title: siRNA_XBP1_DKFZ_Replicate2_dyeswap

status: Public on Jan 29 2009

type: RNA

city: Heidelberg

first: Mark

last: Fellmann

address: INF 580

department: Molecular Genome Analysis

country: Germany

institute: DKFZ

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down XBP1
siRNA_XBP1_DKFZ_Replicate2_dyeswap

hyb_protocol: ch1 and ch2 together are solved in 50 ?l 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x DenhardtÆs solution and 2 ng/?l 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 26629 cDNA clones were given in the data table

molecule: total RNA

organism: Homo sapiens

source_name: cell line MCF7 siRNA _non-silencing_control_4

label_protocol: direct fluorescent labelling of 2 ?g amplified RNA, anneling of 0.5?g 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 ?g/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 ?g/ml insulin bovine

extract_protocol: total RNA was extracted using Rneasy mini-prep kit (Qiagen, Hilden, Germany; 2?g 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 non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA XBP1_2-2

label_protocol: direct fluorescent labelling of 2 ?g amplified RNA, anneling of 0.5?g 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 siRNA XBP1_Replicate2_2


title: siRNA_STC2_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate1

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: siRNA_XBP1_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down XBP1
siRNA_XBP1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA XBP1_1-2

tag: construct siRNA XBP1_Replicate1_2


title: siRNA_STC2_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA STC2_2-2

tag: construct siRNA STC2_Replicate2_2


title: siRNA_HSPB8_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down HSPB8
siRNA_HSPB8_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA HSPB8_2-2

tag: construct siRNA HSPB8_Replicate2_2


title: siRNA_HSPB8_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down HSPB8
siRNA_HSPB8_DKFZ_Replicate2

source_name: cell line MCF7 siRNA HSPB8_2-1

tag: construct siRNA HSPB8_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: siRNA_XBP1_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down XBP1
siRNA_XBP1_DKFZ_Replicate2

source_name: cell line MCF7 siRNA XBP1_2-1

tag: construct siRNA XBP1_Replicate2_1


title: siRNA_STC2_DKFZ_Replicate3_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate3_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: siRNA_STC2_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate2

source_name: cell line MCF7 siRNA STC2_2-1

tag: construct siRNA STC2_Replicate2_1


title: siRNA_STC2_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA STC2_1-2

tag: construct siRNA STC2_Replicate1_2


title: siRNA_STC2_DKFZ_Replicate3

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down STC2
siRNA_STC2_DKFZ_Replicate3

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: siRNA_LOC120224_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down LOC120224
siRNA_LOC120224_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA LOC120224_2-2

tag: construct siRNA LOC120224_Replicate2_2


title: siRNA_HSPB8_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down HSPB8
siRNA_HSPB8_DKFZ_Replicate1

source_name: cell line MCF7 siRNA HSPB8_1-1

tag: construct siRNA HSPB8_Replicate1_1


title: siRNA_GDF15_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate1

source_name: cell line MCF7 siRNA GDF15_1-1

tag: construct siRNA GDF15_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: siRNA_GDF15_DKFZ_Replicate4_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate4_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_8

tag: construct non-silencing control siRNA_Replicate8

source_name: cell line MCF7 siRNA GDF15_4-2

tag: construct siRNA GDF15_Replicate4_2


title: siRNA_FOXA1_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down FOXA1
siRNA_FOXA1_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA FOXA1_2-2

tag: construct siRNA FOXA1_Replicate2_2


title: siRNA_LOC120224_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down LOC120224
siRNA_LOC120224_DKFZ_Replicate1

source_name: cell line MCF7 siRNA LOC120224_1-1

tag: construct siRNA LOC120224_Replicate1_1


title: siRNA_LOC120224_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down LOC120224
siRNA_LOC120224_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA LOC120224_1-2

tag: construct siRNA LOC120224_Replicate1_2


title: siRNA_FOXA1_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down FOXA1
siRNA_FOXA1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA FOXA1_1-2

tag: construct siRNA FOXA1_Replicate1_2


title: siRNA_HSPB8_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down HSPB8
siRNA_HSPB8_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA HSPB8_1-2

tag: construct siRNA HSPB8_Replicate1_2


title: siRNA_GDF15_DKFZ_Replicate4

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate4

source_name: cell line MCF7 siRNA GDF15_4-1

tag: construct siRNA GDF15_Replicate4_1

source_name: cell line MCF7 siRNA _non-silencing_control_7

tag: construct non-silencing control siRNA_Replicate7


title: siRNA_GDF15_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate2

source_name: cell line MCF7 siRNA GDF15_2-1

tag: construct siRNA GDF15_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: siRNA_GPR30_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GPR30
siRNA_GPR30_DKFZ_Replicate2

source_name: cell line MCF7 siRNA GPR30_2-1

tag: construct siRNA GPR30_Replicate2_1


title: siRNA_GPR30_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GPR30
siRNA_GPR30_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA GPR30_2-2

tag: construct siRNA GPR30_Replicate2_2


title: siRNA_ESR1_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down ESR1
siRNA_ESR1_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA ESR1_2-2

tag: construct siRNA ESR1_Replicate2_2


title: siRNA_GDF15_DKFZ_Replicate3

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate3

source_name: cell line MCF7 siRNA GDF15_3-1

tag: construct siRNA GDF15_Replicate3_1

source_name: cell line MCF7 siRNA _non-silencing_control_5

tag: construct non-silencing control siRNA_Replicate5


title: siRNA_GDF15_DKFZ_Replicate3_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate3_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_6

tag: construct non-silencing control siRNA_Replicate6

source_name: cell line MCF7 siRNA GDF15_3-2

tag: construct siRNA GDF15_Replicate3_2


title: siRNA_DDR1_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down DDR1
siRNA_DDR1_DKFZ_Replicate1

source_name: cell line MCF7 siRNA DDR1_1-1

tag: construct siRNA DDR1_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: siRNA_FOXA1_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down FOXA1
siRNA_FOXA1_DKFZ_Replicate2

source_name: cell line MCF7 siRNA FOXA1_2-1

tag: construct siRNA FOXA1_Replicate2_1


title: siRNA_DDR1_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down DDR1
siRNA_DDR1_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA DDR1_2-2

tag: construct siRNA DDR1_Replicate2_2


title: siRNA_GDF15_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA GDF15_1-2

tag: construct siRNA GDF15_Replicate1_2


title: siRNA_GDF15_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GDF15
siRNA_GDF15_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA GDF15_2-2

tag: construct siRNA GDF15_Replicate2_2


title: siRNA_GPR30_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GPR30
siRNA_GPR30_DKFZ_Replicate1

source_name: cell line MCF7 siRNA GPR30_1-1

tag: construct siRNA GPR30_Replicate1_1


title: siRNA_FOXA1_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down FOXA1
siRNA_FOXA1_DKFZ_Replicate1

