title: 1 ng SMART replicate hybridization 1

status: Public on Jun 27 2006

city: London

first: Tatiana

last: Subkhankulova

address: 4 Newark Street

department: Neuroscience

country: United Kingdom

institute: Queen Mary University London

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 pg of total RNA was SMART amplified in two parallel reactions. Replica1 was indirectly labeled with Cy3 and replica2 was indirectly labeled with Cy5 followed by co-hybridization on microarray slide

hyb_protocol: See Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

scan_protocol: Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software

data_processing: Limma packadge: log-ratio were lowess normalized, filtered to exclude spots flagged as bad and backgroud corrected.

label_protocol: Klenow indirect labeling

tag: Product of SMART PCR-based amplification, replica1

tag: Product of SMART PCR-based amplification, replica2


title: Marmoset SNc 14 days after MPTP

status: Public on Jun 29 2006

type: RNA

city: Kagoshima

first: Shin-ichi

last: Iwata

state: Kagoshima

address: Sakuragaoka 8-35-1

department: Pharmacology

country: Japan

institute: Kagoshima University

description: Total RNA was amplified using 2 rounds of in vitro transcription using the RiboAmp HS RNA Amplification Kit (Arcturus).

hyb_protocol: Hybridizations were performed using the In situ Hybridization Kit Plus (Agilent). Doses of 750 ng cyanine 3-labeled cRNA, 750 ng cyanine 5-labeled cRNA were used.

scan_protocol: Agilent G2565BA Microarray Scanner System. Data were analyzed using the Agilent Feature Extraction Software version 7.1.

data_processing: A rank consistency filter and LOWESS were used for dye normalization.

molecule: total RNA

organism: Callithrix jacchus

source_name: substantia nigra pars compacta, vehicle control

label_protocol: The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: Total RNA was extracted by the PicoPure RNA Isolation Kit and eluted in approximately 10 ul buffer as per the manufacturer's protocol.

treatment_protocol: vehicle administraion iv

tag: Gender

value: male, Age:3 years, Tissue:substantia nigra pars compacta

source_name: substantia nigra pars compacta, 14 days after MPTP

treatment_protocol: 14 days after MPTP (2.5 mg/kg) iv


title: Delta4 ligand treatment for 24 hours APV012

city: Villejuif

first: Cyril

last: Catelain

address: 39, rue Camille Desmoulins

country: France

institute: INSERM

description: aRNA sample from HSC was labeled in Cy5 and hybridized against aRNA sample from Lin- cells labeled in Cy3.

data_processing: lowess normalization using BioConductor with method printTipLowess and span 0.4

organism: Mus musculus

tag: Organism Part:Bone marrow

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium without Delta4 ligand during 24 hours.

source_name: HSC-Lin-

tag: Lin- fresh cells were sorted by FACS and used as a commun reference for all experiments


title: 10 pg GA replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy3 and replica2 was indirectly labeled with Cy5 followed by co-hybridization on microarray slide

tag: Product of GA PCR-based amplification, replica1

tag: Product of GA PCR-based amplification, replica2


title: Human decidual CD56+CD3-CD16- cells

status: Public on Jun 28 2006

city: Jerusalem

first: Ofer

last: Mandelboim

department: The Lautenberg Center for General and Tumor Immunology

country: Israel

institute: The Hebrew University of Jerusalem

description: Microarray analysis was performed on highly purified CD56brightCD16- decidual NK (dNK) cells pooled from 23 health elective 1st trimester elective terminations (6-10 weeks). Subsequently, each purified subset from all donors was pooled and used to obtain a total RNA extract. We confirmed that the cRNA samples were fragmented to uniform size by using Agilent Bioanalyzer before continuing with sample labeling and hybridization procedures.  The labeled cRNA samples were hybridized in duplicate to enhance the significance of the hybridization intensities and to eliminate random noise especially from probe sets at the borderline of expression. The aim of experiment to uncover genes expressed in this NK subset.

data_processing: Hybridization Intensity value after substracting average non-specific background value

organism: Homo sapiens

source_name: Microarray analysis was performed on highly purified human CD56brightCD16- decidual NK (dNK) cells pooled from healthy elective 1st trimester terminations


title: Delta4 ligand treatment for 24 hours APV007

description: aRNA sample from HSC was labeled in Cy3 and hybridized against aRNA sample from Lin- cells labeled in Cy5.

tag: Lin- Sca+ c-kit+ fresh cells were cultured in growth medium with Delta4 ligand during 24 hours.


title: 1 ng GA replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 1 ng of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy5 and replica2 was indirectly labeled with Cy3 followed by co-hybridization on microarray slide


title: Single cells GA hybridization 2

description: 8-10 neural progenotor cells were freshely isolated from embrio neocortex (age E11.5), RNA was exreacted, divided into 4 parts and each aliquote was used for independent GA amplification procedure. Replica 1 was labeled with Cy5 and replica 2 was lebeled with Cy3 followed by co-hybridization on the microarray slide

source_name: Progenitor cells, mouse neocortex E11.5

tag: Progenitor cells from mouse neocortex E11.5, replica2

tag: Progenitor cells from mouse neocortex E11.5, replica1


title: 100 pg SMART replicate hybridization 1


title: 10 pg GA different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was GA amplified. Ovary DNA was indirectly labeled with Cy3 and 3T3 DNA was indirectly labeled with Cy5 followed by co-hybridization on microarray slide

tag: Product of GA PCR-based amplification starting from 10 pg of total RNA

source_name: 3T3 fibroblast cell line


title: Single cells SMART hybridization2

description: 8-10 neural progenotor cells were freshely isolated from embrio neocortex (age E11.5), RNA was exreacted, divided into 4 parts and each aliquote was used for independent SMART amplification procedure. Replica 1 was labeled with Cy5 and replica 2 was lebeled with Cy3 followed by co-hybridization on the microarray slide

tag: Progenitor cells, mouse neocortex E11.5,replica1


title: 10 pg SMART replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA was SMART amplified in two parallel reactions. Replica1 was indirectly labeled with Cy5 and replica2 was indirectly labeled with Cy3 followed by co-hybridization on microarray slide


title: Single cells SMART hybridization1

description: 8-10 neural progenotor cells were freshely isolated from embrio neocortex (age E11.5), RNA was exreacted, divided into 4 parts and each aliquote was used for independent SMART amplification procedure. Replica 1 was labeled with Cy3 and replica 2 was lebeled with Cy5 followed by co-hybridization on the microarray slide


title: GA different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ng of total RNA from both cell lines was amplified by global poyadenilated PCR method in two parallel reactions. Ovary DNA was labeled with Cy5, 3T3 DNA was labeled with Cy3 followed by co-hybridization on microarray slide

tag: Product of GA-PCR amplification, replica1


title: 100 pg GA replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 pg of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy3 and replica2 was indirectly labeled with Cy5 followed by co-hybridization on microarray slide

tag: Product of GA PCR-based amplification, replica 2


title: 100 pg SMART replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 pg of total RNA was SMART amplified in two parallel reactions. Replica1 was indirectly labeled with Cy5 and replica2 was indirectly labeled with Cy3 followed by co-hybridization on microarray slide


title: 1ng GA replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 1 ng of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy3 and replica2 was indirectly labeled with Cy5 followed by co-hybridization on microarray slide


title: Single cells GA hybridization1

description: 8-10 neural progenotor cells  were freshely isolated from embrio neocortex (age E11.5), RNA was exreacted, divided into 4 parts and each aliquote was used for independent GA amplification procedure. Replica 1 was labeled with Cy3 and replica 2 was lebeled with Cy5 followed by co-hybridization on the microarray slide.


title: 10 pg GA different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was GA amplified. Ovary DNA was indirectly labeled with Cy5 and 3T3 DNA was indirectly labeled with Cy3 followed by co-hybridization on microarray slide


title: 100 pg GA replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 pg of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy5 and replica2 was indirectly labeled with Cy3 followed by co-hybridization on microarray slide


title: 10 pg SMART replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA was SMART amplified in two parallel reactions. Replica1 was indirectly labeled with Cy3 and replica2 was indirectly labeled with Cy5 followed by co-hybridization on microarray slide


title: 10 pg GA different samples hybridization 2

tag: Product of SMART amplification starting with 10 pg


title: 10 pg GA different samples hybridization 1

tag: Product of GA PCR-based amplification starting with 10 pg of total RNA


title: 10 pg SMART different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was SMART amplified. Ovary DNA was indirectly labeled with Cy5 and 3T3 DNA was indirectly labeled with Cy3, followed by co-hybridization on microarray slide

tag: Product of SMART PCR-based amplification starting with 10 pg of total RNA

label_protocol: Kleenow indirect labeling


title: 10 pg SMART different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was SMART amplified. Ovary DNA was indirectly labeled with Cy3 and 3T3 DNA was indirectly labeled with Cy5 followed by co-hybridization on microarray slide

tag: Product of SMART PCR-based amplification starting from 10 pg of total RNA


title: 1 ng SMART replicate hybridization 2

tag: Product of SMART PCR-based amplification, replica2

tag: Product of SMART PCR-based amplification, replica1


title: 10 pg SMART different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was SMART amplified.  Ovary DNA was indirectly labeled with Cy5 and  3T3 DNA was indirectly labeled  with Cy3, followed by co-hybridization on microarray slide


title: cDNA replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 mg of total RNA was reverse transcribed in two parallel reactions.  Replica1 was indirectly labeled  with Cy5, replica2 was labeled with Cy3 followed by co-hybridization on microarray slide

label_protocol: Indirect labeling during reverse transription

tag: cDNA, replica2

tag: cDNA, replica1


title: SM37 different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SM37 PCR-based amplificastion technique. Ovary DNA was labeled with Cy5 and 3T3 DNA was labeled with Cy3 followed by co-hybridization on microarray slide.

tag: Product of SMT7 PCR-based amplification, replica2


title: SM37 replicate hybridization

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified by SM37 PCR-based amplification technique in two parllel reactions. Replica1 was labeled with Cy3 and replica2was labeled with Cy5 followed by co-hybridization on microarray slide.

tag: Product of SM37 PCR-based amplification, replica1

tag: Product of SM37 PCR-based amplification, replica2


title: cDNA different samples hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 mg of total RNA from each cell line was indirectly labeled during reverse transcription in two parllel reactions. 3T3 cDNA was labeled with Cy5 and ovary cRNA was labeled with Cy3 followed by co-hybridization on microarray slide.

