title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down XBP1 Replicate 2

status: Public on Jul 29 2009

type: RNA

city: Heidelberg

first: Mark

last: Fellmann

address: INF 580

department: Molecular Genome Analysis

country: Germany

institute: DKFZ

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardts solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) including VSN normalization method; after removal of bad quality clones, generalized log ratios from 26618 cDNA clones were given in the data table

molecule: total RNA

organism: Homo sapiens

source_name: cell line MCF7 siRNA XBP1_2-1

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.

growth_protocol: cells were cultivated in Minimum Essential Media (1x) (MEM, Invitrogen, Grand Island, NY, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 µg/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 µg/ml insulin bovine

extract_protocol: total RNA was extracted using Rneasy mini-prep kit (Qiagen, Hilden, Germany; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)

treatment_protocol: chemically synthesized siRNAs (Qiagen, Hilden, Germany) were transfected with HiPerFect (Qiagen, Hilden, Germany) according to standard transfection procedure

tag: construct siRNA XBP1_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.

tag: construct non-silencing control siRNA_Replicate3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TP53 Replicate 1

source_name: cell line MCF7 siRNA TP53_1-1

tag: construct siRNA TP53_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TMEM45B Replicate 1 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA TMEM45B_1-2

tag: construct siRNA TMEM45B_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TMEM45B Replicate 1

source_name: cell line MCF7 siRNA TMEM45B_1-1

tag: construct siRNA TMEM45B_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TMEM45B Replicate 2 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA TMEM45B_2-2

tag: construct siRNA TMEM45B_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 2 dyeswap

source_name: cell line MCF7 control 4

treatment_protocol: 100 nM Tamoxifen solved in ethanol

tag: construct control_Replicate4

source_name: cell line MCF7 TAM 4

tag: construct TAM_Replicate4


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 2

source_name: cell line MCF7 TAM 3

tag: construct TAM_Replicate3

source_name: cell line MCF7 control 3

tag: construct control_Replicate3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 3 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_6

tag: construct non-silencing control siRNA_Replicate6

source_name: cell line MCF7 siRNA STC2_3-2

tag: construct siRNA STC2_Replicate3_2


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 1

source_name: cell line MCF7 TAM 1

tag: construct TAM_Replicate1

source_name: cell line MCF7 control 1

tag: construct control_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 3

source_name: cell line MCF7 siRNA STC2_3-1

tag: construct siRNA STC2_Replicate3_1

source_name: cell line MCF7 siRNA _non-silencing_control_5

tag: construct non-silencing control siRNA_Replicate5


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down XBP1 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA XBP1_1-2

tag: construct siRNA STAT5B_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down XBP1 Replicate 1

source_name: cell line MCF7 siRNA XBP1_1-1

tag: construct siRNA XBP1_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TP53 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA TP53_1-2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

source_name: cell line MCF7 siRNA STC2_2-2

tag: construct siRNA STC2_Replicate2_2


title: Alc-NTO2 Neural tube open alcohol treated mouse embryo_MeDIP_Replicate 2

status: Public on Jul 30 2009

type: genomic

city: Indianapolis

first: GUOHUA

last: WANG

state: IN

address: 410 West 10th Street, Suite 5000

department: Medicine

country: USA

institute: Indiana University Center for Computational Biology and Bioinformatics

description: No description

hyb_protocol: Hybridization performed according to standard procedures by Nimblegen

scan_protocol: Scanning performed according to standard procedures by Nimblegen

data_processing: VALUE is the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

molecule: genomic DNA

organism: Mus musculus

source_name: Cy3, total input sonicated DNA from neural tube open alcohol treated mouse embryos

label_protocol: Labeling performed by Nimblegen

extract_protocol: Total genomic DNA sonicated to give fragments between 200bp and 1000bp

tag: Mouse embryos

source_name: Cy5, methylated DNA from neural tube open alcohol treated mouse embryos enriched by MeDIP

label_protocol: Labeling performed according to standard procedures by Nimblegen

extract_protocol: Methylated DNA purified from total sonicated DNA by MeDIP


title: Alc-NTC1 Neural tube closed alcohol treated mouse embryo_MeDIP_Replicate 1

description: No description

source_name: Cy3, total input sonicated DNA from neural tube closed alcohol treated mouse embryos

source_name: Cy5, methylated DNA from neural tube closed alcohol treated mouse embryos enriched by MeDIP


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STAT5B Replicate 1

source_name: cell line MCF7 siRNA STAT5B_1-1

tag: construct siRNA STAT5B_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA STC2_1-2

tag: construct siRNA STC2_Replicate1_2


title: Alc-NTO3 Neural tube open alcohol treated mouse embryo_MeDIP_Replicate 3

description: No description


title: Alc-NTO1 Neural tube open alcohol treated mouse embryo_MeDIP_Replicate 1

description: No description


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TP53 Replicate 2

source_name: cell line MCF7 siRNA TP53_2-1

tag: construct siRNA TP53_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: Alc-NTC2 Neural tube closed alcohol treated mouse embryo_MeDIP_Replicate 2

description: No description


title: C3 Control mouse embryo_MeDIP_Replicate 3

description: No Description

source_name: Cy3, total input sonicated DNA from control mouse embryos

source_name: Cy5, methylated DNA from control mouse embryos enriched by MeDIP


title: Alc-NTC3 Neural tube closed alcohol treated mouse embryo_MeDIP_Replicate 3

description: No description


title: C2 Control mouse embryo_MeDIP_Replicate 2

description: No Description


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TP53 Replicate 2 dyeswap

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA TP53_2-2

tag: construct siRNA STAT5B_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down TMEM45B Replicate 2

source_name: cell line MCF7 siRNA TMEM45B_2-1

tag: construct siRNA TMEM45B_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 3

source_name: cell line MCF7 TAM 5

tag: construct TAM_Replicate5

source_name: cell line MCF7 control 5

tag: construct control_Replicate5


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 3 dyeswap

source_name: cell line MCF7 control 6

tag: construct Control_Replicate6

source_name: cell line MCF7 TAM 6

tag: construct TAM_Replicate6


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 and STAT5B Replicate 2

source_name: cell line MCF7 siRNA MAPK1_STAT5B_2-1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 Replicate 2

source_name: cell line MCF7 siRNA MAPK1_2-1

tag: construct siRNA MAPK1_Replicate2_1


title: C1 Control mouse embryo_MeDIP_Replicate 1

description: No Description


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 2

source_name: cell line MCF7 siRNA STC2_2-1

tag: construct siRNA STC2_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, Tamoxifen Treatment Replicate 1 dyeswap

source_name: cell line MCF7 control 2

tag: construct control_Replicate2

source_name: cell line MCF7 TAM 2

tag: construct TAM_Replicate2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STC2 Replicate 1

source_name: cell line MCF7 siRNA STC2_1-1

tag: construct siRNA STC2_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down FOXA1 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA FOXA1_1-2

tag: construct siRNA FOXA1_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and MAPK1 Replicate 2 dyeswap

description: siRNA_ESR1_MAPK1_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

source_name: cell line MCF7 siRNA ESR1_MAPK1_2-2

tag: construct siRNA ESR1_MAPK1_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STAT5B Replicate 2 dyeswap

source_name: cell line MCF7 siRNA STAT5B_2-2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and MAPK1 Replicate 1 dyeswap

description: siRNA_ESR1_MAPK1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA ESR1_MAPK1_1-2

tag: construct siRNA ESR1_MAPK1_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STAT5B Replicate 2

