title: liver and spike ins vs. synthetic miRNA pool (4)

description: PMID

hyb_protocol: 0.5 µg of respective total RNA were mixed with 75 spike in synthetic RNAs (which are not expressed in mouse liver) and 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 2.5 fmol of each of  891 non redundant miRNAs sequences and miRControl 3 seqeunces. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). Subsequently,the array data was normalized by calculating the median of the miRControl 3 present in the liver and UR sample.

source_name: liver + 75 synthetic RNAs (spike ins)

label_protocol: 0.5 µg total RNA and the spike ins (0.3125-20 fmol) were labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon)  following the instructions of the manufacturer

extract_protocol: total RNA as described in: Chomczynski P. (1993). A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques. 1993 Sep;15(3):532-4, 536-7

value: liver

label_protocol: 2.5 fmol of each of 889 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

value: 2.5 fmol of each of 889 synthetic miRNAs were pooled and labelled.


title: Normal_B3

status: Public on Mar 17 2010

type: genomic

city: Frankfurt am Main

first: Sylvia

last: Hartmann

department: Pathology

country: Germany

institute: University Frankfurt

description:
healthy reference
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

hyb_protocol: Affymetrix 500k SNP array manual

scan_protocol: Affymetrix 500k SNP array manual

data_processing: GCOS, GTYPE, CNAG, CNAT, dCHIP, BRLMM

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Affymetrix 500k SNP array manual

extract_protocol: Qiagen DNA Mini Kit

tag: disease state

value: normal

tag: tissue

value: peripheral blood


title: liver and spike ins vs. synthetic miRNA pool (5)

status: Public on Oct 27 2009

type: mixed

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

institute: Miltenyi Biotec GmbH

description: PMID

hyb_protocol: 1 µg of respective total RNA were mixed with 75 spike in synthetic RNAs (which are not expressed in mouse liver) and 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 2.5 fmol of each of  891 non redundant miRNAs sequences and miRControl 3 seqeunces. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

scan_protocol: Image capture was done with Agilent DNA-Microarray Scanner (Agilent, Santa Clara, CA)

molecule: total RNA

organism: Mus musculus

label_protocol: 1 µg total RNA and the spike ins (0.3125-20 fmol) were labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon)  following the instructions of the manufacturer

molecule: other

organism: synthetic construct

source_name: synthetic miRNA pool (miRXploreTM Universal Reference, Miltenyi Biotec)

tag: composition


title: liver and spike ins vs. synthetic miRNA pool (2)

description: PMID


title: liver and spike ins vs. synthetic miRNA pool (1)

description: PMID

hyb_protocol: 1 µg of respective total RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 2.5 fmol of each of  891 non redundant miRNAs sequences and miRControl 3 seqeunces. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

source_name: liver

label_protocol: 1 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon)  following the instructions of the manufacturer

label_protocol: 2.5 fmol of each of 889 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer.


title: liver total RNA vs. brain total RNA (3)

type: RNA

description: PMID

hyb_protocol: 5 µg of respective total RNA was mixed with 5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus 5 µg of a second labelled total RNA. The second labelled total RNA was mixed with 5 fmol of 18 RNA oligonucleotides reverse complement to miRControl 3 as well. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 18 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes.

label_protocol: 5 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array labeling kit, Exiqon)  following the instructions of the manufacturer

tag: strain

tag: gender

value: female

tag: age

value: 8 weeks

tag: type

value: WT

source_name: brain

value: brain


title: synthetic RNA pool vs. synthetic miRNA pool (7)

description: PMID

hyb_protocol: An equimolar mixture of synthetice miRNA, with 1 to 10,000 amol of each individual miRNA and 1 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 954 non redundant miRNAs sequences. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots). Subsequently,the array data was normalized by calculating the median of the miRControl 3 present in both samples.

value: 10 amol of each of 954 synthetic miRNAs were pooled and labelled.

label_protocol: 1 fmol of each of 954 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

value: 1 fmol of each of 954 synthetic miRNAs were pooled and labelled.


title: CD34(+)/CD133(-) cells vs. synthetic miRNA pool (1)

description: PMID

hyb_protocol: 1 µg of respective total RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 2.5 fmol of each of  954 non redundant miRNAs sequences and

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). Subsequently,the array data was normalized by calculating the median of the miRControl 3 present in the CD34(+)/CD133(-) and UR sample.

source_name: CD34(+)/CD133(-)/bone marrow

extract_protocol: total RNA as described in: Chomczynski P. (1993). A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques. 1993 Sep;15(3):532-4, 536-7"

value: male

value: 71 years

value: bone marrow

source_name: synthetic miRNA pool

label_protocol: 2.5 fmol of each of 954 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturertotal RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon)  following the instructions of the manufacturer

value: synthetic miRNA


title: brain total RNA vs. synthetic miRNA pool (2)

description: PMID

hyb_protocol: 5 µg of respective total RNA was mixed with 5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 5 fmol of each of  816 non redundant miRNAs sequences and miRControl 3 sequences. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

tag: barin

label_protocol: 5 fmol of each of 816 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array labeling kit, Exiqon) following the instructions of the manufacturer

tag: synthetic miRNA


title: CD34(+)/CD133(-) cells vs. synthetic miRNA pool (3)

description: PMID

hyb_protocol: 1 µg of respective total RNA was mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 2.5 fmol of each of  954 non redundant miRNAs sequences and miRControl 3 seqeunces. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec). Briefly, volume of labelled sample was adjusted to 100 µl with nuclease-free water and 100 µl 2x Hybridization Solution pre-warmed at 42°C was added. After mixing, the solution was pre-heated to 60 °C for 2 min prior to application to the a-Hyb. Microarray processing in the a-Hyb was as follows: incubation in Pre-Hyb Solution for 5 min at 42°C, hybridization with the labeled RNAs for 960 min at 42°C, wash with Wash Buffer I for 1 min at 10°C (2 cycles), and  second wash with Wash Buffer II for 1 min at 10°C (2 cycles). Pump speed at all incubations was set to 1 ml/min. Microarrays were blow-dried and scanned with the ScanArray Lite (GSI Lumonics, Watertown, MA) and the Agilent DNA-Microarray Scanner.

value: 70 years

label_protocol: 2.5 fmol of each of 954 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer

value: synthetic miRNA pool


title: liver and spike ins vs. synthetic miRNA pool (3)

description: PMID


title: brain total RNA vs. synthetic miRNA pool (1)

description: PMID

tag: brain


title: liver vs. synthetic miRNA pool (2)

description: PMID

hyb_protocol: 5 µg of respective total RNA was fluorescently labelled by 3’ ligation. Total RNA was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The synthetic miRNA pool consisted of 5 fmol of each of  816 non redundant miRNAs sequences and miRControl 3 sequences. Hybridization was performed using an automated hybridization machine (a-Hyb, Miltenyi Biotec).