label_protocol: Indirect labeling during reverse transcription


title: 10 pg SMART different samples hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA from each cell line was SMART amplified.  Ovary DNA was indirectly labeled with Cy3 and  3T3 DNA was indirectly labeled  with Cy5, followed by co-hybridization on microarray slide

tag: Product of SMART amplification, starting with 10 pg of total RNA


title: cDNA self-self hybridization

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 mg of total RNA was indirectly labeled during reverse transcription with Cy5 or Cy3 followed by co-hybridization on microarray slide


title: cDNA different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 100 mg of total RNA from each cell line was indirectly labeled during reverse transcription in two two parllel reactions. 3T3 cDNA was labeled with Cy3 and ovary cRNA was labeled with Cy5 followed by co-hybridization on microarray slide.


title: 10 pg GA replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 pg of total RNA was GA amplified in two parallel reactions. Replica1 was indirectly labeled with Cy5 and replica2 was indirectly labeled with Cy3 followed by co-hybridization on microarray slide

tag: Product of GA PCR-based amplification, replica2

tag: Product of GA PCR-based amplification, replica1


title: SM37 different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SM37 PCR-based amplification technique. Ovary DNA was labeled with Cy3 and 3T3 DNA was labeled with Cy5 followed by co-hybridization on microarray slide.


title: cDNA different samples hybridization 4

tag: cDNA, replica 2


title: cDNA different samples hybridization 3

scan_protocol: Scan protocol Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software


title: SM37 different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SM37 PCR-based amplification technique. Ovary DNA was labeled with Cy5 and 3T3 DNA was labeled with Cy3 followed by co-hybridization on microarray slide.


title: SM37 different samples hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SM37 PCR-based amplificastion technique. Ovary DNA was labeled with Cy3 and 3T3 DNA was labeled with Cy5 followed by co-hybridization on microarray slide.

tag: Product of SM37

tag: PCR-based amplification, replica1


title: SM37 replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified by SM37 PCR-based amplification technique in two parllel reactions. Replica2 was labeled with Cy3 and replica1 was labeled with Cy5 followed by co-hybridization on microarray slide.


title: cRNA different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA from both cell lines was amplified in 3 rounds of T7-based amplification (MessageAmpII aRNA Kit, Ambion) in two parallel reactions. cRNA from 3T3 cells was indirectly labeled with Cy5, cRNA from ovary epithelium cell line (OV) was indirectrly labeled with Cy3 followed by co-hybridisation on the slide

source_name: ovary epithelium cell line

label_protocol: Indirect labeling during in vitro amplification

tag: in vitro amplified cRNA, replica2

tag: in vitro amplified cRNA, replica 2


title: GA different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ng of total RNA from both cell lines was amplified by global poyadenilated PCR method in two parallel reactions. Ovary DNA was labeled with Cy3, 3T3 DNA was labeled with Cy5 followed by co-hybridization on microarray slide

hyb_protocol: See Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10  Scan protocol

label_protocol: Klenow indirect lableling

tag: product of GA-PCR amplification, replica2


title: GA self-self hybridization

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified by global poyadenilated PCR method. Amplified DNA was labeled with Cy3 or Cy followed by co-hybridization on microarray slide.

tag: product of GA-PCR amplification

tag: Product of GA-PCR amplification


title: GA different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA from both cell lines was amplified  by global poyadenilated PCR method. 3T3 DNA was labeled with Cy3, ovary DNA was labeled with Cy5 followed by co-hybridization on microarray slide.

tag: product of GA-PCR amplification, replica1


title: cRNA different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA from both cell lines was amplified in 3 rounds of T7-based amplification (MessageAmpII aRNA Kit, Ambion) in two parallel reactions. cRNA from 3T3 cells was indirectly labeled with Cy3, cRNA from ovary epithelium cell line (OV) was indirectrly labeled with Cy5 followed by co-hybridisation on the slide

source_name: ovary ephithelium cell line


title: GA differnet samples hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ng of total RNA was amplified by global poyadenilated PCR method in two parallel reaction. DNA replica1 was labeled with Cy5, DNA replica2 was labeled with Cy3 followed by co-hybridization on microarray slide.

label_protocol: Klenow inderect labeling


title: SMART different samples hybridization 4

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SMART PCR-based amplificastion technique. Ovary DNA was labeled with Cy3 and 3T3 DNA was labeled with Cy5 followed by co-hybridization on microarray slide.

hyb_protocol: Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software

tag: Product of SMART PCR-based amplification, replica2

label_protocol: Klenow indirect labelingSee Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

tag: Product of SMART PCR-based amplification, replica1


title: SMART replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified by SMART PCR-based amplification technique in two parallel reactions. Replica1 was labeled with Cy5 and replica2 was labeled with Cy3 followed by co-hybridization on microarray slide.


title: GA replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified  by global poyadenilated PCR method in two parallel reaction. DNA replica1 was labeled with Cy3, DNA replica2 was labeled with Cy5 followed by co-hybridization on microarray slide.


title: SMART different samples hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SMART PCR-based amplificastion technique. Ovary DNA was labeled with Cy3 and 3T3 DNA  was labeled with Cy5 followed by co-hybridization on microarray slide.


title: SMART different samples hybridization 3

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SMART PCR-based amplificastion technique. Ovary DNA was labeled with Cy5 and 3T3 DNA was labeled with Cy3 followed by co-hybridization on microarray slide.

tag: Characteristics Product of SMART PCR-based amplification, replica 2

label_protocol:
Klenow indirect labelingSee Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

Scan protocol


title: SMART replicate hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ng of total RNA was amplified by SMART PCR-based amplification technique in two parallel reactions. Replica1 was labeled with Cy3 and replica2 was labeled with Cy5 followed by co-hybridization on microarray slide.


title: GA replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA from both cell lines was amplified  by global poyadenilated PCR method. Amplified DNA was labeled with Cy5 (replica1) or with Cy3 (replica2) followed by co-hybridization on microarray slide.


title: cRNA replicate hybridization1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified in 3 rounds of T7-based amplification MessageAmpII aRNA Kit, Ambion) in two parallel reactions. cRNA replica1 and 2 were indirectly labeled with Cy3 and with Cy5 correspondently following by co-hybridisation on the slide

tag: in vitro amplified cRNA, replica1


title: cRNA different samples hybridization 2

tag: in vitro amplified cRNA,replica1


title: WM983B

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: Lymph node metastasis of melanoma.

label: biotin

source_name: culture of metastasis of melanoma

tag: unknown


title: WM983C

description: Lymph node metastasis of melanoma.


title: WM3451

description: Undescribed metastatic melanoma.


title: WM793B

description: Primary (VGP-like) metastasis of melanoma.

source_name: culture of primary metastasis of melanoma

tag: Gender

value: male

tag: Age


title: WM51

description: Undescribed metastasis of melanoma.


title: cRNA self-self hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified in 3 rounds of T7-based amplification (MessageAmpII aRNA Kit, Ambion). cRNA was indirectly labeled with Cy3/Cy5 and co-hybridised on the slide

tag: in vitro amplified RNA, replica 1

tag: in vitro amplified RNA, replica1


title: WM39


title: WM852

description: Cutaneous metastasis of melanoma of the abdomen.

source_name: culture of cutaneous metastasis of melanoma


title: SMART different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total from each cell line RNA was amplified by SMART PCR-based amplificastion technique. Ovary DNA was labeled with Cy5 and 3T3 DNA  was labeled with Cy3 followed by co-hybridization on microarray slide.


title: WM278

description: Primary (VGP-like) metastatic melanoma.

value: female


title: WM1617

description: Metastatic melanoma resulting from primary melanoma WM278.

tag: unknwon


title: WM3248

description: Primary (VGP-like) metastatic melanoma.


title: WM858

description: Lymph node metastasis of melanoma of the axilla.


title: cRNA replicate hybridization 2

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA was amplified in 3 rounds of T7-based amplification MessageAmpII aRNA Kit, Ambion) in two parallel reacxtions. cRNA replica2 and 1 were indirectly labeled with Cy3 and with Cy5 correspondently, following by co-hybridisation on the slide

tag: in vitro amplified cRNA, replica2

tag: in vitro amplified cRNA, replica 1


title: WM239A

description: Lymph metastasis of melanoma to the right groin.


title: WM1727A

description: Undescribed metastasis of melanoma.


title: WM1799

description: Undescribed metastasis of melanoma.


title: WM1382

description: Undescribed metastatic melanoma.


title: WM3211

description: Primary (RGP-like) metastatic melanoma.


title: cRNA different samples hybridization 1

description: RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. 10 ug of total RNA from both cell lines was amplified in 3 rounds of T7-based amplification (MessageAmpII aRNA Kit, Ambion) in two parallel reactions. cRNA from 3T3 cells was indirectly labeled with Cy3, cRNA from ovary epithelium cell line (OV) was indirectrly labeled with Cy5 followed by co-hybridisation on the slide

tag: 3T3 in vitro amplified cRNA, replica1

label_protocol: Ovary epithelial cell line in vitro amplified cRNA, replica1

tag: OV in vitro amplified cRNA, replica1


title: WM3268V

description: Primary (VGP-like) metastatic melanoma.


title: WM1361B

description: Primary (VGP-like) melanoma of the forearm.


title: 1205Lu 2

description: Derived from a lung metastasis in a mouse after injection with human melanoma WM793.


title: WM164

description: Lymph node metastasis of melanoma to the arm.


title: WM115

description: Primary melanoma of the right groin.

value: Female


title: WM1819

description: Undescribed metastasis of melanoma.


title: WM1366

description: Undescribed primary melanoma.


title: WM1346

description: Undescribed metastatic melanoma.


title: 1205Lu 1

source_name: metastatic melanoma culture


title: WM88

description: Primary metastasis of melanoma.


title: WM1321

description: Undescribed metastatic melanoma.


title: WM35

description: Primary (RGP-like) metastasis of melanoma.


title: WM983A

description: Undescribed primary metastasis of melanoma.


title: Mel2_A

description: Culture made from normal human infant foreskin.

source_name: normal melanocyte culture

tag: Source tissue

value: foreskin


title: M010308_A

description: Culture was derived from a cutanous metastasis of melanoma from the left occipital.