source_name: cell line MCF7 siRNA STAT5B_2-1

tag: construct siRNA STAT5B_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down STAT5B Replicate 1 dyeswap

source_name: cell line MCF7 siRNA STAT5B_1-2

tag: construct siRNA STAT5B_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 and STAT5B Replicate 1 dyeswap

description: siRNA_MAPK1_STAT5B_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA MAPK1_STAT5B_1-2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 and STAT5B Replicate 1

source_name: cell line MCF7 siRNA MAPK1_STAT5B_1-1


title: MCF7 ESRalpha positive breast cancer cell line, treatment with 17-beta Estradiol Replicate 2

source_name: cell line MCF7 17-beta Estradiol

growth_protocol: cells were cultivated inRPMI  Media (1x) (Invitrogen, Grand Island, NY, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 µg/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 µg/ml insulin bovine

treatment_protocol: 10 nM 17-beta Estradiol solved in ethanol

tag: 17-beta Estradiol_Replicate2_1

source_name: cell line MCF7 control


title: MCF7 ESRalpha positive breast cancer cell line, treatment with 17-beta Estradiol Replicate 2 dyeswap

tag: 17-beta Estradiol_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 Replicate 2 dyeswap

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA MAPK1_2-2

tag: construct siRNA MAPK1_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA MAPK1_1-2

tag: construct siRNA MAPK1_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down HSPB8 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA HSPB8_2-2

tag: construct siRNA HSPB8_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and CCNG2 Replicate 1

source_name: cell line MCF7 siRNA ESR1_CCNG2_1-1

tag: construct siRNA ESR1_CCNG2_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down HSPB8 Replicate 2

source_name: cell line MCF7 siRNA HSPB8_2-1

tag: construct siRNA HSPB8_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 3

source_name: cell line MCF7 siRNA CCNG2_3-1

tag: construct siRNA CCNG2_Replicate3_1

source_name: cell line MCF7 siRNA _non-silencing_control_5

tag: construct non-silencing control siRNA_Replicate5


title: MCF7 ESRalpha positive breast cancer cell line, treatment with 17-beta Estradiol Replicate 1 dyeswap


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down FOXA1 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

source_name: cell line MCF7 siRNA FOXA1_2-2

tag: construct siRNA FOXA1_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 and STAT5B Replicate 2 dyeswap

description: siRNA_MAPK1_STAT5B_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA MAPK1_STAT5B_2-2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down HSPB8 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA HSPB8_1-2

tag: construct siRNA HSPB8_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down HSPB8 Replicate 1

source_name: cell line MCF7 siRNA HSPB8_1-1

tag: construct siRNA HSPB8_Replicate1_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down FOXA1 Replicate 2

source_name: cell line MCF7 siRNA FOXA1_2-1

tag: construct siRNA FOXA1_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA ESR1+AK14_2-2

tag: construct siRNA ESR1_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 1

source_name: cell line MCF7 siRNA CCNG2_1-1

tag: construct siRNA CCNG2_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA CCNG2_1-2

tag: construct siRNA CCNG2_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down FOXA1 Replicate 1

source_name: cell line MCF7 siRNA FOXA1_1-1

tag: construct siRNA FOXA1_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 Replicate 1

source_name: cell line MCF7 siRNA ESR1_1-1

tag: construct siRNA ESR1_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 Replicate 2

source_name: cell line MCF7 siRNA ESR1_2-1

tag: construct siRNA ESR1_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 2

source_name: cell line MCF7 siRNA CCNG2_2-1

tag: construct siRNA CCNG2_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT2 Replicate 2 dyeswap

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA AKT2_2-2

tag: construct siRNA AKT2_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down MAPK1 Replicate 1

source_name: cell line MCF7 siRNA MAPK1_1-1

tag: construct siRNA MAPK1_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT2 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA AKT2_1-2

tag: construct siRNA AKT2_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and MAPK1 Replicate 2

source_name: cell line MCF7 siRNA ESR1_MAPK1_2-1

tag: construct siRNA ESR1_MAPK1_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA ESR1_1-2

tag: construct siRNA ESR1_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and MAPK1 Replicate 1

source_name: cell line MCF7 siRNA ESR1_MAPK1_1-1

tag: construct siRNA ESR1_MAPK1_Replicate1_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT2 Replicate 1

source_name: cell line MCF7 siRNA AKT2_1-1

tag: construct siRNA AKT2_Replicate1_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and CCNG2 Replicate 2 dyeswap

description: siRNA_ESR1_CCNG2_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

source_name: cell line MCF7 siRNA ESR1_CCNG2_2-2

tag: construct siRNA ESR1_CCNG2_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT1 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA AKT1_1-2

tag: construct siRNA AKT1_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT1 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA AKT1_2-2

tag: construct siRNA AKT1_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and CCNG2 Replicate 1 dyeswap

description: siRNA_ESR1_CCNG2_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA ESR1_CCNG2_1-2

tag: construct siRNA ESR1_CCNG2_Replicate1_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down ESR1 and CCNG2 Replicate 2

source_name: cell line MCF7 siRNA ESR1_CCNG2_2-1

tag: construct siRNA ESR1_CCNG2_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 3 dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_6

tag: construct non-silencing control siRNA_Replicate6

source_name: cell line MCF7 siRNA CCNG2_3-2

tag: construct siRNA CCNG2_Replicate3_2


title: SPI 159

status: Public on Jul 23 2009

city: Little Rock

first: Ying

last: Su

state: AR

address: 1120 Marshall St. South Campus

department: physiology

institute: UAMS

description: Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.

hyb_protocol: 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.

data_processing: Value column are raw signal intensity generated from MAS 5.0.

label: biotin

organism: Rattus norvegicus

source_name: Weaning rat mammary gland, life-time expose to soy protein isolate based AIN-93G diet

label_protocol: RNA from PND21 rat was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool

extract_protocol: TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.

tag: Female Sprague-Dawley rat, postnatal day 21, life-time expose to soy protein isolate based AIN-93G diet


title: MCF7 ESRalpha positive breast cancer cell line, treatment with 17-beta Estradiol Replicate 1

source_name: cell line MCF7 17-beta Estradiol

tag: 17-beta Estradiol_Replicate1_1

source_name: cell line MCF7 control


title: SPI 147


title: Danio_rerio_Larvae_MicrocystisAlgae_rep2

city: Knoxville

first: Julia

last: Gouffon

state: TN

address: 1215 West Cumberland Ave, RM 229

department: Nutrition

institute: Univ. of TN

description: Emily D. Rogers, Theodore B. Henry, Julia S. Gouffon, Jackson McPherson, Gregory L. Boyer, Gary S. Sayler, Steven W. Wilhelm

hyb_protocol: Protocol follows the Affymetrix Hybridization, Wash and Stain kit for Eukaryotic Target Hybridization for 49Format array using 15µg fragmented cRNA and 45°C hyb temp for 16 hours at 60rpm.  Washed with Affymetrix 450 Fluidics using FS450_001.

scan_protocol: Affymetrix 7G GeneChip Scanner standard parameters for Zebrafish Array

data_processing: Affymetrix GCOS MAS5.0 Algorithm

label: Biotin

organism: Danio rerio

label_protocol: Ambion Message Amp II-Biotin Enhanced Method with 1µg Total RNA

growth_protocol: Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained in the Center for Environmental Biotechnology at the University of Tennessee.  Fish husbandry, spawning, and experimental procedures were conducted with approval from the University of Tennessee Institutional Animal Care and Use Committee (Protocol #1690-1007).  Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl.  Embryos were obtained by spawning adult fish with no history of contaminant exposure.  Fertilization of embryos took place at the same time (± 15 min.), such that larvae used in experiments were of similar age at the time of exposure.  All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27± 1 ºC and 14:10h light:dark photoperiod.

