title: L. lactis_3.5h glucose starvation_CDM medium_replicate 3

status: Public on Feb 23 2008

type: RNA

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr). Spots with intensities below the detection threshold were discarded. Detection threshold was defined as the mean intensity plus two standard deviations of empty spots. Data were normalized by the all spot’s mean with Bioplot software.

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

molecule: total RNA

organism: Lactococcus lactis

source_name: L. lactis IL1403 3.5h glucose starvation

tag: strain IL1403

tag: growth status

value: 3.5 h of glucose starvation


title: L. lactis_deceleration phase_CDM medium_replicate 3

scan_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr). Spots with intensities below the detection threshold were discarded. Detection threshold was defined as the mean intensity plus two standard deviations of empty spots. Data were normalized by the all spot’s mean with Bioplot software.

source_name: L. lactis IL1403 deceleration phase

value: deceleration


title: L. lactis_1.25h glucose starvation_CDM medium_replicate 2

source_name: L. lactis IL1403 1.25h glucose starvation

label_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

value: 1.25 h of glucose starvation


title: L. lactis_1.25h glucose starvation_CDM medium_replicate 3

growth_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.


title: L. lactis_deceleration phase_CDM medium_replicate 2

extract_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.


title: L. lactis_deceleration phase_CDM medium_replicate 1


title: L. lactis_exponential phase_CDM medium_replicate 1

source_name: L. lactis IL1403 exponential phase

value: exponential


title: L. lactis_3.5h glucose starvation_CDM medium_replicate 2


title: L. lactis_1.25h glucose starvation_CDM medium_replicate 1


title: L. lactis_3.5 h isoleucine starvation_ILV0.1 medium_replicate 3

description: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France). Spots with intensities below the detection threshold were discarded. Detection threshold was defined as the mean intensity plus two standard deviations of empty spots. Data were normalized by the all spots mean with Bioplot software.

source_name: L. lactis 3.5 h isoleucine starvation

growth_protocol: see manuscript Redon et al. (in preparation). Comparative transcriptomic analysis of isoleucine starvation, CodY regulon and stringent response in Lactococcus lactis.

tag: 3.5 h isoleucine starvation


title: L. lactis_1.7 h isoleucine starvation_ILV0.1 medium_replicate 2

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France). Spots with intensities below the detection threshold were discarded. Detection threshold was defined as the mean intensity plus two standard deviations of empty spots. Data were normalized by the all spots mean with Bioplot software.

source_name: L. lactis IL1403 1.7 h isoleucine starvation

tag: 1.7 h isoleucine starvation


title: L. lactis_3.5 h isoleucine starvation_ILV0.1 medium_replicate 2

source_name: L. lactis IL1403 3.5 h isoleucine starvation


title: L. lactis_30 min isoleucine starvation_ILV0.1 medium_replicate 3

source_name: L. lactis IL1403 30 min isoleucine starvation

tag: 30 min isoleucine starvation


title: L. lactis_30 min isoleucine starvation_ILV0.1 medium_replicate 2


title: L. lactis_3.5h glucose starvation_CDM medium_replicate 1


title: L. lactis_exponential phase_CDM medium_replicate 2


title: L. lactis_exponential phase_CDM medium_replicate 3


title: L. lactis_1.7 h isoleucine starvation_ILV0.1 medium_replicate 1


title: L. lactis_exponential phase_ILV0.1 medium_replicate 3

tag: exponential growth phase


title: L. lactis_1.7 h isoleucine starvation_ILV0.1 medium_replicate 3


title: L. lactis_3.5 h isoleucine starvation_ILV0.1 medium_replicate 1


title: L. lactis_30 min isoleucine starvation_ILV0.1 medium_replicate 1


title: L. lactis_exponential phase_ILV0.1 medium_replicate 2


title: spxB3 allelle Spn_D39vsD39spxB3_BHI_rep2

status: Public on Feb 22 2008

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

country: USA

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

data_processing: Data were normalized with GeneTraffic 3.2 software (Iobion Informatics) using the Lowess (subgrid) method without background subtraction.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae bacterial strain D39

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight. Overnight cultures which displayed no lysis were diluted to an OD620 of ~0.005 into BHI and grown at 37C and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520

tag: S. pneumoniae bacterial strain D39 (NCTC), virulent, type 2 capsule

source_name: S. pneumoniae bacterial strain D39 (NCTC) spxB3

label_protocol: see above

growth_protocol: see above

extract_protocol: see above

tag: S. pneumoniae bacterial strain D39 (NCTC) with spxB3 allelle, virulent, type 2 capsule


title: spxB3 allelle Spn_D39vsD39spxB3_BHI_rep3

scan_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.


title: L. lactis_exponential phase_ILV0.1 medium_replicate 1


title: spxB3 allelle Spn_D39vsD39spxB3_BHI_rep1

source_name: D39 (NCTC) spxB3

tag: S. pneumoniae bacterial strain D39 (NCTC) with spxB3 allelle, virulent, type 2 capsule ,


title: Treatment 5

status: Public on Feb 21 2008

city: Bethesda

first: Azik

last: Schwechter

state: MD

address: NIH/NIMH 10 Center Drive Room 4D/14

department: NIMH

institute: NIH

description: Jurkat T-cells transfected with siRNA #6 for Sp3 for 48 hours

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1 Hybridize Date	Dec 16 2005 11:10AM

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scanner ID	50103010 Number of Scans	1 Scanner Type	M10 Scanner Type	M10

label: biotin

organism: Homo sapiens

label_protocol: GeneChip IVT Labeling Kit

extract_protocol: Ambion RNAeasy Kit


title: Mtg16 null NULL_BM_rep2

city: Nashville

first: Isabel

last: Moreno-Miralles

state: TN

address: 512 PRB 23rd and Pierce Ave

department: Biochemistry

institute: Vanderbilt University School of Medicine

description: Hybridization controls were used per Manufacturer’s instruction (see Hybridization procedures).

hyb_protocol: All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed.  Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol.  During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed.  Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber.  The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM.  The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes.  Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.

scan_protocol: Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).

data_processing:
Data is exported from the 1700 scanner as a tab-delimited text file. The raw data includes signal (background-corrected, unnormalized raw signal of the feature), S/N (the signal to noise ratio, expresses the confidence of the feature's etectibility) and Flags (erros in measurement encountered while scanning).
A quantile-based normalization of the data was performed with an R script designed by Applied Biosystems. This provides the normalized signal intensity (Value data).

label: Digoxigenin

organism: Mus musculus

source_name: Lineage negative fraction of bone marrow, NULL

label_protocol: One (1) ug of total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer's protocol (ABI, Cat# 4365715). Following first strand synthesis, second strand synthesis was completed. The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA. The cRNA was then purified using a kit provied column and assessed for quality on an Agilent Bioanalyzer. All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and used for hybridization.

extract_protocol: Total RNA was extracted using the Versagene Total RNA Purification Kit (Gentra Systems). All RNA Preps submitted to the VMSR were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays.

treatment_protocol: Bone marrow harvested from femur and tibia of 4 mice was pooled. The lineage negative fraction was separated using the Lineage Cell Depletion Kit and MACS Columns (Miltenyi Biotec).

tag: Strain

value: N4 backcrossed into C57BL/6

tag: Gender

value: females

tag: Age

value: 8-12 weeks old

tag: Tissue

value: bone marrow


title: Wild type WT_BM_rep1

source_name: Lineage negative fraction of bone marrow, WT

value: Bone marrow


title: Mtg16 null NULL_BM_rep1


title: Treatment 4

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	2 Hybridize Date	Dec 14 2005 11:08AM

source_name: Jurkat T-cells transfected with siRNA #6 for Sp3 for 48 hours


title: Treatment 3

description: Jurkat T-cells transfected with siRNA #2 for Sp3 for 48 hours

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	4 Hybridize Date	Dec 22 2005 11:27AM


title: Wild type WT_BM_rep2

value: 8-12 weeks


title: Treatment 6

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	3 Hybridize Date	Dec 22 2005 11:27AM

tag: Jurkat T-cells transfected with siRNA #6 for Sp3 for 48 hours


title: Control 6

description: Jurkat T-cells non-transfected grown for 48 hours

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1 Hybridize Date	Dec 22 2005 11:26AM

source_name: Jurkat T-cells non transfected

tag: Jurkat T-cells non transfected


title: E_coli _control2

status: Public on Feb 12 2008

city: Knoxville

first: James

middle: Thomas

last: Fleming

address: 676 Dabney Hall

department: Center for Environmental Biotechnology

institute: University of Tennessee

description: no additional information

hyb_protocol: Arrays were prehybridized with ULTRArrayTM hybridization buffer (Ambion, Austin, TX) in hybridization bottles in a hybridization oven (Isotemp, Fisher Scientific, Suwanee, GA) at 50C for 1 h after which fresh hybridization buffer and the labeled probe were added.   The membranes in hybridization solution were incubated overnight at a rolling rate of 6 rpm at 50C for 18 h.  The following day membranes were washed at 2 X 30 min at 50C at low stringency (2 X SSC, 0.5% SDS)  followed by 2 X 30 min washes at high stringency (0.5 x SSC, 0.5% SDS).  Membranes were briefly air dried, heat-sealed inside light weight freezer bags and applied to phosphoimaging plates (Molecular Dynamics, Sunnydale, CA) for 3-7 days, depending on the specific activity of the probe.

