm culture

description: No further information.

source_name: Pseudomonas aeruginosa non-clonal biofilm culture

value: Pseudomonas aeruginosa

value: Non-clonal isolate 5


title: Pseudomonas aeruginosa (non-clonal isolate 6) biofilm culture

description: No further information.

value: Non-clonal isolate 6


title: Pseudomonas aeruginosa AES-1 (clonal isolate 1) biofilm culture

description: No further information.

source_name: Pseudomonas aeruginosa biofilm culture


title: Pseudomonas aeruginosa (non-clonal isolate 7) planktonic culture

description: No further information.

source_name: Pseudomonas aeruginosa unique planktonic culture

value: isolate 7


title: Pseudomonas aeruginosa AES-1 (clonal isolate 3) biofilm culture

description: No further information.

value: Clonal isolate 3


title: Pseudomonas aeruginosa PAO1 - biofilm culture

description: No further information

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: Cells were grown to mid-log phase (optical density (OD600) = 0.5±0.05) with shaking (200 rpm) at 35 degrees C. Cells were then inoculated into 800ml Luria Broth in a Bioreactor (CDC Atlanta, GA, USA) at a 1:100 dilution and the reactor incubated in a water bath at 35C for 3 days, with a constant stir rate of 100 rpm.

extract_protocol: Glass slides containing attached biofilm were washed with ice-cold 1xPBS to remove biofilm. Cells were pelleted and washed again in ice-cold 1xPBS before resuspension in RNAprotect™ Bacteria Reagent. Total RNA was extracted using the RNeasy Mini Purification kit (QIAGEN Pty Ltd, Victoria, Australia) as per the manufacturer’s protocols. Briefly, 500μl aliquots of cells in RNAprotect™ were lysed using 5 mg/ml lysozyme (L6876, Sigma-Aldrich, MO USA). DNA was removed using the RNase-Free Dnase Set (QIAGEN) and the RNA eluted in 30μl RNase-free water. RNA concentration was measured at A260 nm, with a minimum concentration of ca. 500 ng/µl required to proceed to cDNA synthesis. The quality of the RNA and presence of residual DNA were checked by formaldehyde agarose gel electrophoresis (Ausubel et al., Current protocols in molecular biology, 2003).

value: Pseudomonas aeruginosa biofilm culture


title: Pseudomonas aeruginosa AES-1 (clonal isolate 2) planktonic culture

description: No further information.

source_name: Psuedomonas aeruginosa AES-1 planktonic culture

value: Clonal isolate 2


title: Pseudomonas aeruginosa (non-clonal isolate 7) biofilm culture

description: No further information.

value: Non-clonal isolate 7


title: Pseudomonas aeruginosa (non-clonal isolate 6) planktonic culture

description: No further information.

value: Non clonal

value: isolate 6


title: Pseudomonas aeruginosa AES-1 (clonal isolate 3) planktonic culture

description: No further information.

tag: ID clonal isolate 3


title: Pseudomonas aeruginosa PAO1 planktonic culture

description: No further information

value: PAO1Pseudomonas aeruginosa planktonic culture


title: Pseudomonas aeruginosa (non-clonal isolate 8) biofilm culture

description: No further information.

source_name: Pseudomonas aeruginosa nonclonal biofilm culture

value: Non-clonal isolate 8


title: Pseudomonas aeruginosa AES-1 (clonal isolate 2) biofilm culture

description: No further information.


title: Pseudomonas aeruginosa (non-clonal isolate 8) planktonic culture

description: No further information.

value: non-clonal

value: isolate 8


title: Placenta tissue from patients with severe preeclampsia, replicate 10 of 17

status: Public on Jun 20 2008

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

description: Biological replicate 36 of 43. Placenta tissue from patients with severe preeclampsia

hyb_protocol: The labelled DIG-cRNA (10 micrograms per microarray) was then injected into each microarray hybridization chamber. Following hybridization at 55°C for 16 hours, the unbound material was washed from the microarrays. Features that retained bound DIG- labeled cRNA were visualized using the Applied Biosystems Chemiluminescent Detection Kit. Anti-GIG alkaline phosphatase (Roche Applied Science) was used to hydrolyze a chemiluminescence substrate to generate light at 458 nm.

scan_protocol: Images were quantified using the integrated ABI1700 software

data_processing: The data were pre-processed using the R software (version 2.4.1). A quantile normalization (ABarray package) was carried out prior to further analysis. This comes in addition to the internal preprocessing and filtering carried out by the ABI 1700 software (http=//www.amebioscience.com/ABI1700.htm).

