title: C_094_065_02_PDS275_D F

description: Control genomic dna (untreated)

source_name: HELA ATCC; Control genomic dna (untreated)

growth_protocol: RPMI 1640 medium with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

tag: HELA ATCC


title: C_094_75_06_PDS278_D F

status: Public on Jun 23 2007

type: genomic

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

country: USA

institute: Altius Institute / University of Washington

description: Control genomic dna (untreated)

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: SKMC ATCC; Control genomic dna (untreated)

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K

tag: SKMC Cambrex


title: E_098_043_02_DS7118_W F

description: DnaseI enriched

source_name: HL60 ATCC; DnaseI enriched

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: HL60 ATCC


title: C_094_75_02_PDS276_D F

description: Control genomic dna (untreated)

source_name: HepG2 ATCC; Control genomic dna (untreated)

tag: HepG2 ATCC


title: C_094_75_01_PDS273_D F

description: Control genomic dna (untreated)

source_name: CACO2 ATCC; Control genomic dna (untreated)

tag: CACO2 ATCC


title: C_094_065_03_PDS273_D F

description: Control genomic dna (untreated)


title: 99-007-02_DS7135_wga D

description: DnaseI enriched

source_name: HESC G.Stam; DnaseI enriched

tag: HESC G.Stam


title: C_094_065_01_PDS275_D F

description: Control genomic dna (untreated)


title: 99-048-02_DS7077_gp_5ug F

description: DnaseI enriched

source_name: HELA ATCC; DnaseI enriched


title: 098-32-03_DS7034_WGA D

description: DnaseI enriched

source_name: CACO2 ATCC; DnaseI enriched


title: E_098_048_02_DS7213_W D

description: DnaseI enriched


title: 098-32-01_DS6998_WGA D

description: DnaseI enriched


title: 94-56-02_PDS275_cont_d F

description: DnaseI enriched


title: E_098_048_04_DS7229_W D

description: DnaseI enriched

source_name: HepG2 ATCC; DnaseI enriched


title: E_099_077_03_DS7168_W D

description: DnaseI enriched

source_name: K562 ATCC; DnaseI enriched

tag: K562 ATCC


title: 99-032-10_DS7190_WGA_4ug D

description: DnaseI enriched


title: 99-007-03_DS7136_wga D

description: DnaseI enriched


title: C_094_80_02_PDS277_D D

description: Control genomic dna (untreated)

source_name: K562 ATCC; Control genomic dna (untreated)


title: C_094_75_01_PDS273_D D

description: Control genomic dna (untreated)


title: C_094_065_03_PDS273_D D

description: Control genomic dna (untreated)


title: E_099_077_15_DS6897_W D

description: DnaseI enriched

source_name: HTH2 Wilson; DnaseI enriched

tag: HTH2 Wilson


title: C_094_75_06_PDS278_D D

description: Control genomic dna (untreated)


title: C_094_80_06_PDS276_D D

description: Control genomic dna (untreated)


title: 99-048-02_DS7077_gp_5ug D

description: DnaseI enriched


title: C_094_80_04_DS7457_D D

description: Control genomic dna (untreated)

source_name: HL60 ATCC; Control genomic dna (untreated)


title: E_099_077_04_DS7273_W D

description: DnaseI enriched

source_name: SKMC Cambrex; DnaseI enriched


title: C_094_065_02_PDS275_D D

description: Control genomic dna (untreated)


title: C_094_75_02_PDS276_D D

description: Control genomic dna (untreated)


title: 99-007-02_DS7135_wga B

description: DnaseI enriched


title: 94-56-02_PDS275_cont_d D

description: DnaseI enriched


title: C_094_065_01_PDS275_D D

description: Control genomic dna (untreated)


title: 99-048-04_DS7104_gp_5ug D

description: DnaseI enriched


title: 99-048-04_DS7104_gp_5ug F

description: DnaseI enriched


title: E_099_077_02_DS7124_W B

description: DnaseI enriched


title: E_098_048_03_DS7226_W B

description: DnaseI enriched


title: 098-32-01_DS6998_WGA B

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug B

description: DnaseI enriched


title: E_099_077_04_DS7273_W B

description: DnaseI enriched


title: E_098_048_04_DS7229_W B

description: DnaseI enriched


title: 99-032-10_DS7190_WGA_4ug B

description: DnaseI enriched


title: E_099_086_04_DS6883_W B

description: DnaseI enriched

source_name: HCD4 Wilson; DnaseI enriched

tag: HCD4 Wilson


title: E_098_048_02_DS7213_W B

description: DnaseI enriched


title: E_099_077_06_DS7275_W F

description: DnaseI enriched


title: E_099_077_03_DS7168_W B

description: DnaseI enriched


title: 99-048-05_DS7147_gp_5ug B

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug D

description: DnaseI enriched


title: 098-32-03_DS7034_WGA B

description: DnaseI enriched


title: C_094_75_06_PDS278_D B

description: Control genomic dna (untreated)


title: 99-007-03_DS7136_wga B

description: DnaseI enriched


title: 94-32-03_DS7244_d B

description: Control genomic dna (untreated)


title: C_094_81_01_DS7456_D B

description: Control genomic dna (untreated)


title: C_094_75_01_PDS273_D B

description: Control genomic dna (untreated)


title: C_094_065_03_PDS273_D B

description: Control genomic dna (untreated)


title: 99-048-02_DS7077_gp_5ug B

description: DnaseI enriched


title: 94-56-02_PDS275_cont_d B

description: DnaseI enriched


title: E_099_077_15_DS6897_W B

description: DnaseI enriched


title: 99-048-04_DS7104_gp_5ug B

description: DnaseI enriched


title: 99-007-03_DS7136_wga C

description: DnaseI enriched


title: C_094_065_01_PDS275_D B

description: Control genomic dna (untreated)


title: 99-007-02_DS7135_wga C

description: DnaseI enriched


title: C_094_065_02_PDS275_D B

description: Control genomic dna (untreated)


title: C_094_75_02_PDS276_D B

description: Control genomic dna (untreated)


title: 098-32-01_DS6998_WGA C

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug C

description: DnaseI enriched


title: E_098_048_02_DS7213_W C

description: DnaseI enriched


title: E_099_077_15_DS6897_W C

description: DnaseI enriched


title: 99-032-10_DS7190_WGA_4ug C

description: DnaseI enriched


title: E_099_077_01_DS7119_W C

description: DnaseI enriched


title: E_099_077_03_DS7168_W C

description: DnaseI enriched


title: E_099_086_04_DS6883_W C

description: DnaseI enriched


title: E_098_048_03_DS7226_W C

description: DnaseI enriched


title: 098-32-03_DS7034_WGA C

description: DnaseI enriched


title: C_094_75_01_PDS273_D C

description: Control genomic dna (untreated)


title: E_099_077_04_DS7273_W C

description: DnaseI enriched


title: C_094_065_03_PDS273_D C

description: Control genomic dna (untreated)


title: C_094_80_01_PDS276_D C

description: Control genomic dna (untreated)


title: C_094_80_03_PDS279_D C

description: Control genomic dna (untreated)

source_name: SK-N-SH ATCC; Control genomic dna (untreated)

tag: SK-N-SH ATCC


title: C_094_80_05_PDS277_D C

description: Control genomic dna (untreated)


title: C_094_065_02_PDS275_D C

description: Control genomic dna (untreated)


title: C_094_75_06_PDS278_D C

description: Control genomic dna (untreated)


title: C_094_065_01_PDS275_D C

description: Control genomic dna (untreated)


title: 99-048-04_DS7104_gp_5ug C

description: DnaseI enriched


title: Sample 2

status: Public on Jun 26 2007

type: mixed

city: Boston

first: Arjun

middle: Kumar

last: Manrai

state: MA

address: 44 Binney Street, Mail Stop LW225

department: Department of Biostatistics and Computational Biology

institute: Dana Farber Cancer Institute

description: Raw and processed data

hyb_protocol: Performed by NimbleGen Systems Inc.

scan_protocol: Performed by NimbleGen Systems Inc.

data_processing: Cy5/Cy3 ratios normalized with MA2C

source_name: Human genomic DNA

label_protocol: Random primer labeling

extract_protocol: (genomic DNA extraction)

tag: Human genomic DNA

molecule: other

source_name: Spike A

extract_protocol: (spiked sample extraction)

tag: Spike A DNA


title: 99-048-05_DS7147_gp_5ug C

description: DnaseI enriched


title: 94-56-02_PDS275_cont_d C

description: DnaseI enriched


title: E_098_048_04_DS7229_W C

description: DnaseI enriched


title: 99-048-02_DS7077_gp_5ug C

description: DnaseI enriched


title: 99-032-10_DS7190_WGA_4ug A

description: DnaseI enriched


title: 098-32-01_DS6998_WGA A

description: DnaseI enriched


title: E_099_086_04_DS6883_W A

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug A

description: DnaseI enriched


title: E_098_048_03_DS7226_W A

description: DnaseI enriched


title: 99-007-03_DS7136_wga G

description: DnaseI enriched


title: 99-048-06_DS7179_gp_5ug G

description: DnaseI enriched


title: 99-048-05_DS7147_gp_5ug G

description: DnaseI enriched


title: E_099_077_06_DS7275_W G

description: DnaseI enriched


title: E_098_043_03_DS7167_W G

description: DnaseI enriched


title: E_098_048_04_DS7229_W A

description: DnaseI enriched


title: 94-32-03_DS7244_d C

description: Control genomic dna (untreated)


title: 99-048-05_DS7147_gp_5ug A

description: DnaseI enriched


title: E_099_077_03_DS7168_W G

description: DnaseI enriched


title: E_099_077_03_DS7168_W A

description: DnaseI enriched


title: 098-32-01_DS6998_WGA G

description: DnaseI enriched


title: 098-32-03_DS7034_WGA G

description: DnaseI enriched


title: E_099_077_04_DS7273_W G

description: DnaseI enriched


title: 99-032-10_DS7190_WGA_4ug G

description: DnaseI enriched


title: 098-32-03_DS7034_WGA A

description: DnaseI enriched


title: C_094_75_01_PDS273_D G

description: Control genomic dna (untreated)


title: E_099_077_15_DS6897_W G

description: DnaseI enriched


title: E_099_077_15_DS6897_W A

description: DnaseI enriched


title: E_099_077_04_DS7273_W A

description: DnaseI enriched


title: 94-45-21_DS7257_C_cont_d G

description: Control genomic dna (untreated)

source_name: IMR90 ATCC; Control genomic dna (untreated)

tag: IMR90 ATCC


title: 94-45-08_DS7260_B_cont_d G

description: Control genomic dna (untreated)

source_name: SKMC ATCC; Control genomic dna (untreated)


title: C_094_81_02_PDS279_D G

description: Control genomic dna (untreated)


title: C_094_75_06_PDS278_D G

description: Control genomic dna (untreated)


title: E_098_054_04_DS7317_W G

description: DnaseI enriched

source_name: MCF7 ATCC; DnaseI enriched

tag: MCF7 ATCC


title: E_099_086_04_DS6883_W G

description: DnaseI enriched


title: C_094_065_03_PDS273_D A

description: Control genomic dna (untreated)

source_name: CACO2 ATCC; Control genomic dna (untreated)


title: 99-007-02_DS7135_wga G

description: DnaseI enriched

source_name: HESC G.Stam; DnaseI enriched


title: E_098_048_02_DS7213_W A

description: DnaseI enriched

source_name: HL60 ATCC; DnaseI enriched


title: C_094_80_07_PDS279_D G

description: Control genomic dna (untreated)