scan_protocol: The arrays were scanned at 50 um resolution on a phosphoimager (Storm840, Molecular Dynamics, Sunnydale, CA).  The acquired phosphoimages were analyzed using ArrayVisonTM software version 6.0 (Imaging Research, St. Catharines, Ontario).

data_processing: ArrayVison files are not normalized at this stage.  Normalization occurs in the subsequent step using the statistical program ArrayStat after values are log-transformed.

organism: Escherichia coli

source_name: Escherichia coli, control

label_protocol: 33P labeled cDNA probes were synthesized using the StripAbleTM cDNA Synthesis method (Ambion, Austin, TX )

growth_protocol: Overnight cultures (18 h) were grown in NaCl-free LB (10 g tryptone and 5 g yeast extract per liter, pH 7.5) from single colonies picked from agar plates. Cells were grown to stationary phase for the experiments.

extract_protocol: Fleming, J. T., W. H. Yao, and G. S. Sayler. 1998. Optimization of differential display of prokaryotic mRNA: Application to pure culture and soil microcosms. Applied and Environmental Microbiology 64:3698-3706.

treatment_protocol: Stationary phase cells were exposed to electric current using disposable electroporation cuvettes with a 2 mm plate gap (VWR Scientific Products, West Chester, PA; #47727-642) that were loaded into an apparatus to permit three cell suspensions in three cuvettes to be stimulated simultaneously in series.  DC was supplied by an electrophoresis power supply (Hoefer Instrument Co., San Francisco, model #PS500X).  Cell solutions (2 ml) were placed in each cuvette and exposed to 5mA DC (2 V) at a curre.nt density of   2.5 mA/cm2.  An equal volume of cells was held at room temperature to serve as a control.

tag: K-12 strain MG1655


title: E_coli _current induced1

description: no additional information

source_name: Escherichia coli, electric current induced

label_protocol: 33P labeled cDNA probes were synthesized using the StripAbleTM cDNA Synthesis method (Ambion, Austin, TX ).


title: Treatment 1

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1 Hybridize Date	Dec 14 2005 11:08AM

source_name: Jurkat T-cells transfected with siRNA #2 for Sp3 for 48 hours


title: E_coli _current_induced3

description: no additional information


title: Treatment 2

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	2 Hybridize Date	Dec 16 2005 11:10AM

tag: Jurkat T-cells transfected with siRNA #2 for Sp3 for 48 hours


title: Control 1

description: See above

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	3 Hybridize Date	Dec 14 2005 11:09AM

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Dec 14 2005 01:24PM Scanner ID	50103010 Number of Scans	1 Scanner Type	M10

source_name: Jurkat T-cells transfected with siRNA for GAPDH

tag: Jurkat T-cells 48 hour transfection


title: Control 3

description: Jurkat T-cells transfected with siRNA for GAPDH for 48 hours

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	2 Hybridize Date	Dec 22 2005 11:27AM


title: Control 5

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	3 Hybridize Date	Dec 16 2005 11:10AM


title: Control 4

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	4 Hybridize Date	Dec 14 2005 11:09AM

tag: Jurkat T-cells non-transfected


title: E_coli _control3

description: no additional information


title: E_coli _current_induced2

description: no additional information


title: E_coli _control1

description: no additional information

label_protocol: 33P—labeled cDNA probes were synthesized using the StripAbleTM cDNA Synthesis method (Ambion, Austin, TX )


title: Control 2

hyb_protocol: Protocol	Midi_euk2v3_450 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	4 Hybridize Date	Dec 16 2005 11:11AM

scan_protocol: Pixel Size	1.56 Filter	570 Scan Temperature Scan Date	Dec 16 2005 11:34AM Scanner ID	50103010 Number of Scans	1 Scanner Type	M10 Scanner Type	M10


title: IKKa_Genotype_IKKa-/-_Replicate_1

status: Public on Feb 06 2008

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Gene expression data of mouse embryonic fibroblasts regulated by IKKa

hyb_protocol: Illumina Standard protocol

scan_protocol: Illumina scanner

data_processing: The data was analyzed with bioconductor and GeneSpring

source_name: IKKa-/- mouse embryonic fibroblasts

label_protocol: Illumina TotalPrep

growth_protocol: Cells were grown in 10% FCS and at 80% confluency

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: IKKa-/- mouse embryonic fibroblasts

tag: Embryonic


title: IKKa_Genotype_IKKa-/-_Replicate_2


title: IKKa_Genotype_IKKa+/+reconstituted_Replicate_1

source_name: IKKa+/+reconstituted mouse embryonic fibroblasts


title: IKKa_Genotype_wild-type_Replicate_2

source_name: wild-type mouse embryonic fibroblasts

treatment_protocol: wild-type mouse embryonic fibroblasts


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX33882T

status: Public on Feb 01 2008

type: other

city: Seoul

first: DONG HYUK

last: KI

address: sinchon-dong 134

country: South Korea

institute: NBRC

description: In CRC patients without liver metastasis for 3 years after surgery, we obtained surgical specimens of colon tumor at the time of surgery.

hyb_protocol: The probes were hybridized onto the pre-blocked microarray in 25 % formamide, 5 X SSC, and 0.1 % SDS at 42 degrees C for 16 h

scan_protocol: Scanned on Axon GenePix 4000B scanner

data_processing: Data were extracted by GenePix 4.1 software (Axon)

molecule: other

source_name: The Yonsei refernece RNA

label_protocol: 2 ug amplified mRNA was labeled with Cy3-dUTP during reverse transcription. The final probe was concentrated to 40 ul

extract_protocol: Trizol & T7 linear mRNA amplification

tag: reference RNA in indirect design of microarray

label_protocol: 2 ug amplified mRNA was labeled with Cy5-dUTP during reverse transcription. The final probe was concentrated to 40 ul

tag: human colorectal primary tumor (adenocarcinoma)


title: IKKa_Genotype_IKKa+/+reconstituted_Replicate_2

treatment_protocol: IKKa+/+reconstituted mouse embryonic fibroblasts


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX68531T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX31470T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX28973T


title: IKKa_Genotype_wild-type_Replicate_1


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX18618T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX33896T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX62184T


title: T.rubrum_TRB_rep1

status: Public on Feb 04 2008

city: Beijing

first: Qi

last: Jin

address: Rongjing East Road 6#

country: China

institute: State Key Lab of Virus Gene Engineering

description: Signals were normalized using a locally weighted scatterplot smoothing regression (LOWESS) algorithm in the MIDAS software package.

hyb_protocol: Labeled cDNA was purified using QIAquick columns and mixed with 2μl polyA; 5× Denharts; 3× SSC; yeast tRNA 24 μg; 25 mM HEPES, pH 7.0; 0.25% SDS, the mixture was heated at 100 °C for 2 min and cooled to room temperature and applied to the array slides under glass coverslips. Hybridization was performed at 65°C overnight in a Micro hybridization incubator (Robbins Scientific; Sunnyvale, CA).

scan_protocol: GenePix 6.0 software (Axon Instruments, Inc.) was used for image analysis and data visualization.

data_processing: Genes were considered to be differentially expressed if (i) average expression changed by at least 1.5-fold in three independent experiments performed with triplicate RNA samples or (ii) the change in gene expression was in the same direction (“increased” or “decreased”) in three experiments.

molecule: polyA RNA

organism: Trichophyton rubrum

source_name: T.rubrum_TRB, labelled with Cy5

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime? DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy5-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy? Plant Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions. Poly(A)+ mRNA was isolated with Oligotex mRNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: T.rubrum treated with TRB

source_name: T.rubrum_DMSO, labelled with Cy3

label_protocol: Double strand cDNA were then fluorescently labeled using BioPrime? DNA Labeling System (Life Technologies/Invitrogen; Carlsbad, CA) following the manufacturer’s instructions. ds cDNA was added to 2.5× random primers solution (50 mM Tris-HCl, pH6.8; 5 mM MgCl2; 10 mM 2-mercaptoethanol; 300 μg/ml oligodeoxyribonucleotide primer), boiled at 100 °C for 5 min and then chilled on ice. 10× dNTP Mix for DNA labelling (0.12 mM dATP, dGTP,dTTP; 0.06 mM dCTP; 1 mM Tris-HCl, pH 8.0; 0.1 mM EDTA); Cy3-dCTP (0.06 mM); Klenow fragment (40 U) were added. The mixture was briefly centrifugated and was incubated at 37°C overnight away from light. 5μl 0.5 M EDTA (pH 8.0) was used to stop reaction.