value: cutaneous metastasis of melanoma

tag: Tumor stage

value: III

tag: BRAF

value: wt

tag: NRAS


title: Mel3_A


title: M990514_A

description: Culture was derived from a cutanous metastasis of melanoma from the right groin.

value: IV


title: Mel1_A


title: M010817_A

description: Culture was derived from a cutanous metastasis of melanoma from the left upper arm.


title: M010322_A

description: Culture was derived from a cutanous metastasis of melanoma from the left side of the chest.


title: Sup fraction for normalization of Nse5 after DSB in G2/M phase

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: Sup fraction for normalization of Nse5 distribution after break induction in G2/M phase on chromosome VI

hyb_protocol: Hybridization, blocking and washing were carried out as previously described (http://chromosomedynamics.bio.titech.ac.jp). Each sample was hybridized to the array in 150 ul containing 6xSSPE; 0.005% TritonX-100; 15 ug fragmented denatured salmon sperm DNA (Gibco-BRL); 1 nmole 3?biotin labelled control oligonucleotide (oligo B2, Affymetrix). Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 42C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: S. cerevisiae arrays were scanned using the Genechip Scanner3000 7G following the library array description. All the cel files data and processed data files can be downloaded from GEO database or from our Web sites.

data_processing: The primary analysis of tiling chip data was performed following exactly the statistical algorithm used for Affymetrix GeneChip Operating Software (GCOS). The detailed information for the algorithm used can be downloaded from the Affymetrix web site at http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: SUP fraction after IP (identical to WCE fraction)

label_protocol: DNA fragments were end-labeled by addition of 25 U of Terminal Transferase and 1 nmol Biotin-N6ddATP (NEN) or Biotin-11-ddATP for 1 hour at 37C as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). The entire sample was used for hybridization.

growth_protocol: Cultured in YP+raf at 23C

extract_protocol: Extract preparation was processed following the Shirahige lab protocol (http://everythingchromosomevi.gsc.riken.go.jp ). 5x10^8 cells were disrupted using Multi-Beads Shocker (MB400U, YASUI KIKAI, Osaka). Whole cell extract was sonicated to obtain 400-600 bp genomic DNA fragments. Anti-Flag monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) coupled to Dynabeads (Dynal, protein A Dynabeads) were used for chromatin immunoprecipitation. The immunprecipates were eluted and incubated over night at 65??C to reverse the cross-link. Immunoprecipitated genomic DNA was incubated with proteinase K, extracted 2 times with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RnaseA. The DNA was then purified using the Qiagen PCR purification kit, and concentrated by ethanol precipitation. The DNA was amplified by PCR after random priming. 10 ug of amplified DNA was digested with Dnase I to a mean size of 100 bp.

treatment_protocol: G2/M arrest was achieved 2.5 h after addition of benomyl (Sigma, 80?g/ml), or nocodazole (Sigma, 1.5?g/ml) to logarithmically growing cells. G1, S and G2/M arrests were checked microscopically and by FACS. DSBs were induced by activation of the HO endonuclease from the GAL1-10-promoter by addition of 2% galactose to cell cultures initially grown in 2% raffinose.

tag: Strain W303

tag: Nse5 was tagged by 3XFLAG


title: M990115_A

description: Culture was derived from a cutanous metastasis of melanoma from under the left breast.


title: M000921_A

description: Culture was derived from a cutanous metastasis of melanoma from the epigastrium.


title: M010119_A

description: Culture was derived from a cutanous metastasis of melanoma from the left shoulder.


description: Nse4 distribution after break induction in G2/M phase on chromosome VI

source_name: Chromatin Immuno-precipitated DNA

tag: Strain W303.

tag: Nse4 was tagged by 3XFLAG


title: Sup fraction for normalization of Nse4 after DSB in G2/M phase

description: Sup fraction for normalization of Nse4 distribution after break induction in G2/M phase on chromosome VI


title: M010718_A

description: Culture was derived from a cutanous metastasis of melanoma from the right thigh.

tag: Gender


title: Nse5 distribution in G2/M phase

description: Nse5 distribution in G2/M phase

growth_protocol: Cultured in YPD at 23C


title: Smc5 distribution in G2/M phase

description: Smc5 distribution in G2/M phase

tag: Smc5 was tagged by 3XFLAG


title: Sup fraction for normalization of Smc5 and Nse5 after DSB in cycling cells

description: Sup fraction for normalization of Smc5 and Nse5 distribution in cycling cells after DSB

treatment_protocol: DSBs were induced by activation of the HO endonuclease from the GAL1-10-promoter by addition of 2% galactose to cell cultures initially grown in 2% raffinose.


title: Smc5 distribution in cycling cells after DSB


description: Nse5 distribution after break induction in G2/M phase on chromosome VI


title: Sup fraction for normalization of Smc6 at G2/M phase after DSB at 37 in scc2-4

description: Sup fraction for normalization of Smc6 distribution at G2/M phase after DSB in scc2-4 mutant at 37C

tag: Strain W303 (scc2-4 mutant).

tag: Smc6 was tagged by 3XFLAG


description: Smc5 distribution after break induction in G2/M phase on chromosome VI


title: Nse4 distribution in G2/M phase

description: Nse4 distribution in G2/M phase


title: M000216_A

description: Culture was derived from a cutanous metastasis of melanoma from the left groin.


title: Smc6 distribution in G2/M phase in scc2-4 mutant at 37C after DSB

description: Smc6 distribution at G2/M phase after DSB in scc2-4 mutant at 37C


title: Smc6 distribution in G2/M phase at 37C after DSB

description: Smc6 distribution at G2/M phase after DSB on chromosome VI at 37C


title: M991121_A

description: Culture was derived from a cutanous metastasis of melanoma from the lower left leg.


title: Sup fraction for normalization of Smc6 at G2/M phase after DSB at 37

description: Sup fraction for normalization of Smc6 distribution data after DSB induction in G2/M phase at 37C


title: M000907_A

description: Culture was derived from a cutanous metastasis of melanoma from the right shoulder.


title: Sup fraction for normalization of Smc6 after DSB induction data (mec1 deletion mutant)

description: Sup fraction for the normalization of Smc6 distribution in G2/M phase on chromosome VI (mec1 deletion mutant, HU 1hour)

tag: Strain W303 (mec1 deletion mutant).


title: Smc6 distribution after DSB induction (rad53 deletion mutant)

description: Smc6 distribution after DSB indcution on chromosome VI (rad53 deletion mutant)

tag: Strain W303 (rad53 deletion mutant).


title: WM1361A

description: Primary (VGP-like) melanoma of the forearm.

tag: Age


title: Mel3_B

description: Culture made from normal human infant foreskin.


title: Smc6 distribution in S phase (rad53 deletion mutant)

description: Smc6 distribution in S phase on chromosome VI (HU 1hour, rad53 deletion mutant)

treatment_protocol: For S-phase arrest, cells were grown to log phase and arrested in G1 with alpha factor for 2 h, and then incubated in the presence of 200 mM hydroxyurea (HU) (Sigma) for 30 min. Cells were then washed twice with rich medium containing 100?g/ml pronase (Calbiochem). Finally cells were resuspended in medium containing HU and pronase, and growth continued for indicated time periods.


title: M990514_B

description: Culture was derived from a cutanous metastasis of melanoma of the right groin.


title: Sup fraction for normalization of Smc6 after DSB induction data (mre11 deletion mutant)

description: Sup fraction for the normalization of Smc6 distribution in G2/M phase on chromosome VI (mre11 deletion mutant)

tag: Strain W303 (mre11 deletion mutant).


title: Smc6 distributionafter DSB induction (mec1 deletion mutant)

description: Smc6 distribution in G2/M phase on chromosome VI (mec1 deletion mutant)


title: M000921_B

description: Culture was derived from a cutanous metastasis of melanoma of the epigastrium.


title: M010817_B

description: Culture was derived from a cutanous metastasis of melanoma of the left upper arm.


title: Sup fraction for normalization of Smc6 S phase data (rad53 deletion mutant)

description: Sup fraction for the normalization of Smc6 distribution in S phase on chromosome VI (rad53 deletion mutant, HU 1hour)


title: Mel1_B


title: Smc6 distribution after DSB induction (mre11 deletion mutant)

description: Smc6 distribution in G2/M phase on chromosome VI (mre11 deletion mutant)


title: M980513_A

description: Culture was derived from a cutanous metastasis of melanoma of the left iliac.


title: M991121_B


title: Mel2_B


title: M010308_B

description: Culture was derived from a cutanous metastasis of melanoma from the left occipital.


title: Sup fraction for normalization of Smc6 S phase data_HU 1hour

description: Sup fraction for the normalization of Smc6 distribution in S phase on chromosome VI (HU 1hour)


title: Sup fraction for normalization of Nse1 G2/M phase

description: Sup fraction for normalization of Nse1 distribution after DSB induction at G2/M phase data


title: Smc6 distribution in S phase_HU 1hour

description: Smc6 distribution in S phase on chromosome VI (HU 1hour)


title: M010119_B

description: Culture was derived from a cutanous metastasis of melanoma of the left shoulder.


description: Nse1 distribution after break induction in G2/M phase on chromosome VI (time 180)

tag: Nse1 was tagged by 3XFLAG


title: M010718_B

description: Culture was derived from a cutanous metastasis of melanoma of the right thigh.

tag: Source tissue


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA89scan1.gpr

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

data_processing: Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.

organism: Gossypium hirsutum

tag: Non-Fibre Epidermal Pavement Cells (c.v. Deltapine 16), Biological Repl

value: 2, Technical repl:2

source_name: Fibre Initial Cells (c.v. Deltapine 16)

tag: Fibre Initial Cells (c.v. Deltapine 16), Biological Repl


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA90scan1.gpr

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: false

value: 1, Technical repl:3

source_name: Non-Fibre Epidermal Pavement Cells (c.v. Deltapine 16)


title: Sup fraction for normalization of Nse5 distribution in G2/M phase


title: M000907_B

description: Culture was derived from a cutanous metastasis of melanoma of the right shoulder.

tag: Tumor stage

tag: BRAF

tag: NRAS


title: Sup fraction for normalization of Smc6 and Smc5 G2/M phase timecourse data

description: Sup fraction for normalization of Smc6 and Smc5 DSB induction at G2/M phase data

tag: Strain W303.