title: E_098_048_04_DS7229_W G

description: DnaseI enriched


title: C_094_75_02_PDS276_D G

description: Control genomic dna (untreated)

source_name: HepG2 ATCC; Control genomic dna (untreated)


title: C_094_81_04_DS7475_D A

description: Control genomic dna (untreated)


title: 94-56-02_PDS275_cont_d G

description: DnaseI enriched

source_name: HELA ATCC; DnaseI enriched


title: C_094_065_01_PDS275_D G

description: Control genomic dna (untreated)

source_name: HELA ATCC; Control genomic dna (untreated)


title: C_094_75_02_PDS276_D A

description: Control genomic dna (untreated)


title: 098-32-03_DS7034_WGA E

description: DnaseI enriched

source_name: CACO2 ATCC; DnaseI enriched


title: 99-048-04_DS7104_gp_5ug G

description: DnaseI enriched


title: C_094_065_02_PDS275_D G

description: Control genomic dna (untreated)


title: 99-048-06_DS7179_gp_5ug E

description: DnaseI enriched

source_name: HepG2 ATCC; DnaseI enriched


title: C_094_81_03_DS7475_D A

description: Control genomic dna (untreated)

source_name: HL60 ATCC; Control genomic dna (untreated)


title: C_094_75_01_PDS273_D A

description: Control genomic dna (untreated)


title: E_099_086_01_DS6851_W E

description: DnaseI enriched


title: C_094_75_06_PDS278_D A

description: Control genomic dna (untreated)

source_name: SKMC Cambrex; Control genomic dna (untreated)


title: 99-007-02_DS7135_wga E

description: DnaseI enriched


title: C_094_75_07_PDS279_D G

description: Control genomic dna (untreated)


title: 99-048-05_DS7147_gp_5ug E

description: DnaseI enriched


title: E_098_048_02_DS7213_W E

description: DnaseI enriched


title: E_099_086_03_DS6747_W E

description: DnaseI enriched

source_name: HCD4 Wilson; DnaseI enriched


title: 098-32-02_DS7010_WGA E

description: DnaseI enriched


title: E_099_077_09_DS6127_W E

description: DnaseI enriched


title: 99-048-02_DS7077_gp_5ug G

description: DnaseI enriched


title: 99-048-02_DS7077_gp_5ug A

description: DnaseI enriched


title: E_098_043_01_DS6997_W E

description: DnaseI enriched


title: 94-56-02_PDS275_cont_d A

description: DnaseI enriched


title: 99-048-04_DS7104_gp_5ug A

description: DnaseI enriched


title: C_094_065_01_PDS275_D A

description: Control genomic dna (untreated)


title: E_099_086_04_DS6883_W E

description: DnaseI enriched


title: E_099_077_12_DS6879_W E

description: DnaseI enriched

source_name: HTH1 Wilson; DnaseI enriched

tag: HTH1 Wilson


title: E_099_077_05_DS7274_W E

description: DnaseI enriched

source_name: SKMC ATCC; DnaseI enriched


title: 098-32-01_DS6998_WGA E

description: DnaseI enriched


title: C_094_065_02_PDS275_D A

description: Control genomic dna (untreated)


title: 99-032-10_DS7190_WGA_4ug E

description: DnaseI enriched


title: E_099_077_13_DS6890_W E

description: DnaseI enriched


title: E_098_065_03_DS7347_W E

description: DnaseI enriched

source_name: HMEC Cambrex; DnaseI enriched

tag: HMEC Cambrex


title: E_098_054_01_DS7106_W E

description: DnaseI enriched


title: E_099_077_15_DS6897_W E

description: DnaseI enriched

source_name: HTH2 Wilson; DnaseI enriched


title: E_098_065_04_DS7348_W E

description: DnaseI enriched

source_name: K562 ATCC; DnaseI enriched


title: E_099_077_04_DS7273_W E

description: DnaseI enriched

source_name: SKMC Cambrex; DnaseI enriched


title: E_099_077_16_DS6929_W E

description: DnaseI enriched


title: E_099_077_10_DS6881_W E

description: DnaseI enriched


title: E_098_054_02_DS7107_W E

description: DnaseI enriched


title: E_098_065_01_DS6898_W E

description: DnaseI enriched


title: C_094_082_02_PDS277_D E

description: Control genomic dna (untreated)

source_name: K562 ATCC; Control genomic dna (untreated)


title: C_094_065_03_PDS273_D E

description: Control genomic dna (untreated)

source_name: CACO2 ATCC; Control genomic dna (untreated)


title: C_094_75_06_PDS278_D E

description: Control genomic dna (untreated)

source_name: SKMC ATCC; Control genomic dna (untreated)


title: E_099_077_03_DS7168_W E

description: DnaseI enriched


title: C_094_082_04_PDS279_D E

description: Control genomic dna (untreated)

source_name: SK-N-SH ATCC; Control genomic dna (untreated)


title: E_099_077_14_DS6895_W E

description: DnaseI enriched


title: C_094_082_03_DS7457_D E

description: Control genomic dna (untreated)


title: C_094_75_01_PDS273_D E

description: Control genomic dna (untreated)


title: C_094_082_01_DS7456_D E

description: Control genomic dna (untreated)

source_name: HepG2 ATCC; Control genomic dna (untreated)


title: E_099_077_06_DS7275_W E

description: DnaseI enriched


title: E_098_048_01_DS7105_W E

description: DnaseI enriched


title: C_094_75_02_PDS276_D E

description: Control genomic dna (untreated)


title: C_094_065_04_PDS276_D E

description: Control genomic dna (untreated)


title: E_098_065_02_DS7346_W E

description: DnaseI enriched


title: C_094_065_02_PDS275_D E

description: Control genomic dna (untreated)

source_name: HELA ATCC; Control genomic dna (untreated)


title: C_094_065_01_PDS275_D E

description: Control genomic dna (untreated)


title: 94-56-02_PDS275_cont_d E

description: DnaseI enriched

source_name: HELA ATCC; DnaseI enriched


title: E_098_054_03_DS7108_W E

description: DnaseI enriched


title: 99-048-04_DS7104_gp_5ug E

description: DnaseI enriched


title: 99-048-02_DS7077_gp_5ug E

description: DnaseI enriched


title: 99-007-03_DS7136_wga E

description: DnaseI enriched

source_name: HESC G.Stam; DnaseI enriched


title: G60 vs G60 (self-self) - 3000148352R

status: Public on Jun 22 2007

type: RNA

city: São Paulo

first: Raphaela

middle: Castro

last: Georg

state: São Paulo

address: Av. Prof Lineu Prestes, 748

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization.

molecule: total RNA

organism: Blastocladiella emersonii

label_protocol: 10ug of total RNA was reverse transcribed and labeled using CyScribe Post-labelling kit (GE Healthcare). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

extract_protocol: total RNA was extracted using Trizol regent (Invitrogen)

tag: 60 min germination cells


title: G60 vs G60 (self-self) - 3000148352L


title: E60_HS vs E60 – 3000148364L

tag: 60 min sporulation cells submitted previously to heat shock (38oC) for 30 min

tag: 60 min sporulation cells.


title: G60_HS vs G60 - 3000148355L

tag: 60 min germination cells submitted previously to heat shock (38oC) for 30 min


title: G60_HS vs G60 - 3000148355R


title: E60_HS vs E60 – 3000148364R


title: E60_HS vs E60 – 3000148359L


title: E60 vs E60 (self-self) - 3000148627R

tag: 60 min sporulation cells


title: G60_HS vs G60 - 3000148353R


title: G60_Cd200uM vs G60 – 3000148604R

tag: 60 min germination cells submitted previously to 200uM CdCl2 for 30 min

tag: 60 min germination cells.


title: G60_HS vs G60 - 3000148353L


title: E60 vs E60 (self-self) - 3000148627L


title: E60_HS vs E60 – 3000148356R


title: G60_Cd200uM vs G60 – 3000148611R


title: E60_HS vs E60 – 3000148356L


title: G60_Cd200uM vs G60 – 3000148611L


title: G60_HS vs G60 - 3000148354R


title: E60_HS vs E60 – 3000148363R


title: G60_Cd100uM vs G60 – 3000148619R

tag: 60 min germination cells submitted previously to 100uM CdCl2 for 30 min


title: E60_HS vs E60 – 3000148359R


title: E60_HS vs E60 – 3000148363L


title: G60_Cd100uM vs G60 – 3000148616L


title: G60_Cd200uM vs G60 – 3000148604L


title: G60_Cd200uM vs G60 – 3000148609L


title: G60_Cd200uM vs G60 – 3000148609R


title: G60_HS vs G60 - 3000148354L


title: G60_Cd100uM vs G60 – 3000148615R


title: G60_Cd100uM vs G60 – 3000148615L


title: E60_Cd200uM vs E60 – 3000148349R

tag: 60 min sporulation cells submitted previously to 200uM CdCl2 for 30 min


title: E60_Cd200uM vs E60 – 3000148350R


title: E60_Cd200uM vs E60 – 3000148351R


title: 12981328cy5Sce2965_cy3ControlRep2

status: Public on Jun 21 2007

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

department: Biology

country: Canada

institute: University of Toronto

description:
Isopropanol precipitation
 _ Add 1 volume (I added 120 µL) of isopropanol.
 _ Precipitate the DNA on at -20C for 30 minutes (or place at –20°C); spin 10 minutes at 4°C. _ Remove isopropanol from pellet; rinse pellet with ice cold 70% ethanol (200ul). Scott rinses twice in 70% EtOH, the second time with EtOH that has been sitting at RT.
 _ Pulse centrifuge the samples, and remove all remaining alcohol by pipetting.
 _ Do not allow the labeled cDNA to dry completely.
Resuspend the pellet in 5 ul of dH2O (SigmaW4502).
Often, some colour can be observed in the resuspended pellet; however, lack of colour does not necessarily indicate a failed reaction.