tag: T.rubrum treated with DMSO


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX52497T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX25011T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX45134T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX36208T


title: T.rubrum_TRB_rep-2


title: T.rubrum_TRB_rep3


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX16165T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX33570T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX24121T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX22237T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX18679T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX31056T


title: Human normal liver tissue NBRC-DD13676Y

description: In CRC patients with liver metastasis, we obtained surgical specimens of nomal liver at the time of surgery.

tag: human normal liver tissue


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX18306T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX14048T


title: Human normal colorectal mucosa NBRC-DD13676N

description: In CRC patients with liver metastasis, we obtained surgical specimens of normal mucosa at the time of surgery.

tag: human normal colorectal mucosa


title: Human colorectal primary tumor (adenocarcinoma after chemoradiation therapy) NBRC-DD13676T

description: In CRC patients with liver metastasis, we obtained surgical specimens of colon tumor at the time of surgery.

tag: human colorectal primary tumor (adenocarcinoma after chemoradiation therapy)


title: Human colorectal primary tumor (gastrointestinal stromal tumor) NBRC-DX27754T

tag: human colorectal primary tumor (gastrointestinal stromal tumor)


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX26025T


title: Human normal liver tissue NBRC-DA09647Y


title: Human colorectal liver metastasis tumor (invasive squamous cell carcinoma) NBRC-DA09647L

description: In CRC patients with liver metastasis, we obtained surgical specimens of liver metastasis tumor at the time of surgery.

tag: human colorectal liver metastasis tumor (invasive squamous cell carcinoma)


title: Human colorectal primary tumor (adenocarcinoma) NBRC-EA71820T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-AX11903L

tag: human colorectal liver metastasis tumor (adenocarcinoma)


title: Human normal colorectal mucosa NBRC-DX27754N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX86797T


title: Human normal colorectal mucosa NBRC-EX36605N


title: Human colorectal primary tumor (invasive squamous cell carcinoma) NBRC-DA09647T

tag: human colorectal primary tumor (invasive squamous cell carcinoma)


title: Human colorectal liver metastasis tumor (gastrointestinal stromal tumor) NBRC-DX27754L

tag: human colorectal liver metastasis tumor (gastrointestinal stromal tumor)


title: Human colorectal primary tumor (invasive squamouse cell carcinoma) NBRC-DA09647T2

description: In CRC patients with liver metastasis, we obtained surgical specimens of colon tumor at the time of surgery.(replication)

tag: human colorectal primary tumor (invasive squamouse cell carcinoma)


title: Human normal colorectal mucosa NBRC-DX86797N


title: Human colorectal liver metastasis tumor (adenocarcinoma after chemoradiation therapy) NBRC-DD13676L

tag: human colorectal liver metastasis tumor (adenocarcinoma after chemoradiation therapy)


title: Human normal colorectal mucosa NBRC-DA09647N


title: Human normal liver tissue NBRC-EX36605Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-EA71820L


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX86797L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-AX11903T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-EX36605T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-EX36605L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX73169T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX73339T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX73339L


title: Human normal colorectal mucosa NBRC-DX73339N


title: Human normal liver tissue NBRC-DX86797Y


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX72875T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX72875T2


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX72875L


title: Human normal colorectal mucosa NBRC-DX73169N


title: Human normal colorectal mucosa NBRC-DX72875N


title: Human normal liver tissue NBRC-DX73339Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX73169L


title: Human normal liver tissue NBRC-DX70008Y


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX70008T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX63421T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX63421L


title: Human normal colorectal mucosa NBRC-DX63421N


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX64153L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX67096T


title: Human normal colorectal mucosa NBRC-DX67096N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX64153T


title: Human normal colorectal mucosa NBRC-DX57828N


title: Human normal colorectal mucosa NBRC-DX57828N2

description: In CRC patients with liver metastasis, we obtained surgical specimens of normal mucosa at the time of surgery.(replication)


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX67096L


title: Human normal colorectal mucosa NBRC-DX64153N


title: Human normal colorectal mucosa NBRC-DX70008N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX46644T2


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX70008L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX57828T2


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX57828L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX46644T


title: Human normal colorectal mucosa NBRC-DX46644N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DC54343T


title: Human normal colorectal mucosa NBRC-DC54343N


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX57828L2

description: In CRC patients with liver metastasis, we obtained surgical specimens of liver metastasis tumor at the time of surgery.(replication)


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DC10136L


title: Human normal colorectal mucosa NBRC-DC10136N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DC10136T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX46644L


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DX46644L2


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DC54343L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DB33368T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DX57828T


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DB33368L


title: Human normal colorectal mucosa NBRC-DX46644N2


title: Human normal liver tissue NBRC-DB33368Y


title: Human normal colorectal mucosa NBRC-DB33368N


title: Human normal liver tissue NBRC-DB14731Y


title: Human normal colorectal mucosa NBRC-DB14731N


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DB14731T


title: Human normal colorectal mucosa NBRC-DA86595N


title: Human normal liver tissue NBRC-DA86595Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DB14731L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DA86595T2

description: In CRC patients with liver metastasis, we obtained surgical specimens of colon tumor at the time of surgery.(REPLICATION)


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DA86595T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-DA85401T


title: Human normal colorectal mucosa NBRC-DA86595N2


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DA86595L


title: Human normal colorectal mucosa NBRC-DA85401N


title: Human normal liver tissue NBRC-DA85401Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-CH76639L


title: CD8_0Gy_3h_5

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

description: The TIFF images were imported into GenePix Pro 6.0.1.00 (Axon, http://www.moleculardevices.com/pages/software/gn_genepix_pro.html). This program was used for image and grid alignment, spot detection and extraction of Cy5 (635 nm) and Cy3 (532 nm) intensities for all detected spots. Spots with little or no signal and obvious defects were flagged as non utilizable spots and labeled ‘not assigned’ (NA), to exclude them from further analysis.

hyb_protocol: The sample to be tested was first labeled with Cy3 and the reference pool, with Cy5. We then inversed fluorochrome labeling: Cy5 was used to label the test sample and Cy3, the reference pool (dye swap protocol). We added 10 µg of Cot-1 cDNA (Gibco-BRL Life Technologies), 10 µg of poly(A) (Amersham Pharmacia Biotech) and 10 µg of yeast tRNA (Gibco-BRL Life Technologies) to the labeled amplified RNA to prevent nonspecific hybridization. The nucleic acids were collected by centrifugation at 15,000 g for 1 hour at 4°C, and the resulting pellet was dissolved in 120 µl of 2x SSC (Sigma), 0.1% SDS (Sigma) and 0.1% salmon sperm DNA (Invitrogen), and denatured by heating for 2 min at 100°C. The glass microarray slides were placed in hybridization chambers (Corning) and incubated with the test sample and the reference pool overnight at 50°C. The microarray slides were washed at room temperature on an orbital shaker in 2x SSC, 0.1% SDS for 5min, in 1x SSC for 5min, 0.2x SSC for 5min and at last in 0.05x SSC for 5 min. The slides were dried by aerosol of pure compressed gas (AF France).

scan_protocol: slides were scanned with DNA Microarray Scanner (Agilent), with 10 µm resolution.

data_processing:
Data for each slide were imported into statistical data analysis system R (http://www.R-project.org). We then analyzed the log Cy5, log Cy3 and log ratio of non normalized probe signals, using the functions of the BioConductor marray package (http://www.bioconductor.org/) to check for the absence of abnormal bias during hybridization. Data were then normalized, using the Loess approach (window of 40%) implemented in the BioConductor marray package.

Sample data table VALUE column reports log base 2 ratio (test/ref).

source_name: Common reference amplified RNA

label_protocol: The amino-allyl amplified RNA samples were indirectly labeled by incubation with NH2-cyanin 5 (Cy5, Amersham) or NH2-cyanin 3 (Cy3, Amersham) as described in Amino Allyl MessageAmpTM II aRNA amplification kit protocol.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer protocol. RNA were amplified and labelled with the Amino Allyl MessageAmpTM II aRNA amplification kit (Ambion), following the protocol supplied by the manufacturer.

tag: The reference RNA for all hybridizations consisted of a mixture of total RNA from MNC obtained from 20 independent healthy donors.

source_name: CD8 cells irradiated 0Gy 3h

tag: For each dose and at each time, CD4+, CD8+, B and NK cells were isolated using CD4 Negative Isolation Kit, CD8 Negative Isolation Kit, B cell Negative Isolation Kit and NK Cell Negative Isolation Kit (Dynal) respectively according to the manufacturer protocol.