extract_protocol: Total RNA Extraction Larvae were centrifuged for 10 min. at 13,000 rpm to separate larvae from exposure water, and pellets containing larvae were stored at –80ºC until RNA extraction was performed.  Total larval RNA was extracted using the RNeasy mini extraction kit for animal tissues (Qiagen, Valencia, CA) and quantified using a spectrophotometer (Nanodrop, Wilmington, DE).

treatment_protocol: The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa.  M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined.  Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture).  For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L.


title: Danio_rerio_Larvae_1000µgMCLR_rep3

treatment_protocol:
Microcystin Treated Preparation of Exposure Solutions
The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa.  M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined.  Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture).  For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L. Solutions for microcystin-LR (MC-LR) treatments were prepared by dissolving 1mg of purified MC-LR (Alexis Biochemicals, San Diego, CA) in 0.5 mL ethanol and diluting to appropriate concentrations using fish water.  The concentration of ethanol in all treatments was = 0.05%, and a treatment of 0.05% ethanol was used as a vehicle control.  Fish water served as the negative control.

tag: Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained in the Center for Environmental Biotechnology at the University of Tennessee.  Fish husbandry, spawning, and experimental procedures were conducted with approval from the University of Tennessee Institutional Animal Care and Use Committee (Protocol #1690-1007).  Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added

value: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl.  Embryos were obtained by spawning adult fish with no history of contaminant exposure.  Fertilization of embryos took place at the same time (± 15 min.), such that larvae used in experiments were of similar age at the time of exposure.  All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27± 1 ºC and 14:10h light:dark photoperiod.


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down BCL2 Replicate 1 dyeswap

source_name: cell line MCF7 siRNA BCL2_1-2

tag: construct siRNA BCL2_Replicate1_2


title: Danio_rerio_Larvae_100µgMCLR_rep2

treatment_protocol:
Microcystin Treated Preparation of Exposure Solutions
The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa.  M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined.  Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture).  For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L.
Solutions for microcystin-LR (MC-LR) treatments were prepared by dissolving 1mg of purified MC-LR (Alexis Biochemicals, San Diego, CA) in 0.5 mL ethanol and diluting to appropriate concentrations using fish water.  The concentration of ethanol in all treatments was = 0.05%, and a treatment of 0.05% ethanol was used as a vehicle control.  Fish water served as the negative control.


title: Danio_rerio_Larvae_100µgMCLR_rep3


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down BCL2 Replicate 2 dyeswap

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA BCL2_2-2

tag: construct siRNA BCL2_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down BCL2 Replicate 2

source_name: cell line MCF7 siRNA BCL2_2-1

tag: construct siRNA BCL2_Replicate2_1


title: Danio_rerio_Larvae_Control_EthanolExposure_rep3

treatment_protocol:
Ethanol Treated Preparation of Exposure Solutions
The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa.  M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined.  Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture).  For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L.
Solutions for microcystin-LR (MC-LR) treatments were prepared by dissolving 1mg of purified MC-LR (Alexis Biochemicals, San Diego, CA) in 0.5 mL ethanol and diluting to appropriate concentrations using fish water.  The concentration of ethanol in all treatments was = 0.05%, and a treatment of 0.05% ethanol was used as a vehicle control.  Fish water served as the negative control.


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down CCNG2 Replicate 2 dyeswap

source_name: cell line MCF7 siRNA CCNG2_2-2

tag: construct siRNA CCNG2_Replicate2_2


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT2 Replicate 2

source_name: cell line MCF7 siRNA AKT2_2-1

tag: construct siRNA AKT2_Replicate2_1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down BCL2 Replicate 1

source_name: cell line MCF7 siRNA BCL2_1-1

tag: construct siRNA BCL2_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT1 Replicate 1

source_name: cell line MCF7 siRNA AKT1_1-1

tag: construct siRNA AKT1_Replicate1_1


title: CAS 18

source_name: Weaning rat mammary gland, life-time ingestion of casein based AIN-93G diet

tag: Female Sprague-Dawley rat, postnatal day 21, life-time ingestion of casein based AIN-93G diet


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down AKT1 Replicate 2

source_name: cell line MCF7 siRNA AKT1_2-1

tag: construct siRNA AKT1_Replicate2_1


title: Danio_rerio_Larvae_Control_fishwateronly_rep1

treatment_protocol:
Preparation of Exposure Solutions No Exposure for Fish Water Only Controls
The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa.  M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined.  Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture).  For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L.
Solutions for microcystin-LR (MC-LR) treatments were prepared by dissolving 1mg of purified MC-LR (Alexis Biochemicals, San Diego, CA) in 0.5 mL ethanol and diluting to appropriate concentrations using fish water.  The concentration of ethanol in all treatments was = 0.05%, and a treatment of 0.05% ethanol was used as a vehicle control.  Fish water served as the negative control.


title: Danio_rerio_Larvae_MicrocystisAlgae_rep3


title: SPI 157


title: Danio_rerio_Larvae_Control_fishwateronly_rep2


title: Danio_rerio_Larvae_MicrocystisAlgae_rep1


title: SPI 155


title: PSY3642_to_PSY3639_SC_aerobic

status: Public on Jul 24 2009

city: Boston

first: Caleb

middle: John

last: Kennedy

state: MA

address: 200 Longwood Avenue, WAB 536

department: Systems Biology

institute: Harvard Medical School

hyb_protocol: Described in detail in Casolari, J.M., Brown, C.R., Komili, S., West, J., Hieronymus, H., and Silver, P.A. 2004. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117: 427–439.

scan_protocol: GenePix (see reference above for specific details)

data_processing: Rosetta Resolver, Data were processed in biological triplicate. Note: One sample was processed with the fluorescently labeled nucleotide in the reverse orientation to minimize the effects of incorporation bias.

label: Cy3, Cy5

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: PSY3642, mutant (alt2 fdh1 fdh2 fum1 zwf1)

label_protocol: fluorescent dUTP (Cy3)

extract_protocol: Trizol

tag: SC aerobic

label: Cy5, Cy3

source_name: PSY3639, parent (fdh1 fdh2)

label_protocol: fluorescent dUTP (Cy5)


title: CD32-6h

status: Public on Jul 20 2009

city: Singapore

first: Jayapal

last: Manikandan

country: Singapore

institute: NUS

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
crosslinked CD32-6h

source_name: U937 cell line crosslinked CD32-6h


title: CD-64-2h-Duplicate

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
crosslinked CD64-2h

source_name: U937 cell line crosslinked CD64-2h


title: CAS 7

source_name: Weaning rat mammary gland, life-time expose to casein based AIN-93G diet

tag: Female Sprague-Dawley rat, postnatal day 21, life-time expose to casein based AIN-93G diet


title: CD32-6h-Duplicate

source_name: u937 cell line crosslinked CD32-6h


title: Danio_rerio_Larvae_1000µgMCLR_rep2


title: SPI 149

source_name: Weaning rat mammary gland, life-time expose to soy protein isolate based AIN-93G diet


title: CAS 6


title: Danio_rerio_Larvae_100µgMCLR_rep1


title: Danio_rerio_Larvae_1000µgMCLR_rep1


title: CAS 20

source_name: Weaning rat mammary gland, life-time exposure to casein based AIN-93G diet

tag: Female Sprague-Dawley rat, postnatal day 21, life-time exposure to casein based AIN-93G diet


title: Danio_rerio_Larvae_Control_EthanolExposure_rep2


title: Danio_rerio_Larvae_Control_EthanolExposure_rep1


title: Danio_rerio_Larvae_Control_fishwateronly_rep3


title: CAS 10

source_name: Weaning rat mammary gland, life-time exposures to casein based diet AIN-93G diet

tag: Female Sprague-Dawley rat, postnatal day 21, life-time exposures to casein based diet AIN-93G diet


title: CD64-6h-Duplicate

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
crosslinked CD64-6h

source_name: U937 cell line crosslinked CD64-6h


title: CD64-2h

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
cross linked CD64-2h

source_name: U937 cell line cross linked CD64-2h


title: UNC93B-/-1  NS-8h

status: Public on Jul 15 2009

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: This sample was treated with no stimuli.