hyb_protocol: Hybridization A prehybridization step is not required. Although the best results are generally obtained from using the cDNA immediately after labeling, it can be stored in the dark at –20°C for several days. _ To each 100 µL of DIG Easy Hyb solution (Roche), add 5 µL of yeast tRNA (Invitrogen; 10 mg/ml) and 5 µL of calf thymus DNA (Sigma; 10 mg/ml). (I used ss salmon sperm DNA 10mg/ml). _Incubate the mixture at 65°C for 2 minutes and cool to room temperature. Add 77.5ul of DIG easy Hyb soln to each pooled pair of Cyanine 5 and Cyanine 3-labeled cDNA (about 5 µL). Pipette well to mix.  _Incubate at 65°C for 3 minutes, and cool to room temperature. Vortex and quick spin. _prewarm the hyb chamber and container with SDW.37C.  _ For the hybridizations involving the use of coverslips, the hyb mixture should be pipetted directly onto the coverslip. Place coverslip onto a reliable surface (the corner of a tip box works well) and add the hyb mixture. Lay the slide “array-side” down on top of the coverslip. Use a 24 x 50 mm coverslip for the yeast arrays. _ Carefully place the slide(s) into hybridization chamber(s). The hybridization chambers that we use are plastic microscope slide boxes containing a small amount of DIG Easy Hyb solution in the bottom (to keep a humid environment). Clean plain microscope slides are placed at every second or third slide position in the slide box to create rails or a platform onto which the hybridization arrays can be placed. Each hybridization chamber can hold two or three hybridization slides (depending on which direction the slides are placed). The lid is carefully placed onto the box and the box is then wrapped with plastic wrap.  _ Incubate on a level surface in a 37 °C incubator overnight (about 18 hours). Washing _ Critical that gloves be worn during this procedure  _Disassemble the hybridization chamber and remove the coverslip by quickly but gently dipping the array in 1X SSC (let the coverslip slide off gently, let the CV slide off gently). _ When all of the arrays have been removed from the hybridization chambers, wash 3 times for 15 minutes each at 50°C in 50 ml Falcon tubes containing pre-warmed (at 50oC) 1X SSC/0.1% SDS with gentle occasional agitation. I wash 2 slides per falcon tube back to back for all washes except the very last one before scanning. _After the washes are complete, rinse the slides twice in room temperature 1X SSC (plunging 4-6 times) and then in 0.1X SSC. The last wash is the most stringent for the array so do this wash at the last minute before scanning. Shake vigorously in this wash, do not be afraid of washing off the dyes in this step, it is critical for removing background. Also must use fresh 0.1X SSC for each slide. _ I dry the slides from the last wash in the Westwood lab with the pressurized air sprayer. _ Arrays should be stored in the dark. It is recommended that arrays be scanned as soon as possible after they are washed

scan_protocol: Scanning and data analysis Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and quantified with QuantArray software (v3.0, Perkin Elmer). The adaptive quantification algorithm was used. Further analysis, including data normalization, was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.).  The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess (Locally Weighted Scatter Plot Smoother) normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100.

data_processing:
Normalization
This method normalizes the data to the intensity for each spot and its surrounding area. This method compensates for the effects of dim spots and ensures that normalization is not influenced by the absolute values or the distribution of the bright spots. This method compares the channel 1 intensity /channel 2 intensity normalized (treated/over normalized reference sample) for all non flagged spots in each sub grid (Reference Gene traffic 2.8 Duo Manual Rev. C).
Once the data was normalized the criteria used for filtering the microarray data and selection of  significantly unregulated or down regulated genes were for each gene the mean log 2 ratio up 0.67 for all valid spots of that gene. Coefficient of variance  for all valid spots of that gene less than 1, Number of valid spots greater at 75% for the gene. The covariance of Variance is the standard deviation expressed as a percentage of the mean. This is a measure of the precision of the outcome over several replications. The higher the precision the lower the covariance so that outliers are not counted in the results as valid data spots.
Usable spot pairs were identified. (Usable spot pairs were defined as having the signal intensities of each channel greater than twice the average background for that channel and having the fluorescence intensity of at least one channel greater than the average intensity of the background.) The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100. The three hybridizations were treated as replicates, and a distribution of the mean log2-transformed ratios of the Cy5/Cy3 intensities was plotted (Fig. 4, dotted line). For replicate experiments, at least two-thirds of the spots for a given gene (n ≥4) had to meet the aforementioned validation criteria for the ratio to be included in the distribution. For 95% of the data, the average fold change between the two channels was less than 1.2. Over 99% of the spots exhibited Cy3 and Cy5 signal intensities within ±1.3-fold of each other. The average number of usable spot pairs per slide in these trials was 5542.
Genes were considered in the analysis only if the covariance of the aggregate data from all six arrays was less than 100%.

organism: Saccharomyces cerevisiae

source_name: sce2713 and sce2902

label_protocol:
Protocols from the UHN Microarray Centre 2003.05.15 ©2003 University Health Network/Ontario Cancer Institute
Direct Labeling Protocol from the University Health Network (UHN) Microarray Centre
RNA Isolation
 There are a variety of protocols available that will yield RNA of sufficient quality for microarrays. Many microarray users rely on the Qiagen RNeasy kit for the isolation or cleanup of total RNA. We have not observed any appreciable difference between images derived from the use of total RNA versus mRNA.
Determine the final concentration of purified RNA by measuring A260 and A280. Prepare RNA to a final concentration of at least 1 µg/µL.
I used the hot phenol/chloroform protocol from this website site: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
Reverse Transcription
For 10-20 µg of Qiagen purified total RNA or 0.1-0.5 µg of mRNA, the RT reaction volume is 40 µl. I aimed for 20ug.
Combine the following on ice:
8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen)
1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/_l)
3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP)
1.0 µL 2 mM dCTP
1.0 µL 1 mM Cyanine 3 or Cyanine 5-dCTP (NEN)
 4.0 µL 0.1 M DTT
 0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA)
to 40 µL dH20 (Sigma)
 _ Label the two different samples to be analyzed (i.e. control and experimental) on an array with different fluors (i.e. Cyanine 3 or Cyanine 5). It is also suggested that you perform reciprocal labeling (For more information on reciprocal labeling see the microFAQ).
 _ Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Ensure that the reactions are kept in the dark as the dyes are light sensitive. If the incubator is not covered use aluminum foil to create a cover preventing light from photo bleaching the fluors.
_ Add 2 µL of reverse transcriptase (Superscript II, Invitrogen). Incubate at 42 °C for 3 hours.
Stop Reaction
 _ Briefly centrifuge the reaction and place on ice.
_ Add 5 µL of 50 mM EDTA (pH 8.0), and 4 µL of 5 N NaOH. Mix well by pipetting
_ Incubate at 65°C for 20 minutes to hydrolyse the RNA.
_ Add 4.5 µL of 5 M acetic acid. (A small aliquot of the reaction can be pipetted onto pH paper to ensure the solution is neutralized. Checking the pH is also an optional step that is not necessary for every reaction.)
_ Combine the two reactions that will be hybridized to the same slide (i.e. control and experimental). (I added Cy5 to Cy3).

extract_protocol:
Reference for this protocol: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
This is a standard Yeast hot acid phenol/chloroform RNA extraction protocol followed by a total RNA clean up using Qiagen RNeasy mini spin columns. The RNA is then quantified  by measuring A260 and A280 and then checked by running a DEPC 1% Agarose gel.
RNA extraction:
1.	Centrifuge cells at room temperature, wash with sterile water and centrifuge again. Usually, 50ml of culture at OD 0.6-0.8 are enough.
2.	If necessary, store cell pellets at -80°C.
3.	Resuspend cell pellets in TES buffer (10mM Tris pH 7.5, 10mM EDTA, 0.5%SDS, autoclaved) (1.2ml buffer for 50 OD of cells).
4.	Transfer 400ul aliquots of the resuspended cells in three 1.5ml eppendorf tubes.
5.	Add 400ul of Phenol:Chloroform 5:1 (from Sigma ref: P-1944).
6.	Incubate at 65°C for 20min and vortex 30sec every 5min (be very careful with hot phenol!!).
7.	Cool at -80°C for 30min.
8.	Centrifuge at room temperature for 15min at 15000rpm.
9.	Keep the aqueous phase and add 400ul of Phenol:Chlorofom 5:1.
10.	Vortex tubes three times for 30sec then centrifuge.
Repeat steps 8 to 10 one more time.
11.	Add 300µl of Chloroform (ready red from Sigma) to the aqueous phase.
12.	Vortex tubes three times 20sec.
13.	Centrifuge 2' at 15000rpm.
14.	Transfer aqueous phase in tubes containing 30µl of 3M Na Ac pH 5.3 (autoclaved).
15.	Add 600µl Ethanol absolute.
16.	Incubate one hour at -20°C.
17.	Centrifuge 15min at 15000rpm at 4°C.
18.	Dry pellets and resuspend the three pellets in the same 100µl of bidistilled autoclaved water (Sigma W4502).
19.	Carefully quantify RNA and use 100µg for RNA clean up.
RNA clean up:
1.	The RNA clean up is an essential step for the quality of the Reverse Transcription. Use a Rneasy minikit (Qiagen, ref : 74106) for RNA clean up. Just follow the recommendations of Qiagen.
2.	Elute the column with 50µl of water a first time, then re-elute a second time with the same 50µl.
3.	Quantify your purified RNA. You will need 20µg for cDNA synthesis.

tag: Equal mixture of total RNA from 2 evolved lines s6 and m12

tag: Hybrid diploid of s6 and m12


title: E60_Cd200uM vs E60 – 3000148349L


title: E60_Cd200uM vs E60 – 3000148350L


title: E60_Cd100uM vs E60 - 3000148612L

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)]

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked? in water for 10s and dried with nitrogen gas.

data_processing: filtering low intensity spots, LOWESS normalization

extract_protocol: Total RNA was isolated using Trizol (Invitrogen)

tag: 60 min sporulation cells submitted previously to 100uM CdCl2 for 30 min


title: E60_Cd200uM vs E60 – 3000148351L


title: E60_Cd100uM vs E60 – 3000148613R


title: 13449519cy5Sce2965_cy3ControlRep3

tag: Equal mixture of RNA from 2 evolved pure lines s6 and m12

tag: Hybrid Diploid od s6 and m12


title: 12981217cy5COntrol_cy3Sce2965Rep1

tag: Equal mixture of RNA from 2 evolved lines s6 and m12


title: E60_Cd100uM vs E60 – 3000148613L


title: 13449518cy5COntrol_cy3Sce2950Rep4

source_name: Sce2709 and sce2898

tag: Equal mixture of RNA from 2 pure evolved lines s2 and m8

tag: Hybrid Diploid of s2 and m8


title: Sham infected HIGK cells, biological rep2

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

description: Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)

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

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

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

source_name: Gene expression data from sham infected HIGK cells.

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

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

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

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

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

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


title: E60_Cd100uM vs E60 – 3000148614L


title: HIGK cells infected with Fusobacterium nucleatum, biological rep4

source_name: Gene expression data from Fusobacterium nucleatum-infected HIGK cells.

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


title: Sham infected HIGK cells, biological rep3


title: Sham infected HIGK cells, biological rep1


title: 13449521Cy3Sce2965_cy5ControlRep4

source_name: Sce2713 and sce2902

tag: Hybrid Diplod of s6 and m12


title: E60_Cd100uM vs E60 – 3000148614R


title: Sham infected HIGK cells, biological rep4


title: 12781192cy5sce2950_cy3ControlRep1

source_name: sce2709 and sce2898

tag: Reference strain. Equal mixture of evolved pure lines sce2709 and sce2898

tag: Hybrid diploid of evolved pure line s2 and m8


title: HIGK cells infected with Fusobacterium nucleatum, biological rep2


title: G60_Cd100uM vs G60 – 3000148616R


title: HIGK cells infected with Fusobacterium nucleatum, biological rep1


title: 13449517cy3Control_cy5Sce2950Rep3

tag: Equal mixture of RNA from 2 evolved pure lines s2 and m8

tag: Hybrid diplod of s2 and m8


title: 12781186cy5control_cy3sce2950Rep2

description: A 10-ml culture of a single colony was grown at  30°C and 250 rpm to saturation (~1 × 108 cells/ml) overnight in 0.5xYPD (1% glucose, 1% Difco peptone, 0.5% Difco yeast extract). The culture was diluted to an OD600 of 0.03 and used to inoculate 50 mls of fresh medium in a 250 ml flask and grown to an OD600 of 0.3.  Cells were collected by centrifugation at 1500 rpm for 3 minutes at 4C. The cell pellet was rinsed once in 1ml DEPC water, transferred to a 1.5 ml microfuge tube, spun at maximum speed for 10s, the supernatant removed and pellet immediately frozen in liquid nitrogen and stored at –80oC until RNA extraction. RNA preparation and hybridization to Yeast Y6.4k4 arrays from the UHN Microarray Centre() were performed according to a standard hot acid phenol/chloroform extraction followed by a total RNA clean up with Qiagen RNeasy mini spin columns (cat# 74106). Protocols are described at http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php. The RNA was quantified by measuring A260 and A280 and checked on a DEPC 1% agarose gel. Direct labeling of cDNA was carried out according to protocols from the University Health Network (UHN) Microarray Centre. (http://www.angiogenesis.ca/protocols/Molecular_Biology/Microarray.html.Reverse transcription used 20ug of prepared RNA and the reaction purified by isopropanol precipitation with hybridization overnight at 37oC in Corning hybridization chambers (cat# 2551).