title: CD4_0.05Gy_3h_1

source_name: CD4 cells irradiated 0.05Gy 3h


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-DA85401L


title: CD8_0Gy_3h_2


title: Human normal colorectal mucosa NBRC-CH76639N


title: CD4_0.05Gy_3h_5


title: CD4_0.05Gy_24h_3

source_name: CD4 cells irradiated 0.05Gy 24h


title: CD8_0.05Gy_3h_8

source_name: CD8 cells irradiated 0.05Gy 3h


title: Human normal colorectal mucosa NBRC-CA75662N


title: Human normal liver tissue NBRC-CA75662Y


title: Human colorectal primary tumor (adenocarcinoma) NBRC-CA75662T


title: CD8_0.05Gy_3h_3


title: Human normal liver tissue NBRC-CH76639Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-CA75662L


title: Human colorectal primary tumor (adenocarcinoma) NBRC-CH76639T


title: Human colorectal primary tumor (adenocarcinoma) NBRC-BF95674T


title: CD8_0.05Gy_24h_2

source_name: CD8 cells irradiated 0.05Gy 24h


title: CD8_0.05Gy_24h_6


title: CD8_0.05Gy_24h_3


title: Human normal colorectal mucosa NBRC-BH27060N


title: CD4_0.5Gy_24h_2

source_name: CD4 cells irradiated 0.5Gy 24h


title: Human colorectal primary tumor (adenocarcinoma) NBRC-BH27060T


title: CD4_0.05Gy_24h_7


title: Human normal liver tissue NBRC-AD15889Y


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-BH27060L


title: CD8_0.5Gy_24h_8

source_name: CD8 cells irradiated 0.5Gy 24h


title: CD4_0.5Gy_3h_6

source_name: CD4 cells irradiated 0.5Gy 3h


title: CD4_0.05Gy_3h_6


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-BF95674L


title: CD4_0.5Gy_3h_5


title: Human normal colorectal mucosa NBRC-BF95674N


title: CD8_0.05Gy_24h_7


title: Human colorectal primary tumor (adenocarcinoma) NBRC-AD15889T2


title: CD4_0.05Gy_3h_2


title: Human colorectal primary tumor (adenocarcinoma) NBRC-AD15889T


title: CD8_0.05Gy_24h_5


title: CD4_0.5Gy_24h_6


title: CD4_0.5Gy_3h_2


title: NK_0.5Gy_3h_3

source_name: NK cells irradiated 0.5Gy 3h


title: Human normal colorectal mucosa NBRC-AD15889N


title: CD4_0.05Gy_3h_8


title: NK_0.05Gy_3h_4

source_name: NK cells irradiated 0.05Gy 3h


title: CD8_0.05Gy_24h_8


title: CD4_0Gy_3h_7

source_name: CD4 cells irradiated 0Gy 3h


title: CD8_0.05Gy_24h_4


title: CD8_0.5Gy_24h_3


title: NK_0.05Gy_3h_2


title: CD8_0.05Gy_24h_1


title: CD4_0.5Gy_3h_1


title: CD8_0Gy_24h_6

source_name: CD8 cells irradiated 0Gy 24h


title: Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-AD15889L


title: CD4_0Gy_3h_3


title: CD4_0.05Gy_3h_4


title: CD4_0Gy_3h_8


title: CD4_0.5Gy_24h_4


title: CD4_0Gy_3h_5


title: NK_0.05Gy_3h_1


title: CD8_0Gy_24h_3


title: CD4_0Gy_3h_4


title: CD8_0.05Gy_3h_7


title: NK_0.5Gy_24h_1

source_name: NK cells irradiated 0.5Gy 24h


title: CD4_0Gy_3h_1


title: NK_0.05Gy_3h_3


title: CD4_0.05Gy_24h_8


title: CD8_0.05Gy_3h_4


title: CD4_0Gy_3h_6


title: CD8_0.05Gy_3h_2


title: CD4_0Gy_3h_2


title: NK_0.5Gy_24h_3


title: NK_0.5Gy_24h_4


title: CD4_0.5Gy_24h_8


title: CD4_0.05Gy_24h_4


title: NK_0.05Gy_24h_1

source_name: NK cells irradiated 0.05Gy 24h


title: NK_0.5Gy_3h_1


title: CD8_0.5Gy_3h_3

source_name: CD8 cells irradiated 0.5Gy 3h


title: CD8_0.5Gy_3h_1


title: CD8_0Gy_3h_1


title: CD8_0.05Gy_3h_9


title: CD8_0Gy_3h_4


title: CD4_0Gy_24h_1

source_name: CD4 cells irradiated 0Gy 24h


title: NK_0.05Gy_24h_4

source_name: Common reference amplified RNA


title: CD8_0.05Gy_3h_1


title: CD8_0.5Gy_24h_2


title: CD4_0Gy_24h_6


title: CD8_0.5Gy_24h_9


title: CD4_0.5Gy_24h_1


title: CD4_0Gy_24h_4


title: CD4_0.05Gy_24h_1


title: NK_0Gy_24h_3

source_name: NK cells irradiated 0Gy 24h


title: CD8_0.05Gy_3h_5


title: NK_0Gy_24h_4


title: CD8_0.05Gy_3h_10


title: CD4_0.05Gy_24h_5


title: CD8_0.5Gy_24h_7


title: NK_0.5Gy_24h_2


title: CD8_0Gy_3h_6

source_name: CD8 cells irradiated 0Gy 3h


title: CD4_0.5Gy_3h_4


title: CD8_0.5Gy_24h_4


title: CD4_0Gy_24h_3


title: NK_0Gy_24h_2


title: NK_0Gy_24h_1


title: NK_0.05Gy_24h_2

source_name: NK cells irrdiated 0.05Gy 24h


title: CD8_0.5Gy_24h_10


title: NK_0Gy_3h_1

source_name: NK cells irradiated 0Gy 3h


title: CD4_0Gy_24h_2


title: CD4_0.5Gy_3h_3

scan_protocol: Slides were scanned with DNA Microarray Scanner (Agilent), with 10 µm resolution.


title: CD4_0.5Gy_24h_7


title: CD8_0.5Gy_3h_2


title: CD4_0.05Gy_3h_7

source_name: CD4 cells irradiated 0.05Gy 3h


title: CD8_0Gy_24h_1


title: CD8_0Gy_24h_4


title: NK_0.5Gy_3h_4


title: CD4_0.05Gy_3h_3


title: NK_0.5Gy_3h_2


title: CD4_0.05Gy_24h_6

source_name: CD4 cells irradiated 0.05Gy 24h


title: CD4_0.5Gy_24h_3

source_name: CD4 cells irradiated 0.5Gy 24h


title: CD8_0Gy_3h_3


title: CD8_0.5Gy_24h_6

source_name: CD8 cells irradiated 0.5Gy 24h


title: CD8_0.5Gy_24h_1


title: CD4_0.05Gy_24h_2


title: NK_0Gy_3h_3


title: CD8_0.5Gy_3h_4


title: NK_0Gy_3h_2


title: CD8_0Gy_24h_5

source_name: CD8 irradiated 0Gy 24h


title: CD8_0Gy_24h_2


title: CD4_0.5Gy_3h_7

source_name: CD4 cells irradiated 0.5Gy 3h


title: CD4_0.5Gy_3h_8


title: CD8_0.05Gy_3h_6

source_name: CD8 cells irradiated 0.05Gy 3h


title: CD4_0.5Gy_24h_5


title: CD4_0Gy_24h_5


title: hippocampus rattus_norvegicus_strain NP animal_number 12

city: Westfield

first: Mark

middle: William

last: Kimpel

address: 15032 Hunter Court

department: Psychiatry

description: Gene expression data from brain of adult rats

hyb_protocol: Fifteen µg of fragmented, biotinylated cRNA was mixed into 300 µl of hybridization cocktail, of which 200 µl was used for each hybridization. Hybridization was for 17 hr at 42°C. Washing, staining and scanning were carried out according to the standard protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with BioConductor package 'affy', function justRMA using using default analysis settings. The mean target intensity of all arrays was arbitrarily set to log21000.

organism: Rattus norvegicus

source_name: hippocampus

label_protocol: RNA from each individual rat was labeled and analyzed separately. Starting with 10 µg of total RNA, first and second-strand cDNA synthesis was carried out according to the standard protocol. Biotinylated cRNA was synthesized in vitro from the double-stranded cDNA using the ENZO BioArray High Yield RNA Transcript Labeling Kit according to the Affymetrix protocol.

growth_protocol: Animals were received in our facilities 3 weeks prior to the experiment. Rats were double housed on a 12:12 light dark cycle with lights on at 0700 hours. Rats had water and rat chow ad libitum. Animals were habituated (by the same experimenter) to handling and to the guillotine daily between 0900 - 1000 hr for 10 days prior to sacrifice.