source_name: cell line MCF7 siRNA FOXA1_1-1

tag: construct siRNA FOXA1_Replicate1_1


title: siRNA_BCL2_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down BCL2
siRNA_BCL2_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA BCL2_1-2

tag: construct siRNA BCL2_Replicate1_2


title: siRNA_CCNG2_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA CCNG2_1-2

tag: construct siRNA CCNG2_Replicate1_2


title: siRNA_ESR1_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down ESR1
siRNA_ESR1_DKFZ_Replicate1

source_name: cell line MCF7 siRNA ESR1_1-1

tag: construct siRNA ESR1_Replicate1_1


title: siRNA_ESR1_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down ESR1
siRNA_ESR1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA ESR1_1-2

tag: construct siRNA ESR1_Replicate1_2


title: siRNA_ESR1_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down ESR1
siRNA_ESR1_DKFZ_Replicate2

source_name: cell line MCF7 siRNA ESR1_2-1

tag: construct siRNA ESR1_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: siRNA_DDR1_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down DDR1
siRNA_DDR1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA DDR1_1-2

tag: construct siRNA DDR1_Replicate1_2


title: siRNA_AKT2_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT2
siRNA_AKT2_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA AKT2_2-2

tag: construct siRNA AKT2_Replicate2_2


title: siRNA_DDR1_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down DDR1
siRNA_DDR1_DKFZ_Replicate2

source_name: cell line MCF7 siRNA DDR1_2-1

tag: construct siRNA DDR1_Replicate2_1


title: siRNA_AKT1_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT1
siRNA_AKT1_DKFZ_Replicate2

source_name: cell line MCF7 siRNA AKT1_2-1

tag: construct siRNA AKT1_Replicate2_1


title: siRNA_CCNG2_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA CCNG2_2-2

tag: construct siRNA CCNG2_Replicate2_2


title: siRNA_AKT2_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT2
siRNA_AKT2_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA AKT2_1-2

tag: construct siRNA AKT2_Replicate1_2


title: siRNA_CCNG2_DKFZ_Replicate3_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate3_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: siRNA_AKT2_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT2
siRNA_AKT2_DKFZ_Replicate1

source_name: cell line MCF7 siRNA AKT2_1-1

tag: construct siRNA AKT2_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: siRNA_XBP1_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down XBP1
siRNA_XBP1_DKFZ_Replicate1

source_name: cell line MCF7 siRNA XBP1_1-1

tag: construct siRNA XBP1_Replicate1_1


title: siRNA_BCL2_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down BCL2
siRNA_BCL2_DKFZ_Replicate2

source_name: cell line MCF7 siRNA BCL2_2-1

tag: construct siRNA BCL2_Replicate2_1


title: siRNA_BCL2_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down BCL2
siRNA_BCL2_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA BCL2_2-2

tag: construct siRNA BCL2_Replicate2_2


title: siRNA_CCNG2_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate2

source_name: cell line MCF7 siRNA CCNG2_2-1

tag: construct siRNA CCNG2_Replicate2_1


title: siRNA_BCL2_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down BCL2
siRNA_BCL2_DKFZ_Replicate1

source_name: cell line MCF7 siRNA BCL2_1-1

tag: construct siRNA BCL2_Replicate1_1


title: siRNA_CCNG2_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate1

source_name: cell line MCF7 siRNA CCNG2_1-1

tag: construct siRNA CCNG2_Replicate1_1


title: siRNA_AKT2_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT2
siRNA_AKT2_DKFZ_Replicate2

source_name: cell line MCF7 siRNA AKT2_2-1

tag: construct siRNA AKT2_Replicate2_1

source_name: cell line MCF7 siRNA _non-silencing_control_3

tag: construct non-silencing control siRNA_Replicate3


title: SloR mutant, experiment E

status: Public on Jan 18 2009

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

country: USA

institute: University of Vermont

description: SloR mutant, experiment E

hyb_protocol: Samples were applied to Affymetrix Gene Chip at 45C for 16 hr.

scan_protocol: Biotinylated anti-streptavadin antibodies were used to amplify the signal. Probe arrays were scanned using a Hewlett-Packard Gene Array Scanner (Agilent Technologies).

data_processing: RMA

label: Biotin

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans UA159 SloR mutant, experiment E

label_protocol: RNA samples were amplified using a Two-Cycle cDNA Synthesis Kit according to the manufacturerÕs instructions (Affymetrix, Santa Clara, CA). Following second cycle, second strand cDNA synthesis, and cleanup, biotinylated-cRNA was prepared by in vitro transcription, fragmented and labeled using a streptavadin-phycoerythrin conjugate.

growth_protocol: Grown in semi-defined medium

extract_protocol: Cells resuspended in TRI Reagent (Ambion) were disrupted in BIO101 FastPrep machine.  Ethanol-precipitated nucleic acid was DNAse treated on an RNAeasy column according to the recommendation of the supplier (Qiagen).

treatment_protocol: semi-defined medium ~ 2micromolar MnCl2 via ICP

tag: mid-log planktonic


title: High Mn, experiment B

description: High Mn, experiment B

source_name: Streptococcus mutans UA159 High Mn, experiment B

growth_protocol: Grown in reconstituted chelex-treated semi-defined medium

treatment_protocol: Chelex-treated semi-defined medium was supplemented with ferric citrate, magnesium chloride, and 10 micromolar (High) MnCl2


title: siRNA_CCNG2_DKFZ_Replicate3

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down CCNG2
siRNA_CCNG2_DKFZ_Replicate3

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: Cy5 Slide1 first scan

status: Public on Jan 16 2009

city: Copenhagen

first: Shila

last: Mortensen

address: Bülowsvej 27

department: Dep. for Veterinary Diagnostics and Research

country: Denmark

institute: National Veterinary Institute, Technical University of Denmark

description: Comparison of different fluorescent dyes.

hyb_protocol: Hybridization and washing were performed according to the manufacturer’s instructions (Genisphere) using Corning hybridization chambers. For one cDNA hybridization reaction; 6.5µl cDNA from each synthesis, 0.5µl Salmon sperm (10µg/µl) and 13.5µl 2 x Formamide-Based Hybridization Buffer (3DNA Array 900, Genisphere) was used. A total hybridization mix of 29µl was applied under a 22I x 25 mm LifterSlip (Erie Scientific, Portsmouth, NH, USA) carefully avoiding air bubbles. Slides were incubated at 44oC in a water bath over night. Wash buffer 1 (3DNA Array 900, Genisphere) was preheated to 44oC for the post cDNA hybridization wash. For two 3DNA hybridization reaction mixes; 2.5µl of each Capture reagent and 26µl SDS-Based hybridization buffer was mixed to a final volume of 52µl. 26µl 3DNA hybridization mix was applied to each slide, and incubated in darkness in a water bath at 50oC for 4 hours. Wash buffer 1 was preheated to 60oC for the post 3DNA hybridization wash.