source_name: total RNA from placenta tissue

label_protocol: 0.5 micrograms of total RNA was processed into digoxigenen (DIG)- labeled cRNA using the Applied Biosystems NanoAmp™ RT-IVT Labeling kit (Applied Biosystems)

growth_protocol: Patient material

extract_protocol: MagNa Pure Compact RNA Isolation Kit (Roche Applied Science)

tag: Placenta tissue


title: Placenta tissue from patients with severe preeclampsia, replicate 8 of 17

description: Biological replicate 34 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 12 of 17

description: Biological replicate 38 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 14 of 17

description: Biological replicate 40 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 7 of 17

description: Biological replicate 33 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 16 of 17

description: Biological replicate 42 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 11 of 17

description: Biological replicate 37 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 6 of 17

description: Biological replicate 32 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 15 of 17

description: Biological replicate 41 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 13 of 17

description: Biological replicate 39 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 9 of 17

description: Biological replicate 35 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 17 of 17

description: Biological replicate 43 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patients with severe preeclampsia, replicate 5 of 17

description: Biological replicate 31 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 22 of 26

description: Biological replicate 23 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 13 of 26

description: Biological replicate 14 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 16 of 26

description: Biological replicate 17 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patients with severe preeclampsia, replicate 3 of 17

description: Biological replicate 29 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 14 of 26

description: Biological replicate 15 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patients with severe preeclampsia, replicate 4 of 17

description: Biological replicate 30 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 25 of 26

description: Biological replicate 26 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 20 of 26

description: Biological replicate 21 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 12 of 26

description: Biological replicate 13 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 17 of 26

description: Biological replicate 18 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 15 of 26

description: Biological replicate 16 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 26 of 26

description: Biological replicate 27 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 21 of 26

description: Biological replicate 22 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 11 of 26

description: Biological replicate 11 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 9 of 26

description: Biological replicate 9 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 24 of 26

description: Biological replicate 25 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 18 of 26

description: Biological replicate 19 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 8 of 26

description: Biological replicate 8 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 23 of 26

description: Biological replicate 24 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 7 of 26

description: Biological replicate 7 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patients with severe preeclampsia, replicate 2 of 17

description: Biological replicate 28 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 19 of 26

description: Biological replicate 20 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 5 of 26

description: Biological replicate 5 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 10 of 26

description: Biological replicate 10 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 4 of 26

description: Biological replicate 4 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patients with severe preeclampsia, replicate 1 of 17

description: Biological replicate 12 of 43. Placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 3 of 26

description: Biological replicate 3 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 1 of 26

description: Biological replicate 1 of 43. Placenta tissue from patients with normal labor vs. placenta tissue from patients with severe preeclampsia


title: Placenta tissue from patient with normal labor, replicate 2 of 26

description: Biological replicate 2 of 43. Placenta tissue from patients with normal labour


title: Placenta tissue from patient with normal labor, replicate 6 of 26

description: Biological replicate 6 of 43. Placenta tissue from patients with normal labour


title: smoldering myeloma patient U133Plus-P1353-01

status: Public on Oct 06 2006

city: Little Rock

first: Shaughnessy

middle: Jr.

last: John

state: AR

address: 4301 West Markham St., Slot 776

country: USA

institute: Myeloma Institute for Research and Therapy

description:
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA)
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining

source_name: Bone marrow, smoldering multiple myeloma patient

tag: Human bone marrow plasma cells, U133Plus-P1353-01


title: smoldering myeloma patient U133Plus-P398

tag: Human bone marrow plasma cells, U133Plus-P398


title: smoldering myeloma patient U133Plus-P1255

tag: Human bone marrow plasma cells, U133Plus-P1255


title: MGUS patient U133Plus-P680

source_name: Bone marrow, patient diagnosed with Monoclonal gammopathy of undetermined significance (MGUS)