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots).


title: CD34(+)/CD133(-) cells vs. synthetic miRNA pool (2)

description: PMID

extract_protocol: total RNA was isolated using a commercial kit (miRNeasy Mini kit, Qiagen)  following the instructions of the manufacturer

value: 74 years


title: liver total RNA vs. brain total RNA (1)

description: PMID

value: liver


title: liver vs. synthetic miRNA pool (1)

description: PMID


title: liver total RNA vs. synthetic miRNA pool (1)

description: PMID


title: liver and spike ins vs. synthetic miRNA pool (6)

description: PMID

data_processing: Signal processing and quantification was done with ImaGene software version 8.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the mean of the net signal intensities of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). Subsequently,the array data was normalized by calculating the median of the miRControl 3 present in the liver and UR sample.

label_protocol: 1 µg total RNA and the spike ins (0.15625-10 fmol) were labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon)  following the instructions of the manufacturer

label_protocol: 2.5 fmol of each of 891 synthetic miRNAs were pooled and labelld using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer


title: brain total RNA vs. synthetic miRNA pool (3)

description: PMID


title: liver total RNA vs. brain total RNA (2)

description: PMID


title: Normal_B4


title: In vivo treatment of mice with rFVIII rep. 6

status: Public on Apr 30 2009

city: Kingston

first: Mohammad

last: Qadura

state: Ontario

address: 88 Stuart St.

country: Canada

institute: Queen's University

description: Gene expression 24 hours post treatment

hyb_protocol: hybridized to the micro-array chip according to the manufacturer’s guidelines (Agilent Technologies, Santa Clara CA, USA)

scan_protocol: The arrays were then washed and scanned using an Agilent scanner according to the manufacturer’s guidelines (Agilent Technologies, Santa Clara CA, USA).

data_processing: The data was normalized and the replicates were filtered as previously described by Stekel (Stekel D. Microarray Bioinformatics. 2003) and Quackenbush (Quackenbush J. Microarray data normalization and transformation. Nat Genet. 2002;32 Suppl:496-501).

source_name: DC splenocytes 24hrs

label_protocol: The isolated RNA was labeled with Cyanine 3-CTP according to the manufacturer’s guidelines (Agilent Technologies, Santa Clara CA, USA).

growth_protocol: CD11c+ dendritic cells were isolated from mouse spleens using magnetic beads coated with anti-CD11c

extract_protocol: The CD11c cellular pellets were resuspended in Trizol (Invitrogen, Carlsbad, CA, USA). RNA isolation and purification steps were performed according to the manufacturer’s guidelines

treatment_protocol: Hemophilic mice were treated with either HBSS, plasma derived or recombinant factor VIII

value: Spleens

value: Balb/c hemophilic mice

tag: treatment

value: rFVIII

tag: replicate


title: In vivo treatment of mice with rFVIII rep. 7

description: Gene expression 24 hours post treatment


title: AD Amygdala

status: Public on Sep 15 2009

city: Tokushima

first: Yuta

last: Yamamoto

address: 3-18-15 Kuramoto-cho

department: Stress Science

country: Japan

institute: Institue for Health Biosciences, The University of Tokushima Graduate School

description:
An equal amount of RNA from 4 mice was pooled and used for microarray analysis.

Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at Agilent's website.

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).

data_processing:
Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value for data points labeled as Present.

The raw data were transformed to log2 by GeneSpring 7.3, and divided with the logarithmic AD value.

source_name: AD, Amygdala

label_protocol: Labeled cRNAs were generated from 400 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).

extract_protocol: After systemic perfusion with cold phosphate-buffered saline through the heart using a syringe attached to a 21-G needle, whole mouse brains were removed. Coronal sections (1 mm thickness) of mouse brain were prepared on ice. The amygdala was sliced between 1.5 and 2.5 mm posterior to bregma. Total RNA was immediately prepared from these samples using an RNeasy kit (Qiagen, Hilden, Germany). The quality of purified RNA was assessed by an Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: We tested three feeding regimens. One group of mice had ad libitum (AD) access to food, and was used as a control group. The repeated fasting and refeeding (RFR) group of mice were fasted on day 0 and allowed to feed ad libitum on day 1. Amounts of food consumed by the three mice on day 1 were measured. The half amount of food consumed by the RFR mice was given to three mice in another cage for two days (days 0 and 1) (CR group). The fasting followed by refeeding (RFR) and the restriction of food (CR) were repeated up to day 16. Body weights and consumed chow were measured at 20:00 every day, and then the fasting or feeding period was started. In RFR mice, fasting was started on day 0. Four mice of each group were sacrificed at 14:00 under general anesthesia with diethyl ether.

tag: genotype

value: Male

value: 8-9 wks

value: amygdala

value: AD (ad libitum)

tag: time of sacrifice

value: day 8


title: In vivo treatment of mice with rFVIII rep. 4

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with rFVIII rep. 3

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with rFVIII rep. 8

description: Gene expression 24 hours post treatment


title: Embryonic Drosophila cells, Kc167 cells, diffusible Dam in brahma RNAi vs. white RNAi

status: Public on Nov 05 2009

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Replicates were averaged: deltaAccessibility.1 and deltaAccessibility.2

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridiaztion station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Slides were scanned on an Agilent scanner with 2 micron resolution at full intensity.

data_processing: Scans were processed with NimbleScan 2.5 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values from 2 replicates were median centered and averaged and are represented in 'deltaAccess.norm.txt'. Values from reporters in the same GATC fragments in FlyBase release 5 were averaged. Mean values of GATC fragments are given in 'GATCfragments_deltaAcc.gff'.

label: Cy3 (replicate 1, array 182095), Cy5 (replicate 2, array 182097)

organism: Drosophila melanogaster

source_name: Dam-methylated DNA from Kc167 cells after brm RNAi

label_protocol: 1 µg purified methyl-PCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.0 (http://www.nimblegen.com/products/lit/lit.html). Reactions were repeated until total 13 ug labeled material per channel was obtained.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Dam methylase was expressed from pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

treatment_protocol: cells treated with 15 ug/ul brahma dsRNA on days 0,2 and 4 and transfected with 20 ug Dam expression plasmid/2*10e6 cells on day 4; harvested on day 5

tag: cells

tag: protocol

value: brm knockdown

label: Cy5 (replicate 1, array 182095), Cy3 (replicate 2, array 182097)

source_name: Dam-methylated DNA from Kc167 cells after w RNAi

treatment_protocol: cells treated with 15 ug/ul white dsRNA on days 0,2 and 4 and transfected with 20 ug Dam expression plasmid/2*10e6 cells on day 4; harvested on day 5

value: control


title: In vivo treatment of mice with rFVIII rep. 2

description: Gene expression 24 hours post treatment


title: dscDNA_A_3

status: Public on Nov 25 2009

city: Emeryville

first: Mario

last: Ouellet

state: CA

address: 5885 Hollis St., 4th Floor

country: USA

institute: Joint BioEnergy Institute

description: no additional information

hyb_protocol: Samples were randomly distributed on 5 4-plex slides. Hybridization and washes were performed as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.] simultaneously for all arrays.