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

treatment_protocol: Animal was sacrificed by decapitation between 0900 and 1000 hr. The head was immediately placed in a cold box maintained at -15ºC, where the brain was rapidly removed and placed on a glass plate for dissection. All equipment used to obtain tissue was treated with RNAse Zap.

tag: Genotype

value: Strain NP

tag: _Age_90-100 days old


title: frontal_cortex rattus_norvegicus_strain NP animal_number 12


title: accumbens rattus_norvegicus_strain NP animal_number 12

source_name: accumbens


title: NK_0Gy_3h_4

tag: The reference RNA for all hybridizations consisted of a mixture of total RNA from mononuclear cells obtained from 20 independent healthy donors.


title: amygdala rattus_norvegicus_strain NP animal_number 12

source_name: amygdala


title: amygdala rattus_norvegicus_strain congenic animal_number 9

value: Strain congenic


title: hippocampus rattus_norvegicus_strain congenic animal_number 9


title: amygdala rattus_norvegicus_strain NP animal_number 11


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 9


title: hippocampus rattus_norvegicus_strain NP animal_number 11


title: striatum rattus_norvegicus_strain NP animal_number 12

source_name: striatum


title: NK_0.05Gy_24h_3

source_name: NK cells irradiated 0.05Gy 24h


title: frontal_cortex rattus_norvegicus_strain NP animal_number 11


title: accumbens rattus_norvegicus_strain congenic animal_number 9


title: amygdala rattus_norvegicus_strain NP animal_number 8


title: striatum rattus_norvegicus_strain NP animal_number 11


title: accumbens rattus_norvegicus_strain NP animal_number 11


title: amygdala rattus_norvegicus_strain congenic animal_number 10


title: hippocampus rattus_norvegicus_strain NP animal_number 7


title: frontal_cortex rattus_norvegicus_strain NP animal_number 8


title: accumbens rattus_norvegicus_strain congenic animal_number 10


title: striatum rattus_norvegicus_strain congenic animal_number 10


title: amygdala rattus_norvegicus_strain NP animal_number 7


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 10


title: hippocampus rattus_norvegicus_strain congenic animal_number 10


title: striatum rattus_norvegicus_strain congenic animal_number 9


title: striatum rattus_norvegicus_strain NP animal_number 8


title: accumbens rattus_norvegicus_strain NP animal_number 7


title: hippocampus rattus_norvegicus_strain NP animal_number 8


title: accumbens rattus_norvegicus_strain NP animal_number 8


title: frontal_cortex rattus_norvegicus_strain NP animal_number 7


title: amygdala rattus_norvegicus_strain NP animal_number 5


title: accumbens rattus_norvegicus_strain NP animal_number 5


title: striatum rattus_norvegicus_strain NP animal_number 6


title: amygdala rattus_norvegicus_strain congenic animal_number 4


title: hippocampus rattus_norvegicus_strain congenic animal_number 3


title: hippocampus rattus_norvegicus_strain congenic animal_number 4


title: hippocampus rattus_norvegicus_strain NP animal_number 5


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 3


title: amygdala rattus_norvegicus_strain congenic animal_number 3


title: amygdala rattus_norvegicus_strain NP animal_number 6


title: striatum rattus_norvegicus_strain congenic animal_number 4


title: hippocampus rattus_norvegicus_strain NP animal_number 6


title: striatum rattus_norvegicus_strain NP animal_number 7


title: accumbens rattus_norvegicus_strain congenic animal_number 3


title: frontal_cortex rattus_norvegicus_strain NP animal_number 6


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 2


title: frontal_cortex rattus_norvegicus_strain NP animal_number 5


title: accumbens rattus_norvegicus_strain NP animal_number 6


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 4


title: striatum rattus_norvegicus_strain NP animal_number 5


title: striatum rattus_norvegicus_strain congenic animal_number 2


title: accumbens rattus_norvegicus_strain congenic animal_number 4


title: Au_Time8hoursSize80nmreplicate0Concentration10%

status: Public on Jan 20 2008

description: Gene expression data of Human Skin Fibroblast treated with Au nanoparticles

source_name: Human Skin Fibroblast

growth_protocol: Cells were 100% confluent when treatment.

treatment_protocol: Au particles of 80nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.

tag: Young male


title: hippocampus rattus_norvegicus_strain congenic animal_number 2


title: frontal_cortex rattus_norvegicus_strain congenic animal_number 1


title: striatum rattus_norvegicus_strain congenic animal_number 3


title: accumbens rattus_norvegicus_strain congenic animal_number 2


title: amygdala rattus_norvegicus_strain congenic animal_number 1


title: striatum rattus_norvegicus_strain congenic animal_number 1


title: Au_Time2hoursSize80nmreplicate0Concentration10%

treatment_protocol: Au particles of 80nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize5nmreplicate0Concentration100%

treatment_protocol: Au particles of 5nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: amygdala rattus_norvegicus_strain congenic animal_number 2


title: hippocampus rattus_norvegicus_strain congenic animal_number 1


title: Au_Time2hoursSize5nmreplicate0Concentration10%

treatment_protocol: Au particles of 5nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize5nmreplicate0Concentration100%

treatment_protocol: Au particles of 5nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize80nmreplicate0Concentration100%

treatment_protocol: Au particles of 80nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize40nmreplicate0Concentration10%

treatment_protocol: Au particles of 40nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize5nmreplicate0Concentration10%

treatment_protocol: Au particles of 5nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize80nmreplicate0Concentration100%

treatment_protocol: Au particles of 80nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize200nmreplicate0Concentration10%

treatment_protocol: Au particles of 200nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize30nmreplicate0Concentration10%

treatment_protocol: Au particles of 30nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize30nmreplicate0Concentration100%

treatment_protocol: Au particles of 30nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: accumbens rattus_norvegicus_strain congenic animal_number 1


title: Au_Time2hoursSize30nmreplicate0Concentration10%

treatment_protocol: Au particles of 30nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize40nmreplicate0Concentration100%

treatment_protocol: Au particles of 40nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize200nmreplicate0Concentration100%

treatment_protocol: Au particles of 200nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize30nmreplicate0Concentration100%

treatment_protocol: Au particles of 30nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize40nmreplicate0Concentration10%

treatment_protocol: Au particles of 40nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize40nmreplicate0Concentration100%

treatment_protocol: Au particles of 40nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize200nmreplicate0Concentration100%

treatment_protocol: Au particles of 200nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize200nmreplicate0Concentration10%

treatment_protocol: Au particles of 200nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize2nmreplicate0Concentration100%

treatment_protocol: Au particles of 2nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize20nmreplicate0Concentration10%

treatment_protocol: Au particles of 20nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize20nmreplicate0Concentration100%

treatment_protocol: Au particles of 20nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize20nmreplicate0Concentration10%

treatment_protocol: Au particles of 20nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize20nmreplicate0Concentration100%

treatment_protocol: Au particles of 20nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize2nmreplicate0Concentration10%

treatment_protocol: Au particles of 2nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize2nmreplicate0Concentration100%

treatment_protocol: Au particles of 2nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize15nmreplicate0Concentration100%

treatment_protocol: Au particles of 15nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time2hoursSize10nmreplicate0Concentration100%

treatment_protocol: Au particles of 10nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Periprosthetic_membrane_infectious_CodeAB223

status: Public on Jan 01 2008

city: Berlin

first: Lars

last: Morawietz

address: Chariteplatz 1

department: Institute for Pathology

country: Germany

institute: Charite University Hospital

description: The features at the corner- and edge-regions were control markers. About 80 pixels within each feature were averaged after discarding outliers and pixels near feature boundaries. The quantitative expression level for each gene was calculated by the average differences representing the perfectly matched versus the mismatched specific probe. Arrays were scaled to an average intensity of 500 degrees per gene and analyzed independently. Text files were exported for the intensity information for each interrogating oligonucleotide.

hyb_protocol: 15 micrograms of each fragmented cRNA sample was hybridized for 16 hours at 45 degrees Celsius to an Affymetrix HG-U133A GeneChip Array. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to protocols recommended by Affymetrix.

scan_protocol: Probe arrays were scanned at 3 micrometers resolution using the Affymetrix GeneChip System confocal scanner 2500 with argon laser instrument, controlled by Microarray Suite 5.0 software (AFFYMETRIX). After a scan of the array surface, the computer-generated image of the array was overlayed with a virtual grid, controlled by Microarray Suite 5.0 software. This allowed for each feature to be defined, and the interrogating features aligned to known dimensions of the array.

data_processing: The Data Mining Tool 3.0 (AFFYMETRIX) and GeneSpring software package 6.1 (SILICON GENETICS) were used to average results from different replicates and perform statistical analysis to compare between treatments. The data were normalized to account for variability in hybridization for probe pairs and other hybridization artifacts. The normalization consists of the following 3 steps: first, data transformation (set measurements less than 300.0 to 300.0), second, per chip (normalize each chip to the 50th percentile of the measurements taken from that chip) and third, per gene (normalize each gene to the median of the measurements for that gene).

label: Biotin

source_name: Periprosthetic membrane, infectious type, internal code number AB223

label_protocol: Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (AFFYMETRIX) according to the manufacturer’s instruction. After cleanup (QIAGEN), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mmol/L Tris-acetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate) at 94 degrees Celsius for 35 minutes.