scan_protocol: Slides were scanned on a CCD ArrayWoRxe auto (Applied Precision, Issaquah, WA, USA) using different exposure times (0.3 for 595 nm and 1.2 for 685 nm). Each slide was scanned 3 times, immediately after hybridization, after 1 month of storage in darkness and after 1 month in the dark followed by 24 hours on the bench (12 hours of daylight and 12 hours of artificial light).

data_processing: Raw data are used

label: 3DNA Cy5

organism: Sus scrofa

source_name: 3DNA Cy5 color

label_protocol: Cy3/Cy5 3DNA Array 900 expression array detection kit (Genisphere Inc., Hatfield, PA, USA) were used for the labeling and cDNA synthesis reaction of the RNA in the present study. Labeling was done according to the manufacturer’s protocol for large-scale cDNA synthesis. For the cDNA synthesis 9.2µg total RNA from each liver sample was used and mixed with 20U AmpliQ RTenzyme and 10x first strand buffer (Bie og Berntsen, Rødovre, Denmark).

extract_protocol: Total RNA from the infected and control liver samples were extracted using RNeasy midi kit (Qiagen, Denmark) and DNase treated using RNase-Free DNase Set (Qiagen).

tag: Healthy animal is labled with red color


title: Cy3 Slide1 24 hour

description: Comparison of different dyes tested. This slide is identical to Cy3_Slide1_first scan

label: 3DNA Cy3

source_name: 3DNA Cy3 color

tag: Infected animal is labled with green color


title: siRNA_GPR30_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down GPR30
siRNA_GPR30_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_2

tag: construct non-silencing control siRNA_Replicate2

source_name: cell line MCF7 siRNA GPR30_1-2

tag: construct siRNA GPR30_Replicate1_2


title: WT, experiment E

description: WT, experiment E

source_name: Streptococcus mutans UA159 WT, experiment E


title: siRNA_AKT1_DKFZ_Replicate1_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT1
siRNA_AKT1_DKFZ_Replicate1_dyeswap

source_name: cell line MCF7 siRNA AKT1_1-2

tag: construct siRNA AKT1_Replicate1_2


title: siRNA_LOC120224_DKFZ_Replicate2

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down LOC120224
siRNA_LOC120224_DKFZ_Replicate2

source_name: cell line MCF7 siRNA LOC120224_2-1

tag: construct siRNA LOC120224_Replicate2_1


title: siRNA_AKT1_DKFZ_Replicate2_dyeswap

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT1
siRNA_AKT1_DKFZ_Replicate2_dyeswap

source_name: cell line MCF7 siRNA _non-silencing_control_4

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA AKT1_2-2

tag: construct siRNA AKT1_Replicate2_2


title: Cy3 Slide2 24 hours

description: Comparison of different dyes tested. This slide is identical to Cy3_Slide2_first scan


title: Cy3 slide1 first scan

description: Comparison of different dyes are tested.


title: SloR mutant, experiment D

description: SloR mutant, experiment D

source_name: Streptococcus mutans UA159 SloR mutant, experiment D


title: siRNA_AKT1_DKFZ_Replicate1

description:
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down AKT1
siRNA_AKT1_DKFZ_Replicate1

source_name: cell line MCF7 siRNA AKT1_1-1

tag: construct siRNA AKT1_Replicate1_1

source_name: cell line MCF7 siRNA _non-silencing_control_1

tag: construct non-silencing control siRNA_Replicate1


title: Oyster650 slide2 first scan

label: Oyster 650

source_name: 3DNA Oyster color

label_protocol: Oyster 550/650 3DNA Array 900 expression array detection kit (Genisphere Inc., Hatfield, PA, USA) were used for the labeling and cDNA synthesis reaction of the RNA in the present study. Labeling was done according to the manufacturer’s protocol for large-scale cDNA synthesis. For the cDNA synthesis 9.2µg total RNA from each liver sample was used and mixed with 20U AmpliQ RTenzyme and 10x first strand buffer (Bie og Berntsen, Rødovre, Denmark).


title: Cy5 Slide2 1 month

description: Comparison of dirrefent fluorescent dyes. This slide is identical to Cy5_Slide2_first scan


title: Cy5 slide2 first scan

description: Comparison of dirrefent fluorescent dyes.


title: Oyster650 slide2 1month

description:
Comparison of different fluorescent dyes.
This slide is identical to Oyster650_slide2_first scan


title: Low Mn, experiment B

description: Low Mn, experiment B

source_name: Streptococcus mutans UA159 Low Mn, experiment B

treatment_protocol: Chelex-treated semi-defined medium was supplemented with ferric citrate, magnesium chloride, and 0.1 micromolar (Low) MnCl2


title: High Mn, experiment C

description: High Mn, experiment C

source_name: Streptococcus mutans UA159 High Mn, experiment C


title: WT, experiment D

description: WT, experiment D

source_name: Streptococcus mutans UA159 WT, experiment D


title: Cy3 Slide2 first scan

description: Comparison of different dyes tested.


title: Cy5 Slide1 1month

description: Comparison of dirrefent fluorescent dyes. This slide is identical to Cy5_Slide1_first scan


title: Cy5 Slide2 24 hours


title: Cy5 Slide1 24 hour


title: Oyster550 slide2 first scan

label: Oyster 550


title: Oyster550 slide1 1month

description:
Comparison of different fluorescent dyes.
This slide is identical to Oyster550_slide1_first scan


title: Oyster550 slide1 first scan


title: Oyster650 slide2 24 hour


title: Cy3 Slide2 1month


title: Oyster650 slide1 first scan


title: Oyster650 slide1 1month

description:
Comparison of different fluorescent dyes.
This slide is identical to Oyster650_slide1_first scan


title: Cy3 Slide1 1month

description: Comparison of different dyes are tested. This slide is identical to Cy3_Slide1_first scan


title: Low Mn, experiment A

description: Low Mn, experiment A

source_name: Streptococcus mutans UA159 Low Mn, experiment A


title: Oyster550 slide2 24 hour

description:
Comparison of different fluorescent dyes.
This slide is identical to Oyster550_slide2_first scan


title: Oyster550 slide2 1month


title: Oyster550 slide1 24 hour


title: High Mn, experiment A

description: High Mn, experiment A

source_name: Streptococcus mutans UA159 High Mn, experiment A


title: Alexa647 Slide2 first scan

description: Comparison of different fluorephores.

label: 3DNA alexa 647

source_name: 3DNA Alexa color

label_protocol: Alexa 546/647 3DNA Array 900 expression array detection kit (Genisphere Inc., Hatfield, PA, USA) were used for the labeling and cDNA synthesis reaction of the RNA in the present study. Labeling was done according to the manufacturer’s protocol for large-scale cDNA synthesis. For the cDNA synthesis 9.2µg total RNA from each liver sample was used and mixed with 20U AmpliQ RTenzyme and 10x first strand buffer (Bie og Berntsen, Rødovre, Denmark).