scan_protocol: Individual arrays were scanned independently using a GenePix Professional 4200A scanner (Axon Instruments), adjusting the PMT gain for each array as recommended [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.]. Image analysis was performed with the NimbleScan software and features intensities were exported as .pair files

data_processing: ArrayStar 3.0 (DNASTAR) was used for probe summarization and normalization (RMA algorithm, quantile normalization) and data analysis

organism: Saccharomyces cerevisiae

source_name: Sample A (strain EPY330)

label_protocol:
10 µg of total RNA was used as starting material regardless of the labeling method used.
1) ds-cDNA method: the labeling method was carried as recommended by NimbleGen [NimbleGen Arrays User's Guide - Gene Expression Analysis v.3.0.], except that the components for the ds-cDNA synthesis were purchased separately and SuperScriptIII was used for the first strand cDNA synthesis. As recommended, 4 µg of labeled ds-cDNA was used for hybridization to each array.
2) Direct Random method:  7 µg of 5’Cy3 random nonamers (TriLink Biotechnologies, San Diego, CA) were added to the total RNA for a volume of 18.5 µl, heat denatured at 70°C for 5 minutes and placed on ice immediately. The remainder of the reverse transcription reaction components (6 µl of 5X First-Strand buffer, 1.5 µl of 0.1M DTT, 1 µl of 10mM dNTPs, 2 µl of 400U/µl SuperScriptIII and 1 µl of 40U/µl RNAseOut) were added and the reaction incubated at 25°C for 5 minutes and at 42°C for 3h. Template RNA was chemically hydrolysed by addition of 1 volume of a 200 mM NaOH, 20mM EDTA solution and incubation at 65°C for 10 minutes. The hydrolysis reaction was neutralized with 1 volume of 1M HEPES and the labeled cDNA purified on a Qiaquick column (QIAGEN) following the manufacturer’s recommendations for PCR purification. 5µg of labeled cDNA was hybridized to each array.
3) Indirect method: The SuperScript Plus Indirect cDNA Labeling System (Invitrogen) was used with Alexa Fluor 555 reactive dye following the manufacturer's recommendations, except for the chemical hydrolysis of RNA and cDNA purifications, which were carried as described above for the Direct random method with the exception that the kit wash buffer in the first cDNA purification was replaced with 80% ethanol. 300ng of labeled cDNA was hybridized to each array.

growth_protocol: 3 colonies for each strain were pre-cultured in SD-His-Met-Leu medium and used to inoculate 5 ml of YPG inducing medium [Ro et al. BMC Biotechnol 2008, 8(1):83] for induction at 30°C in culture tubes for 24h

extract_protocol: Cells were harvested by quick centrifugation and immediately frozen in liquid nitrogen, disrupted with glass beads in a bead-beater and total RNA was extracted using the RNeasy Mini kit (QIAGEN), including the on-column DNAse treatment. RNA was quantified by spectrophotometry with a Nanodrop ND-1000 and its integrity verified on a 2100 Bioanalyzer (Agilent). Equal amounts of RNA from each replicate culture were pooled for each strain.

tag: labeling method

value: ds-cDNA

tag: induction time (h)


title: In vivo treatment of mice with rFVIII rep. 5

description: Gene expression 24 hours post treatment

tag: tissue


title: kidney_high-weight-difference-steroids_rep2

status: Public on Jul 22 2009

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

department: Bioinformatics

hyb_protocol: The hybridization procedure was performed according to the “One-colour Microarray-based Gene expression analysis protocol” (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65µg Cy3-labelled fragmented cRNA was hybridized overnight (17 hours, 65°C) to Agilent Whole Rat Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37°C) containing 0.005% N-lauroylsarcosine for 1min. The last washing step was performed with acetonitrile for 30sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner. The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

organism: Rattus norvegicus

source_name: kidney, transplanted from Dark Agouti rats into Lewis rats, high weight difference between donor and recipient, treatment with prednisolone immediately after transplantation

label_protocol: Sample labelling was performed as detailed in the “One-colour Microarray-based Gene expression analysis protocol” (version 5.5, part number G4140-90040). Briefly, one µg of each total RNA sample was used for amplification and labelling using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP (Perkin Elmer). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 sprectophotometer (NanoDrop Technologies).

growth_protocol: Naïve male 120-250 g inbred rats (Harlan-Winkelmann GmbH, Borchen, Germany) were used throughout the experiments. Lewis rats (LEW; RT1l) were used as graft recipients, and Dark Agouti (DA; RT1a) or Lewis animals as donors. Rats received a standard diet and water ad libitum and were cared for in strict accordance to the guidelines of the FELASA (Federation of European Laboratory Animal Science Associations).

extract_protocol: Animals were sacrificed at 24-h after transplantation, tissue samples were snap-frozen in liquid nitrogen and stored at –70°C. Total RNA was isolated using the Strataprep-Total-RNA-Miniprep-KitTM (Stratagene, Heidelberg, Germany).

treatment_protocol: Orthotopic kidney transplantations were performed from DA to the MHC-incompatible Lewis rat strain using a technique described previously [Pascher A. et al (2003)Transplantation 76:1560-1568]. Briefly, the animals were anesthetized, the donor kidneys were harvested, cooled with UW (University of Wisconsin) solution (Dupont Pharma, USA), kept at 4°C for 25 min, and transplanted orthotopically into bilaterally nephrectomized male LEW recipients. This study project was divided into four groups. The recipients in the first group received allografts from low-weight donors, designated as high-weight difference (-20 to -50% difference in body weight with the percentage reflecting the weight difference in g divided by the weight of the recipient). The recipients of the second group received kidney grafts from donors demonstrating a similar body weight, designated as lower-weight difference (-0 to -20% difference in body weight). Group three recipients received in addition a single injection i.v. of 500µg neutralizing anti-IL6 receptor antibody (BIOZOL, Eching, Germany) immediately after transplantation. Group four recipients received a single injection of prednisolone (Solu-Decortin H, 15mg/kg i.v., Merck, Germany) immediately after transplantation.

value: Dark Agouti (DA; RT1a)


title: kidney_low-weight-difference_rep2

source_name: kidney, transplanted from Dark Agouti rats into Lewis rats, low weight difference between donor and recipient


title: Control C3 vs. Exp E6, skeletal muscle

status: Public on Jun 02 2009

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: Skeletal muscle

hyb_protocol: According to Agilent protocol

scan_protocol: Agilent Scanner, according to Agilent protocol

data_processing: Feature Extraction Software, then log2 transformation and lowess normalization using Bioconductor packages

source_name: Control, C3, skeletal muscle

label_protocol: Agilent Low RNA Input FluorescentLinear Amplification Kit

growth_protocol: 6-month old mice

extract_protocol: Trizol

value: WT

value: skeletal muscle

source_name: KIKO, E6, skeletal muscle

value: KIKO


title: hMSCs_BV-transduced_rep1

city: Hsinchu

first: Yu-Chen

last: Hu

address: 101, Section 2, Kuang-Fu Road

department: Chemical Engineering

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Cy5-labeled aRNA were suspended in OneArray™ hybridization buffer (provided in HOA product package) at a final volume of 180 ul per bridization. The pre-hybridization blocking, array hybridization, and post-hybridization washes were performed according to the instruction provided in the HOA User Guide.