extract_protocol: Total RNA was isolated using Trizol (INVITROGEN) followed column based clean up (RNeasy, QIAGEN). Total RNA was quantified by UV-spectroscopy and its quality was checked by analysis on a LabChip (BioAnalyzer, AGILENT TECHNOLOGIES). Three micrograms from each sample were synthesized into double-stranded cDNA using SuperScript transcriptase (LIFE TECHNOLOGIES, INC.) and with an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL BIOL). After second strand cDNA synthesis (LIFE TECHNOLOGIES, INC.), the product was purified and served as template in the subsequent in vitro transcription reaction.

treatment_protocol: The samples was excised during endoprosthetic revision surgery. Inside the operation room, the sample was macroscopically described, measured, and cut into pieces of 3x3x3 mm. One piece was fixed in 4% buffered formalin, and the immediately adjacent piece was snap frozen in liquid nitrogen and then stored at -80 degrees Celsius. HE stained section was made from the formalin fixed tissue. As the HE slide showed the typical morphology of an endoprosthesis loosening membrane, the adjacent kryopreserved sample was used for RNA-extraction.

tag: Gender

value: Female

tag: Age

value: 81 years

tag: Time between primary arthroplasty and revision surgery

value: 3.2 years

tag: Microbiological culturing result

value: Staphylococcus epidermidis

tag: Localization

value: Left knee joint

tag: Cementation


title: Au_Time2hoursSize15nmreplicate0Concentration100%

treatment_protocol: Au particles of 15nm were added in culture medium at concentration of 100%. Cells were collected 2hours after treatment.


title: Au_Time2hoursSize0nmreplicate0Concentration0%

treatment_protocol: Au particles of 0nm were added in culture medium at concentration of 0%. Cells were collected 2hours after treatment.


title: Au_Time8hoursSize0nmreplicate0Concentration0%

treatment_protocol: Au particles of 0nm were added in culture medium at concentration of 0%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize10nmreplicate1Concentration10%

treatment_protocol: Au particles of 10nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time0hoursSize0nmreplicate0Concentration0%

treatment_protocol: Au particles of 0nm were added in culture medium at concentration of 0%. Cells were collected 0hours after treatment.


title: Periprosthetic_membrane_wear_CodeAB91

source_name: Periprosthetic membrane, wear-particle induced type, internal code number AB91

value: Male

value: 67 years

value: 7.2 years

value: Negative


title: Au_Time2hoursSize10nmreplicate0Concentration10%

treatment_protocol: Au particles of 10nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: Periprosthetic_membrane_wear_CodeAB207

source_name: Periprosthetic membrane, wear-particle induced type, internal code number AB207

value: 88 years

value: 11.8 years

value: Yes


title: Periprosthetic_membrane_wear_CodeAB233

source_name: Periprosthetic membrane, wear-particle induced type, internal code number AB233

value: 74 years

value: 15.5 years

value: Right hip joint


title: Periprosthetic_membrane_infectious_CodeAB211

source_name: Periprosthetic membrane, infectious type, internal code number AB211

value: 64 years

value: 1.0 years

value: Left hip joint


title: Periprosthetic_membrane_infectious_CodeAB228

source_name: Periprosthetic membrane, infectious type, internal code number AB228

value: Female

value: 0.6 years

value: Right knee joint


title: Periprosthetic_membrane_infectious_CodeAB217

source_name: Periprosthetic membrane, infectious type, internal code number AB217

value: 58 years

value: 4.3 years

value: Staphylococcus epidermidis


title: Periprosthetic_membrane_infectious_CodeAB88

source_name: Periprosthetic membrane, infectious type, internal code number AB88

value: Male

value: 81 years

value: 5.1 years

value: Streptococcus orales


title: Periprosthetic_membrane_wear_CodeAB212

source_name: Periprosthetic membrane, wear-particle induced type, internal code number AB212

value: 68 years

value: 3.0 years

value: Negative


title: Au_Time8hoursSize15nmreplicate0Concentration10%

treatment_protocol: Au particles of 15nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize10nmreplicate0Concentration100%

treatment_protocol: Au particles of 10nm were added in culture medium at concentration of 100%. Cells were collected 8hours after treatment.


title: Au_Time8hoursSize2nmreplicate0Concentration10%

treatment_protocol: Au particles of 2nm were added in culture medium at concentration of 10%. Cells were collected 8hours after treatment.


title: Periprosthetic_membrane_wear_CodeAB201

source_name: Periprosthetic membrane, wear-particle induced type, internal code number AB201

value: 65 years

value: 23.9 years

value: Yes


title: Au_Time2hoursSize15nmreplicate0Concentration10%

treatment_protocol: Au particles of 15nm were added in culture medium at concentration of 10%. Cells were collected 2hours after treatment.


title: 628D_genomic

type: genomic

city: Vancouver

first: Heather

last: Maughan

state: BC

address: Life Sciences Centre

department: Zoology

country: Canada

institute: University of British Columbia

description: For hybridization of samples to each slide, both Cy3 and Cy5 labeled samples were re-suspended in 50 µM EDTA and denatured at 98°C for 10 minutes.  140 µl of Hybridization Buffer #3 (Ambion) was added to each sample and loaded onto the slides.  Hybridization was performed for 16 hours at 42º C, followed by washes at 50º C for 2 minutes each in medium stringency wash buffer, high stringency wash buffer, and post-wash buffer in a GENE TAC hybridization station (all buffers are GENE TAC).  Scanning of slides on an Applied Precision Array Worx scanner was immediately done following hybridization.  Spot finding and general image analyses were done in Scanalyze v. 2.35

data_processing: log base 2 ratio of background subtracted intensity (Ch1/Ch2)

molecule: genomic DNA

organism: Bacillus subtilis

source_name: 628D evolved strain in sporulation-inducing medium

tag: Strain is a 168 derivative and was evolved in sporulation-inducing medium for 6,000 generations.

source_name: 628 Ancestor

tag: Strain is a 168 derivative.


title: 628C_genomic

source_name: 628C evolved strain in sporulation-inducing medium


title: 628B_genomic

source_name: 628B evolved strain in sporulation-inducing medium

tag: Strain is a 168 derivative and was evolved for 6,000 generations in sporulation-inducing medium

tag: Strain is a 168 derivative


title: 628E_genomic

source_name: 628E evolved strain in sporulation-inducing medium


title: 624B_genomic

source_name: 624B evolved strain in sporulation-repressing medium

tag: Strain is 168 derivative and was evolved in sporulation-repressing medium for 6,000 generations.

source_name: 624 Ancestor

tag: Strain is 168 derivative.


title: 624C_genomic

source_name: 624C evolved strain in sporulation-repressing medium

tag: Strain is 168 derivative and was evolved for 6,000 generations in sporulation-repressing medium


title: 1139

source_name: Bacteria evolved for 6,000 generations in sporulation-repressing medium

tag: Bacteria are strain 168 derivatives and were evolved for 6,000 generations in sporulation-repressing medium. RNA was isolated at the onset of stationary phase in sporulation-repressing medium.

source_name: Ancestor

tag: Bacteria are strain 168 derivatives. RNA was isolated at the onset of stationary phase in sporulation-repressing medium.


title: 624A_genomic

source_name: 624A evolved strain in sporulation-repressing medium

tag: Derivative of strain 168, evolved for 6,000 generations in sporulation-repressing medium

tag: Strain 168 derivative.


title: 624D_genomic

source_name: 624D evolved strain in sporulation-repressing medium

tag: Strain is 168 derivative and was evolved for 6,000 generations in sporulation-repressing medium.


title: 1143

tag: Bacteria are strain 168 derivatives and were evolved in sporulation-repressing medium for 6,000 generations. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.

tag: Bacteria are strain 168 derivatives. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 628A_genomic

source_name: 628A evolved strain in sporulation-inducing medium


title: 624E_genomic

source_name: 624E evolved strain in sporulation-repressing medium


title: 1138

tag: Bacteria are derivatives of strain 168 and were evolved for 6,000 generations in sporulation-repressing medium. RNA was isolated at the onset of stationary phase in sporulation-repressing medium.


title: 1141

source_name: Bacteria evolved for 6,000 generations in sporulation-inducing medium

tag: Bacteria are strain 168 derivatives and were evolved in sporulation-inducing medium for 6,000 generations. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 1142

tag: Bacteria are strain 168 derivatives and were evolved for 6,000 generations in sporulation-repressing medium. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 1137

description: Microarray slides were purchased from Eurogentec and were glass slides spotted in duplicate with 4,096 PCR products, representing each annotated ORF.  For hybridization of samples to each slide, both Cy3 and Cy5 labeled samples were re-suspended in 50 µM EDTA and denatured at 98°C for 10 minutes.  140 µl of Hybridization Buffer #3 (Ambion) was added to each sample and loaded onto the slides.  Hybridization was performed for 16 hours at 42º C, followed by washes at 50º C for 2 minutes each in medium stringency wash buffer, high stringency wash buffer, and post-wash buffer in a GENE TAC hybridization station (all buffers are GENE TAC).  Scanning of slides on an Applied Precision Array Worx scanner was immediately done following hybridization.  Spot finding and general image analyses were done in Scanalyze v. 2.35

tag: Bacteria are derivatives of strain 168 and were evolved for 6,000 generations in sporulation-repressing medium. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.