tag: Human bone marrow plasma cells, U133Plus-P680


title: smoldering myeloma patient U133Plus-P1280-01

tag: Human bone marrow plasma cells, U133Plus-P1280-01


title: smoldering myeloma patient U133Plus-P0338-01

tag: Human bone marrow plasma cells, U133Plus-P0338-01


title: MGUS patient U133Plus-P987

tag: Human bone marrow plasma cells, U133Plus-P987


title: MGUS patient U133Plus-P786

tag: Human bone marrow plasma cells, U133Plus-P786


title: MGUS patient U133Plus-P900

tag: Human bone marrow plasma cells, U133Plus-P900


title: MGUS patient U133Plus-P869

tag: Human bone marrow plasma cells, U133Plus-P869


title: smoldering myeloma patient U133Plus-P840

tag: Human bone marrow plasma cells, U133Plus-P840


title: smoldering myeloma patient U133Plus-P331

tag: Human bone marrow plasma cells, U133Plus-P331


title: smoldering myeloma patient U133Plus-P664

tag: Human bone marrow plasma cells, U133Plus-P664


title: MGUS patient U133Plus-P819

tag: Human bone marrow plasma cells, U133Plus-P819


title: smoldering myeloma patient U133Plus-P1499-01

tag: Human bone marrow plasma cells, U133Plus-P1499-01


title: MGUS patient U133Plus-P814

tag: Human bone marrow plasma cells, U133Plus-P814


title: MGUS patient U133Plus-P645

tag: Human bone marrow plasma cells, U133Plus-P645


title: MGUS patient U133Plus-P980

tag: Human bone marrow plasma cells, U133Plus-P980


title: smoldering myeloma patient U133Plus-P1413-01

tag: Human bone marrow plasma cells, U133Plus-P1413-01


title: MGUS patient U133Plus-P948

tag: Human bone marrow plasma cells, U133Plus-P948


title: MGUS patient U133Plus-P493

tag: Human bone marrow plasma cells, U133Plus-P493


title: MGUS patient U133Plus-P904

tag: Human bone marrow plasma cells, U133Plus-P904


title: MGUS patient U133Plus-P618

tag: Human bone marrow plasma cells, U133Plus-P618


title: smoldering myeloma patient U133Plus-P407

tag: Human bone marrow plasma cells, U133Plus-P407


title: MGUS patient U133Plus-P652

tag: Human bone marrow plasma cells, U133Plus-P652


title: smoldering myeloma patient U133Plus-P1643-01

tag: Human bone marrow plasma cells, U133Plus-P1643-01


title: MGUS patient U133Plus-P613

tag: Human bone marrow plasma cells, U133Plus-P613


title: MGUS patient U133Plus-P469

tag: Human bone marrow plasma cells, U133Plus-P469


title: MGUS patient U133Plus-P710

tag: Human bone marrow plasma cells, U133Plus-P710


title: MGUS patient U133Plus-P479

tag: Human bone marrow plasma cells, U133Plus-P479


title: MGUS patient U133Plus-P466

tag: Human bone marrow plasma cells, U133Plus-P466


title: MGUS patient U133Plus-P1615-01

tag: Human bone marrow plasma cells, U133Plus-P1615-01


title: MGUS patient U133Plus-P1318-01

tag: Human bone marrow plasma cells, U133Plus-P1318-01


title: MGUS patient U133Plus-P439

tag: Human bone marrow plasma cells, U133Plus-P439


title: MGUS patient U133Plus-P1508-01

tag: Human bone marrow plasma cells, U133Plus-P1508-01


title: MGUS patient U133Plus-P1306-01

tag: Human bone marrow plasma cells, U133Plus-P1306-01


title: MGUS patient U133Plus-P1268

tag: Human bone marrow plasma cells, U133Plus-P1268


title: MGUS patient U133Plus-P348

tag: Human bone marrow plasma cells, U133Plus-P348


title: MGUS patient U133Plus-P167

tag: Human bone marrow plasma cells, U133Plus-P167


title: MGUS patient U133Plus-P1467-01

tag: Human bone marrow plasma cells, U133Plus-P1467-01


title: MGUS patient U133Plus-P1472-01

tag: Human bone marrow plasma cells, U133Plus-P1472-01


title: MGUS patient U133Plus-P268

tag: Human bone marrow plasma cells, U133Plus-P268


title: MGUS patient U133Plus-P1426-01

tag: Human bone marrow plasma cells, U133Plus-P1426-01


title: MGUS patient U133Plus-P1032

tag: Human bone marrow plasma cells, U133Plus-P1032


title: MGUS patient U133Plus-P302

tag: Human bone marrow plasma cells, U133Plus-P302


title: MGUS patient U133Plus-P417

tag: Human bone marrow plasma cells, U133Plus-P417


title: MGUS patient U133Plus-P1020

tag: Human bone marrow plasma cells, U133Plus-P1020


title: MGUS patient U133Plus-P1026-2

tag: Human bone marrow plasma cells, U133Plus-P1026-2


title: MGUS patient U133Plus-P1014

tag: Human bone marrow plasma cells, U133Plus-P1014


title: MGUS patient U133Plus-P1115

tag: Human bone marrow plasma cells, U133Plus-P1115


title: MGUS patient U133Plus-P021