scan_protocol: The arrays were scanned using DNA Microarray Scanner (Agilent Technologies) and the fluorescent intensities are extracted from the generated images by following the instructions and the conditions described in HOA User Guide.

data_processing: The raw data was preprocessed by log2 transformation and Global Lowess normalization. The preprocessed data was then analyzed by Limma package of R software. In this study, the significantly changed genes were identified and filtered based on one-way ANOVA (adjusted p<0.05).

source_name: hMSCs, BV-transduced

label_protocol: cDNA were synthesized from the extracted total RNA by reverse transcription followed by second strand synthesis using the Amino Allyl MessageAmpII aRNA amplification Kit (Ambion) according to the manufacturer's specification. Amino allyl modified aRNA produced was subsequently coupled to Cy5 dye label.

growth_protocol: Bone marrow-derived hMSCs were obtained from Cambrex Co., selected, enriched, cultured in a-MEM medium containing 10% fetal bovine serum (FBS, Hyclone) , and expanded to passage 11 for all experiments.

extract_protocol: Total RNA was extracted with the RNeasy® Mini Kit (Qiagen) according to manufacturer's specification.

treatment_protocol: The virus transduction was performed on 6-well plates. Depending on the MOI, a certain volume of virus supernatant was mixed with NaHCO3-deficient  a-MEM medium to adjust the final volume to 500 ml (per well). The transduction was initiated by adding the virus mixture to the cells and continued by gently shaking the plates on a rocking plate for 4 h at 25-27 oC. For mock-transduction, the cells were incubated under the same conditions with the solution consisting of 400  ml NaHCO3-deficient a-MEM and 100  ml fresh TNM-FH medium.

tag: cell type

value: Human mesenchymal stem cells (hMSCs)

tag: hmscs passage number

value: 11th passage


title: kidney_high-weight-difference_rep1

source_name: kidney, transplanted from Dark Agouti rats into Lewis rats, high weight difference between donor and recipient

tag: strain


title: kidney_high-weight-difference-anti-IL6R-mAb_rep1

source_name: kidney, transplanted from Dark Agouti rats into Lewis rats, high weight difference between donor and recipient, treatment with anti-IL6R antibody immediately after transplantation


title: kidney_low-weight-difference_rep1


title: hMSCs_BV-transduced_rep3


title: In vivo treatment of mice with rFVIII rep. 1

description: Gene expression 24 hours post treatment

value: Spleens


title: kidney_high-weight-difference-anti-IL6R-mAb_rep2


title: kidney_high-weight-difference-steroids_rep1


title: In vivo treatment of mice with pdFVIII rep. 7

description: Gene expression 24 hours post treatment

value: Balb/c hemophilic mice

value: pdFVIII


title: In vivo treatment of mice with pdFVIII rep. 8

description: Gene expression 24 hours post treatment


title: Control C3 vs. Exp E6, heart

description: Heart

source_name: Control, C3, heart

value: heart

source_name: KIKO, E6, heart


title: hMSCs_BV-transduced_rep4


title: hMSCs_mock-transduced_rep4

source_name: hMSCs, mock-transduced


title: In vivo treatment of mice with pdFVIII rep. 5

description: Gene expression 24 hours post treatment


title: hMSCs_BV-transduced_rep2


title: In vivo treatment of mice with pdFVIII rep. 4

description: Gene expression 24 hours post treatment


title: hMSCs_mock-transduced_rep3


title: In vivo treatment of mice with pdFVIII rep. 1

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with pdFVIII rep. 2

description: Gene expression 24 hours post treatment


title: hMSCs_mock-transduced_rep1


title: In vivo treatment of mice with HBSS rep. 7

description: Gene expression 24 hours post treatment

value: HBSS


title: In vivo treatment of mice with pdFVIII rep. 6

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 4

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 5

description: Gene expression 24 hours post treatment


title: hMSCs_mock-transduced_rep2


title: In vivo treatment of mice with HBSS rep. 2

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 6

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with pdFVIII rep. 3

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 1

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 8

description: Gene expression 24 hours post treatment


title: In vivo treatment of mice with HBSS rep. 3

description: Gene expression 24 hours post treatment


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 030 Liver-1

status: Public on Apr 28 2009

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

description: 150 mg/kg X 24 hr

hyb_protocol: Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the array for 17 hours prior to washing and scanning.

scan_protocol: Pixel intensity data were extracted from scanned images using the Agilent Technologies Scanner and Feature Extraction Software (Agilent Technologies).  See the header of the Agilent data files for more details of the scanning and data acquisition harware and software versions and parameters.

data_processing: log base 2 ratio of Dye Normalized rProcessedSignal to gProcessedSignal

source_name: 0 mg/kg Thioacetamide 24hr Rat Liver Control Pool

label_protocol: 1 ug of total RNA was amplified and labeled with a fluorescent dye using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer's protocol.

extract_protocol: RNA was isolated from the flash frozen portion of the left lateral liver lobe using RNeasy Midi columns (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

tag: gender

value: male

tag: age

value: 10-12 weeks

value: Liver

source_name: 150mg/kg Thioacetamide 24hr Rat 030 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 030 Liver-2

description: 150 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 032 Liver-2

description: 150 mg/kg X 24 hr

source_name: 150mg/kg Thioacetamide 24hr Rat 032 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 029 Liver-1

description: 150 mg/kg X 24 hr

source_name: 150mg/kg Thioacetamide 24hr Rat 029 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 026 Liver-2

description: 50 mg/kg X 24 hr

source_name: 50mg/kg Thioacetamide 24hr Rat 026 Liver


title: dscDNA_A_1

description: no additional information


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 026 Liver-1

description: 50 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 029 Liver-2

description: 150 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 031 Liver-2

description: 150 mg/kg X 24 hr

source_name: 150mg/kg Thioacetamide 24hr Rat 031 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 027 Liver-2

description: 50 mg/kg X 24 hr

source_name: 50mg/kg Thioacetamide 24hr Rat 027 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 028 Liver-1

description: 50 mg/kg X 24 hr

source_name: 50mg/kg Thioacetamide 24hr Rat 028 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 025 Liver-1

description: 50 mg/kg X 24 hr

source_name: 50mg/kg Thioacetamide 24hr Rat 025 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 025 Liver-2

description: 50 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 031 Liver-1

description: 150 mg/kg X 24 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 043 Liver-2

description: 50 mg/kg X 48 hr

source_name: 50mg/kg Thioacetamide 48hr Rat 043 Liver

source_name: 0 mg/kg Thioacetamide 48hr Rat Liver Control


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 027 Liver-1

description: 50 mg/kg X 24 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 042 Liver-1