title: Alexa647 Slide2 24 hours

description:
Comparison of different fluorephores.
This slide is identical to Alexa647_Slide2_first scan


title: Low Mn, experiment C

description: Low Mn, experiment C

source_name: Streptococcus mutans UA159 Low Mn, experiment C


title: Alexa546 Slide2 1 month

description: Comparison of different fluorephores. This slide is identical to Alexa546_Slide2_first scan

label: 3DNA alexa 546

tag: Infected animal is labled whit green color


title: Alexa546 Slide1 1month

description:
Comparison of different fluorephores.
This slide is identical to Alexa546_Slide1_first scan

tag: Infected animal is labled to green color


title: Alexa647 Slide2 1 month


title: Alexa647 Slide1 24 hour

description:
Comparison of different fluorephores.
Thil slide is identical to Alexa647_Slide1_first scan

tag: Healthy animal is labled to red color


title: Alexa647 Slide1 first scan

description: Comparison study for different fluorescent dyes

hyb_protocol: Hybridization and washing were performed according to the manufacturers instructions (Genisphere) using Corning hybridization chambers. For one cDNA hybridization reaction; 6.5µl cDNA from each synthesis, 0.5µl Salmon sperm (10µg/µl) and 13.5µl 2 x Formamide-Based Hybridization Buffer (3DNA Array 900, Genisphere) was used. A total hybridization mix of 29µl was applied under a 22I x 25 mm LifterSlip (Erie Scientific, Portsmouth, NH, USA) carefully avoiding air bubbles. Slides were incubated at 44oC in a water bath over night. Wash buffer 1 (3DNA Array 900, Genisphere) was preheated to 44oC for the post cDNA hybridization wash. For two 3DNA hybridization reaction mixes; 2.5µl of each Capture reagent and 26ul SDS-Based hybridization buffer was mixed to a final volume of 52µl. 26ul 3DNA hybridization mix was applied to each slide, and incubated in darkness in a water bath at 50oC for 4 hours. Wash buffer 1 was preheated to 60oC for the post 3DNA hybridization wash.

scan_protocol: Slide were scanned on a CCD ArrayWoRxe auto (Applied Precision, Issaquah, WA, USA) using different exposure times (0.3 for 595 nm and 1.2 for 685 nm). Slide was scanned 3 times, immediately after hybridization, after 1 month of storage in darkness and after 1 month in the dark followed by 24 hours on the bench (12 hours of daylight and 12 hours of artificial light).

label_protocol: Alexa 546/647 3DNA Array 900 expression array detection kits (Genisphere Inc., Hatfield, PA, USA) were used for the labeling and cDNA synthesis reaction of the RNA in the present study. Labeling was done according to the manufacturers protocol for large-scale cDNA synthesis. For the cDNA synthesis 9.2ug total RNA from each liver sample was used and mixed with 20U AmpliQ RTenzyme and 10x first strand buffer (Bie og Berntsen, Rødovre, Denmark).

tag: Healthy animal labled to red dye


title: Alexa546 Slide1 first scan


title: Alexa647 Slide1 1month

description:
Comparison of different fluorephores.
This slide is identical to Alexa647_Slide1_first scan


title: Oyster650 slide1 24 hour


title: Alexa546 Slide2 24 hours


title: Alexa546 Slide1 24 hour

tag: infected animal is labled to green color


title: Alexa546 Slide2 first scan

description: Comparison of different fluorephores.


title: Ct_strain L2R biological rep 1

status: Public on Jan 15 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Ct_strain L2R biological rep 1

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Chlamydia trachomatis

source_name: Ct_strain L2R biological rep 1

label_protocol: Biotinylated cRNA were prepared

growth_protocol: Eighteen T75 flasks containing McCoy cells (4x107) were divided into three groups (6 each) and infected with L2/434, L2 (25667R) (MOI of 10), or mock infected and grown for 24 hr at 37°C with 5% CO2.  The media was removed by aspiration and 5 ml of RLT plus buffer (Qiagen, Allprep 96-well Kit, Valencia, CA  91355) added to each flask in randomized order.

extract_protocol: RNA was extracted from all 18 samples using the Allprep 96-well Kit (Qiagen) according to manufacturer’s specifications


title: Ct_strain L2R biological rep 5

description: Gene expression data from_Ct_strain L2R biological rep 5

source_name: Ct_strain L2R biological rep 5


title: Tomato_leaf_In vitro_rep2

status: Public on Jan 07 2009

city: Québec

first: Jean-François

last: Dubuc

address: 2440 boul. Hochelaga

country: Canada

institute: Université Laval

description: Hybridization and study was conducted to identify genes regulated by the in vitro culture conditions.

hyb_protocol: SlideHyb buffer #1 (Applied Biosystems) was preheated to 68ºC for 30 minutes. Labelled cDNA was resuspended in 4 μl 10 mM EDTA and heat denatured at 95ºC for 10 min. SlideHyb buffer #1 was added to the labelled cDNA. Hybridization was performed by using a SlideBooster from Advalytix AG (Brunnthal, Germany). For this purpose, a lifterSlip (Erie Scientific Company, Partsmouth, NH) was laid down on the array and the hybridization solution injected. After 17-h of hybridization at 55ºC, slides were washed in a low and high stringency buffer as mentioned in the SlideHyb buffer #1 protocol.

scan_protocol: Slides were scanned using a VersArray ChipReader (BioRad, Mississauga, ON, Canada). Digital image were acquired with the ChipReader 3.1 software (Bio-Rad).

data_processing: Data image were transferred to the Array-Pro Analyzer v.4.5 software (Media Cybernetics, Silver Spring, MD, USA) to detect the intensity of each spot on the array and for background subtraction using the local ring method. Net intensity data were log2 transformed. Data were normalized using the global Loess method included in the Microarray Analysis of Variance (MAANOVA) software. Normalization was performed in order to consider possible intensity-dependent variations in dye bias. Statistical analysis was accomplished by using the F-test of the R/maanova package (Wu et al., 2002), which work under the R programming environment. The false discovery rate (FDR) procedure was applied to the p-values in order to minimize the number of false positives associated to multiple testing. Differentially expressed genes were selected according to the adjusted p-values. Only genes showing an adjusted p-value under 0.01 were kept for further analysis. In addition, the fold change in expression between the two treatments had to be higher than 1.5 to be considered.