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: Illumina BeadStation 500

data_processing: Following background subtraction, the raw signal values extracted with Illumina Beadstudio version 2 software were scaled to the mean intensity of the dataset.

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: Rneasy Kit

tag: Fibroblasts derived from UNC93B-/-deficient patient

tag: Incubation time

value: 8 hours

tag: Primary immune deficiency

value: UNC93B1 Deficiency

tag: This sample was treated with no stimuli


title: CD64-6h


title: CD32-2h- Duplicate

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
cross linked with CD32-2h

source_name: u937 cell line crosslinked with CD32-2h


title: UNC93B-/- 2 IL1B-2h

description: This sample was stimulated  with IL1B

value: 2 hours

tag: This sample was stimulated with IL1B


title: CD32-2h

description:
Human Monocytic cell line(u937) differentiated with IFN gamma-
CD 32 crosslinked for 2 hrs

source_name: u937 cell line crosslinked CD332 for 2 h


title: UNC93B-/- 1 IL1B-2h

description: This sample was stimulated  with IL1B


title: UNC93B-/- 1 TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: UNC93B-/- 1 TNFa-2h

tag: This sample was stimulated with TNF-a


title: UNC93B-/- 1 TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: UNC93B-/- 1 TNFa-8h


title: Control-2

description: Human Monocytic cell line(u937) differentiated with IFN gamma

source_name: Human Monocytic cell line(u937)


title: STAT1-/- NS-8h

source_name: STAT1-/- NS-8h

tag: Fibroblasts derived from STAT1 deficient patient

value: STAT1 Deficiency


title: UNC93B-/- 2 TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: UNC93B-/- 2 TNFa-2h


title: STAT1-/- Poly(I:C)-2h

description: This sample was stimulated  with Poly(I:C)

source_name: STAT1-/- Poly(I:C)-2h


title: Control-1


title: STAT1-/- -NS-2h

source_name: STAT1-/- -NS-2h


title: UNC93B-/- 2 Poly(I:C)-8h

source_name: UNC93B-/- 2 Poly(I:C)-8h

tag: This sample was stimulated with Poly(I:C)


title: UNC93B-/- 2 TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: UNC93B-/- 2 TNFa-8h


title: STAT1-/- IL1B-8h

description: This sample was stimulated  with IL1B

source_name: STAT1-/- IL1B-8h


title: UNC93B-/- 2 Poly(I:C)-2h

source_name: UNC93B-/- 2 Poly(I:C)-2h


title: NEMO-/- TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: NEMO-/- TNFa-8h

tag: Fibroblasts derived from NEMO deficient foetus

value: NEMO Deficiency


title: UNC93B-/- 2 -NS-2h


title: UNC93B-/- 2 IL1B-8h

description: This sample was stimulated  with IL1B


title: NEMO-/- IL1B-2h

description: This sample was stimulated  with IL1B

source_name: NEMO-/- IL1B-2h


title: UNC93B-/- 2 NS-8h


title: UNC93B-/- 1 Poly(I:C)-2h

source_name: UNC93B-/- 1 Poly(I:C)-2h


title: UNC93B-/- 1 IL1B-8h

description: This sample was stimulated  with IL1B


title: STAT1-/- TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: STAT1-/- TNFa-2h


title: UNC93B-/- 1 Poly(I:C)-8h

source_name: UNC93B-/- 1 Poly(I:C)-8h


title: STAT1-/- TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: STAT1-/- TNFa-8h


title: MyD88-/- Poly(I:C)-8h

source_name: MyD88-/- Poly(I:C)-8h

tag: Fibroblasts derived from MyD88 deficient patient

value: MyD88 Deficiency


title: UNC93B-/- 1 -NS-2h


title: IRAK4-/- Poly(I:C)-2h

source_name: IRAK4-/- Poly(I:C)-2h

tag: Fibroblasts derived from IRAK4 deficient patient

value: IRAK4 Deficiency


title: STAT1-/- Poly(I:C)-8h

source_name: STAT1-/- Poly(I:C)-8h


title: STAT1-/- IL1B-2h

description: This sample was stimulated  with IL1B

source_name: STAT1-/- IL1B-2h


title: IRAK4-/--TNFa-2h

description: This sample was stimulated  with TNF-a


title: NEMO-/- IL1B-8h

description: This sample was stimulated  with IL1B

source_name: NEMO-/- IL1B-8h


title: IRAK4-/- NS-2h

source_name: IRAK4-/- NS-2h


title: NEMO-/- -NS-2h

source_name: NEMO-/- -NS-2h


title: NEMO-/- Poly(I:C)-2h

source_name: NEMO-/- Poly(I:C)-2h


title: control 3-TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: control TNFa-8h

tag: Fibroblasts derived from healthy donors


title: IRAK4-/- Poly(I:C)-8h

source_name: IRAK4-/- Poly(I:C)-8h


title: NEMO-/- NS-8h

source_name: NEMO-/- NS-8h


title: MyD88-/- TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: MyD88-/- TNFa-2h


title: NEMO-/- Poly(I:C)-8h

source_name: NEMO-/- Poly(I:C)-8h


title: MyD88-/- TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: MyD88-/- TNFa-8h


title: IRAK4-/- NS-8h

source_name: IRAK4-/- NS-8h


title: NEMO-/- TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: NEMO-/- TNFa-2h


title: MyD88-/- NS-8h


title: MyD88-/- Poly(I:C)-2h

source_name: MyD88-/- Poly(I:C)-2h


title: IRAK4-/- TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: IRAK4-/- TNFa-8h


title: control 3-Poly(I:C)-8h

source_name: control Poly(I:C)-8h


title: MyD88-/- NS-2h


title: control 3-TNFa-2h

description: This sample was stimulated  with TNF-a

source_name: control TNFa-2h


title: control 3-IL1B-8h

description: This sample was stimulated  with IL1B

source_name: control IL1B-8h


title: control 2-Poly(I:C)-8h


title: MyD88-/- IL1B-2h

description: This sample was stimulated  with IL1B


title: control 3-IL1B-2h

description: This sample was stimulated  with IL1B

source_name: control IL1B-2h


title: IRAK4-/- IL1B-8h

description: This sample was stimulated  with IL1B

source_name: IRAK4-/- IL1B-8h


title: control 2-NS-2h

source_name: control NS-2h


title: control 2-TNFa-8h

description: This sample was stimulated  with TNF-a


title: MyD88-/- IL1B-8h

description: This sample was stimulated  with IL1B


title: control 2-TNFa-2h

description: This sample was stimulated  with TNF-a


title: control 3-NS-8h

source_name: control NS-8h


title: IRAK4-/- IL1B-2h

description: This sample was stimulated  with IL1B

source_name: IRAK4-/- IL1B-2h


title: control 3-Poly(I:C)-2h

source_name: control Poly(I:C)-2h


title: control 3-NS-2h


title: Untreated, replicate 2, set 5

city: Baltimore

first: Aik Choon

last: Tan

state: MD

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human 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: Tumor