description: 50 mg/kg X 48 hr

source_name: 50mg/kg Thioacetamide 48hr Rat 042 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 028 Liver-2

description: 50 mg/kg X 24 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 043 Liver-1

description: 50 mg/kg X 48 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 016 Liver-1

description: 150 mg/kg X 6 hr

source_name: 0 mg/kg Thioacetamide 6hr Rat Liver Control Pool

source_name: 150mg/kg Thioacetamide 6hr Rat 016 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 041 Liver-1

description: 50 mg/kg X 48 hr

source_name: 50mg/kg Thioacetamide 48hr Rat 041 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 044 Liver-2

description: 50 mg/kg X 48 hr

source_name: 50mg/kg Thioacetamide 48hr Rat 044 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 016 Liver-2

description: 150 mg/kg X 6 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 042 Liver-2

description: 50 mg/kg X 48 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 015 Liver-2

description: 150 mg/kg X 6 hr

source_name: 150mg/kg Thioacetamide 6hr Rat 015 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 041 Liver-2

description: 50 mg/kg X 48 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 040 Liver-2

description: 15 mg/kg X 48 hr

source_name: 15mg/kg Thioacetamide 48hr Rat 040 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 040 Liver-1

description: 15 mg/kg X 48 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 024 Liver-2

description: 15 mg/kg X 24 hr

source_name: 15mg/kg Thioacetamide 24hr Rat 024 Liver

source_name: 0 mg/kg Thioacetamide 24hr Rat Liver Control Pool


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 022 Liver-1

description: 15 mg/kg X 24 hr

source_name: 15mg/kg Thioacetamide 24hr Rat 022 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 039 Liver-2

description: 15 mg/kg X 48 hr

source_name: 15mg/kg Thioacetamide 48hr Rat 039 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 015 Liver-1

description: 150 mg/kg X 6 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 023 Liver-2

description: 15 mg/kg X 24 hr

source_name: 15mg/kg Thioacetamide 24hr Rat 023 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 013 Liver-1

description: 150 mg/kg X 6 hr

source_name: 150mg/kg Thioacetamide 6 hr Rat 013 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 014 Liver-1

description: 150 mg/kg X 6 hr

source_name: 150mg/kg Thioacetamide 6hr Rat 014 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 012 Liver-1

description: 50 mg/kg X 6 hr

source_name: 50mg/kg Thioacetamide 6hr Rat 012 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 038 Liver-2

description: 15 mg/kg X 48 hr

source_name: 15mg/kg Thioacetamide 48hr Rat 038 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 022 Liver-2

description: 15 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 021 Liver-2

description: 15 mg/kg X 24 hr

source_name: 15mg/kg Thioacetamide 24hr Rat 021 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 024 Liver-1

description: 15 mg/kg X 24 hr


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 021 Liver-1

description: 15 mg/kg X 24 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 012 Liver-2

description: 50 mg/kg X 6 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 014 Liver-2

description: 150 mg/kg X 6 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 011 Liver-1

description: 50 mg/kg X 6 hr

source_name: 50mg/kg Thioacetamide 6 hr Rat 011 Liver


title: Thioacetamide 24hr Rat Liver Control Pool vs. Thioacetamide 24hr Rat 023 Liver-1

description: 15 mg/kg X 24 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 013 Liver-2

description: 150 mg/kg X 6 hr

source_name: 0 mg/kg Thioacetamide 6hr Rat Liver Control Pool


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 009 Liver-1

description: 50 mg/kg X 6 hr

source_name: 50mg/kg Thioacetamide 6hr Rat 009 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 009 Liver-2

description: 50 mg/kg X 6 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 011 Liver-2

description: 50 mg/kg X 6 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 010 Liver-2

description: 50 mg/kg X 6 hr

source_name: 50mg/kg Thioacetamide 6 hr Rat 010 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 039 Liver-1

description: 15 mg/kg X 48 hr

source_name: 0 mg/kg Thioacetamide 48hr Rat Liver Control


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 037 Liver-1

description: 15 mg/kg X 48 hr

source_name: 15mg/kg Thioacetamide 48hr Rat 037 Liver


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 008 Liver-2

description: 15 mg/kg X 6 hr

source_name: 15mg/kg Thioacetamide 6hr Rat 008 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 037 Liver-2

description: 15 mg/kg X 48 hr


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6 hr Rat 010 Liver-1

description: 50 mg/kg X 6 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 038 Liver-1

description: 15 mg/kg X 48 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48 hr Rat 048 Liver-2

description: 150 mg/kg X 48 hr

source_name: 150mg/kg Thioacetamide 48 hr Rat 048 Liver


title: kidney_high-weight-difference_rep2

source_name: kidney, transplanted from Dark Agouti rats into Lewis rats, high weight difference between donor and recipient


title: Thioacetamide 6hr Rat Liver Control Pool vs. Thioacetamide 6hr Rat 008 Liver-1

description: 15 mg/kg X 6 hr


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 047 Liver-2

description: 150 mg/kg X 48 hr

source_name: 150mg/kg Thioacetamide 48hr Rat 047 Liver


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 047 Liver-1

description: 150 mg/kg X 48 hr


title: expression, 120 min after TRAP+PTX stimulation, rep2

city: Berlin

first: Solveig

last: Grossmann

address: Robert-Rössle-Str. 10

institute: FMP Berlin

description: Gene expression data from stimualted vascular smooth smucle cells

hyb_protocol: 15 µg of cRNA were hybridized for 16-18 h at 45°C and 60 rpm in a Gene Chip Hybridization Oven 640. Gene chips were washed and stained in the Gene Chip Fluidics Station 450.

scan_protocol: Gene Chips were scanned in a Gene Chip Scanner 7G

data_processing: The data were analyzed with Gene Chip Operating Software 1.4 (GCOS 1.4)

source_name: neonatal rat aortic smooth muscle cells, stimulated with 25 µM TRAP for 120 min after pre-treatment with 200 ng/ml PTX for 24 h

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

growth_protocol: primary cultures of newborn rat aortic smooth muscle cells were maintained in MEM Earl's medium supplemented with 10 % FCS, 2 % tryptose phosphate broth, 4 mM glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin

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

treatment_protocol: cells were serum-starved in quiescent medium supplemented with 1 % BSA overnight. Cells were stimulated with 2 U/ml thrombin, 25 µM TRAP or 25 µM TRAP after pre-treatment with 200 ng/ml pertussis toxin for 24 h

value: aortic vascular smooth muscle cells

tag: agent


title: Thyroid tissue cultured with IL-1 alpha 24 hours

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

institute: Tokyo Women's Medical University

description: Thyroid follicles were cultured with or without IL-1 alpha for 24 hours

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: Images were quantified using Agilent Microarray Scanner