organism: Solanum lycopersicum

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep2

label_protocol: cDNA was produced by reverse transcription of 40 μg of total RNA using the Superscript III (Invitrogen). Aminoallyl-dUTP (Applied Biosystems, Streetsville, ON, Canada) were added to the cDNA synthesis reaction to make possible further indirect labelling. The RNA of the hybrid cDNA-RNA was hydrolysed by addition of NaOH 1M and 15 min heating at 65ºC. Reaction was neutralized by adding HCL 1M. A purification step was realized using the Qiaquick PCR purification kit (Qiagen, Mississauga, ON, Canada). Sample where labelled using AlexaFluor 555 reactive dye packs (Invitrogen) according to the manufacturer. Briefly, 1 μg of cDNA from each sample were evaporated with Savant speedvac concentrator (Thermo Fisher Scientific, Waltham, MA), resuspended in 5 μl double-distilled water and 3 μl labelling buffer. DMSO (2 μl) was added to each single-use fluorophore vial and vortexed. Sample cDNA was added to AlexaFluor 555 reactive dye vial. Labelling was performed for a three hour period. Following a purification step, 600 ng of labelled cDNA of each probes were speedvac-evaporated.

extract_protocol: The second leaves from tomato plantlets grown under in vitro culture conditions were harvested after 20 days in vitro. Tissue were immediately frozen in liquid nitrogen and stored at -80˚C for further grinding. Total RNA was isolated using Plant RNA Reagent following manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). RNA concentration was measured using a ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Possible contamination was access with the 260/280nm ratio. RNA quality was visualized with a 1.5% denatured agarose gels.

treatment_protocol: For the experiment, plantlets were grown in vitro in stacked doubled magenta vessel (Sigma, Oakville, ON, Canada). Each vessel contained a single plantlet. Axillary apex of single node cuttings were grown for 20 days on MS medium containing 8% bacto-agar (BD Diagnostic System, Sparks, MD, USA), and 3% sucrose. In the growth room, plantlets were submitted to a 16-h photoperiod at 60 μmol photons m-2 s-1 and 23/20°C day/night temperature. After 20 days, the plantlets second leaf was harvested.

tag: Solanum Lycopersicum cv. Trust

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep2

label_protocol: cDNA was produced by reverse transcription of 40 μg of total RNA using the Superscript III (Invitrogen). Aminoallyl-dUTP (Applied Biosystems, Streetsville, ON, Canada) were added to the cDNA synthesis reaction to make possible further indirect labelling. The RNA of the hybrid cDNA-RNA was hydrolysed by addition of NaOH 1M and 15 min heating at 65ºC. Reaction was neutralized by adding HCL 1M. A purification step was realized using the Qiaquick PCR purification kit (Qiagen, Mississauga, ON, Canada). Sample where labelled using AlexaFluor 647 reactive dye packs (Invitrogen) according to the manufacturer. Briefly, 1 μg of cDNA from each sample were evaporated with Savant speedvac concentrator (Thermo Fisher Scientific, Waltham, MA), resuspended in 5 μl double-distilled water and 3 μl labelling buffer. DMSO (2 μl) was added to each single-use fluorophore vial and vortexed. Sample cDNA was added to AlexaFluor 647 reactive dye vial. Labelling was performed for a three hour period. Following a purification step, 600 ng of labelled cDNA of each probes were speedvac-evaporated.

extract_protocol: After 12 days of growth ex vitro, the second leaves of tomato plant were harvested. Tissue were immediately frozen in liquid nitrogen and stored at -80˚C for further grinding. Total RNA was isolated using Plant RNA Reagent following manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). RNA concentration was measured using a ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Possible contamination was access with the 260/280nm ratio. RNA quality was visualized with a 1.5% denatured agarose gels.

treatment_protocol: Axillary apex of single node cuttings were grown for 20 days on MS medium containing 8% bacto-agar (BD Diagnostic System, Sparks, MD, USA), and 3% sucrose. In the growth room, plantlets were submitted to a 16-h photoperiod at 60 μmol photons m-2 s-1 and 23/20°C day/night temperature. After 20 days, plantlets were transferred ex vitro for a 12 days acclimatization. For the first 4 days, tomato plants were maintained in an Arabidopsis chamberTM (Conviron, Winnipeg, MB, Canada) under high humidity condition and 16-h photoperiod at 200 μmol photons m-2 s-1. Plantlets were transferred to a greenhouse under natural daylight (august) for the remaining 8 days in order to complete the acclimatization process. Plantlets second leaf was harvested after 12 days ex vitro. The second leaf corresponded to a newly ex vitro formed leaf by opposition to old, permanent in vitro leaves


title: RNA from mock infected biological rep 3

description: Gene expression data from_RNA from mock infected biological rep 3

source_name: RNA from mock infected biological rep 3


title: Tomato_leaf_In vitro_rep3

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep3

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep3


title: Tomato_leaf_In vitro_rep3_dye swap

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep3_dye swap

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep3_dye swap


title: Ct_strain L2R biological rep 3

description: Gene expression data from_Ct_strain L2R biological rep 3

source_name: Ct_strain L2R biological rep 3


title: RNA from mock infected biological rep 4

description: Gene expression data from_RNA from mock infected biological rep 4

source_name: RNA from mock infected biological rep 4


title: Ct_strain L2R biological rep 6

description: Gene expression data from_Ct_strain L2R biological rep 6

source_name: Ct_strain L2R biological rep 6


title: Ct_strain L2 biological rep 5

description: Gene expression data from_Ct_strain L2 biological rep 5

source_name: Ct_strain L2 biological rep 5


title: Ct_strain L2 biological rep 4

description: Gene expression data from_Ct_strain L2 biological rep 4

source_name: Ct_strain L2 biological rep 4


title: RNA from mock infected biological rep 2

description: Gene expression data from_RNA from mock infected biological rep 2

source_name: RNA from mock infected biological rep 2


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_6_1)

status: Public on Jan 06 2009

type: genomic

city: San Francisco

first: Antoine

last: Snijders

state: CA

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

description: Array CGH experiments of cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

hyb_protocol: We combined and precipitated 50 ml Cy3 labeled test DNA, 50 ml Cy5 labeled reference DNA and 100 mg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol. We collected the precipitate by centrifugation and dissolved the pellet in a final hybridization mixture containing 50% formamide, 2xSSC and 4% SDS. We denatured the hybridization mixture at 75°C for 10-15 min and then incubated the samples at 37°C for 1 hour to block repetitive DNA sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 ml of a pre-incubation solution containing 250 mg salmon sperm DNA, 50% formamide, 2xSSC and 4% SDS.  After a 30 min incubation at room temperature, we removed ~30 ml of the pre-incubation solution and added the denatured and re-annealed hybridization mixture.  We placed a silicone gasket around each hybridization area, placed a microscope slide on top of the gasket, which was thick enough to prevent the microscope slide from contacting the hybridization solution and clamped the whole unit together using binder clips to create an air tight environment.  We carried out the hybridization to the arrays for ~48 hrs on a slowly rocking table at 37°C.  After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min.  Subsequently, we removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system

data_processing:
We used “UCSF SPOT” software to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the August, 2001 freeze of the draft human genome sequence (http://genome.ucsc.edu).
SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.