tag: Bacteria are derivatives of strain 168. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 1134

tag: Bacteria are derivatives of strain 168 and were evolved in sporulation-inducing medium for 6,000 generations. RNA was isolated at the onset of stationary phase.


title: 1136

tag: Bacteria are strain 168 derivatives and were evolved for 6,000 generations in sporulation-inducing medium. RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 1140


title: 1135

tag: Bacteria are strain 168 derivatives and were evolved for 6,000 generations in sporulation-inducing medium.  RNA was isolated at the onset of stationary phase in sporulation-inducing medium.


title: 1133

tag: Strain 168 derivatives.  Evolved for 6,000 generations in sporulation repressing medium.RNA isolated during the onset of stationary phase.

tag: Strain 168 derivative. Ancestor of evolved lines.  RNA extracted during the onset of stationary phase.


title: Grade 2 (113898_vs_10699-9_s59_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

status: Public on Dec 31 2007

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent (www.agilent.com).

data_processing: Global median normalized value of the log2ratio.

source_name: 11389-8_mammary carcinoma

tag: 10 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G2 (moderately differentiated)

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer's instruction (Gentra).

tag: 8 months, liver, female, Balb/c WAP-T1 x WAP-mutp53, n.a.d. (no abnormalities detected)


title: 1132

tag: Bacteria are derivatives of strain 168. RNA was isolated during the onset of stationary phase.

tag: Bacteria are derivatives of strain 168.  Evolved for 6,000 generations in sporulation-repressing medium. RNA was isolated during the onset of stationary phase.


title: Grade 3 (11391-3_vs_10699-9_s68_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

hyb_protocol: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

source_name: 11391-3_mammary carcinoma

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer's instruction (Gentra)

tag: 7 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G3 (undifferentiated)


title: HOS

city: Toronto

first: Shamini

last: Selvarajah

state: Ontario

address: 555 University Ave

department: Cancer Institute

institute: Hospital for Sick Children

description: osteosarcoma derived cell line vs. normal male

hyb_protocol: Experimental and reference labelled DNA for each hybridization were pooled, mixed with 50 ug of human Cot-1 DNA (Invitrogen, USA), 52 ul of Agilent 10X Blocking Agent and 260 ul of Agilent 2X Hybridization Buffer.  Prior to hybridization to the array, the 520 ul hybridization mixtures were denatured at 100C for 1 min 30 s and incubated at 37C for 30 min.  The sample was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40h at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm.

scan_protocol: Arrays were washed according to the manufacturer's recommendations, air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing:
Agilent CGH Data Analysis
The data quality of each microarray was assessed using the Quality Metrics report provided by Agilent's CGH Analytics software (v.3.4) (Agilent Technologies, Inc).  This report provides acceptable ranges for quality control parameters from each microarray experiment that are based on analysis of numerous well characterized cell lines.  All CGH data (reported in VALUE column below) represent the average of dye-flip experiments for each of the samples, using the Aberration Detection Method 1 (ADM-1) based on computing significance ratios for all genomic intervals.  To make aberration calls, a robust estimate of the noise was obtained by calculating the spread of the ratio differences between consecutive probes (DLRSpread) along all chromosomes.  The ability of the DLRSpread to measure the noise of the ratios independently of the number and severity of aberrations was used to assess the overall quality of each experiment.  The ADM-1 algorithm searches for chromosomal intervals of any length, for which the mean interval ratio is significantly different from zero.  An interval has a ratio significantly different from zero if it is more than the threshold standard deviations.  For this study, the threshold was optimized to a value of 10 to reduce inherent sample noise, without negating true consistent imbalances along each chromosome.
Raw data for individual hybridizations are linked as supplementary files at the foot of the Sample record.

label: Cy3, Cy5

source_name: osteosarcoma; tumor from 13yr old Caucasian female patient

label_protocol: Genomic DNA samples were digested with AluI (12.5 units) and RsaI (12.5 units) (Promega) for a minimum of 2 hours at 37C.  Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies).  Individual reference and experimental samples were purified using the Qiaquick PCR Cleanup Kit (Qiagen Inc., Cologne, Germany).  Labelling reactions were performed with purified digested DNA using the Bioprime labeling kit (Invitrogen, USA) according to the manufacturer's directions.

extract_protocol: Cell line was grown in ATCC complete growth medium: Minimum essential medium (Eagle) with 2 mM L-glutamine and Earle's BSS adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids, and 1.0 mM sodium pyruvate, 90%; fetal bovine serum, 10%; temperature: 37.0C; atmosphere: air, 95%; carbon dioxide (CO2), 5%.  Samples not treated.  Genomic DNA was prepared using the Puregene DNA Purification Tissue Kits (Gentra Systems, Inc., Minneapolis, USA).   Samples were RNase A treated for 1 hour at 37C.

tag: HOS osteosarcoma derived cell line

source_name: normal male DNA (reference sample)

label_protocol: Same as for CH1

extract_protocol: Purchased from Promega Corporation, Madison, USA

tag: Human Genomic DNA from multiple anonymous male donors


title: U-2 OS

source_name: osteosarcoma; tumor from 15yr old Caucasian female patient

tag: U-2 OS osteosarcoma derived cell line


title: MG-63

source_name: osteosarcoma; tumor from 14yr old Caucasian male patient

tag: MG-63 osteosarcoma derived cell line


title: SAOS-2

source_name: osteosarcoma; tumor from 11yr old Caucasian female patient

tag: SAOS-2 osteosarcoma derived cell line


title: Grade 2 (11155-7_vs_11155-9_s40_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11155-7_mammary carcinoma

label_protocol: protocols according to Snijders,A.M. et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet., 29, 263-264.

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G2 (moderately differentiated)

tag: 9 months, liver, female, Balb/c WAP-T1, n.a.d.


title: Grade 1 (11383-3_vs_10699-9_s51_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11383-3_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G1 (differentiated)


title: Grade 2 (11389-3_vs_10699-9_s58_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11389-3_mammary carcinoma


title: Grade 1 (11389-1_vs_10699-9_s55_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11389-1_mammary carcinoma

tag: 10 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G1 (differentiated)


title: Grade 1 (11389-1_vs_10699-9_s74_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)


title: Grade 3 (11263-4_vs_11155-9_s46_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11263-4_mammary carcinoma

tag: 7 months, mammary carcinoma, female, Balb/c WAP-T1, G3 (undifferentiated)


title: Grade 2 (11390-3_vs_10699-9_s60_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11390-3_mammary carcinoma


title: Grade 2 (11361-7_vs_10699-9_s61_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11361-7_mammary carcinoma

tag: 7 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G2 (moderately differentiated)


title: Grade 2 (11389-3_vs_10699-9_s76_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)


title: Grade 3 (11088-3_vs_10699-9_s67_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11088-3_mammary carcinoma

tag: 8 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G3 (undifferentiated)


title: Grade 2 (11046-7_vs_11155-9_s38_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11046-7_mammary carcinoma


title: Grade 4 (11275-8_vs_10699-9_s71_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11275-8_mammary carcinoma

tag: 7 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G4 (anaplastic)


title: Grade 1 (11084-6_vs_11155-9_s35_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11084-6_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G1 (differentiated)


title: Grade 3 (11191-2_vs_11155-9_s45_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11191-2_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G3 (undifferentiated)


title: Grade 3 (10777-6_vs_11155-9_s47_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10777-6_mammary carcinoma


title: Grade 1 (11046-2_vs_11155-9_s54_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11046-2_mammary carcinoma


title: Grade 4 (11043-4_vs_11155-9_s48_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11043-4_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G4 (anaplastic)


title: Grade 3 (11089-1_vs_11155-9_s44_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11089-1_mammary carcinoma

tag: 10 months, mammary carcinoma, female, Balb/c WAP-T1, G3 (undifferentiated)


title: Grade 2 (11155-4_vs_11155-9_s39_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11155-4_mammary carcinoma


title: Wild type liver (10714-9_vs_10699-9_s77_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

tag: 4 months, liver, female, Balb/c wild type, n.a.d.