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: human thyroid follicles

label_protocol: 1 µg of total RNA were primed with 5 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNTP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10-8M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without IL-1 alpha 5ng/ml for 24 hours

value: untreated (control)

value: IL-1 alpha

tag: concentration

tag: time

value: 24 hours


title: basal expression, prior to TRAP+PTX stimulation, rep1

description: Gene expression data from vascular smooth smucle cells

source_name: neonatal rat aortic smooth muscle cells, unstimulated


title: expression, 120 min after TRAP+PTX stimulation, rep1

value: 25 µM TRAP for 120 min after pre-treatment with 200 ng/ml PTX for 24 h


title: expression, 120 min after TRAP stimulation, rep2

source_name: neonatal rat aortic smooth muscle cells, stimulated with 25 µM TRAP for 120 min

value: 25 µM TRAP for 120 min


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 046 Liver-1

description: 150 mg/kg X 48 hr

source_name: 150mg/kg Thioacetamide 48hr Rat 046 Liver


title: expression, 120 min after thrombin stimulation, rep2

source_name: neonatal rat aortic smooth muscle cells, stimulated with 2 U/ml thrombin for 120 min

value: 2 U/ml thrombin for 120 min


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 046 Liver-2

description: 150 mg/kg X 48 hr


title: expression, 120 min after thrombin stimulation, rep1


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48 hr Rat 048 Liver-1

description: 150 mg/kg X 48 hr


title: expression, 120 min after TRAP stimulation, rep1


title: basal expression, prior to TRAP stimulation, rep1


title: Thioacetamide 48hr Rat Liver Control vs. Thioacetamide 48hr Rat 045 Liver-2

description: 150 mg/kg X 48 hr

source_name: 150mg/kg Thioacetamide 48hr Rat 045 Liver


title: basal expression, prior to thrombin stimulation, rep2


title: BL308

status: Public on Apr 24 2009

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

description:
allergic asthma 03, post ICS treatment
DV020808HGA13.CEL

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized  at 45C overnight (16–20 hours). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Following washing, the specifically bound probe was detected by incubating the arrays with SAPE (streptavidin phycoerthryin, Molecular Probes) and scanning the chips using a Gene Array Scanner (Agilent).

data_processing: The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix). Data was extracted using MAS5 and filtered to exclude genes that were not expressed (taken to be equivalent to a MAS5 absent call) in all samples.

source_name: Bronchial biopsies from lung tissue

label_protocol: Biotinylated probe was prepared from the entire cDNA reaction mixture with the ENZO bioarray high-yield RNA transcript labeling kit (ENZO diagnostics).

extract_protocol: Biopsies were obtained from the sub-segmental and segmental bronchial carinae of the lower (3–5 biopsies) and upper (1–2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1–2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). When bronchoscopy was repeated after ICS treatment, biopsies were taken from the left lung at similar bronchial levels. The samples were mechanically homogenized (Rotor/Stator homogeniser, PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The tissue samples were immediately placed in RNAlater (Ambion) to stabilize intracellular RNA during transport.

value: adult

value: female

value: lung


title: CLE264

description:
allergic asthma 03
YF020711HGA05aa.CEL

source_name: Bronchial biopsies from lung tissue (pool of six bronchial biopsies)


title: BL307

description:
allergic asthma 02, post ICS treatment
DV020808HGA12.CEL


title: BL306

description:
allergic asthma, post ICS treatment
not the same patient - same phenotype
DV020808HGA11.CEL


title: Thyroid tissue cultured with IFN gamma 48 hours.

description: Thyroid follicles were cultured with or without IFN gamma for 48 hours.

label_protocol: 0.5 µg of total RNA were primed with 1.2 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without IFN gamma 1000U/ml for 48 hours.

value: IFN gamma

value: 48 hours


title: Thyroid tissue cultured with TNF alpha 24 hours

description: Thyroid follicles were cultured with or without TNF alpha for 24 hours

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Green signal/processed Red signal. Agilent software was used.

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without TNF alpha 20ng/ml for 24 hours

value: TNF alpha


title: BL151

description:
allergic asthma 02
AS020523HGA11aa.CEL


title: BL305

description:
allergic asthma 01, post ICS treatment
DV020808HGA10.CEL


title: basal expression, prior to TRAP+PTX stimulation, rep2


title: BL126

description:
allergic asthma
AS020523HGA08aa.CEL


title: basal expression, prior to TRAP stimulation, rep2


title: BL136

description:
control
AS020523HGA09aa.CEL


title: BL150

description:
control
AS020523HGA10aa.CEL


title: BL120

description:
allergic asthma 01
AS020523HGA06aa.CEL


title: BL121

description:
control
AS020523HGA07aa.CEL


title: BL005

description:
control
RS020319HU02ba.CEL


title: group-2-pt-t6495589

status: Public on Apr 13 2009

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS 1.3) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix).

extract_protocol: Total RNA was harvested using the RNeasy RNA Isolation kit  standard protocol (Qiagen, Valencia, CA)

tag: final disposition

value: control


title: group-2-pt-t8624689

value: male


title: group-2-pt-t33433141

value: 01:Inpatient rehabilitation facility


title: group-2-pt-t5045596


title: group-2-pt-t3554510


title: group-2-pt-t33640716


title: group-2-pt-t9308516


title: group-2-pt-t4508690


title: group-2-pt-t7212104


title: group-2-pt-t6243678


title: group-2-pt-t4965319


title: group-2-pt-t32091878

value: 02:Skilled nursing facility


title: group-2-pt-t30640843


title: group-2-pt-t34247523


title: group-2-pt-t8209678


title: group-2-pt-t32937784


title: group-2-pt-t32342344

value: 88:Other (specify)