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA88scan1.gpr

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

value: 2, Technical repl:1


title: M010322_B

description: Culture was derived from a cutanous metastasis of melanoma from the left side of the chest.


title: Smc6 distribution after break induction in G2/M phase_time 180

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 180)


title: Nse5 distribution in cycling cells after DSB

tag: Nse5 was tagged by 3XFLAG


title: M000216_B

description: Culture was derived from a cutanous metastasis of melanoma of the left groin.

tag: Gender


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA91scan1.gpr

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 2, Technical Replicate: 3, Dye Swapped: true

value: 2, Technical repl:3


title: Sup fraction for normalization of Smc6 G2/M phase timecourse data_time 45

description: Sup fraction for normalization of Smc6 DSB induction at G2/M phase data (time 45)


title: Smc6 distribution after break induction in G2/M phase_time 70

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 70)


title: Sup fraction for normalization of Smc6 G2/M phase timecourse data_time 30

description: Sup fraction for normalization of Smc6 DSB induction at G2/M phase data (time 30)


title: Sup fraction for normalization of Smc6 G2/M phase timecourse data_time 60 and 70

description: Sup fraction for normalization of Smc6 DSB induction at G2/M phase data (time 60 and 70)


title: Smc6 distribution after break induction in G2/M phase_time 45

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 45)


title: M990115_B

description: Culture was derived from a cutanous metastasis of melanoma from under the left breast.


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA87scan1.gpr

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true

value: 1, Technical repl:2


title: Smc6 distribution after break induction in G2/M phase_time 60

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 60)


title: Sup fraction for normalization of Smc6 after DSB induction data (rad53 deletion mutant)

description: Sup fraction for the normalization of Smc6 distribution after DSB induction on chromosome VI (rad53 deletion mutant)


title: Smc6 distribution after break induction in G2/M phase_time 20

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 20)


title: Smc6 distribution after break induction in G2/M phase_time 30

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 30)


title: Sup fraction for normalization of Smc6 G2/M phase timecourse data_time 0 and 20

description: Sup fraction for normalization of Smc6 distribution data after DSB induction at G2/M phase data (time 0 and 20). Also used for normalization of Nse4 distribution data.


title: M980513_B

description: Culture was derived from a cutanous metastasis of melanoma of the left iliac.


title: Smc6 distribution after break induction in G2/M phase_time 0

description: Smc6 distribution after break induction in G2/M phase on chromosome VI (time 0)


title: Sup fraction for normalization of Nse1 G2/M phase data

treatment_protocol: G2/M arrest was achieved 2.5 h after addition of benomyl (Sigma, 80?g/ml), or nocodazole (Sigma, 1.5?g/ml) to logarithmically growing cells.


title: Nse1 distribution in G2/M phase

description: Nse1 distribution in G2/M phase on chromosome VI


title: Sup fraction for normalization of Nse1 S phase data


title: Sup fraction for normalization of Nse1 G1 phase data

description: Nse1 distribution in G1 phase on chromosome VI

treatment_protocol: For synchronization in G1, alpha factor was added (Zymo research and Innovagen AB) at 3 ?g/ml final concentrations to logarithmically growing cells, and G1 arrest was obtained at indicated temperatures for 2.5 h.


title: Fibre Initial Cells (c.v. Deltapine 16) F/NF, ghA86scan1.gpr

description:
0dpa fibre vs epidermal LCM comparison
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

value: 1, Technical repl:1


title: Nse1 distribution in S phase

description: Nse1 distribution in S phase on chromosome VI


title: Sup fraction for normalization of Smc6 S phase data

description: Sup fraction for the normalization of Smc6 distribution in S phase on chromosome VI


title: Sup fraction for normalization of Smc6 G1 phase data

description: Smc6 distribution in G1 phase on chromosome VI


title: Nse1 distribution in G1 phase


title: Smc6 distribution in G1 phase


title: Sup fraction for normalization of Smc6 distribution after DSB induction (mre11 deletion mutant) at whole genome scale

description: Sup fraction for the normalization of Smc6 distribution in G2/M phase after DSB induction (mre11 deletion mutant) at whole genome scale


title: Sup fraction for normalization of Smc6 at G2/M phase at 37C in scc1-73 (whole genome level)

description: Sup fraction for normalization of Smc6 distribution data  in G2/M phase at 37C in scc1-73 (whole genome data)

treatment_protocol: G2/M arrest was achieved 2.5 h after addition of benomyl (Sigma, 80?g/ml), or nocodazole (Sigma, 1.5?g/ml) to logarithmically growing cells. G1, S and G2/M arrests were checked microscopically and by FACS.

tag: Strain W303 (scc1-73).


title: Sup fraction for normalization of Smc6 distribution in S phase with DSB induction at chromosome VI (whole genome data)

description: Sup fraction for the normalization of Smc6 distribution in S phase with DSB induction at chromosome VI (whole genome data)

treatment_protocol: For S-phase arrest, cells were grown to log phase and arrested in G1 with alpha factor for 2 h, and then incubated in the presence of 200 mM hydroxyurea (HU) (Sigma) for 30 min. Cells were then washed twice with rich medium containing 100?g/ml pronase (Calbiochem). Finally cells were resuspended in medium containing HU and pronase, and growth continued for indicated time periods.DSBs were induced by activation of the HO endonuclease from the GAL1-10-promoter by addition of 2% galactose to cell cultures initially grown in 2% raffinose.


title: Sup fraction for normalization of Smc6 at G2/M phase at 37C in scc2-4 (whole genome level)

description: Sup fraction for normalization of Smc6 distribution data  in G2/M phase at 37C in scc2-4 (whole genome data)

tag: Strain W303 (scc2-4).


title: Sup fraction for normalization of Smc6 after DSB in G2/M phase (whole genome data)

description: Sup fraction for normalization of Smc6 distribution after break induction (at chromosome V) in G2/M phase (whole genome data)

tag: Strain W303


title: hTERT_EXTENDED_HD2_REP2

status: Public on Jun 24 2006

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

institute: Swiss Institute of Bioinformatics

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  2, rep2

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr on human U133Plus 2.0  GeneChip, Chips were washed and stained in the Fluidics Station 400.

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

data_processing: The .cel files data were analyzed with the R library affy, using RMA default  settings and the quantile normalization method.

source_name: CD8 T lymphocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Cell are cultures in RPMI 1640 medium supplemented with 8% Human Serum and 150U/ml of rIL-2 (GlaxoSmithKline) and stimulated using PHA (Sodiag) and irradiated feeder cells.

extract_protocol: RNA from 30x10E6 cells was extracted, purified and used for cDNA synthesis following standard procedures (www.Affymetrix.com).

treatment_protocol: Mycoplasma-free cells were harvested after 15 to 18 days of mitogen stimulation (PHA), Annexin-V expression <10%.

tag: late passage CD8 T cells  expressing hTERT


title: Smc6 distribution in S phase

description: Smc6 distribution in S phase on chromosome VI

tag: Smc6 was tagged by 3XFLAG


title: GFP_OLD_HD1_REP3

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep3

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr on human U133A GeneChip, Chips were washed and stained in the Fluidics Station 400.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 micrograms total RNA.

tag: late passage CD8 T cells clones expressing GFP.


title: GFP_OLD_HD2_REP3

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  2, rep3

tag: late passage CD8 T cells  expressing GFP.


title: hTERT_EXTENDED_HD2_REP1

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  2, rep1


title: GFP_OLD_HD2_REP2

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  2, rep2


title: hTERT_EXTENDED_HD2_REP3

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  2, rep3


title: hTERT_EXTENDED_HD1_REP3

description: hTERT expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep3

tag: late passage CD8 T cells clones expressing hTERT.


title: Smc6 distribution after DSB induction (mre11 deletion mutant) at whole genome scale

description: Smc6 distribution in G2/M phase after DSB induction (mre11 deletion mutant) at whole genome scale

tag: Strain W303 (mre11 deletion mutant).


title: GFP_OLD_HD2_REP1

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  2, rep1


title: hTERT_YOUNG_HD2_REP3

tag: early passage CD8 T cells  expressing hTERT


title: hTERT_YOUNG_HD1_REP3

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  1, rep3

tag: early passage CD8 T cells clones expressing hTERT.


title: hTERT_EXTENDED_HD1_REP2

description: hTERT expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep2


title: GFP_OLD_HD1_REP1

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep1


title: Scc1 distribution in G2/M phase (whole genome scale)

description: Scc1 distribution in G2/M phase at whole genome scale

tag: Scc1 was tagged by 3XFLAG


title: GFP_OLD_HD1_REP2

description: GFP expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep2


title: Smc6 distribution after break induction at chromosome V in G2/M phase (whole genome data)

description: Smc6 distribution after break induction (at chromosome V) in G2/M phase (whole genome data)


title: GFP_YOUNG_HD1_REP3

description: GFP expressing transduced CD8 T Lymphocytes, early passage, healthy donor  1, rep3

tag: early passage CD8 T cells  expressing GFP.


title: Sup fraction for normalization of Smc6 S phase data (whole genome scale)

description: Sup fraction for the normalization of Smc6 distribution in S phase (whole genome scale)


title: Sup fraction for normalization of Smc6 and Scc1 G2/M phase data (whole genome scale)

description: Sup fraction for normalization of Smc6 and Scc1 G2/M phase data at whole genome scale


title: Sup fraction for normalization of Smc6 S phase data (rad53 deletion mutant) at whole genome scale

description: Sup fraction for the normalization of Smc6 distribution in S phase at whole genome level (rad53 deletion mutant, HU 1hour)

tag: Strain W303 (rad53 deletion mutant).


title: Smc6 distribution in G2/M phase at 37C in scc1-73 (whole genome level)

description: Smc6 distribution at G2/M phase at 37C in scc1-73 (whole genome data)

tag: Strain W303 (scc1-73 mutant).


title: hTERT_YOUNG_HD2_REP1

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  2, rep1


title: hTERT_YOUNG_HD2_REP2

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  2, rep2


title: Sup fraction for normalization of Smc6 at G2/M phase at 37

description: Sup fraction for normalization of Smc6 distribution data  in G2/M phase at 37C (whole genome data)

tag: Strain W303.