molecule: genomic DNA

source_name: HT1080 GLI2 cell line

label_protocol: We labeled genomic DNA by random priming in a 50 ml reaction by combining 300 ng genomic DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1x dNTP solution (0.2 mM each of dATP, dTTP, dGTP, 0.05 mM dCTP, 1 mM Tris base (pH 7.6), 0.1 mM EDTA), 40 mM Cy3 or Cy5-dCTP (Amersham) and 40 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL).  We incubated the DNA and the random primers in a volume of 42 ml at 100°C for 10-15 min, placed the reaction on ice and added the dNTP solution, labeled nucleotides and Klenow fragment. We incubated the random priming reaction overnight at 37°C. We removed unincorporated nucleotides using a Sephadex spin-column.

extract_protocol: We incubated cells from a T75 flask overnight at 55°C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 mg/ml proteinase K. We precipitated the DNA with ethanol, recovered it by spooling and then dissolved it in ~300 ml H2O.

tag: cell line DNA

tag: control HT1080 cells, or HT1080 cells infected with a lentivirus expressing eGFP, GLI2-eGFP or CCND1-RFP

source_name: Genomic DNA isolated from male blood sample

tag: reference sample


title: Tomato_leaf_In vitro_rep1_dye swap

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep1_dye swap

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep1_dye swap


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_8_1)


title: Ct_strain L2R biological rep 2

description: Gene expression data from_Ct_strain L2R biological rep 2

source_name: Ct_strain L2R biological rep 2


title: Ct_strain L2 biological rep 2

description: Gene expression data from_Ct_strain L2 biological rep 2

source_name: Ct_strain L2 biological rep 2


title: Ct_strain L2 biological rep 1

description: Gene expression data from_Ct_strain L2 biological rep 1

source_name: Ct_strain L2 biological rep 1


title: Ct_strain L2R biological rep 4

description: Gene expression data from_Ct_strain L2R biological rep 4

source_name: Ct_strain L2R biological rep 4


title: RNA from mock infected biological rep 6

description: Gene expression data from_RNA from mock infected biological rep 6

source_name: RNA from mock infected biological rep 6


title: RNA from mock infected biological rep 1

description: Gene expression data from_RNA from mock infected biological rep 1

source_name: RNA from mock infected biological rep 1


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_3_1)


title: Ct_strain L2 biological rep 3

description: Gene expression data from_Ct_strain L2 biological rep 3

source_name: Ct_strain L2 biological rep 3


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_2_1)


title: Tomato_leaf_In vitro_rep2_dye swap

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep2_dye swap

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep2_dye swap


title: RNA from mock infected biological rep 5

description: Gene expression data from_RNA from mock infected biological rep 5

source_name: RNA from mock infected biological rep 5


title: Ct_strain L2 biological rep 6

description: Gene expression data from_Ct_strain L2 biological rep 6

source_name: Ct_strain L2 biological rep 6


title: Tomato_leaf_In vitro_rep1

description: Hybridization and study was conducted to identify genes regulated by the in vitro culture conditions.

source_name: Tomato plantlet_leaf_in vitro grown_20 days_rep1

source_name: Tomato plantlet_leaf_ex vitro grown_12 days_rep1


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_1_1)

source_name: HT1080 GLI2 cell line


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_8_1)

source_name: Genomic DNA isolated from male blood sample


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_7_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_9_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_6_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_5_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_4_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_4_1_1)

source_name: HT1080 eGFP cell line


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_12_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_4_10_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_4_2_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_4_4_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_4_5_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_11_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_2_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_3_1_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_3_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_3_2_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_8_1)

source_name: HT1080 CCND1 cell line


title: Methotrexate treated HT1080_eGFP cell line (GFP_3_10_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_7_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_4_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_2_1)


title: Methotrexate treated HT1080_eGFP cell line (GFP_3_3_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_3_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_10_1)


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_1_1)


title: Methotrexate treated HT1080 cell line (4_3_1)

source_name: HT1080 cell line


title: Methotrexate treated HT1080 cell line (4_9_1)


title: Methotrexate treated HT1080 cell line (4_2_1)


title: Methotrexate treated HT1080 cell line (X070917d_3_4_1)


title: Methotrexate treated HT1080 cell line (3_3_1)


title: Methotrexate treated HT1080 cell line (X071102_3_4_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_4_4_1)


title: Methotrexate treated HT1080_GLI2 cell line (gli2_3_1_1)


title: hepatocellular carcinoma-normal liver-50

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

description: hepatocellular carcinoma versus normal liver tissue

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (635 nm) to Channel 1 (532 nm)

source_name: normal liver tissue

tag: normal liver tissue

source_name: hepatocellular carcinoma

tag: AGE

value: 42 SEX:Male Size of tumor:8*10 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-51

value: 52 SEX:Male Size of tumor:12*11*10 Differentiation:Poorly-differentiated


title: Methotrexate treated HT1080 cell line (3_12_1)


title: hepatocellular carcinoma-normal liver-57

value: 76 SEX:Male Size of tumor:NA Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-48

value: 14 SEX:Male Size of tumor:5*4*4 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-49

value: 36 SEX:Male Size of tumor:8*9 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-45

value: 60 SEX:Male Size of tumor:4*4*3 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-47

value: 41 SEX:Male Size of tumor:8.3*8.2*8.2 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-53

value: 47 SEX:Male Size of tumor:10*8*8 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-42

value: 49 SEX:Male Size of tumor:17*12*12 Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-52

value: 44 SEX:Male Size of tumor:3*4 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-43

value: 50 SEX:Male Size of tumor:5*5*3 Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-46

value: 23 SEX:Male Size of tumor:7*6*6 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-44

value: 35 SEX:Male Size of tumor:9*7*4 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-40

value: 60 SEX:Male Size of tumor:4*4*3 Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-41

value: 40 SEX:Male Size of tumor:3*3*3 Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-58

source_name: normal liver

value: 46 SEX:Male Size of tumor:12*10 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-55

value: 45 SEX:Male Size of tumor:6*6 Differentiation:Poorly-differentiated


title: Methotrexate treated HT1080_CCND1 cell line (ccnd1_4_5_1)


title: hepatocellular carcinoma-normal liver-39

value: 52 SEX:Male Size of tumor:15*13*11 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-31

description: hepatocellular carcinoma versus corresponding noncancerous liver tissue

source_name: noncancerous liver tissue

tag: corresponding noncancerous liver tissue

value: SEX:Male Size of tumor:7.2*6 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-38

value: 44 SEX:Male Size of tumor:NA Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-36

value: 42 SEX:Male Size of tumor:10*13*12 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-33

value: 53 SEX:Male Size of tumor:8*7*6 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-35

value: 62 SEX:Male Size of tumor:3*3*3 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-28

value: 42 SEX:Male Size of tumor:13 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-32

value: 37 SEX:Male Size of tumor:10 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-30

value: 41 SEX:Male Size of tumor:6*8 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-37

value: 57 SEX:Male Size of tumor:5*5*4 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-22