tag: Human bone marrow plasma cells, U133Plus-P021


title: MGUS patient U133Plus-P0039-02

tag: Human bone marrow plasma cells, U133Plus-P0039-02


title: Healthy donor U133Plus-N041

source_name: Bone marrow, healthy donor

tag: Human bone marrow plasma cells, U133Plus-N041


title: MGUS patient U133Plus-P014

tag: Human bone marrow plasma cells, U133Plus-P014


title: MGUS patient U133Plus-P1002

tag: Human bone marrow plasma cells, U133Plus-P1002


title: MGUS patient U133Plus-P1300-01

tag: Human bone marrow plasma cells, U133Plus-P1300-01


title: Healthy donor U133Plus-N042

tag: Human bone marrow plasma cells, U133Plus-N042


title: MGUS patient U133Plus-P1018

tag: Human bone marrow plasma cells, U133Plus-P1018


title: Healthy donor U133Plus-N020

tag: Human bone marrow plasma cells, U133Plus-N020


title: Healthy donor U133Plus-N017

tag: Human bone marrow plasma cells, U133Plus-N017


title: Healthy donor U133Plus-N035

tag: Human bone marrow plasma cells, U133Plus-N035


title: Healthy donor U133Plus-N045

tag: Human bone marrow plasma cells, U133Plus-N045


title: Healthy donor U133Plus-N039

tag: Human bone marrow plasma cells, U133Plus-N039


title: Healthy donor U133Plus-N007

tag: Human bone marrow plasma cells, U133Plus-N007


title: Healthy donor U133Plus-N030

tag: Human bone marrow plasma cells, U133Plus-N030


title: Healthy donor U133Plus-N013

tag: Human bone marrow plasma cells, U133Plus-N013


title: Healthy donor U133Plus-N022

tag: Human bone marrow plasma cells, U133Plus-N022


title: Healthy donor U133Plus-N005

tag: Human bone marrow plasma cells, U133Plus-N005


title: Healthy donor U133Plus-N025

tag: Human bone marrow plasma cells, U133Plus-N025


title: Healthy donor U133Plus-N001

tag: Human bone marrow plasma cells, U133Plus-N001


title: Healthy donor U133Plus-N031

tag: Human bone marrow plasma cells, U133Plus-N031


title: Healthy donor U133Plus-N009

tag: Human bone marrow plasma cells, U133Plus-N009


title: Healthy donor U133Plus-N028

tag: Human bone marrow plasma cells, U133Plus-N028


title: Healthy donor U133Plus-N019

tag: Human bone marrow plasma cells, U133Plus-N019


title: Healthy donor U133Plus-N029

tag: Human bone marrow plasma cells, U133Plus-N029


title: Healthy donor U133Plus-N024

tag: Human bone marrow plasma cells, U133Plus-N024


title: Healthy donor U133Plus-N004

tag: Human bone marrow plasma cells, U133Plus-N004


title: Healthy donor U133Plus-N006

tag: Human bone marrow plasma cells, U133Plus-N006


title: Placenta_PE(EO)3

status: Public on Apr 25 2006

address: 1-98 Dengakugakubo Kutsukake-cho

department: Gynecology & Obstetrics

description: Placental biopsies were obtained during Caesarean section from early onset Preeclampsia. A mixture of 3 placentas from normal subjects were used for a template control.

data_processing: Data processed with FeatureExtraction v7.1

source_name: Placenta_PE(EO)3 with Cy5

tag: Placental tissue from early onset Preeclampsia

source_name: Placenta_nl with Cy3

tag: A mixture of placental tissue from normal pregnancy


title: Placenta_PE(EO)1

source_name: Placenta_PE(EO)1 with Cy5


title: Placenta_PE(LO)5

description: Placental biopsies were obtained during Caesarean section from late onset Preeclampsia. A mixture of 3 placentas from normal subjects were used for a template control.

source_name: Placenta_PE(LO)5 with Cy5

tag: Placental tissue from late onset Preeclampsia


title: Placenta_PE(EO)2

source_name: Placenta_PE(EO)2 with Cy5


title: Placenta_PE(LO)3

source_name: Placenta_PE(LO)3 with Cy5


title: Placenta_PE(LO)1

source_name: Placenta_PE(LO)1 with Cy5


title: Placenta_nl3

description: Placental biopsies were obtained during Caesarean section from normotensive patients. A mixture of 3 placentas from normal subjects were used for a template control.

source_name: Placenta_nl3 with Cy5

tag: Placental tissue from normal pregnancy


title: Placenta_PE(LO)2

source_name: Placenta_PE(LO)2 with Cy5


title: Placenta_PE(EO)5

source_name: Placenta_PE(EO)5 with Cy5


title: Placenta_PE(LO)4

source_name: Placenta_PE(LO)4 with Cy5


title: Placenta_nl4

source_name: Placenta_nl4 with Cy5


title: Placenta_nl1

source_name: Placenta_nl1 with Cy5


title: Placenta_PE(EO)4

source_name: Placenta_PE(EO)4 with Cy5


title: Placenta_nl2

source_name: Placenta_nl2 with Cy5