title: Smc6 distribution in S phase with DSB induction at chromosome VI (whole genome data)


title: GFP_YOUNG_HD1_REP1

description: GFP expressing transduced CD8 T Lymphocytes, early passage, healthy donor  1, rep1


title: Smc6 distribution in G2/M phase at 37C in scc2-4 (whole genome level)

description: Smc6 distribution at G2/M phase at 37C in scc2-4  (whole genome data)

tag: Strain W303 (scc2-4 mutant).


title: Mouse Ovary Total RNA 1 ug AFFX1rd Labeling

status: Public on Jun 23 2006

city: Boston

first: Jeff

last: Shearstone

state: MA

address: 70 Fargo Street

department: Biology

country: USA

institute: Acetylon Pharmaceuticals

description: 1 ug of Ambion Ovary Total RNA

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Ambion Mouse Total RNA Tissue Panel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One Cycle Labeling Kit

tag: Total RNA generated from mouse Ovary


title: Smc6 distribution in S phase (rad53 deletion mutant) at whole genome scale

description: Smc6 distribution in S phase at whole genome level  (HU 1hour, rad53 deletion mutant)


title: Smc6 distribution in G2/M phase at 37C

description: Smc6 distribution at G2/M phase at 37C (whole genome data)


title: Mouse Spleen Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Spleen Total RNA

tag: Total RNA generated from mouse Spleen


title: Smc6 distribution in G2/M phase (whole genome scale)

description: Smc6 distribution in G2/M phase at whole genome scale


title: Mouse Brain Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Brain Total RNA

tag: Total RNA generated from mouse brain


title: Mouse Kidney Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Kidney Total RNA

tag: Total RNA generated from mouse Kidney


title: Mouse Embryo Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Embryo Total RNA

tag: Total RNA generated from mouse Embryo


title: Mouse Heart Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Heart Total RNA

tag: Total RNA generated from mouse Heart


title: Mouse Total RNA from 50 RAW267 cells BIIB Labeling Replicate 1

description: 50 flow sorted RAW267 cells

source_name: Flow sorted RAW267 cultured cells

label_protocol: Biotinylated cDNA were prepared according to the BIIB amplification and labeling protocol developed at Biogen Idec. Shearstone JR, Genomics 88 (2006) 111–121

tag: Total RNA generated from flow sorted RAW267 cell line


title: Mouse Total RNA from 500 RAW267 cells BIIB Labeling Replicate 2

description: 500 flow sorted RAW267 cells


title: Mouse Universal Total RNA 1 ug AFFX1rd Labeling Replicate 1

description: 1 ug of Stratagene Mouse Universal Total RNA

source_name: Stratagene Mouse Universal Total RNA

tag: Total RNA pool generated from 11 cell lines


title: Mouse Universal Total RNA 1 ug AFFX1rd Labeling Replicate 4


title: Smc6 distribution in S phase (whole genome scale)

tag: Smc6 was tagged by 3XFLAG


title: Mouse Liver Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Liver Total RNA

tag: Total RNA generated from mouse Liver


title: hTERT_YOUNG_HD1_REP1

description: hTERT expressing transduced CD8 T Lymphocytes, early passage, healthy donor  1, rep1

tag: early passage CD8 T cells clones expressing hTERT.


title: Mouse Universal Total RNA 1 ug AFFX1rd Labeling Replicate 2


title: Mouse Total RNA from 50 RAW267 cells BIIB Labeling Replicate 2

description: 50 flow sorted RAW267 cells


title: Mouse Total RNA from 1000 RAW267 cells BIIB Labeling Replicate 1

description: 1000 flow sorted RAW267 cells


title: Mouse Total RNA from 1000 RAW267 cells BIIB Labeling Replicate 2

description: 1000 flow sorted RAW267 cells


title: Mouse Universal Total RNA 1 ug AFFX1rd Labeling Replicate 3


title: Mouse Total RNA from 5000 RAW267 cells BIIB Labeling Replicate 2

description: 5000 flow sorted RAW267 cells


title: Mouse Total RNA from 500 RAW267 cells BIIB Labeling Replicate 1

description: 500 flow sorted RAW267 cells


title: Mouse Total RNA from 10000 RAW267 cells BIIB Labeling Replicate 1

description: 10000 flow sorted RAW267 cells


title: Mouse Total RNA from 10000 RAW267 cells BIIB Labeling Replicate 2

description: 10000 flow sorted RAW267 cells


title: Mouse Total RNA from 5000 RAW267 cells BIIB Labeling Replicate 1

description: 5000 flow sorted RAW267 cells


title: Mouse Total RNA from 100 T-cells and 400 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes

source_name: Flow sorted T and B-cells out of a splenocyte suspension isolated from a single normal mouse

tag: Total RNA generated from flow sorted T and B-cells from mouse splenocyte population


title: Mouse Total RNA from 400 T-cells and 100 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes


title: Mouse Total RNA from 300 T-cells and 200 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes


title: Mouse Total RNA from 60 T-cells and 40 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 0 T-cells and 500 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes


title: Mouse Total RNA from 40 T-cells and 60 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 20 T-cells and 80 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 100 RAW267 cells BIIB Labeling

description: 100 flow sorted RAW267 cells


title: Mouse Total RNA from 100 T-cells and 0 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Liver Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Liver Total RNA


title: Mouse Total RNA from 40 T-cells and 60 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 0 T-cells and 100 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 500 T-cells and 0 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes


title: Mouse Ovary Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Ovary Total RNA


title: Mouse Total RNA from 20 T-cells and 80 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 0 T-cells and 100 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 80 T-cells and 20 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Lung Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Lung Total RNA

tag: Total RNA generated from mouse Lung


title: Mouse Total RNA from 60 T-cells and 40 B-cells BIIB Labeling Replicate 2

description: 100 flow sorted primary lymphocytes


title: Mouse Total RNA from 100 T-cells and 0 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Kidney Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Kidney Total RNA


title: Mouse Total RNA from 80 T-cells and 20 B-cells BIIB Labeling Replicate 1

description: 100 flow sorted primary lymphocytes


title: Mouse Spleen Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Spleen Total RNA


title: GFP_YOUNG_HD1_REP2

description: GFP expressing transduced CD8 T Lymphocytes, early passage, healthy donor  1, rep2

tag: early passage CD8 T cells  expressing GFP.


title: Mouse Heart Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Heart Total RNA


title: Mouse Embryo Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Embryo Total RNA


title: Mouse Lung Total RNA 1 ug AFFX1rd Labeling

description: 1 ug of Ambion Lung Total RNA


title: hTERT_EXTENDED_HD1_REP1

description: hTERT expressing transduced CD8 T Lymphocytes, late passage, healthy donor  1, rep1

tag: late passage CD8 T cells clones expressing hTERT.


title: Mouse Universal Total RNA 50 pg BIIB Labeling Replicate 3

description: 50 pg of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 10 pg BIIB Labeling Replicate 3

description: 10 pg of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 10 pg BIIB Labeling Replicate 1


title: Mouse Universal Total RNA 1 ng BIIB Labeling Replicate 3

description: 1 ng of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 5 ng BIIB Labeling Replicate 2

description: 5 ng of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 1 ng BIIB Labeling Replicate 1


title: Mouse Universal Total RNA 500 pg BIIB Labeling Replicate 1

description: 500 pg of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 500 pg BIIB Labeling Replicate 2


title: Mouse Universal Total RNA 10 pg BIIB Labeling Replicate 2


title: Mouse Universal Total RNA 50 pg ARCHS Labeling Replicate 2

label_protocol: Biotinylated cRNA were prepared according to the Arcturus RiboAmp HS Amplification Kit


title: Mouse Universal Total RNA 50 pg BIIB Labeling Replicate 4


title: Mouse Total RNA from 200 T-cells and 300 B-cells BIIB Labeling

description: 500 flow sorted primary lymphocytes


title: Mouse Universal Total RNA 500 pg BIIB Labeling Replicate 3


title: Mouse Universal Total RNA 50 pg BIIB Labeling Replicate 1


title: Mouse Universal Total RNA 100 pg BIIB Labeling Replicate 3

description: 100 pg of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 50 pg BIIB Labeling Replicate 2


title: Mouse Universal Total RNA 5 ng BIIB Labeling Replicate 4


title: Mouse Universal Total RNA 1 ng BIIB Labeling Replicate 2


title: Mouse Universal Total RNA 1 ng BIIB Labeling Replicate 4


title: Mouse Universal Total RNA 100 pg BIIB Labeling Replicate 2


title: Mouse Universal Total RNA 100 pg BIIB Labeling Replicate 1


title: Mouse Brain Total RNA 500 pg BIIB Labeling

description: 500 pg of Ambion Brain Total RNA


title: Mouse Universal Total RNA 50 pg ARCHS Labeling Replicate 1


title: Mouse Universal Total RNA 100 pg BIIB Labeling Replicate 4


title: Mouse Universal Total RNA 5 ng BIIB Labeling Replicate 1


title: Mouse Universal Total RNA 500 pg ARCHS Labeling Replicate 2


title: Mouse Universal Total RNA 5 ng ARCHS Labeling Replicate 2


title: Mouse Universal Total RNA 50 ng ARCHS Labeling Replicate 2

description: 50 ng of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 10 pg BIIB Labeling Replicate 4


title: Mouse Universal Total RNA 500 pg ARCHS Labeling Replicate 1


title: Mouse Universal Total RNA 5 ng ARCHS Labeling Replicate 1


title: Mouse Universal Total RNA 50 pg NGN Labeling Replicate 1

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation RNA Amplification and Labeling System


title: Mouse Universal Total RNA 50 ng ARCHS Labeling Replicate 1


title: Mouse Universal Total RNA 500 ng ARCHS Labeling Replicate 1

description: 500 ng of Stratagene Mouse Universal Total RNA


title: Mouse Universal Total RNA 5 ng NGN Labeling Replicate 2


title: Mouse Universal Total RNA 500 ng NGN Labeling Replicate 1


title: Genomic responses to Phenobarbital E25PB2

city: Edmonton

first: Kirst

last: King-Jones

state: AB

address: 77 University Campus

department: Biological Sciences

country: Canada

institute: University of Alberta

description: flies starved overnight. Experiment is designed as follows: Controls +- drug and mutant +- drug (three replicates each = total of 12 chips)