value: 44 SEX:Male Size of tumor:6*6*6 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-29

value: 34 SEX:Male Size of tumor:5*5 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-normal liver-34

value: 43 SEX:Male Size of tumor:7*9*9 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-13

tag: noncancerous liver tissue

value: 36 SEX:Female Size of tumor:9*8*8 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-14

value: 50 SEX:Male Size of tumor:6.5*6*6 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-26

source_name: noncancerous tissue

value: 67 SEX:Male Size of tumor:9.5*9*8 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-23

value: 59 SEX:Male Size of tumor:6.5*6.5*6 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-19

value: 41 SEX:Male Size of tumor:8.3*8.2*8.2 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-25

value: 52 SEX:Male Size of tumor:14.5*10*9 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-21

value: 39 SEX:Male Size of tumor:6*5*5  Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-20

value: 60 SEX:Female Size of tumor:10*9*9 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-27

tag: Age

value: 48 SEX:Male Size of tumor:13*10 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-24

value: 52 SEX:Male Size of tumor:11*8*7 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-15

value: 62 SEX:Male Size of tumor:5.7*5.5*4.5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-9

value: 55 SEX:Male Size of tumor:6*5*5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-10

value: 40 SEX:Female Size of tumor:14*10*7 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-11

value: 53 SEX:Male Size of tumor:2 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-7

value: 59 SEX:Male Size of tumor:6 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-8

value: 62 SEX:Male Size of tumor:6.1*6 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-12

value: 48 SEX:Male Size of tumor:4.5*3*3 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-5

value: 36 SEX:Male Size of tumor:6*5.5*5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous sample-3

value: 55 SEX:Female Size of tumor:3.5*3.5*3.5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-6

value: 52 SEX:Male Size of tumor:2.2*2.2*2 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-1

value: 60 SEX:Male Size of tumor:3.5*3.5*3.5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-normal liver-56

value: 43 SEX:Male Size of tumor:12*16 Differentiation:Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-2

value: 49 SEX:Male Size of tumor:6.5*5*5 Differentiation:Well-differentiated


status: Public on Jan 05 2009

description: Gene expression data from_wild type MW2 for Mli_7 series biological rep 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Staphylococcus aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For microarray experiments, overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37C with shaking at 180rpm for 4 h (post-exponential growth phase).

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

tag: wild type MW2


description: Gene expression data from_wild type MW2 for Mli_7 series biological rep 1


description: Gene expression data from_370 mutant for Mli_7 series biological rep 2

tag: 370 mutant


description: Gene expression data from_wild type MW2 for Mli_7 series biological rep 2


description: Gene expression data from_RNAIII mutant for JQ_3 series biological rep 2

tag: RNAIII mutant


description: Gene expression data from_AGR mutant for JQ_3 series biological rep 3

tag: AGR mutant


title: hepatocellular carcinoma-noncancerous liver-17

tag: SEX

value: Male

tag: Size of tumor

tag: Differentiation

value: Poorly-differentiated


title: hepatocellular carcinoma-noncancerous liver-4

value: 42 SEX:Male Size of tumor:5.5*5 Differentiation:Well-differentiated


title: hepatocellular carcinoma-noncancerous liver-18

value: 52 SEX:Male Size of tumor:4.8*4.4*4.4 Differentiation:Poorly-differentiated


description: Gene expression data from_370 mutant for Mli_7 series biological rep 1


description: Gene expression data from_370 mutant for Mli_7 series biological rep 3


description: Gene expression data from_RNAIII mutant for JQ_3 series biological rep 3


description: Gene expression data from_RNAIII mutant for JQ_3 series biological rep 1


description: Gene expression data from_wild type MW2 for JQ_3 series biological rep 2


description: Gene expression data from_wild type MW2 for JQ_3 series biological rep 1


description: Gene expression data from_hld mutant for JQ_1 series biological rep 3

tag: hld mutant


description: Gene expression data from_hld mutant for JQ_1 series biological rep 2


description: Gene expression data from_hld mutant for JQ_1 series biological rep 1


description: Gene expression data from_wild type MW2 for JQ_3 series biological rep 3


description: Gene expression data from_PSM beta mutant for JQ_1 series biological rep 3

tag: PSM beta mutant


description: Gene expression data from_AGR mutant for JQ_3 series biological rep 1


description: Gene expression data from_PSM beta mutant for JQ_1 series biological rep 2


description: Gene expression data from_PSM alpha mutant for JQ_1 series biological rep 3

tag: PSM alpha mutant


description: Gene expression data from_wild type MW2 for JQ_1 series biological rep 2


description: Gene expression data from_PSM alpha mutant for JQ_1 series biological rep 1


title: Liver, ko ND

status: Public on Jan 03 2009

city: Lund

first: Céline

last: Fernandez

address: BMC C11

department: Experimental Medical Science

country: Sweden

institute: Medical Faculty, Lund University

description: Gene expression data from HSL-null mice on ND

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GA2500.

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.

organism: Mus musculus

source_name: Liver, ko, on a normal diet for 6 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, using the Enzo RNA transcript-labeling kit, from 4.8 ug of total RNA.

growth_protocol: Female mice were sacrificed at 8 months old.

extract_protocol: Total RNA was extracted according to Chomczynski and Sacchi (Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. 1987. Anal Biochem 162: 156-159) and was then purified using an RNeasy Kit (Qiagen).

treatment_protocol: Livers were snap-frozen and stored at -80C. Mice were either fed a normal diet (ND) (11% energy from fat) or a high-fat diet (FD) (58% energy from fat) (Research Diets, New Brunswick, NJ; products no D12310 and D12309, respectively).

tag: Gender

value: female

tag: Tissue

value: liver

tag: Nutritional state

value: fed mice


description: Gene expression data from_PSM alpha mutant for JQ_1 series biological rep 2


description: Gene expression data from_wild type MW2 for JQ_1 series biological rep 3


title: DRIP 25_muscle taken at slaughter, mean end weight of 110 kg

status: Public on Jan 01 2009

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from Muscle Longissimus dorsi sample of F2 animals

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: Muscle Longissimus dorsi, DRIP 25