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

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

tag: Human pancreatic tumor was xenografted in six-week-old female athymic nude mice


title: control 2-Poly(I:C)-2h


title: control 2-IL1B-8h

description: This sample was stimulated  with IL1B


title: Untreated, replicate 2, set 4


title: control 2-NS-8h


title: Untreated, replicate 1, set 5


title: control 1-TNFa-2h

description: This sample was stimulated  with TNF-a


title: Treated set 5


title: control 1-TNFa-8h

description: This sample was stimulated  with TNF-a

source_name: control TNFa-8h


title: Untreated, replicate 1, set 3


title: Untreated, replicate 1, set 4


title: Treated set 4


title: Treated set 3


title: Treated set 2


title: Untreated, replicate 2, set 3


title: Treated set 1


title: Untreated, replicate 1, set 2


title: control 1-Poly(I:C)-8h


title: Untreated, replicate 1, set 1


title: control 1-Poly(I:C)-2h


title: control 2-IL1B-2h

description: This sample was stimulated  with IL1B


title: Untreated, replicate 2, set 1


title: Untreated, replicate 2, set 2


status: Public on Jul 14 2009

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis and Streptococcus gordonii, biological rep4

hyb_protocol: Following fragmentation,  human HG-U133 Plus 2.0 oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).

scan_protocol: GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.

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

source_name: Human Immortalized Gingival Keratinocyte. References: [1] Oda, D., and Watson, E. In Vitro Cell Dev Biol. 1990 Jun;26(6):589-95. PMID: 2358421, [2] Oda, D., Bigler, L., Lee, P., and Blanton, R. Exp Cell Res. 1996 Jul 10;226(1):164-9.PMID: 8660952.

label_protocol: cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted, DNAse-treated, purified and quantified according to standard  methods (Qiagen and Affymetrix).

treatment_protocol: Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.

tag: HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).

tag: HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis and Streptococcus gordonii, biological rep2


title: control 1-NS-8h


title: control 1-NS-2h


title: control 1-IL1B-2h

description: This sample was stimulated  with IL1B


description: Gene expression data from Sham infected HIGK cells, biological rep2

treatment_protocol: HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis, biological rep1


title: MSCs1_2

first: Ivy

last: Ho

address: 11 Hospital Drive

institute: National Cancer Center

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Data obtained are imported into Partek Genomics Suite.  Data were normalized during import using RMA background correction

source_name: MSCs

growth_protocol: Culture in DMEM/F12 with 10% FBS

extract_protocol: Trizol RNA extraction method from Invitrogen

tag: Male.  Hip Arthroplasty


description: Gene expression data from Sham infected HIGK cells, biological rep1


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis, biological rep4


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis and Streptococcus gordonii, biological rep1


description: Gene expression data from HIGK cells infected with Streptococcus gordonii, biological rep3


title: control 1-IL1B-8h

description: This sample was stimulated  with IL1B


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis, biological rep2


description: Gene expression data from HIGK cells infected with Streptococcus gordonii, biological rep2


title: MSCs8_2

scan_protocol: According to standard Affymetrix protocol.

tag: Female, Hip Arthroplasty


description: Gene expression data from HIGK cells infected with Streptococcus gordonii, biological rep4


description: Gene expression data from Sham infected HIGK cells, biological rep4


title: MSCs8_1

label_protocol: According to standard Affymetrix protocol.


description: Gene expression data from Sham infected HIGK cells, biological rep3


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis and Streptococcus gordonii, biological rep3


title: MSCs9_4


description: Gene expression data from HIGK cells infected with Porphyromonas gingivalis, biological rep3


title: MSCs2

tag: Femal, Hip arthroplasty


title: MSCs1


title: MSCs1_1


title: Sprague Dawley rat, Carcinogenic treatment and celecoxib initiation protocol, replicate 1

status: Public on Jul 10 2009

city: Mexico

first: Adriana

last: Marquez-Quiñones

state: DF

address: AV. Instituto Politecnico Nacional No. 2508

department: Cell Biology

country: Mexico

institute: CINVESTAV

description:
Animals were subjected to carcinogenic treatment plus celecoxib since initiation cancer stage.
Normal rats are animals that did not receive none treatment and just were fed a standard 5001 diet.

hyb_protocol: 8h at 42ºC in the automatic hybridization machine discovery from Ventana. After hybridization, slides were washed twice in Ribowash buffer for 5 minutes with agitation and then once with 0.1xSSC buffer.

scan_protocol: Scanning with Genepix 400A microarray scanner (Axon instruments). Image analysis was made by Genepix Pro V6 software, each spot was evaluated and selectioned to be analyzed by Bioplot software.

data_processing: Background subtraction with lowess allowed value 10, log transformation and LOWESS normalization.

source_name: Total RNA from Sprague Dawley rat liver, carcinogenic and celecoxib treatment since initiation stage until sacrifice, labeled with Cyanine-3.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm.

growth_protocol: Animals were fed ad libitum with 5001 diet and housed in a controlled environment with a 12-h light/dark cycle and a temperature of 23°C until sacrifice. Under Institutional Animal Care and Use Committee Guidelines.

extract_protocol: Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNAlater and stored at -80ºC. Isolation of total RNA from liver samples was following the instructions for Quagen Rneasy mini kit. Quality and quantity were determined by capillary electrophoresis (RNA 6000 nano assay, Agilent)

treatment_protocol: Carcinogenic treatment, the rats were initiated with an intraperitoneal injection of 200 mg/kg of body weight of diethylnitrosamine and 7 days later, 2-acetylaminofluorene was orally administered at 20 mg/kg doses for 3 consecutive days before partial hepatectomy, starting from 6 weeks old until sacrifice at 25 days post-hepatocarcinogenesis initiation. Celecoxib was administrated at 1500 ppm mixed in the 5001 diet. The administration was given since a week before until 25 days after of cancer initiation, a total of 32 days of treatment.

tag: Strain

value: Sprague Dawley

tag: Gender

value: Male

tag: Age

value: 9 weeks old

tag: Treatment

value: Carcinogenic treatment plus celecoxib since a week before initiation stage.

tag: Tissue

value: liver

source_name: Total RNA from Sprague Dawley rat liver, normal liver, labeled with Cyanine-5.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm.

growth_protocol: Animals were fed ad libitum with 5001 diet and housed in a controlled environment with a 12-h light/dark cycle and a temperature of 23°C until sacrifice. Under Institutional Animal Care and Use Commitee Guidlines.

treatment_protocol: None.


title: Sprague Dawley rat, Carcinogenic treatment plus celecoxib progression protocol, replicate 2

description:
Animals were subjected to carcinogenic treatment plus celecoxib in progression cancer stage.
Normal rats are animals that did not receive none treatment and just were fed a standard 5001 diet.

source_name: Total RNA from Sprague Dawley rat liver subjected to carcinogenic treatment plus celecoxib in progression stage, labeled with Cyanine-5.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm.