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer’s instruction (Gentra).

tag: 8 months, liver, female, Balb/c WAP-T1 x WAP-mutp53, n.a.d. (no abnormalities detected)


title: Grade 1 (11096-3_vs_11155-9_s36_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11096-3_mammary carcinoma

tag: 10 months, mammary carcinoma, female, Balb/c WAP-T1, G1 (differentiated)


title: Grade 3 (11020-8_vs_11155-9_s43_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 11020-8_mammary carcinoma


title: Wild type liver (10760-8_vs_11155-9_s41_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10760-8_mammary carcinoma


title: B. fragilis IB425 O2-b1

status: Public on Dec 30 2007

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

data_processing: data processed using quantile normalization and RMA algorithm

organism: Bacteroides fragilis

source_name: IB425 oxyR mutant stressed in oxygen

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB425 (oxyR) grown in BHIS complex media and then stressed by shaking aerobically for 30 min


title: Grade 4 (10726-5_vs_10699-9_s70_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10726-5_mammary carcinoma

extract_protocol: Genomic DNA was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer’s instruction (Gentra)

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G4 (anaplastic)


title: Wild type liver (10714-9_vs_10699-9_s72_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)


title: B. fragilis IB425 O2-b2

hyb_protocol: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.


title: Wild type liver (10714-9_vs_11155-9_s49_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)


title: B. fragilis IB397 O2-c2

scan_protocol: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

source_name: IB397 wild type strain stressed with oxygen

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397 (wild-type) grown in BHIS complex media and then stressed by shaking aerobically for 30 min


title: B. fragilis IB425 O2-a1

label_protocol: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.


title: B. fragilis IB425 H2O2-b2

source_name: IB425 oxyR mutant stressed with H2O2

extract_protocol: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB425 (oxyR) grown in BHIS complex media and stressed with 50 micromolar H2O2 two times for 15 min


title: B. fragilis IB425 H2O2-b1


title: Grade 2 (10864-6_vs_11155-9_s34_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma  )

source_name: 10864-6_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1, G2 (moderately differentiated)

tag: 9 months, liver, female, Balb/c WAP-T1, n.a.d.


title: B. fragilis IB425 O2-a2


title: B. fragilis IB425 H2O2-a2


title: Grade 3 (10696-5_vs_10699-9_s62_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10696-5_mammary carcinoma

tag: 9 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G3 (undifferentiated)


title: Grade 3 (10680-7_vs_10699-9_s66_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10680-7_mammary carcinoma


title: Grade 3 (10682-6_vs_10699-9_s65_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10682-6_mammary carcinoma


title: B. fragilis IB425 Anaerobic-a2

source_name: IB425 oxyR mutant anaerobic culture

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB425 (oxyR) grown in BHIS complex media.


title: Grade 4 (10696-4_vs_10699-9_s69_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10696-4_mammary carcinoma


title: Grade 1 (10681-7_vs_10699-9_s75_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10681-7_mammary carcinoma

tag: 8 months, mammary carcinoma, female, Balb/c WAP-T1 x WAP-mutp53, G1 (differentiated)


title: B. fragilis IB425 Anaerobic-b1


title: B. fragilis IB425 H2O2-a1


title: B. fragilis IB425 Anaerobic-b2


title: Grade 1 (10699-7_vs_10699-9_s56_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10699-7_mammary carcinoma


title: Grade 3 (10682-3_vs_10699-9_s64_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)

source_name: 10682-3_mammary carcinoma


title: Grade 1 (10681-7_vs_10699-9_s57_b64_MACF_Influence of mutp53 on progression of mammary adenocarcinoma)


title: B. fragilis IB397 O2-c1


title: B. fragilis IB397 H2O2-c2

source_name: IB397 wild type strain stressed with H2O2

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397 (wild-type) grown in BHIS complex media and stressed with 50 micromolar H2O2 two times for 15 min


title: B. fragilis IB397 Anaerobic-b1

source_name: IB397 wild type strain in anaerobic culture b1

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397 (wild-type) grown in BHIS complex media.


title: B. fragilis IB397 H2O2-c1


title: B. fragilis IB425 Anaerobic-a1


title: B. fragilis IB397 Anaerobic-b2

source_name: IB397 wild type strain in anaerobic culture b2


title: Sample4 2003-10-02 PT3BF5

status: Public on Dec 07 2007

first: Eric

middle: J

last: Hansen

address: 5323 Harry Hines Boulevard

department: Microbiology

institute: University of Texas Southwestern Medical Center

description: cDNA samples were prepared by using the Amersham CyScribe Post-Labelling Kit (RPN5660) and using M. catarrhalis genome-directed primers (GDPs).

data_processing: Gene Pix Pro 5.0 and Acuity 4.0

organism: Moraxella catarrhalis

source_name: Planktonic culture

growth_protocol: Medium: BHI, Temperature: 37 °C with shaking (250 rpm).  Cells harvested in mid-logarithmic phase at a density  of 140 Klett units.

extract_protocol: Qiagen RNeasy Midi Kit

tag: Strain ATCC43617 planktonic culture (Klett Units=140)

source_name: 3-Day Biofilm culture

growth_protocol: Medium: BHI, Temperature: 37 °C.  Cells were grown in the Sorbarod continuous flow biofilm system for three days; cells were obtained from the biofilm that extended up along the feed tube.

tag: Strain ATCC43617 3-day biofilm culture


title: Sample1 2003-07-01 PT3BF5

description: cDNA samples were prepared by using Amersham's CyScribe Post-Labelling Kit (RPN5660) and using M. catarrhalis genome-directed primers.

label_protocol: Amersham CyScribe Post-Labelling Kit (RPN5660)

growth_protocol: Medium: BHI, Temperature: 37 C with shaking (250 rpm).  Cells harvested in mid-logarithmic phase at a density  of 140 Klett units.

growth_protocol: Medium: BHI, Temperature: 37 C.  Cells were grown in the Sorbarod continuous flow biofilm system for three days; cells were obtained from the biofilm that extended up along the feed tube.

tag: Strain ATCC43617 3-Day biofilm culture


title: B. fragilis IB397 Anaerobic-a

description: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure.  The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

source_name: IB397 Anaerobic culture


title: B. fragilis IB397 O2-b

source_name: IB397 wild type strain stressed in oxygen

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397

tag: (wild-type) grown in BHIS complex media and then stressed by shaking aerobically for 30

tag: min


title: Sample5 2003-10-02 PT5BF3

description: cDNA samples were prepared by using Amersham's CyScribe Post-Labelling Kit (RPN5660) and using M. catarrhalis genome-directed primers (GDPs).

scan_protocol: GenePix Personal 4.0

tag: Strain ATCC43617 3-days biofilm culture


title: Sample10 2003-10-24 DF0Cy5-DF30Cy3

description: cDNA samples were prepared by using the CyScribe Post-Labelling Kit (RPN5660, Amersham) and using M. catarrhalis genome-directed primers (GDPs).

source_name: Iron-limited culture

growth_protocol: 37°C with shaking (250 rpm) in iron-limiting  medium (BHI containing 30 μM Desferal, an iron-chelating agent) for 3-4 hrs (cell density equivalent to 60 Klett units)

tag: M. catarrhalis ATCC43617 grown in BHI containing 30 μM Desferal

source_name: Iron-replete culture

growth_protocol: 37°C with shaking (250 rpm) in iron-replete medium (BHI) for 3-4 hours (mid-logarithmic phase; cell density equivalent to 140 Klett units)

tag: M. catarrhalis ATCC43617 grown in BHI


title: Sample2 2003-07-18 PT3BF5


title: Sample8 2003-10-16 DF0Cy5-DF30Cy3


title: Sample11 2004-01-18 DF0Cy3-DF30Cy5


title: Sample3 2003-08-19 PT3BF5


title: Sample7 2003-10-16 DF0Cy3-DF30Cy5

source_name: iron-limited culture


title: Sample12 2004-02-24 DF0Cy5-DF30Cy3


title: B. fragilis IB397 H2O2-a

source_name: IB397 wildtype strain H2O2 stressed


title: B. fragilis IB397 H2O2-b

source_name: IB397 wild type strain H2O2 stressed


title: Wild Type nr 658

status: Public on Nov 29 2007

city: Uppsala

first: Richard

last: Marsell

address: Sjukhusvägen

department: Dep. of Surgical Sciences

country: Sweden

institute: Uppsala University

description: Gene expression data from kidneys of 8 week FGF23 TG mice and WT littermates

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner GA 2500.

data_processing: Subsequent analysis of the gene expression data was carried out in the statistical computing language R using packages available from the Bioconductor project. The raw data was normalized using the GCRMA method.

source_name: Mus Musculus Kidney

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: Kidneys were collected at 8 weeks of age

treatment_protocol: Transgenic mice were produced with microinjection technique with construct of human WT FGF23 behind a 1 alpha col 1 promotor

tag: Genotype

value: FGF23 TG on C57Bl strain

tag: Age

value: 8 weeks


title: Sample9 2003-10-24 DF0Cy3-DF30Cy5


title: Sample6 2004-07-16 PT5BF3


title: Wild Type 650


title: Transgenic nr 661


title: Wild Type nr 663


title: Transgenic nr 652


title: Transgenic nr 619


title: Transgenic nr 657


title: B. fragilis IB397 O2-a

source_name: IB397 wild type strain oxygen stressed

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397 (wild-type) grown in BHIS complex media and then stressed by shaking aerobically for 30 min


title: Wild type 618


title: Wild Type 612