data_processing: gcRMA

organism: Drosophila melanogaster

source_name: adult flies fed with sucrose or Phenobarbital/sucrose

tag: see CSSUC1


title: Genomic responses to Phenobarbital CSPB3


title: Mouse Universal Total RNA 5 ng NGN Labeling Replicate 1


title: Mouse Universal Total RNA 50 pg NGN Labeling Replicate 2


title: Genomic responses to Phenobarbital E25PB3


title: Genomic responses to Phenobarbital CSPB1


title: Mouse Universal Total RNA 500 ng ARCHS Labeling Replicate 2


title: Genomic responses to Phenobarbital CSPB2


title: Mouse Universal Total RNA 500 ng NGN Labeling Replicate 2


title: Mouse Universal Total RNA 50 pg AFFX2rd Labeling Replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two Cycle Labeling Kit


title: Mouse Universal Total RNA 500 pg NGN Labeling Replicate 2


title: Mouse Universal Total RNA 50 pg AFFX2rd Labeling Replicate 1


title: Mouse Universal Total RNA 50 ng NGN Labeling Replicate 2


title: Genomic responses to Phenobarbital E25PB1


title: Mouse Universal Total RNA 50 ng NGN Labeling Replicate 1


title: Mouse Universal Total RNA 500 pg NGN Labeling Replicate 1


title: Mouse Universal Total RNA 500 pg AFFX2rd Labeling Replicate 1


title: Mouse Universal Total RNA 500 pg BIIB Labeling Replicate 4


title: Mouse Universal Total RNA 500 pg AFFX2rd Labeling Replicate 2


title: Mouse Universal Total RNA 5 ng AFFX2rd Labeling Replicate 2


title: Genomic responses to Phenobarbital E25SUC3


title: Genomic responses to Phenobarbital E25SUC2


title: Mouse Universal Total RNA 50 ng AFFX2rd Labeling Replicate 2


title: Genomic responses to Phenobarbital CSSUC3


title: Mouse Universal Total RNA 5 ng AFFX2rd Labeling Replicate 1


title: Genomic responses to Phenobarbital CSSUC2


title: Mouse Universal Total RNA 500 ng AFFX2rd Labeling Replicate 1


title: Mouse Universal Total RNA 50 ng AFFX2rd Labeling Replicate 1


title: Mouse Universal Total RNA 500 ng AFFX2rd Labeling Replicate 2


title: Tobramycin interference

status: Public on Jun 22 2006

city: La Jolla

first: William

middle: A

last: Greenberg

state: CA

address: 10550 N Torrey Pines Rd

department: Chemistry

institute: The Scripps Research Institite

description: Full description can be found in Fu-Sen Liang, William A. Greenberg, Jennifer A. Hammond, Julia Hoffman, Steven R. Head, and Chi-Huey Wong. (2006) Evaluation of RNA Binding Specificity of Aminoglycosides with DNA Microarrays.

data_processing: GCOS

molecule: polyA RNA

source_name: commercial human liver mRNA

tag: Hybridization interference in the presence of 5 micromolar tobramycin.


title: Tblink bead

tag: RNA bound to Tblink bead.


title: 7-OHMTX_biological rep1

city: Stockholm

first: Ali

last: Moshfegh

department: Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from untreated MOLT4 cells

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: ATCC CRL 1582 (lymphoblast)

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

extract_protocol: RNeasy Midi kit in accordance with manufacturer’s instructions

treatment_protocol: MOLT4 cells were exposed to a increased concentrations of 7-OHMTX, until final concentrations of  30000 nM, respectively, were reachedFor this purpose the cells were cultured and sub-cultured bi- weekly in RPMI-1640 medium containing fetal calf serum (10%), penicillin (100 U/ml), streptomycin (100 µg/ml) and L-glutamine (2 mM) and under humidified air containing 5% CO2 and at 37?C. The cultures were tested routinely for contamination by mycoplasma. The cells were cultured in drug-free-medium for at least 3 passages prior to harvesting during logarithmic phase growth (at a density of approximately 0.8-1.5x106/ml) for experimental studies. A Coulter Multi-sizer (Coulter Electronics, Luton, United Kingdom) was used to count the cells.

tag: male 19 years old


title: MTX_biological rep1

treatment_protocol: MOLT4 cells were exposed to a increased concentrations of MTX, until final concentrations of  300 nM, respectively, were reachedFor this purpose the cells were cultured and sub-cultured bi- weekly in RPMI-1640 medium containing fetal calf serum (10%), penicillin (100 U/ml), streptomycin (100 µg/ml) and L-glutamine (2 mM) and under humidified air containing 5% CO2 and at 37?C. The cultures were tested routinely for contamination by mycoplasma. The cells were cultured in drug-free-medium for at least 3 passages prior to harvesting during logarithmic phase growth (at a density of approximately 0.8-1.5x106/ml) for experimental studies. A Coulter Multi-sizer (Coulter Electronics, Luton, United Kingdom) was used to count the cells.


title: MTX_biological rep3


title: Genomic responses to Phenobarbital CSSUC1

tag: control strain is Canton S

tag: mutant strain harbors a null mutation for DHR96


title: 7-OHMTX_biological rep3


title: Cultured HTM cells-B

city: Durham

first: Pedro

last: Gonzalez

state: NC

address: Erwin Road Box 3802

department: Ophthalmology

institute: Duke University

description: RNA samples were amplified using the OvationTM Biotin RNA amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s instructions. Briefly, total RNA (20 ng) was reverse transcribed into cDNA using a reverse transcriptase and a DNA/RNA chimeric primer. This strand is copied by a DNA polymerase with reverse transcriptase activity to give double-stranded cDNA with an RNA-DNA heteroduplex at one end. This double-stranded cDNA is amplified using the novel isothermal linear amplification method Ribo-SPIA. The cDNA amplification products were fragmented and labeled to generate biotinylated cDNA targets. Biotinylated cDNA targets were hybridized on Affymetrix Human Genome U133 Plus 2.0 high density microarrays following the manufacturer’s instructions.

data_processing: Affymetrix Software

label: Biotin

source_name: Cultured trabecular meshwork cells

extract_protocol: Total RNA from dissected TM tissues and RNA later-fixed cultured HTM cells at passage three was isolated using RNeasy kit (Qiagen Inc., Valencia, CA) following the manufacturer’s protocol. After DNase treatment, RNA yields were determined using the RiboGreen® fluorescent dye (Molecular Probes Inc, Eugene, OR).  RNA quality was confirmed using the Agilent 2100 Bioanalyzer.

tag: Cultured human trabecular meshwork cells (passage 3) obtained from a donor with no known history of glaucoma. 25y/female/caucasian. Cause of death

value: pneumonia.


title: Tbr bead

tag: mRNA bound to Tbr beads.


title: Neomycin interference

tag: Hybridization interference in the presence of 5 micromolar neomycin.


title: ControlTM-C

source_name: Trabecular meshwork tissue

tag: Trabecular meshwork tissue from control donor C. 78y/male/africanamerican. Cause of death

value: abdominal aortic aneurism.


title: 7-OHMTX_biological rep2


title: MTX_biological rep2


title: POAG-TM-A

tag: Trabecular meshwork tissue from POAG donor A. 59y/male/caucasian. Cause of death

value: Renal failure. Othe ocular diseases:cataracts. IOP:17-28. Drug therapy:Xalatan


title: Control Bead

source_name: mRNA bound to unmodifed bead

tag: commercial human liver mRNA


title: Genomic responses to Phenobarbital E25SUC1


title: Control_biological rep3

treatment_protocol: For this purpose the cells were cultured and sub-cultured bi- weekly in RPMI-1640 medium containing fetal calf serum (10%), penicillin (100 U/ml), streptomycin (100 µg/ml) and L-glutamine (2 mM) and under humidified air containing 5% CO2 and at 37?C. The cultures were tested routinely for contamination by mycoplasma. The cells were cultured in drug-free-medium for at least 3 passages prior to harvesting during logarithmic phase growth (at a density of approximately 0.8-1.5x106/ml) for experimental studies. A Coulter Multi-sizer (Coulter Electronics, Luton, United Kingdom) was used to count the cells.


title: Control_biological rep2


title: POAG-TM-B

tag: Trabecular meshwork tissue from POAG donor B. 77y/female/africanamerican. Cause of death

value: renal failure. Other ocular diseases:cataracts. IOP:15-25. Drug therapy:Xalatan, cosopt.


title: Cultured TM cells-A

tag: Cultured human trabecular meshwork cells (passage 3) obtained from a donor with no known history of glaucoma. 45y/female/caucasian. Cause of death

value: multi-system organ failure


title: ControlTM-B

tag: Trabecular meshwork tissue from control donor B. 85 y/ female/ caucasian. Cause of death

value: IC bleed


title: Mouse Universal Total RNA 5 ng BIIB Labeling Replicate 3

tag: Total RNA pool generated from 11 cell lines


title: Cultured HTM cells-C

status: Public on Jun 21 2006

tag: Cultured human trabecular meshwork cells (passage 3) obtained from a donor with no known history of glaucoma. 58y/male/caucasian. Cause of death

value: cancer


title: Gene expression in degenerated rat supraspinatus tendon

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

institute: St Vincent's Centre for Applied Medical Research

description: No additional data

data_processing: No processing - raw experimental/control

organism: Rattus norvegicus

source_name: Rat supraspinatus tendon - degenerated

tag: Strain

value: SD

tag: Gender

value: Male

tag: Tissue

value: Supraspinatus tendon

tag: State

value: Degerated (exercised)

source_name: Rat supraspinatus tendon - normal

value: Normal (non-exercised)


title: Ectopic expression of DHR96 (gain of function) gain 1

description: larvae are essentially staged, young third instar feeding larvae. Nutritional source is Bakers yeast.

source_name: young third instar larvae (all tissues)

tag: W1118 served as controls. The experimental samples were derived from trangenic animals that harboured a heat-shock inducible full-length DHR96 cDNA. larvae were staged at the molt from L2 to L3, heat-shocked after three hours and allowed to recover for 4 hours before RNA extraction.


title: Control_biological rep1

tag: male 19 years old


title: ControlTM-A

source_name: Trabecular meshwork

tag: Trabecular meshwork tissue from control donor A (70y/Female/Caucasian). Cause of death


title: Ectopic expression of DHR96 (gain of function) gain 2


title: Ectopic expression of DHR96 (gain of function) control 2


title: bovine granulosa cell_persistent follicle_reps1-5

city: Morgantown

first: Brandon

middle: M

last: Lingenfelter

state: WV

address: G058 Agricultural Sciences Bldg

department: Animal & Veterinary Sciences

institute: West Virginia University

description: This is all of the array data compiled after normalization.