treatment_protocol: Carcinogenic treatment, the rats were initiated with an intraperitoneal injection of 200 mg/kg of body weight of diethylnitrosamine and 7 days later, 2-acetylaminofluorene was orally administered at 20 mg/kg doses for 3 consecutive days before partial hepatectomy, starting from 6 weeks old until sacrifice at 25 days post-hepatocarcinogenesis initiation. Celecoxib was administrated at 1500 ppm mixed in the 5001 diet, between days 18 and 25 post-cancer initiation, a total of 8 days of treatment, when well established preneoplastic lesions starts to appear.

value: Carcinogenic treatment plus celecoxib in progression stage

source_name: Total RNA from Sprague Dawley rat liver, normal liver, labeled with Cyanine-3.

label_protocol: Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm.


title: Sprague Dawley rat, Carcinogenic treatment and celecoxib initiation protocol, replicate 2

source_name: Total RNA from Sprague Dawley rat liver, carcinogenic and celecoxib treatment since initiation stage until sacrifice, labeled with Cyanine-5.


title: 5339-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)

status: Public on Jul 07 2009

city: Paris

first: Jean-Louis

last: Laplanche

address: 4 avenue de l'Observatoire

department: Biologie Cellulaire

country: France

institute: Faculté de Pharmacie Université Paris5

description:
To identify genes implied in prion diseases, we chose the N2a58 subline of neuroblastoma cell line. The cells were infected with the 22L prion strain. Total RNA was extracted using the Qiagen RNeasy kit (Qiagen). All RNA samples were treated with RNase-free DNA I (Qiagen). The quality and quantity were initially estimated on the bioanalyzer (Agilent) and quantity of total RNA were confirmed on Nanodrop spectrophotometer. 1 µg of total RNA was amplified using MessageAmp aRNA kit (Ambion). 2 µg of amplified RNA were processed for microarray analysis. Double-strand cDNA was obtained by the reverse transcription using CyScript reverse transcriptase according to the manufacturer specifications (GE Healthcare).
Incorporation of a nucleotide containing an alkyl amino group (AA-dNTP) allowed post-reverse transcription conjugation of the fluorescence dyes. The reaction was blocked by hydroxylamine hydrochloride. Cy-3 and Cy-5 containing probes were combined and purified.
For each sample, the cDNA of the infected or not infected cells were labeled using the green fluorescence dye (Cy3) and the reference cDNA using the red-fluorescent dye (Cy5).
The same amount of cells and reference cDNA was used for the experiment. Cy-3 and Cy-5 containing probes were dried down and resuspended in 100 µl H2O nuclease free and denaturated for 3 min at 98°C. The hybridization was performed on the mouse developmental array (G4120A, Agilent) in hybridization buffer (Agilent) at 60°C for 17 hours. The slides were then washed 10 min in 6X SSC, 0.005% TritonX-102, then 5 min in 0.1X SSC, 0.005% TritonX-102 on ice. Slides were dried under filtered nitrogen flow.

hyb_protocol: cDNAs coupled to cyanines were hybridised on the mouse developmental array (G4120A, Agilent) in hybridization buffer (Agilent) at 60°C for 17 hours. The slides were then washed 10 min in 6X SSC, 0.005% TritonX-102, then 5 min in 0.1X SSC, 0.005% TritonX-102 on ice.

scan_protocol: Slides were Slides were dried under filtered nitrogen flow then scanned using a GMS418 scanner (Affymetrix) at adequate laser power.

data_processing: Slides were scanned for both Cy3 and Cy5 with a GMS418 scanner (Affymetrix) and images were processed by ImaGene software (BioDiscovery).

label_protocol: One µg of total RNA N2a5822L was taken and linearly amplified (MessageAMP aRNA kit, Ambion). Two micrograms of amplified RNA were used as a template for oligo(dT)-primed reverse transcription and incorporation of aminoallyl-dUTP into the cDNA, then coupled to cyanine 3 (CyScribe Post-Labelling kit, GE Healthcare).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen) then treated with RNase-free DNA I (Qiagen).

tag: Neuroblastoma cells stably transfected with Prnp and infected with 22L prion strain

source_name: Mouse Universal Reference Total RNA, Clontech

label_protocol: One µg of Mouse Universal Reference Total RNA (Clontech) was taken and linearly amplified (MessageAMP aRNA kit, Ambion). Two micrograms of amplified RNA were used as a template for oligo(dT)-primed reverse transcription and incorporation of aminoallyl-dUTP into the cDNA, then coupled to cyanine 5 (CyScribe Post-Labelling kit, GE Healthcare).

extract_protocol: Commercial mouse total RNA.

tag: Commercial mouse total RNA


title: Sprague Dawley rat, Carcinogenic treatment plus celecoxib progression protocol, replicate 3

source_name: Total RNA from Sprague Dawley rat liver subjected to carcinogenic treatment plus celecoxib in progression stage, labeled with Cyanine-3.


title: Sprague Dawley rat, Carcinogenic treatment, replicate 4

description:
Carcinogenic protocol is an efficient treatment to induce cancer in rat liver in a short time period.
Normal rats are animals that did not receive none treatment and just were fed a standard 5001 diet.

source_name: Total RNA from Sprague Dawley rat liver, carcinogenic treatment, labeled with Cyanine-3

treatment_protocol: Carcinogenic treatment, the rats were initiated with an intraperitoneal injection of 200 mg/kg of body weight of diethylnitrosamine and 7 days later, 2-acetylaminofluorene was orally administered at 20 mg/kg doses for 3 consecutive days before partial hepatectomy, starting from 6 weeks old until sacrifice at 25 days post-hepatocarcinogenesis initiation.

value: Carcinogenic Treatment


title: Sprague Dawley rat, Carcinogenic treatment plus celecoxib progression protocol, replicate 1


title: Sprague Dawley rat, Carcinogenic treatment and celecoxib initiation protocol, replicate 4


title: 2155-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


description: Gene expression data from HIGK cells infected with Streptococcus gordonii, biological rep1


title: Sprague Dawley rat, Carcinogenic treatment, replicate 2


title: 5341-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: 5358-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: Sprague Dawley rat, Carcinogenic treatment, replicate 1

source_name: Total RNA from Sprague Dawley rat liver, carcinogenic treatment, labeled with Cyanine-5


title: 5360-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: 5362-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: 5342-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)

label_protocol: One µg of total RNA N2a58 was taken and linearly amplified (MessageAMP aRNA kit, Ambion). Two micrograms of amplified RNA were used as a template for oligo(dT)-primed reverse transcription and incorporation of aminoallyl-dUTP into the cDNA, then coupled to cyanine 3 (CyScribe Post-Labelling kit, GE Healthcare).

tag: Neuroblastoma cells stably transfected with Prnp


title: 5361-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: Sprague Dawley rat, Carcinogenic treatment and celecoxib initiation protocol, replicate 3


title: MSCs9_3

tag: Female.  Hip Arthroplasty


title: 2153-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: MSCs2_1

tag: Female.  Hip arthroplasty


title: MSCs8


title: 2159-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: MSCs2_2


title: Sprague Dawley rat, Carcinogenic treatment, replicate 3


title: Sprague Dawley rat, Carcinogenic treatment plus celecoxib progression protocol, replicate 4


title: 5359-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: MSCs9


title: 2157-N2a5822L vs. Mouse Universal Reference Total RNA (Clontech)


title: 5340-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: Wild Type Keratinocyte vs CHUK-LoxP Mutant Keratinocyte_rep2

city: Smithville

first: Yinling

last: Hu

address: 1808 Park Road 1C

department: Carcinogenesis

institute: UT M.D.Andreson Cancer Center

description: The current analysis was carried out to study the changes in the gene expression profiles of CHUK gene deleted mouse keratinocytes compared to wild type mouse keratinocytes

hyb_protocol: Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

scan_protocol: Scanning and data acquisitions were performed using Agilent scanner and feature extraction protocol GE2-v5-95 (available at www.agilent.com)

data_processing: The data was acquired using Agilent's feature extraction protocol GE2-v5_95 with inbuilt Lowess normalization feature and Log10ratio algorithms, for details visit www.agilent.com

source_name: Wild Type Keratinocytes

label_protocol: Labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF

extract_protocol: Total RNA was extracted from wild type mouse keratinocytes using RNAeasy RNA purification kit (Qiagen, Valencia, CA).