title: group-2-pt-t32627779


title: group-2-pt-t30240283

value: 05:Home with services


title: group-2-pt-t34814188


title: group-2-pt-t32827992


title: group-2-pt-t3217508


title: group-2-pt-t31254381


title: group-2-pt-t322025


title: group-2-pt-t31016255


title: group-2-pt-t7061623


title: group-2-pt-t6861920


title: group-2-pt-t34198779


title: group-2-pt-t28175962


title: group-2-pt-t29544461


title: group-2-pt-t24021044


title: group-2-pt-t27890110


title: group-2-pt-t23355260


title: group-2-pt-t27298010


title: group-2-pt-t26350190


title: group-2-pt-t22676948


title: group-2-pt-t27159239


title: group-2-pt-t22528008


title: group-2-pt-t21347674


title: group-2-pt-t21659093


title: group-2-pt-t18932716


title: group-2-pt-t28856947


title: group-2-pt-t20325754


title: group-2-pt-t1778836


title: group-2-pt-t20710123


title: group-2-pt-t20628135


title: group-2-pt-t23445359


title: group-2-pt-t18368456


title: group-2-pt-t2113833


title: group-2-pt-t18509360


title: basal expression, prior to thrombin stimulation, rep1

value: aortic vascular smooth muscle cells


title: group-2-pt-t18145446


title: group-2-pt-t17593495


title: group-2-pt-t19792345


title: group-2-pt-t17169324


title: group-2-pt-t15733320


title: group-2-pt-t17044501


title: group-2-pt-t14841022


title: group-2-pt-t12881564


title: group-2-pt-t13513185


title: group-2-pt-t15111525


title: group-2-pt-t14755953


title: group-2-pt-t16934338


title: group-2-pt-t13427118


title: group-2-pt-t13856354


title: group-2-pt-t15501307


title: group-2-pt-t13213595


title: group-2-pt-t1129691


title: group-2-pt-t12459034


title: group-2-pt-t13365750


title: group-2-pt-t12449908


title: group-2-pt-t10999830


title: group-2-pt-t12485562


title: group-2-pt-t12149903


title: group-2-pt-t11498346


title: group-2-pt-t11200547


title: group-2-pt-t31980419


title: group-2-pt-t10899813


title: group-2-ctl-c6630359


title: group-2-ctl-c35041110


title: group-2-ctl-c18299580


title: group-2-ctl-c9113824


title: group-2-ctl-c25052454


title: group-2-ctl-c34464946


title: group-2-ctl-c21704142


title: group-2-ctl-c19453182


title: group-2-ctl-c29498112


title: group-1-pt-t9557192


title: group-1-pt-t8859499


title: group-2-ctl-c18243342


title: group-2-ctl-c23203001

value: 07:Another acute care facility


title: group-2-ctl-c21240736


title: group-2-ctl-c21422982


title: group-2-ctl-c13735365


title: group-2-ctl-c14368019


title: group-2-ctl-c33135299


title: group-1-pt-t7660790


title: group-1-pt-t5376310


title: group-1-pt-t7444072


title: group-1-pt-t7726341


title: group-1-pt-t5928763


title: group-1-pt-t936103


title: group-1-pt-t4539940


title: group-1-pt-t4972319


title: group-2-pt-t25959229


title: group-1-pt-t6435853


title: group-1-pt-t4253298


title: group-1-pt-t34670758


title: group-2-pt-t2273448


title: group-1-pt-t32950994


title: group-1-pt-t2684174


title: group-1-pt-t31850232


title: group-1-pt-t3396312


title: group-1-pt-t3896185


title: group-1-pt-t31938349


title: group-1-pt-t30534587


title: group-1-pt-t26802595


title: group-1-pt-t24532226


title: group-1-pt-t32734260


title: group-1-pt-t32042281


title: group-1-pt-t2684459


title: group-1-pt-t29753308


title: group-1-pt-t26407397


title: group-1-pt-t24865344


title: group-1-pt-t34933880


title: group-1-pt-t4009237


title: group-1-pt-t33226222


title: group-1-pt-t27248819


title: group-1-pt-t27151221


title: group-1-pt-t25158203


title: group-1-pt-t5055720


title: group-1-pt-t32750360


title: group-1-pt-t31082981


title: group-1-pt-t3457955


title: group-1-pt-t29636425


title: group-1-pt-t24884150


title: group-1-pt-t2128306


title: group-1-pt-t23306982


title: group-1-pt-t21411022


title: group-1-pt-t21068100


title: group-1-pt-t21452005


title: group-1-pt-t20200060


title: group-1-pt-t224165


title: group-1-pt-t20810880


title: group-1-pt-t23748670


title: group-1-pt-t23767201


title: group-1-pt-t23054365


title: group-1-pt-t20055549


title: group-1-pt-t20209854


title: group-1-pt-t16666198


title: group-1-pt-t16644640


title: group-1-pt-t20153774


title: group-1-pt-t19582578


title: group-1-pt-t19872404


title: group-1-pt-t15812209


title: group-1-pt-t19228402


title: group-1-pt-t18794715


title: group-1-pt-t163143


title: group-1-pt-t19176208


title: group-1-pt-t18691395


title: group-1-pt-t16437161


title: group-1-pt-t16175538


title: group-1-pt-t17649932


title: group-1-pt-t12824413


title: group-1-pt-t19290858


title: group-1-pt-t10999876


title: group-1-ctl-c5367069


title: group-1-pt-t16744186


title: group-1-ctl-c34578412


title: group-1-ctl-c26096349


title: group-1-ctl-c7760396


title: group-1-ctl-c30463616


title: group-1-pt-t12460746


title: group-1-pt-t12718421


title: group-1-pt-t14324609


title: group-1-ctl-c2018336


title: group-1-pt-t13542489


title: group-1-ctl-c10052302


title: group-1-ctl-c25216385


title: group-1-ctl-c25419898


title: group-1-ctl-c19130256


title: group-1-pt-t14821887


title: group-1-pt-t12920964


title: group-1-pt-t11706353


title: Day5 VIN13 #1

status: Public on Jul 01 2008

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Standard Affymetrix Procedure, MAS5.0

label: Biotin

source_name: Day5 VIN13

label_protocol: Standard Affymetrix procedure

extract_protocol: Hot-phenol method

tag: replicate

value: Day 5 of fermentation


title: group-1-pt-t17826449


title: stroma_normal_reduction_sample019_rep2

status: Public on Oct 20 2006

city: Montreal

first: Greg

last: Finak

state: QC

address: 3775 University

department: Mcgill Center For Bioinformatics

institute: McGill University

description: RNA isolated from laser capture microdissected breast tissue. RNA has undergone two rounds of T7 linear amplification.

data_processing:
Raw Cy5 and Cy3 intensities were background corrected using the RMA background
correction algorithm. Data was tranformed to log2 ratios and within array normalization
was performed using spatial  and intensity-dependent loess. Between array normalization
was performed by scaling the arrays to have the same median absolute deviation.

source_name: normal breast stroma from reduction tissue

tag: LN

tag: ESR

tag: GRADE

tag: TT

value: Normal-Connective

tag: PR

tag: AgeOfOperation

tag: TumorSize

tag: MenopauseStatus

tag: TypeOfCase

value: Normal

tag: recurrence

value: No

tag: cellularity

value: High

source_name: Stratagene universal human reference


title: epithelium_normal_reduction_sample044_rep1

source_name: normal breast epithelium from reduction tissue

value: Normal-Epithelial

value: Surgical menopause


title: stroma_normal_adjacent_sample392_rep1

source_name: histologically normal stroma adjacent to I.D.C.

value: Negative

value: III

value: Post-menopause

value: Malignant


title: stroma_normal_reduction_sample132_rep2

value: Pre-menopause


title: epithelium_normal_adjacent_sample122_rep1

source_name: histologically normal epithelium adjacent to I.D.C.