hyb_protocol: Hybridization A prehybridization step is not required. Although the best results are generally obtained from using the cDNA immediately after labeling, it can be stored in the dark at –20°C for several days. _ To each 100 µL of DIG Easy Hyb solution (Roche), add 5 µL of yeast tRNA (Invitrogen; 10 mg/ml) and 5 µL of calf thymus DNA (Sigma; 10 mg/ml). (I used ss salmon sperm DNA 10mg/ml). _Incubate the mixture at 65°C for 2 minutes and cool to room temperature. Add 77.5ul of DIG easy Hyb soln to each pooled pair of Cyanine 5 and Cyanine 3-labeled cDNA (about 5 µL). Pipette well to mix.  _Incubate at 65°C for 3 minutes, and cool to room temperature. Vortex and quick spin. _prewarm the hyb chamber and container with SDW.37C.  _ For the hybridizations involving the use of coverslips, the hyb mixture should be pipetted directly onto the coverslip. Place coverslip onto a reliable surface (the corner of a tip box works well) and add the hyb mixture. Lay the slide “array-side” down on top of the coverslip. Use a 24 x 50 mm coverslip for the yeast arrays. _ Carefully place the slide(s) into hybridization chamber(s). The hybridization chambers that we use are plastic microscope slide boxes containing a small amount of DIG Easy Hyb solution in the bottom (to keep a humid environment). Clean plain microscope slides are placed at every second or third slide position in the slide box to create rails or a platform onto which the hybridization arrays can be placed. Each hybridization chamber can hold two or three hybridization slides (depending on which direction the slides are placed). The lid is carefully placed onto the box and the box is then wrapped with plastic wrap.  _ Incubate on a level surface in a 37 °C incubator overnight (about 18 hours). Washing _ Critical that gloves be worn during this procedure  _Disassemble the hybridization chamber and remove the coverslip by quickly but gently dipping the array in 1X SSC (let the coverslip slide off gently, let the CV slide off gently).

scan_protocol: Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and quantified with QuantArray software (v3.0, Perkin Elmer). The adaptive quantification algorithm was used. Further analysis, including data normalization, was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.).  The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess (Locally Weighted Scatter Plot Smoother) normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100.

source_name: Control(sce2709 and sce2898)

label_protocol: UHN Direct labelling

extract_protocol: Hot Phenol RNA extraction followed by Qiagen RNeasy column

tag: Equal Mixture of total RNA of evolved pure lines (s2 and M8 or s6 amd m12)- Reference strains

label_protocol:
Protocols from the UHN Microarray Centre 2003.05.15 ©2003 University Health Network/Ontario Cancer Institute
Direct Labeling Protocol from the University Health Network (UHN) Microarray Centre
RNA Isolation
 There are a variety of protocols available that will yield RNA of sufficient quality for microarrays. Many microarray users rely on the Qiagen RNeasy kit for the isolation or cleanup of total RNA. We have not observed any appreciable difference between images derived from the use of total RNA versus mRNA.
Determine the final concentration of purified RNA by measuring A260 and A280. Prepare RNA to a final concentration of at least 1 µg/µL.
I used the hot phenol/chloroform protocol from this website site: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
Reverse Transcription
For 10-20 µg of Qiagen purified total RNA or 0.1-0.5 µg of mRNA, the RT reaction volume is 40 µl. I aimed for 20ug.
Combine the following on ice:
8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen)
1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/_l)
3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP)
1.0 µL 2 mM dCTP
1.0 µL 1 mM Cyanine 3 or Cyanine 5-dCTP (NEN)
 4.0 µL 0.1 M DTT
 0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA)
to 40 µL dH20 (Sigma)
 _ Label the two different samples to be analyzed (i.e. control and experimental) on an array with different fluors (i.e. Cyanine 3 or Cyanine 5). It is also suggested that you perform reciprocal labeling (For more information on reciprocal labeling see the microFAQ).
 _ Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Ensure that the reactions are kept in the dark as the dyes are light sensitive. If the incubator is not covered use aluminum foil to create a cover preventing light from photo bleaching the fluors.
_ Add 2 µL of reverse transcriptase (Superscript II, Invitrogen). Incubate at 42 °C for 3 hours.
Stop Reaction
 _ Briefly centrifuge the reaction and place on ice.
_ Add 5 µL of 50 mM EDTA (pH 8.0), and 4 µL of 5 N NaOH. Mix well by pipetting
_ Incubate at 65°C for 20 minutes to hydrolyse the RNA.
_ Add 4.5 µL of 5 M acetic acid. (A small aliquot of the reaction can be pipetted onto pH paper to ensure the solution is neutralized. Checking the pH is also an optional step that is not necessary for every reaction.)
_ Combine the two reactions that will be hybridized to the same slide (i.e. control and experimental). (I added Cy5 to Cy3).
Isopropanol precipitation
 _ Add 1 volume (I added 120 µL) of isopropanol.
 _ Precipitate the DNA on at -20C for 30 minutes (or place at –20°C); spin 10 minutes at 4°C. _ Remove isopropanol from pellet; rinse pellet with ice cold 70% ethanol (200ul). Scott rinses twice in 70% EtOH, the second time with EtOH that has been sitting at RT.
 _ Pulse centrifuge the samples, and remove all remaining alcohol by pipetting.
 _ Do not allow the labeled cDNA to dry completely.
Resuspend the pellet in 5 ul of dH2O (SigmaW4502).
Often, some colour can be observed in the resuspended pellet; however, lack of colour does not necessarily indicate a failed reaction.

tag: Hybrid diploid of the two evolved lines. S2M8 hybrid or S6M12 hybrid.


title: HIGK cells infected with Fusobacterium nucleatum, biological rep3


title: HIGK cells infected with Streptococcus gordonii, biological rep4

source_name: Gene expression data from Streptococcus gordonii-infected HIGK cells.


title: HIGK cells infected with Streptococcus gordonii, biological rep1


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep5

status: Public on Jun 20 2007

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Study the transcriptomic effects of the shear stress on cultured osteoblast-like MC3T3 cells

hyb_protocol: Labeled cDNAs were hybridized overnight at 50C on a microscope slide spotted with ~ 27,000 spotted mouse cDNA sequences produced by the Microarray Core Facility of the Albert Einstein College of Medicine. We used six sets of controls (C1, C2, C3, C4, C5, C6) and shear stressed samples (S1, S2, S3, S4, S5, S6) to ensure statistical relevance of the study, co-hybridized with six microarrays in the “multiple yellow” design described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38.

scan_protocol: Slides were scanned with GenePix 4100A scanner (Axon Instruments, CA) and images were primarily analyzed with GenePixPro 4.0 (Axon Instruments, CA)

data_processing: Data were normalized and analyzed with in house developed algorithms described in Iacobas DA, Iacobas S, Li WEI, et al. Physiol Genomics 20: 211-223, 2005.

organism: Mus musculus

label_protocol: 50 ug of total RNA from each sample was reversed transcribed into labeled cDNAs using fluorescent Cy5-dUTP (Amersham Biosciences, NJ)

growth_protocol: Cells were cultured in minimal essential alpha medium (alpha-MEM, Invitrogen Corporation) containing 1% penicillin-streptomycin (Invitrogen Corporation) and 5% fetal bovine serum (FBS) (Invitrogen Corporation) at 37C with 5% CO2. Confluent monolayers of cells were grown on glass slides in static condition and transferred to the flow apparatus to expose the monolayers to a pulsatile flow with average shear stress of 5dyn/cm2 for 5 h at 1 Hz frequency.

extract_protocol: TRIzol (Invitrogen, CA)

treatment_protocol: The fluid flow setup consisted of a parallel plate flow chamber (Cytodyne, La Jolla, CA), a re-circulating flow loop with a variable speed Masterflex pump (Cole-Palmer Instrument Company) and a reservoir with culture medium (alpha-MEM with 1% FBS) maintained at 37°C with 95% O2/ 5% CO2. This system produces pulsatile flow (1 Hz) over a cell monolayer. A flow rate was chosen to yield a shear stress of 5 dyn/cm2. Control cells were kept under static conditions with the same set up at 37°C.

tag: Cultured osteoblast-like MC3T3-E1 cells (obtained from Dr. Kenneth J. McLeod - Binghamton University) within 3-6 passages subjected to shear stress


title: HIGK cells infected with Streptococcus gordonii, biological rep3


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep4

label_protocol: 50 ug of total RNA from each sample was reversed transcribed into labeled cDNAs using fluorescent Cy3-dUTP (Amersham Biosciences, NJ)


title: E60_Cd100uM vs E60 – 3000148612R

tag: 60 min sporulation cells


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep2


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep6


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep6

tag: Cultured osteoblast-like MC3T3-E1 cells (obtained from Dr. Kenneth J. McLeod - Binghamton University) within 3-6 passages


title: G60_Cd100uM vs G60 – 3000148619L

tag: 60 min germination cells

tag: 60 min germination cells submitted previously to 100uM CdCl2 for 30 min


title: HIGK cells infected with Streptococcus gordonii, biological rep2


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep1


title: Cultured_osteoblast-like_shear-stressed_MC3T3-E1_cells_rep3


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep5

hyb_protocol: Labeled cDNAs were hybridized overnight at 50C on a microscope slide spotted with ~ 27,000 spotted mouse cDNA sequences produced by the Microarray Core Facility of the Albert Einstein College of Medicine. We used six sets of controls (C1, C2, C3, C4, C5, C6) and shear stressed samples (S1, S2, S3, S4, S5, S6) to ensure statistical relevance of the study, co-hybridized with six microarrays in the “multiple yellow” design described in Iacobas DA, Fan C, Iacobas S et al., Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38.