tag: Wild Type Keratinocytes

source_name: CHUK-LoxP Mutant Keratinocytes

tag: CHUK gene deleted mouse keratinocytes


title: 5338-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: Neural crest cells vs Boundary cap cells biological replicate 2

status: Public on Jul 03 2009

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

description: Biological replicate two of two.

hyb_protocol: Microarrays were pre-hybridized during 1 hour at 42¡C in 5x SSC, 0.1% SDS, 1% BSA, washed with distilled water and dried. They were hybridized overnight at 42¡C in 25% formamide, 5x SSC, 0.1%SDS with Cy5- and Cy3-labelled cDNA, washed in 1x SSC, 0.2% SDS at 42¡C, in 0.1x SSC, 0.2% SDS and two times in 0.1x SSC at room temperature and finally were spin-dried.

scan_protocol: The hybridized microarrays were scanned using Genepix 4000B (Axon) and the resulting image files analyzed by GenePix Pro 6.0 software (Axon).

data_processing: Spots flagged by the GenePix software and saturating spots, where the median foreground intensity is greater than 60,000 in one of the two channels, were discarded from the result files. The data were normalized using Goulphar (Lemoine et al.,2006) applying a global Lowess correction followed by a print-tip median normalization step.

source_name: Boudary cap cell pool 2.

label_protocol: The labelling of the RNA (2-5 ug) was carried out by incorporation of amino-allyl dUTP.

extract_protocol: Total RNA was extracted from the different purified cell populations using  the RNAqueous-Micro kit (Ambion). The quality of the RNA was estimated using a Bioanalyser 2100 (Agilent). When required, amplification of the RNA (500 ng) was performed using the Amino Allyl MessageAmp aRNA kit (Ambion).

tag: Boudary cap cells were isolated from Krox20GFP(DT) heterozygous embryos at E12.5. The appropriate embryos were identified by GFP or YFP expression under fluorescent stereomicroscope (Leica, Nussloch, Germany) and head and viscera were eliminated. For boudary cap cell preparation, the meninges, carrying the nerve roots and dorsal root ganglion, were dissected from the neural tube from cervical to lumbo-sacral levels. Meninges from 3-5 litters were pooled and incubated at 37¡C for 20 min in 1 ml of HBSS (Sigma) with 0.05% trypsin (Invitrogen) and 3 mg/ml collagenase type III (Sigma). The digestion was stopped by addition of 0.1 ml of fetal calf serum (FCS), the material was washed 3 times with PBS, triturated, centrifuged at 200 g for 5 min, resuspended in HBSS and passed through nylon mesh of 20 µm pore diameter (Falcon) to get a single cell suspension. FACS was performed with a vantage flow cytometer (Becton-Dickinson, Mountain View, CA). Cells (1-2 x 106/ml) were analyzed for forward scatter, side scatter and GFP fluorescence with an argon laser (488 nm excitation, 520 nm emission). Dead cells and doublets were excluded by gating on forward and side scatter. GFP expressing cells were directly collected in the lysis buffer (Ambion) and stored at -20¡C until use.

source_name: Neural crest cells pool 2.

tag: Neural crest cells were isolated from HtPACre, Rosa26YFP E9.5 embryos. The appropriate embryos were identified by GFP or YFP expression under fluorescent stereomicroscope (Leica, Nussloch, Germany) and head and viscera were eliminated. For neural crest cells preparation, the whole trunk was dissected and subjected to cell dissociation and FACS sorting by using the same procedure as described for BC cells.


title: 2151-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: Schwann cell precursors vs Boundary cap cells biological replicate 1 dye swap

description: Biological replicate one of two.

source_name: Boudary cap cell pool 3.

source_name: Schwann cell precursors pool 1.

tag: Primary Schwann precursor cell cultures were obtained from E12.5 mouse embryos using a modification of a previously described protocol (Manent et al., 2003). Briefly, mouse embryo carcasses were dissected by decapitation and evisceration and trypsinized at 37¡C for 30 min. Dissociated cells were homogenized through a narrowed Pasteur pipette before centrifugation and resuspension in PM medium (DMEM, 10% FCS, 2 mM Forskolin, 10 ng/ml heregulin-b1 (HRG-§1, R&D Systems), 50 mg/ml Gentamycin, 2.5 µg/ml Fungizone. Cells were plated on PLL/laminin coated dishes (Sigma). After 48-72 h in culture, the cells were trypsinized and SCpr were sorted by an indirect magnetic cell sorting protocol based on SCpr specific expression of p75LNGFR (Manent et al., 2003). After sorting, p75-positive cells were replated in N2 medium (DMEM:F12 (1:1) supplemented with N2 complement, 2 mM Forskolin, 10 ng/ml HRG-§1 (R&D Systems), 50 mg/ml Gentamycin, 2.5 µg/ml Fungizone) on PLL/laminin coated dishes. Purity of the SCpr culture was assessed by immunofluorescence with antibodies against p75LNGFR (Chemicon).


title: Wild Type Keratinocyte vs CHUK-LoxP Mutant Keratinocyte_rep1

source_name: Wild Type Keratinocyte

tag: Wild type keratinocytes

source_name: CHUK-LoxP Mutant Keratinocyte


title: 2156-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)

tag: N2a58Neuroblastoma cells stably transfected with Prnp


title: 2158-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)


title: Day 1 control pool vs. Day 1 #6-500ppm

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Immediately after the cessation of COS exposure on the appropriate day of sacrifice (day 1 or day 2) the rats were deeply anesthetized with intraperitoneal sodium pentobarbital. The posterior colliculi were surgically exposed and removed using a pair of corneal scissors and fine forceps. The samples were immediately placed in RNase-free plastic vials and snap frozen in liquid nitrogen.  Three control animals (non-exposed) were processed identically. Total RNAs from frozen brain tissue (posterior colliculus) were isolated with an RNeasy tissue kit (Qiagen, Valencia, CA) according to the manufacturer's protocols. Gene expression analysis was conducted using Agilent Rat Oligo Microarrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Two arrays were utilized for each comparison allowing for dye reversals.  Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

source_name: Day 1 control pool

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNAs from frozen brain tissue (posterior colliculus) were isolated with an RNeasy tissue kit (Qiagen, Valencia, CA) according to the manufacturer's protocols. The quality and integrity of the RNA was verified by 260/280 nm absorbance ratio, formaldehyde agarose gel electrophoresis and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: Strain

value: Fischer 344, Gender:Male, Age:8-9 weeks, Exposure:filtered, conditioned air

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

value: Fischer 344, Gender:Male, Age:8-9 weeks, Exposure:inhalation of 500 ppm of COS, 6 hours per day for 2 consecutive days


title: Day 1 #19-500ppm vs. Day 1 control pool

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

data_processing: Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).