data_processing: Data in value column were subjected to Loess and Quantile normalizations. Gene Pix Auto Processor (http://darwin.biochem.okstate.edu/gpap) and are represented as M-value

organism: Bos taurus

source_name: Granulosa cells from day 8 follicles

tag: Bos Taurus, female, age 4-7 years, tissue

value: granulosa cells, Day 8 of estrous cycle

source_name: Granulosa cells from day 15 follicles

value: granulosa cells, Day 15 of estrous cycle


title: Ectopic expression of DHR96 (gain of function) control 1


title: Mammary MT1-MMP rep3

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: Third biological replicate from three for the transfected 184B5-MT cell line

hyb_protocol: As described in the illumina Human-6 hybridisation protocol. Doc#11176837 Rev E.

scan_protocol: As suggested by Illumina using the Illumina scanner.

data_processing: None: raw data from Beadstudio

label: Streptavidin Cy3

source_name: cell line 184B5-MT

label_protocol: As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)

tag: cell line 184B5-MT. Mammary epithelial. Gender Female. Age. Derived from 184B5 by transfection with a full length MT1-MMP lentiviral construct.


title: Mammary MT1-MMP rep1

description: First biological replicate from three for the transfected 184B5-MT cell line

tag: cell line 184B5-MT is derived from 184B5 by transfecting cells with a lentiviral construct  bearing the full-length MT1-MMP proenzyme gene. MT1-MMP is expressed at significant levels.


title: Mammary MT1-MMP rep2

description: Second biological replicate from three for the transfected 184B5-MT cell line

tag: cell line 184B5-MT. Mammary epithelial. Gender

value: Female. Age:Derived from 184B5 by transfection with a full length MT1-MMP lentiviral construct.


title: Ectopic expression of DHR96 (gain of function) control 3


title: Ectopic expression of DHR96 (gain of function) gain 3


title: Rat 4 vehicle-treated in the Nighttime

city: Philadelphia

first: Gregory

last: Miller

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

description: Adult Sprague-Dawley rats (100-150g) housed individually and entrained to 12:12 light-dark cycles for at least two weeks were rapidly sacrificed between 10:00AM and 12:00PM for daytime treatments and between 4:00 and 6:00 PM for night treatments according to a protocol approved by TJU IACUC. Brains were excised quickly, placed in ice-cold, oxygenated artificial cerebral spinal fluid (ACSF) (10 mM HEPES, pH 7.4, 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, 24 mM D-Glucose), and cut into 500 µm coronal sections using a vibroslice vibratome (752M, Camden Instruments, Leica, UK). The resulting SCN slices were cultured in oxygenated ACSF for at least 60 minutes at 35°C. After incubation, slices were bisected along the third ventricle, separating the “left” and “right” SCN, and transferred into a new media containing the treatment (20 nM EGF or vehicle). Slices were incubated in treatment for 60 minutes before taking 0.75 mm micropunches (Stoelting, Chicago, IL). Punches for day treatment were taken at 2 PM (8 hours after lights on) while punches for night treatment were taken at 8PM (2 hrs after lights off). RNA was extracted using the Rneasy mini kit (Qiagen), yielding ~200 nanograms of total RNA/punch. Two hundred to four hundred nanograms total RNA were amplified using two rounds of antisense RNA (aRNA) amplification using the RNA MessageAmp kit (Ambion), yielding no less than 130 µg aRNA. aRNA quality was assessed using Bioanalyzer Picochip (Agilent Technologies, Palo Alto, CA). 2.25 µg of aRNA was used to generate amino-allyl and Cy dye conjugated labeled cDNA (Cy5, Amersham) using the indirect aminoallyl-dNTP approach. Experimental details for hybridization, scanning, and quantification are in the Supporting Information (Materials & Methods) in Zak, Hao, et al (2006).

data_processing: log2((ch2 median - ch2 median background)/(ch1 median - ch1 median background))

organism: synthetic construct

source_name: Reference RNA

tag: PCR of vector of empty clone. Hybridizes to all spots evenly.

source_name: Sample RNA

tag: 'Strain:Sprague-Dawley', 'Gender:Male', 'Tissue:Suprachiasmatic Nucleus"


title: Rat 2 vehicle-treated in the Daytime


title: PPAR in Rat  EDL_2-Wy-14,643_d06_010.0mkd_#1188

status: Public on Jun 20 2006

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_2-Wy-14,643_d06_010.0mkd_#1188

data_processing: Local background correction

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Vehicle Treated, extensor digitorum longus (EDL)

tag: Sprague Dawley CD, Approximately 8 wks at the onset of dosing, Fenofibrate; Wy-14,643; bezafibrate; rosiglitazone; all trans retinoic acid, extensor digitorum longus (EDL)


title: Rat 1 vehicle-treated in the Daytime


title: Rat 2 EGF-treated in the Daytime

description: Adult Sprague-Dawley rats (100-150g) housed individually and entrained to 12:12 light-dark cycles for at least two weeks were rapidly sacrificed between 10:00AM and 12:00PM for daytime treatments and between 4:00 and 6:00 PM for night treatments according to a protocol approved by TJU IACUC.  Brains were excised quickly, placed in ice-cold, oxygenated artificial cerebral spinal fluid (ACSF) (10 mM HEPES, pH 7.4, 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, 24 mM D-Glucose), and cut into 500 µm coronal sections using a vibroslice vibratome (752M, Camden Instruments, Leica, UK). The resulting SCN slices were cultured in oxygenated ACSF for at least 60 minutes at 35°C. After incubation, slices were bisected along the third ventricle, separating the “left” and “right” SCN, and transferred into a new media containing the treatment (20 nM EGF or vehicle). Slices were incubated in treatment for 60 minutes before taking 0.75 mm micropunches (Stoelting, Chicago, IL). Punches for day treatment were taken at 2 PM (8 hours after lights on) while punches for night treatment were taken at 8PM (2 hrs after lights off). RNA was extracted using the Rneasy mini kit (Qiagen), yielding ~200 nanograms of total RNA/punch. Two hundred to four hundred nanograms total RNA were amplified using two rounds of antisense RNA (aRNA) amplification using the RNA MessageAmp kit (Ambion), yielding no less than 130 µg aRNA. aRNA quality was assessed using Bioanalyzer Picochip (Agilent Technologies, Palo Alto, CA). 2.25 µg of aRNA was used to generate amino-allyl and Cy dye conjugated labeled cDNA (Cy5, Amersham) using the indirect aminoallyl-dNTP approach.  Experimental details for hybridization, scanning, and quantification are in the Supporting Information (Materials & Methods) in Zak, Hao, et al (2006).


title: Rat 1 EGF-treated in the Daytime


title: PPAR in Rat  EDL_2-Wy-14,643_d06_010.0mkd_#1187

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_2-Wy-14,643_d06_010.0mkd_#1187


title: PPAR in Rat  EDL_5-Retinoic acid_d06_002.5mkd_#1298

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_5-Retinoic acid_d06_002.5mkd_#1298

source_name: EDL_5-Retinoic acid_d06_002.5mkd_#1298


title: Rat 3 EGF-treated in the Nighttime


title: Rat 4 EGF-treated in the Nighttime


title: PPAR in Rat  EDL_2-Wy-14,643_d06_010.0mkd_#1186

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_2-Wy-14,643_d06_010.0mkd_#1186


title: PPAR in Rat  EDL_5-Retinoic acid_d06_002.5mkd_#1297

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_5-Retinoic acid_d06_002.5mkd_#1297

source_name: EDL_5-Retinoic acid_d06_002.5mkd_#1297


title: PPAR in Rat  EDL_1-Fenofibrate_d06_050.0mkd_#1131

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_1-Fenofibrate_d06_050.0mkd_#1131


title: Rat 3 vehicle-treated in the Nighttime


title: PPAR in Rat  EDL_2-Wy-14,643_d05_010.0mkd_#1184

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d05_010.0mkd_#1184


title: PPAR in Rat  EDL_4-Rosiglitazone_d06_010.0mkd_#1353

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_4-Rosiglitazone_d06_010.0mkd_#1353


title: PPAR in Rat  EDL_2-Wy-14,643_d05_010.0mkd_#1182

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d05_010.0mkd_#1182


title: PPAR in Rat  EDL_5-Retinoic acid_d05_002.5mkd_#1295

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_5-Retinoic acid_d05_002.5mkd_#1295

source_name: EDL_5-Retinoic acid_d05_002.5mkd_#1295


title: PPAR in Rat  EDL_3-Bezafibrate_d06_025.0mkd_#1242

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_3-Bezafibrate_d06_025.0mkd_#1242


title: Mammary normal rep2

description: Second biological replicate from three for the untransformed 184B5 cell line

source_name: cell line 184B5

tag: cell line

value: 184B5. Mammary epithelial. Gender Female. Age:


title: PPAR in Rat  EDL_3-Bezafibrate_d06_025.0mkd_#1241

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_3-Bezafibrate_d06_025.0mkd_#1241


title: PPAR in Rat  EDL_3-Bezafibrate_d05_025.0mkd_#1238

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_3-Bezafibrate_d05_025.0mkd_#1238


title: PPAR in Rat  EDL_1-Fenofibrate_d06_050.0mkd_#1129

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_1-Fenofibrate_d06_050.0mkd_#1129


title: Mammary normal rep3

description: Third biological replicate from three for the untransformed 184B5 cell line

tag: cell line 184B5. Mammary epithelial. Gender Female. Age:


title: PPAR in Rat  EDL_4-Rosiglitazone_d05_010.0mkd_#1352

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_4-Rosiglitazone_d05_010.0mkd_#1352


title: PPAR in Rat  EDL_5-Retinoic acid_d05_002.5mkd_#1293

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_5-Retinoic acid_d05_002.5mkd_#1293

source_name: EDL_5-Retinoic acid_d05_002.5mkd_#1293


title: PPAR in Rat  EDL_5-Retinoic acid_d06_002.5mkd_#1300

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_5-Retinoic acid_d06_002.5mkd_#1300

source_name: EDL_5-Retinoic acid_d06_002.5mkd_#1300


title: Mammary normal rep1

description: First biological replicate from three for the untransformed cell line

hyb_protocol: As described in the illumina Human-6 hyb protocol. Doc#11176837 Rev E.

scan_protocol: As suggested by illumina using the illumina scanner.