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep2


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep1


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep4


title: Large Scale Identification of DNaseI Hypersensitive Regions in Genomic DNA (HepG2)

description:
Digestion of purified HepG2 nuclei with low levels of DNaseI results
in the release of low mw DNA fragments adjoining multiple DNaseI cut
sites. These fragments were enriched using high speed centrifugation
through sucrose step gradients. The small fragments were purified then
labeled using random primer extension with Cy5 labeled random heximers.

hyb_protocol: http://www.nimblegen.com ChIP-chip Hybridization protocols.

scan_protocol: http://www.nimblegen.com ChIP-chip scan protocols.

data_processing: Data values are the log ratio of red and green channel intensities, scaled by the tukey-biweight mean of array control probes

source_name: HepG2 liver

label_protocol: According to Nimblegen ChIP-chip total input DNA protocol. http://www.nimblegen.com

tag: Total genomic DNA (Control). Fragmented by DNaseI. Labeled using primer extension with cy3 labeled random hexamers.

label_protocol: According to Nimblegen ChIP-chip published protocol. http://www.nimblegen.com

tag: DNaseI hypersensitive enriched fraction. HS sites enriched by sucrose gradient fractionation. DNA labeled using primer extension with cy5 labeled random hexamers.


title: Cultured_osteoblast-like_control_MC3T3-E1_cells_rep3


title: Connexin43 null neonatal mouse brain2 (K43-2)

description:
Cy3-labeled cDNA from brains of neonatal Cx43 null C57BL mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = Cx43 null neonatal mouse brain

source_name: pool of ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, stomach)


title: wildtype neonatal mouse brain4 (W-4)

description:
Cy5-labeled cDNA was obtained from RNA sample reference, prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = wildtype mouse brain

source_name: sample reference (S)

source_name: wildtype neonatal mouse brain4 (W-4)


title: 26-Cy3-LTB & Cy5-FE

city: Sapporo

first: Sorin

middle: Vasile

last: Sabau

address: 5-1-1-1 Minamisawa, Minamiku

country: Japan

institute: Tokai University

hyb_protocol: Hybridization and washing protocols were according to the manufacturer’s instructions (Agilent Technologies).

scan_protocol: The microarrays were scanned with a GenePix4000B DNA Microarray Scanner (Axon Instruments, Foster City, CA). The resulting fluorescence intensity for each spot was quantified using GENEPIX PRO 4.0 microarray analysis software (Axon Instruments).

data_processing: Quantified images were exported into text files for statistical analysis. After removing the flagged features and subtracting the background value we took the logarithm (base 2) of the intensity signals.

organism: Ciona intestinalis

source_name: late tailbud embryo

label_protocol: Two micrograms of poly (A)+RNA was labeled with Cy3 using an Agilent Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: To prepare total RNA from C. intestinalis eggs, embryos and juveniles, the acid guanidine thiocyanate-phenol/chloroform (AGPC) method was used.

tag: Late tailbud embryo stage

source_name: fertilized egg

label_protocol: Two micrograms of poly (A)+RNA was labeled with Cy5 using an Agilent Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: To prepare total RNA from C. intestinalis eggs, the acid guanidine thiocyanate-phenol/chloroform (AGPC) method was used.

tag: C. intestinalis was cultivated at the Maizuru Fisheries Research Station of Kyoto University, Maizuru, Kyoto, Japan. Adults were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. After insemination, eggs were washed and maintained in seawater at room temperature (18-20˚C).


title: 24-Cy3-MTB & Cy5-FE

source_name: middle tailbud embryo

tag: Middle tailbud embryo stage


title: 36-Cy3-4.0 & Cy5-2.5

source_name: 4.0 month-old adult

extract_protocol: For total RNA preparation from C. intestinalis adults, tunics were removed and the inner whole bodies of three individuals per stage were homogenized and RNA isolated by ultracentrifugation .

tag: 4.0 month-old adult stage

source_name: 2.5 month-old adult

tag: 2.5 month-old adult stage


title: wildtype neonatal mouse brain2 (W-2)

description:
Cy3-labeled cDNA from brains of neonatal C57BL/6j wildtype mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
Keywords = wildtype mouse brain

source_name: wildtype neonatal mouse brain2 (W-2)


title: 34-Cy3-2.5 & Cy5-1.5

source_name: 1.5 month-old adult

tag: 1.5 month-old adult stage


title: wildtype neonatal mouse brain3 (W-3)


title: 32-Cy3-1.5 & Cy5-Ju

source_name: juvenile embryo

tag: Juvenile embryo stage


title: 14-Cy3-EG & Cy5-FE

source_name: early gastrulae embryo

tag: Early gastrulae embryo stage


title: 30-Cy3-Ju & Cy5-LV

source_name: juveniles

tag: Juveniles stage

source_name: larvae embryo

tag: Larvae embryo stage


title: 18-Cy3-EN & Cy5-FE

source_name: early neurulae embryo

tag: Early neurulae embryo stage


title: 16-Cy3-LG & Cy5-FE

source_name: late gastrulae embryo

tag: Late gastrulae embryo stage


title: wildtype neonatal mouse brain1 (W-1)

description:
Cy3-labeled cDNA from brains of neonatal C57BL/6j wildtype mice was compared to Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.

Keywords = wildtype mouse brain

source_name: wildtype neonatal mouse brain1 (W-1)


title: Connexin43 null neonatal mouse brain4 (K43-4)

source_name: pool of ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, stomach)


title: Connexin43 null neonatal mouse brain3 (K43-3)


title: 20-Cy3-ITB & Cy5-FE

source_name: initial tailbud embryo

tag: Initial tailbud embryo　stage


title: 22-Cy3-ETB & Cy5-FE

source_name: early tailbud embryo

tag: Early tailbud embryo stage


title: 28-Cy3-LV & Cy5-FE


title: Connexin43 null neonatal mouse brain1 (K43-1)


title: 33-Cy3-1.5 & Cy5-2.5

extract_protocol: For total RNA preparation from C. intestinalis adults, tunics were removed and the inner whole bodies of three individuals per stage were homogenized and RNA isolated by ultracentrifugation.


title: 12-Cy3-64cell & Cy5-FE

source_name: sixty four cell embryo

tag: Sixty four cell embryo stage


title: 08-Cy3-16cell & Cy5-FE

source_name: sixteen cell embryo

tag: sixteen cell embryo stage

source_name: fertilized egg


title: 10-Cy3-32cell & Cy5-FE

source_name: thirty three cell embryo

tag: Thirty three cell embryo stages


title: 04-Cy3-4cell & Cy5-FE

source_name: four cell embryo

tag: Four cell embryo stage


title: 31-Cy3-Ju & Cy5-1.5


title: 06-Cy3-8cell & Cy5-FE

source_name: eight cell embryo

tag: Eight cell embryo stages

tag: C. intestinalis was cultivated at the Maizuru Fisheries Research Station of Kyoto University, Maizuru, Kyoto, Japan. Adults were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. After insemination, eggs were washed and maintained in seawater at room temperature (18-20˚C).


title: 29-Cy3-LV & Cy5-Ju


title: Large Scale Identification of DNaseI Hypersensitive Regions in Genomic DNA (CACO2)

description:
Digestion of purified CACO2 nuclei with low levels of DNaseI results
in the release of low mw DNA fragments adjoining multiple DNaseI cut
sites. These fragments were enriched using high speed centrifugation
through sucrose step gradients. The small fragments were purified then
labeled using random primer extension with Cy5 labeled random heximers.

source_name: Caco2 colon

extract_protocol: According to Nimblegen ChIP-chip total input DNA protocol. http://www.nimblegen.com

tag: Total genomic DNA (Control). Fragmented by DNaseI. Labeled using primer extension with cy3 labeled random hexamers.

extract_protocol: According to Nimblegen ChIP-chip published protocol. http://www.nimblegen.com

tag: DNaseI hypersensitive enriched fraction. HS sites enriched by sucrose gradient fractionation. DNA labeled using primer extension with cy5 labeled random hexamers.


title: 25-Cy3-FE & Cy5-LTB

source_name: late tailbud embryo

tag: Late tailbud embryo stage


title: 27-Cy3-FE & Cy5-LV


title: 23-Cy3-FE & Cy5-MTB

source_name: middle tailbud embryo

tag: Middle tailbud embryo stage


title: 13-Cy3-FE & Cy5-EG

source_name: early gastrulae embryo

tag: Early gastrulae embryo stage


title: 21-Cy3-FE & Cy5-ETB


title: 19-Cy3-FE & Cy5-ITB

tag: Initial tailbud embryo stage


title: 17-Cy3-FE & Cy5-EN


title: 09-Cy3-FE & Cy5-32cell

source_name: thirty two cell embryo

tag: Thirty two cell embryo stage


title: Pooled sample of adult male D. melanogaster individuals with wash

status: Public on Jun 18 2007

first: Lauren

middle: M.

last: McIntyre

department: Dept. of Molecular Genetics and Microbiology

description: adult D. melanogaster

data_processing: Imagene v6.0 was used to process image and all results from Imagene listed

organism: Drosophila melanogaster

source_name: male adult D. melanogaster

tag: adult pooled individuals; chip treated with Agilent's Stabilization and Drying Solution


title: 07-Cy3-FE & Cy5-16cell

tag: Sixteen cell embryo stage


title: 03-Cy3-FE & Cy5-4cell


title: Sup fraction for the analysis of Distibution of Mde4, Sgo2, Swi6, and Pcs1

type: other

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

description: Sup fraction for the normalization of ChIP data

data_processing: Data was processed following the protocol provided by Affymetrix (GCOS ver 1.4).

organism: Schizosaccharomyces pombe

source_name: Mitotic Growing cells

tag: Wild type S.pombe cell was used.


title: 05-Cy3-FE & Cy5-8cell

tag: Eight cell embryo stage


title: Pooled sample of adult female D. melanogaster individuals with was

description: adult D. melanogaster

source_name: female adult D. melanogaster


title: 02-Cy3-2cell & Cy5-FE

source_name: two cell embryo

tag: Two cell embryo stage

label_protocol: Two micrograms of poly (A)+RNA was labeled with  Cy5 using an Agilent Fluorescent Linear Amplification Kit (Agilent Technologies).


title: Pooled sample of adult male D. melanogaster individuals without wash

description: adult D. melanogaster

tag: adult pooled individuals; chip not treated with Agilent's Stabilization and Drying Solution


title: 11-Cy3-FE & Cy5-64cell

tag: Sixty four cell embryo stage


title: 15-Cy3-FE & Cy5-LG

source_name: late gastrulae embryo

tag: Late gastrulae embryo stage


title: O157:H7 Sakai timecourse, 8h vs 3h rep3

status: Public on Jun 15 2007

city: East Lansing

first: Thomas

middle: S

last: Whittam

state: MI

address: 165 Food Safety & Tox

department: Microbiology

institute: Michigan State University

description: There are probes on the array that target three different E. coli genomes. Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5x SSC, and 1mg/mL BSA at 42C for 1 hour. After blocking, arrays were washed 2x 5 min in 0.1x SSC and 2x 30s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95C for 5 min and then mixed with 40uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47C for 16-18h. After hybridization, arrays were washed in 2x SSC, 0.5% SDS 37C for 5 min, followed by 2x 5 min in 0.1x SSC, 0.1% SDS 37C, and then 2x 2.5min in room temperature 0.1x SSC.