title: Schwann cell precursors vs Boundary cap cells biological replicate 2

description: Biological replicate two of two.

source_name: Boudary cap cell pool 4.

source_name: Schwann cell precursors pool 2.


title: Neural crest cells vs Boundary cap cells biological replicate 2 dye swap

description: Biological replicate two of two.


title: Day 1 #16-500ppm vs. Day 1 control pool


title: Day 0 #3-500ppm vs. Day 0 control pool

value: Fischer 344, Gender:Male, Age:8-9 weeks, Exposure:inhalation of 500 ppm of COS, 6 hours per day for 1 consecutive day

source_name: Day 0 control pool


title: Day 1 #6-500ppm vs. Day 1 control pool


title: Day 0 control pool vs. Day 0 #3-500ppm


title: Day 1 control pool vs. Day 1 #19-500ppm


title: Schwann cell precursors vs Boundary cap cells biological replicate 2 dye swap

description: Biological replicate two of two.


title: Day 0 control pool vs. Day 0 #9-500ppm


title: Neural crest cells vs Boundary cap cells biological replicate 1 dye swap

description: Biological replicate one of two.

source_name: Boudary cap cell pool 1.

source_name: Neural crest cells pool 1.


title: Day 0 #9-500ppm vs. Day 0 control pool


title: Schwann cell precursors vs Boundary cap cells biological replicate 1

description: Biological replicate one of two.


title: Neural crest cells vs Boundary cap cells biological replicate 1

description: Biological replicate one of two.


title: Day 0 #2-500ppm vs. Day 0 control pool


title: Day 0 control pool vs. Day 0 #2-500ppm


title: Day 1 control pool vs. Day 1 #16-500ppm


title: stageII colorectal cancer patient5 with distant recurrence in validation phase

status: Public on Jul 02 2009

city: Suita

first: masakazu

last: miyake

state: Osaka

address: Yamadaoka 2-2

department: Gastroenterological Surgery

country: Japan

institute: Graduate School of Medicine, Osaka University

description: no additional information

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.

source_name: 40 Total RNA mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

treatment_protocol: no treatment

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageII patient with distant recurrence labeled with Cyanine-5 (red).

extract_protocol:
Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.
Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

value: stageII colorectal cancer with distant recurrence


title: stageII colorectal cancer patient4 with distant recurrence in validation phase

description: no additional information

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.


title: stageII colorectal cancer patient1 with distant recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient6 with distant recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient22 with no recurrence in validation phase

description: no additional information

source_name: Total RNA from primary colorectal cancer of stageII patient with no recurrence labeled with Cyanine-5 (red).

value: stageII colorectal cancer with no recurrence


title: stageII colorectal cancer patient3 with distant recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient17 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient7 with distant recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient21 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient16 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient18 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient20 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient6 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient13 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient14 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient2 with distant recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient23 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient19 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient8 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient5 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient10 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient7 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient3 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient4 with no recurrence in validation phase

description: no additional information


title: 2154-N2a58 vs. Mouse Universal Reference Total RNA (Clontech)

source_name: Mouse Universal Reference Total RNA, Clontech


title: stageII colorectal cancer patient9 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient15 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient11 with no recurrence in validation phase

description: no additional information


title: stageII colorectal cancer patient2 with no recurrence in validation phase

description: no additional information


title: stageIII colorectal cancer patient35 with distant recurrence in discovery phase

description: no additional information

source_name: Total RNA from primary colorectal cancer of stageIII patient with distant recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with distant recurrence


title: stageIII colorectal cancer patient36 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient27 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient37 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient28 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient1 with no recurrence in validation phase

description: no additional information


title: stageIII colorectal cancer patient24 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient30 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient26 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient33 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient32 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient29 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient23 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient25 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient34 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient20 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient17 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient22 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient21 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient31 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient16 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient19 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient18 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient14 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient13 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient15 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient12 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient11 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient6 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient24 with no recurrence in discovery phase

description: no additional information

source_name: Total RNA from primary colorectal cancer of stageIII patient with no recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with no recurrence


title: stageIII colorectal cancer patient27 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient8 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient20 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient28 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient1 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient3 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient19 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient2 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient7 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient21 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient4 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient30 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient15 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient18 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient22 with no recurrence in discovery phase

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title: stageIII colorectal cancer patient9 with distant recurrence in discovery phase

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title: stageIII colorectal cancer patient25 with no recurrence in discovery phase

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title: stageIII colorectal cancer patient31 with no recurrence in discovery phase

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title: stageIII colorectal cancer patient26 with no recurrence in discovery phase

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title: stageIII colorectal cancer patient5 with distant recurrence in discovery phase

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title: stageIII colorectal cancer patient16 with no recurrence in discovery phase

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title: stageIII colorectal cancer patient29 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient17 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient23 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient10 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient13 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient14 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient12 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient9 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient7 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient22 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient4 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient15 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient16 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient8 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient6 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient17 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient2 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient20 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient10 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient14 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient9 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient19 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient21 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient11 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient5 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient10 with no recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient3 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient12 with distant recurrence in discovery phase

description: no additional information


title: stageIII colorectal cancer patient1 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient11 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient18 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient13 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient8 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient7 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient4 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient5 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient39 with no recurrence in discovery phase

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title: stageII colorectal cancer patient38 with no recurrence in discovery phase

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title: stageII colorectal cancer patient37 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient1 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient3 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient31 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient36 with no recurrence in discovery phase

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title: stageII colorectal cancer patient30 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient6 with distant recurrence in discovery phase

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title: stageII colorectal cancer patient24 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient35 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient34 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient29 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient21 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient32 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient22 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient33 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient19 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient26 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient27 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient18 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient20 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient28 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient23 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient2 with distant recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient17 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient25 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient15 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient14 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient16 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient13 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient10 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient11 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient12 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient8 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient9 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient4 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient2 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient6 with no recurrence in discovery phase

description: no additional information


title: stageII colorectal cancer patient7 with no recurrence in discovery phase

description: no additional information


title: Gastroc m. Drug Treatment 7 Days Dex 2

status: Public on Jul 01 2009

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

description: dexamethasone

hyb_protocol: Standard Affymetrix protocol for the rat 230-2 array.

data_processing:
Normalization, initial filtering, and determination of significant changes in expression were performed using BRB Array tools v 3.6
Data for each array were normalized using the median for the entire array; expression values were set to 10 if below this value, and excluded from further analysis if more than 20% of the values were at least 1.5-fold greater or smaller than the median for that probe set.

source_name: gastrocnemius muscle

extract_protocol: Muscle (20 mg) was homogenized in guanidine isothiocyanate buffer using a polytron.  Total RNA was extracted using phenol chloroform then cleaned up using RNA easy columgs.

treatment_protocol: Male Wistar rats (250 g) were administered vehicle (propylene glycol), dexamethasone (0.7 mg/kg/day), or dexamethasone plus testosterone (28 mg/kg/day) for 7 days using Alzet pumps.

tag: male Wistar-Hannover rat approx 250 g


title: stageII colorectal cancer patient3 with no recurrence in discovery phase

description: no additional information