value: Positive


title: epithelium_normal_reduction_sample044_rep2


title: epithelium_normal_adjacent_sample122_rep2


title: epithelium_normal_adjacent_sample315_rep2

value: Peri-menopause

value: Yes


title: epithelium_normal_adjacent_sample247_rep1

value: II


title: epithelium_normal_adjacent_sample247_rep2


title: stroma_normal_adjacent_sample057_rep1

value: LowII


title: epithelium_normal_adjacent_sample076_rep2


title: epithelium_normal_reduction_sample193_rep1


title: epithelium_normal_adjacent_sample345_rep1


title: stroma_normal_reduction_sample132_rep1


title: stroma_normal_adjacent_sample076_rep2


title: stroma_normal_adjacent_sample409_rep2


title: epithelium_normal_adjacent_sample344_rep2


title: epithelium_normal_reduction_sample193_rep2


title: epithelium_normal_adjacent_sample076_rep1


title: stroma_normal_adjacent_sample018_rep2

value: LowI


title: epithelium_normal_adjacent_sample344_rep1


title: stroma_normal_adjacent_sample409_rep1

value: Normal-Connective


title: stroma_normal_adjacent_sample057_rep2


title: epithelium_normal_adjacent_sample315_rep1


title: epithelium_normal_adjacent_sample345_rep2


title: stroma_normal_adjacent_sample392_rep2


title: stroma_normal_adjacent_sample076_rep1


title: stroma_normal_adjacent_sample018_rep1


title: stroma_normal_adjacent_sample453_rep2


title: stroma_normal_adjacent_sample453_rep1

value: Low


title: stroma_normal_adjacent_sample083_rep1

value: No


title: stroma_normal_reduction_sample043_rep1

value: Normal

value: High


title: stroma_normal_adjacent_sample281_rep2


title: epithelium_normal_adjacent_sample351_rep2

value: Normal-Epithelial


title: epithelium_normal_adjacent_sample351_rep1

value: Negative


title: stroma_normal_adjacent_sample063_rep2

value: Surgical menopause


title: stroma_normal_adjacent_sample083_rep2

value: Post-menopause


title: stroma_normal_adjacent_sample359_rep2

value: III

value: Malignant


title: stroma_normal_reduction_sample036_rep2

source_name: normal_breast stroma from reduction tissue


title: stroma_normal_adjacent_sample359_rep1


title: epithelium_normal_reduction_sample036_rep2


title: epithelium_normal_reduction_sample036_rep1


title: stroma_normal_adjacent_sample281_rep1

value: Positive

value: Pre-menopause


title: epithelium_normal_adjacent_sample161_rep2


title: epithelium_normal_adjacent_sample301_rep2


title: stroma_normal_adjacent_sample063_rep1


title: epithelium_normal_adjacent_sample161_rep1


title: stroma_normal_reduction_sample153_rep1


title: epithelium_normal_reduction_sample153_rep2


title: stroma_normal_reduction_sample153_rep2


title: epithelium_normal_reduction_sample153_rep1


title: epithelium_normal_reduction_sample_132_rep2


title: stroma_normal_reduction_sample036_rep1


title: epithelium_normal_reduction_sample132_rep1


title: stroma_normal_adjacent_sample351_rep1


title: epithelium_normal_reduction_sample019_rep2


title: epithelium_normal_reduction_sample019_rep1


title: stroma_normal_adjacent_sample351_rep2


title: stroma_normal_adjacent_sample366_rep2


title: stroma_normal_reduction_sample019_rep1


title: stroma_normal_reduction_sample043_rep2


title: stroma_normal_adjacent_sample366_rep1


title: epithelium_normal_adjacent_sample366_rep1


title: epithelium_normal_adjacent_sample057_rep2


title: epithelium_normal_adjacent_sample366_rep2


title: epithelium_normal_adjacent_sample057_rep1


title: stroma_normal_adjacent_sample348_rep2


title: epithelium_normal_adjacent_sample113_rep2


title: epithelium_normal_adjacent_sample063_rep1


title: epithelium_normal_adjacent_sample348_rep2


title: epithelium_normal_adjacent_sample113_rep1


title: epithelium_normal_adjacent_sample348_rep1


title: stroma_normal_adjacent_sample301_rep2


title: epithelium_normal_reduction_sample052_rep2


title: stroma_normal_adjacent_sample027_rep1


title: stroma_normal_adjacent_sample348_rep1


title: epithelium_normal_reduction_sample052_rep1


title: epithelium_normal_reduction_sample043_rep1


title: epithelium_normal_adjacent_sample301_rep1


title: epithelium_normal_adjacent_sample372_rep2


title: epithelium_normal_adjacent_sample372_rep1


title: stroma_normal_adjacent_sample301_rep1


title: epithelium_normal_reduction_sample043_rep2


title: stroma_normal_adjacent_sample027_rep2


title: stroma_normal_reduction_sample101_rep2


title: stroma_normal_reduction_sample101_rep1


title: epithelium_normal_reduction_sample152_rep2


title: epithelium_normal_reduction_sample152_rep1


title: epithelium_normal_adjacent_sample063_rep2


title: epithelium_normal_adjacent_sample075_rep2

value: Yes


title: epithelium_normal_adjacent_sample075_rep1


title: stroma_normal_adjacent_sample259_rep1


title: epithelium_normal_adjacent_sample259_rep1


title: stroma_normal_adjacent_sample259_rep2


title: epithelium_normal_adjacent_sample086_rep2


title: epithelium_normal_adjacent_sample065_rep2

value: II


title: epithelium_normal_adjacent_sample295_rep2


title: stroma_normal_adjacent_sample223_rep2


title: stroma_normal_adjacent_sample295_rep1


title: stroma_normal_adajcent_sample047_rep1


title: epithelium_normal_adjacent_sample136_rep1


title: stroma_normal_adjacent_sample136_rep1


title: epithelium_normal_adjacent_sample259_rep2


title: stroma_normal_adjacent_sample315_rep2

value: Peri-menopause


title: epithelium_normal_adjacent_sample136_rep2


title: stroma_normal_adjacent_sample075_rep2

value: LowII


title: epithelium_normal_adjacent_sample223_rep1


title: stroma_normal_adjacent_sample295_rep2

value: Normal-Connective


title: epithelium_normal_adjacent_sample065_rep1


title: stroma_normal_adjacent_sample075_rep1


title: stroma_normal_adjacent_sample136_rep2


title: epithelium_normal_adjacent_sample295_rep1


title: stroma_normal_adjacent_sample047_rep2


title: epithelium_normal_adjacent_sample070_rep2


title: stroma_normal_adjacent_sample070_rep2


title: stroma_normal_adjacent_sample315_rep1


title: stroma_normal_adjacent_sample190_rep2

value: LowI


title: stroma_normal_adjacent_sample190_rep1

value: No


title: epithelium_normal_adjacent_sample070_rep1


title: stroma_normal_adjacent_sample223_rep1


title: stroma_normal_adjacent_sample086_rep2


title: stroma_normal_adjacent_sample086_rep1


title: epithelium_normal_adjacent_sample190_rep2


title: stroma_normal_adjacent_sample039_rep2


title: epithelium_normal_adjacent_sample190_rep1


title: epithelium_normal_adjacent_sample039_rep2


title: stroma_normal_adjacent_sample070_rep1


title: stroma_normal_adjacent_sample039_rep1


title: epithelium_normal_adjacent_sample223_rep2


title: epithelium_normal_adjacent_sample086_rep1


title: epithelium_normal_adjacent_sample039_rep1