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: Data were first normalized using print-tip lowess in R/MAANOVA v0.98-8. Normalized data from replicate spots were averaged and then converted to log2 values. The 3h samples were used as the common reference for all subsequent time point

organism: Escherichia coli

source_name: O157:H7 Sakai, 3h mid exponential phase in MOPS minimal medium

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP. 30uL reactions were incubated overnight at 42C. cDNA was purified using PCR cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

growth_protocol: The Sakai strain was inoculated into 10mL of LB broth from freezer stocks and grown to OD600 = 0.1. This ~4h period of growth in LB allowed cells to recover before transfer to MOPS minimal media. MOPS minimal media (10x) was prepared as described in Neidhardt et al. with the addition of 20mL of micronutrient solution instead of 10mL. MOPS minimal media contained 100mL of 10x MOPS minimal media, 10mL of 0.132M K2HPO4, and 5mL of 20% D-glucose per liter. Cultures were inoculated into 50mL of MOPS minimal media with 0.1% glucose at a ratio of 1:200 and grown to stationary phase at 37C with shaking. Cultures in MOPS were transferred to 100mL MOPS in 250mL plastic culture flasks at a ratio of 1:75 and grown for 9h before transfer again to 100mL MOPS in 250mL plastic culture flasks at a ratio of 1:30 and this culture was used to sample RNA during growth. Cultures were sampled at 3h (OD600 ≈ 0.22), 4h (OD600 ≈ 0.45), 4.33h (OD600 ≈ 0.73), 4.66h (OD600 ≈ 0.93), 5h (OD600 ≈ 1), 5.5h, 6h, 7h, 7.5h, and 8h. After 5h, the culture density remained at OD600 ≈ 1.

extract_protocol: 4mL of culture was mixed with 8mL of RNAProtect (Qiagen, Valencia, Calif.), vortexed, and centrifuged at 4C, 7500rpm for 10 min to pellet cells. The supernatant was removed and cell pellets stored at –70C for 1 week or less before RNA extraction. Cell pellets were suspended in 700uL of 95C lysis buffer (20mM sodium acetate pH 5.2, 2mM EDTA pH 8.0, and 0.5% SDS), held at 95C for 30s then mixed with 700uL of 65C Acid-Phenol: Chloroform, pH 4.5 (with IAA, 125:25:1) (Ambion, Austin, Tex.). Samples were held at 65C with periodic shaking for at least 6 minutes before centrifuging at 12000 rpm for 10 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated for at least 1 hour at –20C in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA was suspended in 1mM sodium citrate pH 6.5 and stored at –70C. RNA samples were purified and treated with Dnase using the Rneasy kit

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 3

source_name: O157:H7 Sakai, 8h stationary phase in MOPS minimal medium


title: Distribution of Sgo2 at Whole Genome Scale

description: ChIP-chip experiment for Sgo2.

tag: Wild type S.pombe cells were used.


title: Distribution of Pcs1 at Whole Genome Scale

description: ChIP-chip experiment for Pcs1.

tag: Wild type S.pombe strain was used for ChIP-chip.


title: 01-Cy3-FE & Cy5-2cell

tag: C. intestinalis was cultivated at the Maizuru Fisheries Research Station of Kyoto University, Maizuru, Kyoto, Japan.  Adults were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. After insemination, eggs were washed and maintained in seawater at room temperature (18-20˚C).

tag: two cell embryo stage


title: O157:H7 Sakai timecourse, 8h vs 3h rep4

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 4


title: 35-Cy3-2.5 & Cy5-4.0

source_name: 2.5 month-old adult

tag: 2.5 month-old adult stage

source_name: 4.0 month-old adult

tag: 4.0 month-old adult stage


title: O157:H7 Sakai timecourse, 8h vs 3h rep2

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 2


title: O157:H7 Sakai timecourse, 7.5h vs 3h rep2

source_name: O157:H7 Sakai 7.5h stationary phase in MOPS minimal medium

source_name: O157:H7 Sakai 3h, mid exponential phase in MOPS Minimal medium


title: Pooled sample of adult female D. melanogaster individuals without wash

description: adult D. melanogaster


title: O157:H7 Sakai timecourse, 7.5h vs 3h rep4

source_name: O157:H7 Sakai 3h mid exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 8h vs 3h rep1

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 1


title: O157:H7 Sakai timecourse, 7h vs 3h rep2

source_name: O157:H7 Sakai 3h, mid exponential phase in MOPS minimal medium

source_name: O157:H7 Sakai, 7h stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 7h vs 3h rep3


title: O157:H7 Sakai timecourse, 6h vs 3h rep4

source_name: O157:H7 Sakai, 6h, stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 7h vs 3h rep1

source_name: O157:H7 Sakai, 7h, stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 7.5h vs 3h rep1

source_name: O157:H7 Sakai, 7.5h stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5.5h vs 3h rep4

source_name: O157:H7 Sakai, 5.5h early stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 7.5h vs 3h rep3


title: Distribution of Swi6 at Whole Genome Scale

description: ChIP-chip experiment for Swi6.

source_name: Mitotic Growing cells

tag: Wild type S.pombe strain was used.


title: O157:H7 Sakai timecourse, 7h vs 3h rep4


title: O157:H7 Sakai timecourse, 6h vs 3h rep1

source_name: O157:H7 Sakai, 3h, mid exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 6h vs 3h rep2

tag: s 	E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 2


title: O157:H7 Sakai timecourse, 6h vs 3h rep3

source_name: O157:H7 Sakai, 6h stationary phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5h vs 3h rep4

source_name: O157:H7 Sakai 5h, stationary phase transition point in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5h vs 3h rep2

source_name: O157:H7 Sakai, 5h, stationary phase transition in MOPS minimal medium

source_name: O157:H7 Sakai, 3h mid exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5h vs 3h rep3

source_name: O157:H7 Sakai, 5h, stationary phase transition point in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5.5h vs 3h rep2


title: O157:H7 Sakai timecourse, 4.6h vs 3h rep3

data_processing: Data were first normalized using print-tip lowess in R/MAANOVA v0.98-8. Normalized data from replicate spots were averaged and then converted to log2 values. The 3h samples were used as the common reference for all subsequent time points.

tag: E. coli O157:H7 RIMD0509952 (Sakai)

source_name: O157:H7 Sakai, 4.6h late exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse, 5.5h vs 3h rep1


title: O157:H7 Sakai timecourse, 5.5h vs 3h rep3


title: O157:H7 Sakai timecourse, 5h vs 3h rep1

source_name: O157:H7 Sakai 3h mid-exponential phase in MOPS minimal medium

source_name: O157:H7 Sakai, 5h stationary phase transition in MOPS minimal medium


title: O157:H7 Sakai timecourse, 4.6h vs 3h rep4

source_name: O157:H7 Sakai, 3h mid exponential phase in MOPS medium


title: O157:H7 Sakai timecourse, 4.6h vs 3h rep2

source_name: O157:H7 Sakai 4.6h late exponential phase in MOPS minimal medium

source_name: O157:H7 Sakai 3h mid exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse 3h vs 4.3h rep4

source_name: O157:H7 Sakai 4.3h late exponential phase in MOPS minimal medium


title: O157:H7 Sakai timecourse 3h vs 4h rep3

description: There are probes on the array that target three different E. coli genomes.  Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5x SSC, and 1mg/mL BSA at 42C for 1 hour.  After blocking, arrays were washed 2x 5 min in 0.1x SSC and 2x 30s in H2O.  Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95C for 5 min and then mixed with 40uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array.  Hybridizations were carried out at 47C for 16-18h.  After hybridization, arrays were washed in 2x SSC, 0.5% SDS 37C for 5 min, followed by 2x 5 min in 0.1x SSC, 0.1% SDS 37C, and then 2x 2.5min in room temperature 0.1x SSC.

data_processing: Data were first normalized using print-tip lowess in R/MAANOVA v0.98-8.  Normalized data from replicate spots were averaged and then converted to log2 values.  The 3h samples were used as the common reference for all subsequent time points.

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT,  400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP.  30uL reactions were incubated overnight at 42C.  cDNA was purified using PCR cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5).   Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and  coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.).  Uncoupled dye was removed by another purfication using the PCR cleanup kit.  Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

growth_protocol: The Sakai strain was inoculated into 10mL of LB broth from freezer stocks and grown to OD600 = 0.1.  This ~4h period of growth in LB allowed cells to recover before transfer to MOPS minimal media.  MOPS minimal media (10x) was prepared as described in Neidhardt et al. with the addition of 20mL of micronutrient solution instead of 10mL.  MOPS minimal media contained 100mL of 10x MOPS minimal media, 10mL of 0.132M K2HPO4, and 5mL of 20% D-glucose per liter. Cultures were inoculated into 50mL of MOPS minimal media with 0.1% glucose at a ratio of 1:200 and grown to stationary phase at 37C with shaking.  Cultures in MOPS were transferred to 100mL MOPS in 250mL plastic culture flasks at a ratio of 1:75 and grown for 9h before transfer again to 100mL MOPS in 250mL plastic culture flasks at a ratio of 1:30 and this culture was used to sample RNA during growth.  Cultures were sampled at 3h (OD600 ≈ 0.22), 4h (OD600 ≈ 0.45), 4.33h (OD600 ≈ 0.73), 4.66h (OD600 ≈ 0.93), 5h (OD600 ≈ 1), 5.5h, 6h, 7h, 7.5h, and 8h.  After 5h, the culture density remained at OD600 ≈ 1.

extract_protocol: 4mL of culture was mixed with 8mL of RNAProtect (Qiagen, Valencia, Calif.), vortexed, and centrifuged at 4C, 7500rpm for 10 min to pellet cells.  The supernatant was removed and cell pellets stored at –70C for 1 week or less before RNA extraction.  Cell pellets were suspended in 700uL of 95C lysis buffer (20mM sodium acetate pH 5.2, 2mM EDTA pH 8.0, and 0.5% SDS), held at 95C for 30s then mixed with 700uL of 65C Acid-Phenol: Chloroform, pH 4.5 (with IAA, 125:25:1) (Ambion, Austin, Tex.).  Samples were held at 65C with periodic shaking for at least 6 minutes before centrifuging at 12000 rpm for 10 min.  Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1).  RNA was precipitated for at least 1 hour at –20C in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2.  RNA was suspended in 1mM sodium citrate pH 6.5 and stored at –70C.  RNA samples were purified and treated with Dnase using the Rneasy kit

source_name: O157:H7 Sakai, 4h, late exponential phase in MOPS minimal medium

extract_protocol: 4mL of culture was mixed with 8mL of RNAProtect (Qiagen, Valencia, Calif.), vortexed, and centrifuged at 4C, 7500rpm for 10 min to pellet cells.  The supernatant was removed and cell pellets stored at –70C for 1 week or less before RNA extraction.  Cell pellets were suspended in 700uL of 95C lysis buffer (20mM sodium acetate pH 5.2, 2mM EDTA pH 8.0, and 0.5% SDS), held at 95C for 30s then mixed with 700uL of 65C Acid-Phenol: Chloroform, pH 4.5 (with IAA, 125:25:1) (Ambion, Austin, Tex.).  Samples were held at 65C with periodic shaking for at least 6 minutes before centrifuging at 12000 rpm for 10 min.  Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1).  RNA was precipitated for at least 1 hour at –20C in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2.  RNA was suspended in 1mM sodium citrate pH 6.5 and stored at –70C.  RNA samples were purified and treated with Dnase using the Rneasy kit


title: O157:H7 Sakai timecourse 3h vs 4.3h rep3


title: Distribution of Mde4 at Whole Genome Scale

description: ChIP-chip experiment for Mde4.

source_name: Mitotic growing cells

tag: Wild type Schizosaccharomyces pombe.


title: Bladder tumor 1082-1_DK (27g2)