label: Strepavidin Cy3

label_protocol: As described in the illumina Human-6 chip hyb protocol. Briefly, generation of biotin labelled cRNA from product of RT cDNA synthesis and 2nd strand cDNA synth.

value: 184B5. Mammary epithelial. Gender:female. Age:


title: PPAR in Rat  EDL_4-Rosiglitazone_d06_010.0mkd_#1355

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_4-Rosiglitazone_d06_010.0mkd_#1355


title: PPAR in Rat  EDL_3-Bezafibrate_d06_025.0mkd_#1243

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_3-Bezafibrate_d06_025.0mkd_#1243


title: PPAR in Rat  EDL_3-Bezafibrate_d05_025.0mkd_#1237

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_3-Bezafibrate_d05_025.0mkd_#1237


title: PPAR in Rat  EDL_1-Fenofibrate_d05_050.0mkd_#1126

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_1-Fenofibrate_d05_050.0mkd_#1126


title: PPAR in Rat  EDL_3-Bezafibrate_d05_025.0mkd_#1240

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_3-Bezafibrate_d05_025.0mkd_#1240


title: PPAR in Rat  EDL_1-Fenofibrate_d06_050.0mkd_#1132

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_1-Fenofibrate_d06_050.0mkd_#1132


title: PPAR in Rat  EDL_1-Fenofibrate_d05_050.0mkd_#1127

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_1-Fenofibrate_d05_050.0mkd_#1127


title: PPAR in Rat  EDL_4-Rosiglitazone_d06_010.0mkd_#1354

description: EDL_ vehicle control pool_d06_000.0mkd_n=14 vs. EDL_4-Rosiglitazone_d06_010.0mkd_#1354


title: PPAR in Rat  EDL_2-Wy-14,643_d04_010.0mkd_#1180

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_2-Wy-14,643_d04_010.0mkd_#1180


title: PPAR in Rat  EDL_2-Wy-14,643_d05_010.0mkd_#1183

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d05_010.0mkd_#1183


title: PPAR in Rat  EDL_2-Wy-14,643_d04_010.0mkd_#1178

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_2-Wy-14,643_d04_010.0mkd_#1178


title: PPAR in Rat  EDL_5-Retinoic acid_d04_002.5mkd_#1289

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_5-Retinoic acid_d04_002.5mkd_#1289

source_name: EDL_5-Retinoic acid_d04_002.5mkd_#1289


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_100.0mkd_#1375

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_100.0mkd_#1375


title: PPAR in Rat  EDL_4-Rosiglitazone_d05_010.0mkd_#1350

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_4-Rosiglitazone_d05_010.0mkd_#1350


title: PPAR in Rat  EDL_5-Retinoic acid_d04_002.5mkd_#1290

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_5-Retinoic acid_d04_002.5mkd_#1290

source_name: EDL_5-Retinoic acid_d04_002.5mkd_#1290


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_100.0mkd_#1374

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_100.0mkd_#1374


title: PPAR in Rat  EDL_5-Retinoic acid_d04_002.5mkd_#1292

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_5-Retinoic acid_d04_002.5mkd_#1292

source_name: EDL_5-Retinoic acid_d04_002.5mkd_#1292


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_100.0mkd_#1376

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_100.0mkd_#1376


title: PPAR in Rat  EDL_5-Retinoic acid_d05_002.5mkd_#1294

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_5-Retinoic acid_d05_002.5mkd_#1294

source_name: EDL_5-Retinoic acid_d05_002.5mkd_#1294


title: PPAR in Rat  EDL_2-Wy-14,643_d04_010.0mkd_#1177

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_2-Wy-14,643_d04_010.0mkd_#1177


title: PPAR in Rat  EDL_1-Fenofibrate_d05_050.0mkd_#1125

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_1-Fenofibrate_d05_050.0mkd_#1125


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_100.0mkd_#1373

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_100.0mkd_#1373


title: PPAR in Rat  EDL_4-Rosiglitazone_d05_010.0mkd_#1351

description: EDL_ vehicle control pool_d05_000.0mkd_n=16 vs. EDL_4-Rosiglitazone_d05_010.0mkd_#1351


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_010.0mkd_#1345

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_010.0mkd_#1345


title: PPAR in Rat  EDL_3-Bezafibrate_d04_025.0mkd_#1233

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_3-Bezafibrate_d04_025.0mkd_#1233


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_010.0mkd_#1348

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_010.0mkd_#1348


title: PPAR in Rat  EDL_1-Fenofibrate_d04_050.0mkd_#1121

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_1-Fenofibrate_d04_050.0mkd_#1121


title: PPAR in Rat  EDL_3-Bezafibrate_d04_025.0mkd_#1235

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_3-Bezafibrate_d04_025.0mkd_#1235


title: PPAR in Rat  EDL_1-Fenofibrate_d04_050.0mkd_#1124

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_1-Fenofibrate_d04_050.0mkd_#1124


title: PPAR in Rat  EDL_4-Rosiglitazone_d04_010.0mkd_#1346

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_4-Rosiglitazone_d04_010.0mkd_#1346


title: PPAR in Rat  Quad_d02_Retinoic acid_025.0mkd_#1312

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Retinoic acid_025.0mkd_#1312

source_name: Quad_d02_Retinoic acid_025.0mkd_#1312


title: PPAR in Rat  EDL_3-Bezafibrate_d04_025.0mkd_#1234

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_3-Bezafibrate_d04_025.0mkd_#1234


title: PPAR in Rat  Quad_d02_Fenofibrate_400.0mkd_#1143

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Fenofibrate_400.0mkd_#1143


title: SN:Human Glioblastoma Biopsy 30150

city: Los Angeles

first: Cho-Lea

last: Tso

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles

data_processing: rma

source_name: SN:Human Glioblastoma  30150

tag: Human Glioblastoma Biopsy


title: PPAR in Rat  EDL_5-Retinoic acid_d03_002.5mkd_#1286

description: EDL_ vehicle control pool_d03_000.0mkd_n=16 vs. EDL_5-Retinoic acid_d03_002.5mkd_#1286

source_name: EDL_5-Retinoic acid_d03_002.5mkd_#1286


title: PPAR in Rat  EDL_5-Retinoic acid_d03_002.5mkd_#1288

description: EDL_ vehicle control pool_d03_000.0mkd_n=16 vs. EDL_5-Retinoic acid_d03_002.5mkd_#1288

source_name: EDL_5-Retinoic acid_d03_002.5mkd_#1288


title: PPAR in Rat  Quad_d02_Fenofibrate_400.0mkd_#1144

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Fenofibrate_400.0mkd_#1144


title: SN:Human Glioblastoma Biopsy 30164

source_name: SN:Human Glioblastoma  30164


title: SN:Human Glioblastoma Biopsy 30165

source_name: SN:Human Glioblastoma  30165


title: PPAR in Rat  Quad_d02_Bezafibrate_250.0mkd_#1255

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Bezafibrate_250.0mkd_#1255


title: PPAR in Rat  EDL_1-Fenofibrate_d04_050.0mkd_#1122

description: EDL_ vehicle control pool_d04_000.0mkd_n=15 vs. EDL_1-Fenofibrate_d04_050.0mkd_#1122


title: SN:Human Glioblastoma Biopsy 30148

source_name: SN:Human Glioblastoma  30148


title: PPAR in Rat  EDL_2-Wy-14,643_d03_010.0mkd_#1173

description: EDL_ vehicle control pool_d03_000.0mkd_n=16 vs. EDL_2-Wy-14,643_d03_010.0mkd_#1173


title: PPAR in Rat  Quad_d02_Bezafibrate_250.0mkd_#1254

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Bezafibrate_250.0mkd_#1254


title: PPAR in Rat  Quad_d02_Rosiglitazone_100.0mkd_#1365

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Rosiglitazone_100.0mkd_#1365


title: PPAR in Rat  Quad_d02_Bezafibrate_250.0mkd_#1256

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Bezafibrate_250.0mkd_#1256


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1014

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1014


title: PPAR in Rat  Quad_d02_Fenofibrate_400.0mkd_#1142

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Fenofibrate_400.0mkd_#1142


title: PPAR in Rat  Quad_d02_Fenofibrate_400.0mkd_#1141

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Fenofibrate_400.0mkd_#1141


title: PPAR in Rat  Quad_d02_Bezafibrate_250.0mkd_#1253

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Bezafibrate_250.0mkd_#1253


title: PPAR in Rat  Quad_d02_Retinoic acid_025.0mkd_#1310

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_Retinoic acid_025.0mkd_#1310

source_name: Quad_d02_Retinoic acid_025.0mkd_#1310


title: SN:Human Glioblastoma Biopsy 29154

source_name: SN:Human Glioblastoma  29154


title: SN:Human Glioblastoma Biopsy 29152

source_name: SN:Human Glioblastoma  29152


title: SN:Human Glioblastoma Biopsy 12380

source_name: SN:Human Glioblastoma  12380


title: SN:Human Glioblastoma Biopsy 29150

source_name: SN:Human Glioblastoma  29150


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1008

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1008


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1010

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1010


title: SN:Human Glioblastoma Biopsy 12386

source_name: SN:Human Glioblastoma  12386


title: SN:Human Glioblastoma Biopsy 30147

source_name: SN:Human Glioblastoma  30147


title: SN:Human Glioblastoma Biopsy 12384

source_name: SN:Human Glioblastoma  12384


title: SN:Human Glioblastoma Biopsy 12368

source_name: SN:Human Glioblastoma  12368


title: SN:Human Glioblastoma Biopsy 30145

source_name: SN:Human Glioblastoma  30145


title: SN:Human Glioblastoma Biopsy 10516

source_name: SN:Human Glioblastoma  10516


title: SN:Human Glioblastoma Biopsy 12382

source_name: SN:Human Glioblastoma  12382


title: SN:Human Glioblastoma Biopsy 30149

source_name: SN:Human Glioblastoma  30149


title: PPAR in Rat  Quad_d02_ vehicle control_000.0mkd_#1005

description: Quad_d02_ vehicle control pool_000.0mkd_n=14 vs. Quad_d02_ vehicle control_000.0mkd_#1005


title: SN:Human Glioblastoma Biopsy 10517

source_name: SN:Human Glioblastoma  10517


title: SN:Human Glioblastoma Biopsy 12367

source_name: SN:Human Glioblastoma  12367