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: F2 animals of a resource population based on the breeds Duroc and Pietrain


title: DRIP 23_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 23


title: DRIP 17_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 17


title: DRIP 32_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 32


title: Liver, ko FD

description: Gene expression data from HSL-null mice on FD

source_name: Liver, ko, on a high fat diet for 6 months


description: Gene expression data from_wild type MW2 for JQ_1 series biological rep 1


title: DRIP 26_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 26


title: hepatocellular carcinoma-noncancerous liver-16

description: hepatocellular carcinoma versus corresponding noncancerous liver tissue

tag: corresponding noncancerous liver tissue

tag: AGE

value: 35 SEX:Male Size of tumor:9*7*4 Differentiation:Well-differentiated


title: DRIP 21_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 21


title: Liver, wt FD

description: Gene expression data from wildtype mice on FD

source_name: Liver, wt, on a high fat diet for 6 months


title: DRIP 99_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 99


title: DRIP 15_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 15


title: DRIP 13_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 13


title: DRIP 33_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 33


title: DRIP 24_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 24


title: DRIP 98_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 98


title: DRIP 14_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 14


description: Gene expression data from_AGR mutant for JQ_3 series biological rep 2


title: DRIP 96_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 96


title: DRIP 83_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 83


title: DRIP 87_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 87


title: DRIP 93_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 93


title: DRIP 92_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 92


title: DRIP 94_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 94


title: DRIP 77_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 77


title: DRIP 86_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 86


title: DRIP 76_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 76


title: DRIP 85_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 85


title: DRIP 78_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 78


title: DRIP 84_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 84


title: DRIP 88_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 88


title: DRIP 75_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 75


title: DRIP 82_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 82


title: DRIP 90_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 90


title: DRIP 91_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 91


title: DRIP 79_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 79


title: DRIP 73_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 73


title: DRIP 67_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 67


title: DRIP 74_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 74


title: DRIP 70_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 70


title: DRIP 66_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 66


title: DRIP 69_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 69


title: DRIP 68_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 68


description: Gene expression data from_PSM beta mutant for JQ_1 series biological rep 1


title: Liver, wt ND

description: Gene expression data from wildtype mice on ND

source_name: Liver, wt, on a normal diet for 6 months


title: DRIP 72_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 72


title: DRIP 6_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 6


title: DRIP 62_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 62


title: DRIP 63_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 63


title: DRIP 61_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 61


title: DRIP 65_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 65


title: DRIP 64_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 64


title: DRIP 29_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 29


title: DRIP 22_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 22


title: DRIP 18_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 18


title: DRIP 60_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 60


title: DRIP 110_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 110


title: DRIP 114_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 114


title: DRIP 19_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 19


title: DRIP 4_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 4


title: DRIP 20_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 20


title: DRIP 28_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 28


title: DRIP 108_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 108


title: DRIP 112_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 112


title: DRIP 111_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 111


title: DRIP 97_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 97


title: DRIP 107_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 107


title: DRIP 12_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 12


title: DRIP 11_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 11


title: DRIP 106_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 106


title: DRIP 104_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 104


title: DRIP 105_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 105


title: DRIP 109_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 109


title: DRIP 113_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 113


title: DRIP 101_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 101


title: DRIP 102_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 102


title: DRIP 103_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 103


title: DRIP 9_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 9


title: DRIP 10_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 10


title: 13688406 - Anther Col0 set1 vs Root Col0 set1

status: Public on Dec 07 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the gene expressed during meiosis pathway in Arabidopsis thalina.

hyb_protocol: Root Col0 set1 Cy5 / Anther Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Root Col0 set1

label_protocol: labelling  , amplification=,   .

growth_protocol: root - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Root Col0 set1:77.54ug.

tag: Arabidopsis thaliana (col-0)  - harvest date:01-09-07

source_name: Anther Col0 set1

growth_protocol: stamen - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Anther Col0 set1:22.2ug.

tag: Arabidopsis thaliana (col-0)  - harvest date:01-04-07


title: DRIP 100_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 100


title: DRIP 1_muscle taken at slaughter, mean end weight of 110 kg

source_name: Muscle Longissimus dorsi, DRIP 1


title: 13690692 - Leaves Col0 set2 vs Meiocytes Col0 set2

type: other

hyb_protocol: Meiocytes Col0 set2 Cy5 / Leaves Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

molecule: other

source_name: Meiocytes Col0 set2

growth_protocol: meiocyte - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Meiocytes Col0 set2:2.59ug.

tag: Arabidopsis thaliana (col-0)  - harvest date:01-06-07

source_name: Leaves Col0 set2

growth_protocol: leaf - Media=soil 	 hygrometry=70	 Temperature=18	 Light=11h

extract_protocol: Leaves Col0 set2:95ug.

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes = 3.9


title: 13688236 - Leaves Col0 set1 vs Anther Col0 set1

hyb_protocol: Anther Col0 set1 Cy5 / Leaves Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Leaves Col0 set1

extract_protocol: Leaves Col0 set1:59.57ug.


title: 13688044 - Anther L.erecta set1 vs Anther SPL set1

hyb_protocol: Anther SPL set1 Cy5 / Anther L.erecta set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Anther SPL set1

extract_protocol: Anther SPL set1:21.2ug.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (spl1-1) - harvest date:01-04-07

source_name: Anther L.erecta set1

extract_protocol: Anther L.erecta set1:41.65ug.

tag: Arabidopsis thaliana (landsberg erecta)  - harvest date:01-04-07


title: 13688231 - Meiocytes Col0 set1 vs Leaves Col0 set1

hyb_protocol: Leaves Col0 set1 Cy5 / Meiocytes Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Meiocytes Col0 set1

extract_protocol: Meiocytes Col0 set1:1.86ug.


title: 13688228 - Leaves Col0 set1 vs Meiocytes Col0 set1

hyb_protocol: Meiocytes Col0 set1 Cy5 / Leaves Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690696 - Meiocytes Col0 set2 vs Leaves Col0 set2

hyb_protocol: Leaves Col0 set2 Cy5 / Meiocytes Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688401 - Root Col0 set2 vs Meiocytes Col0 set2

hyb_protocol: Meiocytes Col0 set2 Cy5 / Root Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Root Col0 set2

extract_protocol: Root Col0 set2:168.17ug.


title: 13688045 - Anther SPL set1 vs Anther L.erecta set1

hyb_protocol: Anther L.erecta set1 Cy5 / Anther SPL set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688235 - Anther Col0 set1 vs Leaves Col0 set1

hyb_protocol: Leaves Col0 set1 Cy5 / Anther Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688405 - Meiocytes Col0 set2 vs Root Col0 set2

hyb_protocol: Root Col0 set2 Cy5 / Meiocytes Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688030 - Anther Col0 set1 vs Anther L.erecta set1

hyb_protocol: Anther L.erecta set1 Cy5 / Anther Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688043 - Anther Col0 set2 vs Root Col0 set2

hyb_protocol: Root Col0 set2 Cy5 / Anther Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Anther Col0 set2

extract_protocol: Anther Col0 set2:1.56ug.


title: 13688239 - Anther Col0 set2 vs Leaves Col0 set2

hyb_protocol: Leaves Col0 set2 Cy5 / Anther Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688032 - Anther L.erecta set1 vs Anther Col0 set1

hyb_protocol: Anther Col0 set1 Cy5 / Anther L.erecta set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688403 - Meiocytes Col0 set1 vs Root Col0 set1

hyb_protocol: Root Col0 set1 Cy5 / Meiocytes Col0 set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688034 - Leaves Col0 set2 vs Anther Col0 set2

hyb_protocol: Anther Col0 set2 Cy5 / Leaves Col0 set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.