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Gene expression data from a bladder tumor compared to a common reference sample

hyb_protocol: Described in: Dyrskjot L, Zieger K, Kruhoffer M, Thykjaer T, Jensen JL, Primdahl H, Aziz N, Marcussen N, Moller K, Orntoft TF. A molecular signature in superficial bladder carcinoma predicts clinical outcome. Clin Cancer Res. 2005 Jun 1;11(11):4029-36. PMID: 15930337

scan_protocol: Arrays were scanned using a ScanArray4000 scanner - settings: Cy5: 54% PMT, 100% laser power and Cy3: 78% PMT, 100% laser power

data_processing: Raw data were generated using TIGR Spotfinder 2.23 and raw data were lowess print-group normalized using TIGR MIDAS 2.19

source_name: Bladder tumor biopsy

extract_protocol: Total RNA extraction using standard protocols

tag: Bladder tumor

tag: Patient clinical information can be found in a Series supplementary file

source_name: Universal human reference RNA (Stratagene)

extract_protocol: Total RNA from Stratagene Universal human reference RNA

tag: reference sample


title: Bladder tumor 735-1_DK (28g2)

label_protocol: Described in: Dyrskjot L, Zieger K, Kruhoffer M, Thykjaer T, Jensen JL, Primdahl H, Aziz N, Marcussen N, Moller K, Orntoft TF. A molecular signature in superficial bladder carcinoma predicts clinical outcome. Clin Cancer Res. 2005 Jun 1;11(11):4029-36. PMID: 15930337


title: O157:H7 Sakai timecourse 3h vs 4.3h rep1

source_name: O157":H7 Sakai 3h mid exponential phase in MOPS minimal medium

source_name: O157:H7 Sakai, 4.3h late exponential phase in MOPS minimal medium


title: Bladder tumor 1082-1_DK (26g2)


title: O157:H7 Sakai timecourse 3h vs 4h rep2

source_name: O157:H7 Sakai, 4h late exponential phase in MOPS minimal medium


title: Bladder tumor 194_F (32g2)


title: Bladder tumor 194_F (33g2)


title: Bladder tumor 193_F (33g1)


title: Bladder tumor 171_F (31g2)


title: O157:H7 Sakai timecourse 4.6h vs 3h rep1


title: Bladder tumor 193_F (32g1)


title: O157:H7 Sakai timecourse 3h vs 4.3h rep2


title: Bladder tumor 735-1_DK (29g2)


title: O157:H7 Sakai timecourse 3h vs 4h rep4

source_name: O157:H7 Sakai, 3h, mid exponential phase in MOPS minimal medium


title: Bladder tumor 169_F (27g2)


title: Bladder tumor 171_F (30g2)


title: O157:H7 Sakai timecourse 3h vs 4h rep1

source_name: O157:H7 Sakai, 3h mid-exponental phase in MOPS minimal medium


title: Bladder tumor 169_F (26g2)


title: Bladder tumor 113_F (27g1)


title: Bladder tumor 113_F (26g1)


title: Bladder tumor 107_F (25g2)


title: Bladder tumor 105_F (25g1)


title: Bladder tumor 112_F (30g1)


title: Bladder tumor 112_F (31g1)


title: Bladder tumor 107_F (24g2)


title: Bladder tumor 1442 (11g1) F


title: Bladder tumor 102_F (23g2)


title: Bladder tumor 105_F (24g1)


title: Bladder tumor 102_F (22g2)


title: Bladder tumor 1442 (12g1) F


title: Bladder tumor 1434-1 (45g2)


title: Bladder tumor 1430-1 (46g1)


title: Bladder tumor 1413 (72g1) F


title: Bladder tumor 1415-1 (4g1)


title: Bladder tumor 1430-1 (45g1)


title: Bladder tumor 1425-1_DK (19g2)


title: Bladder tumor 1434-1 (46g2)


title: Bladder tumor 1415-1 (33g2)


title: Bladder tumor 1412 (70g2) F


title: Bladder tumor 1413 (71g1) F


title: Bladder tumor 1412 (69g2) F


title: Bladder tumor 1379-1 (22g1)


title: Bladder tumor 1408-1 (57g1)


title: Bladder tumor 1425-1_DK (18g2)


title: Bladder tumor 1390-1 (43g2)


title: Bladder tumor 1379-1 (23g1)


title: Bladder tumor 1408-1 (58g1)


title: Bladder tumor 1379 (24g1) F


title: Bladder tumor 1379 (23g1) F


title: Bladder tumor 1375-1 (10g1)


title: Bladder tumor 1390-1 (44g2)


title: Bladder tumor 1352-1 (8g1)


title: Bladder tumor 1366-1 (44g1)


title: Bladder tumor 1354-1 (8g2)


title: Bladder tumor 1367-1 (37g1)


title: Bladder tumor 1354-1 (7g2)


title: Bladder tumor 1367-1 (36g1)


title: Bladder tumor 1366-1 (43g1)


title: Bladder tumor 1375-1 (9g1)


title: Bladder tumor 1352-1 (7g1)


title: Bladder tumor 1349-1 (75g2)


title: Bladder tumor 1349-1 (6g2)


title: Bladder tumor 1346-1 (75g1)


title: Bladder tumor 1342-1 (45G2)


title: Bladder tumor 1345-2 (28g1)


title: Bladder tumor 1342-1 (46G2)


title: Bladder tumor 1345-2 (27g1)


title: Bladder tumor 1336-1 (56g1)


title: Bladder tumor 1346-1 (6g1)


title: Bladder tumor 1335-1 (20g2)


title: Bladder tumor 1335-1 (21g2)


title: Bladder tumor 1337-1 (55g2 vask2)


title: Bladder tumor 1334-4 (72g1) F


title: Bladder tumor 1336-1 (55g1)


title: Bladder tumor 1325_S (19g2)


title: Bladder tumor 1327-1 (41g2)


title: Bladder tumor 1334-4 (73g1) F


title: Bladder tumor 1327-1 (42g2)


title: Bladder tumor 1303-1 (46G1)


title: Bladder tumor 1293-1 (18g2)


title: Bladder tumor 1325_S (18g2)


title: Bladder tumor 1290-1 (35g2)


title: Bladder tumor 1337-1 (56g2)


title: Bladder tumor 1290-1 (34g2)


title: Bladder tumor 1330-1 (21g1)


title: Bladder tumor 1330-1 (20g1)


title: Bladder tumor 1282-1 (26g1)


title: Bladder tumor 1303-1 (45G1)


title: Bladder tumor 1264-1 (54g1)


title: Bladder tumor 1280-1 (73g1)


title: Bladder tumor 1280-1 (74g1)


title: Bladder tumor 1282-1 (27g1)


title: Bladder tumor 1293-1 (19g2)


title: Bladder tumor 1264-1 (53g1)


title: Bladder tumor 1255-1 (72g2)


title: Bladder tumor 1257-1 (53g2)


title: Bladder tumor 1252-1 (71g1)


title: Bladder tumor 1252-1 (72g1)


title: Bladder tumor 1259-1 (32g1)


title: Bladder tumor 1257-1 (54g2)


title: Bladder tumor 1238-1 (31g2)


title: Bladder tumor 1211-2 (9g2) F


title: Bladder tumor 1224-1 (30g1)


title: Bladder tumor 1238-1 (30g2)


title: Bladder tumor 1250-1 (70g2)


title: Bladder tumor 1255-1 (71g2)


title: Bladder tumor 1259-1 (33g1)


title: Bladder tumor 1250-1 (69g2)


title: Bladder tumor 1209-1 (28g2)


title: Bladder tumor 1211-2 (10g2) F


title: Bladder tumor 1211-1 (26g2)


title: Bladder tumor 1206-1 (26g1)


title: Bladder tumor 1210-1 (70g1)


title: Bladder tumor 1210-1 (69g1)


title: Bladder tumor 1206-1 (25g1)


title: Bladder tumor 1224-1 (31g1)


title: Bladder tumor 1209-1 (29g2)


title: Bladder tumor 1211-1 (25g2)


title: Bladder tumor 1191-1 (35g1)


title: Bladder tumor 1191-1 (34g1)


title: Bladder tumor 1189-1 (68g2)


title: Bladder tumor 1189-1 (67g2)


title: Bladder tumor 1195 (71g2) F


title: Bladder tumor 1195 (70g2) F


title: Bladder tumor 1134-1 (51g2)


title: Bladder tumor 1164-1 (54g1)


title: Bladder tumor 1134-1 (52g2)


title: Bladder tumor 1146-1 (23g2)


title: Bladder tumor 1182-1 (16g2)


title: Bladder tumor 1145-1 (32g2)


title: Bladder tumor 1164-1 (53g1)


title: Bladder tumor 1145-1 (33g2)


title: Bladder tumor 1131-1 (41G2)


title: Bladder tumor 1146-1 (24g2)


title: Bladder tumor 1131-1 (42G2)


title: Bladder tumor 1158-1 (68g1)


title: Bladder tumor 1117-1 (52g2)


title: Bladder tumor 1105-1 (66g1)


title: Bladder tumor 1117-1 (51g2)


title: Bladder tumor 1086-1 (65g1)


title: Bladder tumor 1086-1 (66g1)


title: Bladder tumor 1083-1 (52g1)


title: Bladder tumor 1093-1 (24g1)


title: Bladder tumor 1182-1 (17g2)


title: Bladder tumor 1078-1 (33g1)


title: Bladder tumor 1158-1 (67g1)


title: Bladder tumor 1093-1 (23G1)


title: Bladder tumor 1105-1 (65g1)


title: Bladder tumor 1083-1 (51g1)


title: Bladder tumor 1077-1 (60g2)


title: Bladder tumor 1078-1 (32g1)


title: Bladder tumor 1073-1 (11g1)


title: Bladder tumor 1073-1 (10g1)


title: Bladder tumor 1077-1 (59g2)


title: Bladder tumor 1060-1 (63g1)


title: Bladder tumor 1060-1 (64g1)


title: Bladder tumor 1065-1 (50g2)


title: Bladder tumor 1066-1 (41G1)


title: Bladder tumor 1034-2 (9g2)


title: Bladder tumor 1066-1 (42G1)


title: Bladder tumor 1033 (70g1) F


title: Bladder tumor 1047-1 (33g1)


title: Bladder tumor 1053-1 (42g1)


title: Bladder tumor 1056-4_DK (19g1)


title: Bladder tumor 1058-2 (28g1)


title: Bladder tumor 1053-1 (41g1)


title: Bladder tumor 1056-4_DK (18g1)


title: Bladder tumor 1036-1 (60g1)


title: Bladder tumor 1036-1 (59g1)


title: Bladder tumor 1058-2 (29g1)


title: Bladder tumor 1031-1 (57g2)


title: Bladder tumor 1047-1 (32g1)


title: Bladder tumor 1024-1 (48G1)


title: Bladder tumor 1065-1 (49g2)


title: Bladder tumor 1031-1 (58g2)


title: Bladder tumor 1034-2 (8g2)


title: Bladder tumor 1033 (69g1) F


title: Bladder tumor 1022-1 (9g1)


title: Bladder tumor 1022-1 (8g1)


title: Bladder tumor 1024-1 (47G1)


title: Bladder tumor 1010-1 (31g2)


title: Bladder tumor 1017-1 (65g2)


title: Bladder tumor 1017-1 (66g2)


title: Bladder tumor 1010-1 (30g2)


title: Bladder tumor 1012-1 (17g1)


title: Bladder tumor 01046_E (72g1)


title: Bladder tumor 01046_E (71g1)


title: Bladder tumor 01035_E (64g2)


title: Bladder tumor 01035_E (63g2)


title: Bladder tumor 01048_E (72g2)


title: Bladder tumor 01044_E (69g1)


title: Bladder tumor 01034T_E (62g2)


title: Bladder tumor 01041_E (68g1)


title: Bladder tumor 01034T_E (61g2)


title: Bladder tumor 01048_E (71g2)


title: Bladder tumor 01040_E (65g2)


title: Bladder tumor 01044_E (70g1)


title: Bladder tumor 01033T_E (61g1)


title: Bladder tumor 01033T_E (62g1)


title: Bladder tumor 01041_E (67g1)


title: Bladder tumor 01037_E (66g1)


title: Bladder tumor 1012-1 (16g1)


title: Bladder tumor 01037_E (65g1)


title: Bladder tumor 01032T_E (59g2)


title: Bladder tumor 01040_E (66g2)


title: Bladder tumor 01031T_E (59g1)


title: Bladder tumor 01031T_E (60g1)


title: Bladder tumor 01030T_E (57g2)


title: Bladder tumor 01028T_E (56g2)


title: Bladder tumor 01030T_E (58g2)


title: Bladder tumor 01028T_E (55g2)


title: Bladder tumor 01029T_E (57g1)


title: Bladder tumor 01032T_E (60g2)


title: Bladder tumor 01025_E (42g1)


title: Bladder tumor 01025_E (41g1)


title: Bladder tumor 01022T_E (49g1)


title: Bladder tumor 01027_E (63g1)


title: Bladder tumor 01029T_E (73g1)


title: Bladder tumor 01020T_E (55g1)


title: Bladder tumor 01020T_E (56g1)


title: Bladder tumor 01027_E (64g1)


title: Bladder tumor 01016T_E (51g1)


title: Bladder tumor 01017T_E (51g2)


title: Bladder tumor 01018T_E (54g1)


title: Bladder tumor 01019T_E (54g2)


title: Bladder tumor 01019T_E (53g2)


title: Bladder tumor 01016T_E (52g1)


title: Bladder tumor 01017T_E (52g2)


title: Bladder tumor 01013T_E (48g2)


title: Bladder tumor 01022T_E (50g1)


title: Bladder tumor 01015T_E (43g2)


title: Bladder tumor 01013T_E (47g2)


title: Bladder tumor 01009_E (40g2)


title: Bladder tumor 01008T_E (44g1)


title: Bladder tumor 998-1 (22g2)


title: Bladder tumor 01008T_E (43g1)


title: Bladder tumor 997-1 (66g1)


title: Bladder tumor 01012T_E (46g1)


title: Bladder tumor 998-1 (7g2)


title: Bladder tumor 01009_E (39g2)


title: Bladder tumor 01012T_E (45g1)


title: Bladder tumor 997-1 (65g1)


title: Bladder tumor 01018T_E (53g1)


title: Bladder tumor 992-1 (17g2)


title: Bladder tumor 992-1 (16g2)


title: Bladder tumor 972-1 (40G2)


title: Bladder tumor 972-1 (39G2)


title: Bladder tumor 970-1 (42g1)


title: Bladder tumor 970-1 (41g1)


title: Bladder tumor 967-3 (7g1)


title: Bladder tumor 967-3 (6g1)


title: Bladder tumor 965 (67g2) F


title: Bladder tumor 962-1 (61g2)


title: Bladder tumor 962-1 (62g2)


title: Bladder tumor 943 (31g1) F


title: Bladder tumor 965 (68g2) F


title: Bladder tumor 943 (30g1) F


title: Bladder tumor 944-1 (40g2)


title: Bladder tumor 942-1 (15g2)


title: Bladder tumor 942-1 (14g2)


title: Bladder tumor 944-1 (39g2)


title: Bladder tumor 941-4 (63g2)


title: Bladder tumor 938-1 (17g1)


title: Bladder tumor 926-1 (39g1)


title: Bladder tumor 941-4 (64g2)


title: Bladder tumor 930-1 (50g2)


title: Bladder tumor 927-1 (55g2)


title: Bladder tumor 930-1 (49g2)


title: Bladder tumor 938-1 (16g1)


title: Bladder tumor 925-7 (62g1)


title: Bladder tumor 927-1 (56g2)


title: Bladder tumor 926-1 (40g1)


title: Bladder tumor 916-1 (41g2)


title: Bladder tumor 924-1 (42g1) F


title: Bladder tumor 924-1 (41g1) F


title: Bladder tumor 925-7 (61g1)


title: Bladder tumor 916-1 (42g2)


title: Bladder tumor 910 (21g2) F


title: Bladder tumor 908 (21g1) F


title: Bladder tumor 910 (22g2) F


title: Bladder tumor 898-1 (45g1)


title: Bladder tumor 8908_S (57g2)


title: Bladder tumor 886-1 (15g2)


title: Bladder tumor 886-1 (14g2)


title: Bladder tumor 898-1 (46g1)


title: Bladder tumor 908 (22g1) F


title: Bladder tumor 881-1 (40g2)


title: Bladder tumor 8908_S (56g2)


title: Bladder tumor 881-1 (39g2)


title: Bladder tumor 880-1 (50g1)


title: Bladder tumor 876-1 (35g2)


title: Bladder tumor 867_UK (17g2)


title: Bladder tumor 880-1 (49g1)


title: Bladder tumor 879 (28g2) F


title: Bladder tumor 876-1 (36g1)


title: Bladder tumor 879 (29g2) F


title: Bladder tumor 865-1 (64g1)


title: Bladder tumor 867 (10g1) F


title: Bladder tumor 867_UK (16g2)


title: Bladder tumor 856-2 (15g1)


title: Bladder tumor 861-1 (47g2)


title: Bladder tumor 861-1 (48g2)


title: Bladder tumor 865-1 (63g1)


title: Bladder tumor 856-2 (14g1)


title: Bladder tumor 867 (9g1) F


title: Bladder tumor 855-1 (40g1)


title: Bladder tumor 843-1 (15g1)


title: Bladder tumor 843-1 (14g1)


title: Bladder tumor 842 (66g2) F


title: Bladder tumor 845-1 (38g2)


title: Bladder tumor 855-1 (39g1)


title: Bladder tumor 848 (68g1) F


title: Bladder tumor 845-1 (37g2)


title: Bladder tumor 848 (67g1) F


title: Bladder tumor 841-1 (37g1)


title: Bladder tumor 840-1 (39g2) F


title: Bladder tumor 840-1 (40g2) F


title: Bladder tumor 841-1 (38g1)


title: Bladder tumor 839 (40g1) F


title: Bladder tumor 839 (39g1) F


title: Bladder tumor 842 (65g2) F


title: Bladder tumor 839-1 (44g1)


title: Bladder tumor 837-1 (31g1)


title: Bladder tumor 837-1 (30g1)


title: Bladder tumor 829-1 (12g2)


title: Bladder tumor 825-3 (71g1)


title: Bladder tumor 839-1 (43g1)


title: Bladder tumor 824-1 (53g2) F


title: Bladder tumor 8054_S (42g2)


title: Bladder tumor 825-3 (70g1)


title: Bladder tumor 8054_S (41g2)


title: Bladder tumor 7546_S (67g1)


title: Bladder tumor 7988_S (20g2)


title: Bladder tumor 7988_S (21g2)


title: Bladder tumor 7739_S (65g2)


title: Bladder tumor 7739_S (64g2)


title: Bladder tumor 7184_S (58g1)


title: Bladder tumor 824-1 (54g2) F


title: Bladder tumor 7188_S (66g2)


title: Bladder tumor 7188_S (67g2)


title: Bladder tumor 7184_S (59g1)


title: Bladder tumor 829-1 (13g2)


title: Bladder tumor 6150_S (17g1)


title: Bladder tumor 6150_S (18g1)


title: Bladder tumor 6679_S (58g2)


title: Bladder tumor 6876_S (18g2)


title: Bladder tumor 6876_S (31g2)


title: Bladder tumor 6971_S (19g2)


title: Bladder tumor 6971_S (18g2)


title: Bladder tumor 5911_S (26g1)


title: Bladder tumor 7546_S (66g1)


title: Bladder tumor 5911_S (27g1)


title: Bladder tumor 6679_S (59g2)


title: Bladder tumor 5880_S (31g1)


title: Bladder tumor 5880_S (30g1)


title: Bladder tumor 5731_S (41g1)


title: Bladder tumor 5099_S (34g1)


title: Bladder tumor 5099_S (33g1)


title: Bladder tumor 5731_S (42g1)


title: Bladder tumor 4935_S (69g1)


title: Bladder tumor 4838_S (69g2)


title: Bladder tumor 4776_S (13g1)


title: Bladder tumor 4935_S (68g1)


title: Bladder tumor 4776_S (12g1)


title: Bladder tumor 4753_S (62g2)


title: Bladder tumor 4838_S (68g2)


title: Bladder tumor 4763_S (28g2)


title: Bladder tumor 4763_S (27g2)


title: Bladder tumor 4753_S (61g2)


title: Bladder tumor 4489_S (70g1)


title: Bladder tumor 4482_S (27g2)


title: Bladder tumor 4489_S (71g1)


title: Bladder tumor 4482_S (26g2)


title: Bladder tumor 4134_S (70g2)


title: Bladder tumor 4405_S (5g1)


title: Bladder tumor 2926_S (8g1)


title: Bladder tumor 4405_S (6g1)


title: Bladder tumor 4134_S (71g2)


title: Bladder tumor 2814_S (6g2)


title: Bladder tumor 2477_S (10g2)


title: Bladder tumor 3595_S (30g2)


title: Bladder tumor 2926_S (9g1)


title: Bladder tumor 3595_S (31g2)


title: Bladder tumor 2160_S (13g2)


title: Bladder tumor 1983_S (38g2)


title: Bladder tumor 2477_S (11g2)


title: Bladder tumor 1983_S (52g2)


title: Bladder tumor 2814_S (5g2)


title: Bladder tumor 1950_S (8g2)


title: Bladder tumor 1950_S (9g2)


title: Bladder tumor 1887-1 (34g2)


title: Bladder tumor 1887-1 (35g2)


title: Bladder tumor 1660-1 (35g1)


title: Bladder tumor 1660-1 (34g1)


title: Bladder tumor 1656-1 (27g2)


title: Bladder tumor 2160_S (12g2)


title: Bladder tumor 1571-1 (35g1)


title: Bladder tumor 1574-1 (37g2)


title: Bladder tumor 1574-1 (36g2)


title: Bladder tumor 1571-1 (34g1)


title: Bladder tumor 1656-1 (28g2)


title: Bladder tumor 1533-10 (24g2) F


title: Bladder tumor 1512-6 (74g2) F


title: Bladder tumor 1533-10 (23g2) F


title: Bladder tumor 1443-1_DK (21g1)


title: Bladder tumor 1448-2 (12g2) F


title: Bladder tumor 1482-1 (47g2)


title: Bladder tumor 1484 (74g1) F


title: Bladder tumor 1512-6 (75g2) F


title: Bladder tumor 1456-1 (58g2)


title: Bladder tumor 1484 (75g1) F


title: Bladder tumor 1448-2 (11g2) F


title: Bladder tumor 1473-1 (48g1)


title: Bladder tumor 1456-1 (57g2)


title: Bladder tumor 1008-1 (57g1)


title: Bladder tumor 1498 (41g2) F


title: Bladder tumor 1507-1 (50g1)


title: Bladder tumor 01005T_E (48g1)


title: Bladder tumor 1507-1 (49g1)


title: Bladder tumor 1478-1 (59g1)


title: Bladder tumor 1498 (42g2) F


title: Bladder tumor 1473-1 (47g1)


title: Bladder tumor 01001T_E (46g2)


title: Bladder tumor 1482-1 (48g2)


title: Bladder tumor 01005T_E (47g1)


title: Bladder tumor 01002_E (39g1)


title: Bladder tumor 1443-1_DK (20g1)


title: Bladder tumor 01002_E (40g1)


title: Bladder tumor 1008-1 (58g1)


title: Bladder tumor 9155_S (54g1)


title: Bladder tumor 9286_S (65g1)


title: Bladder tumor 9923_S (16g2)


title: Bladder tumor 9148_S (7g2)


title: Bladder tumor 9148_S (8g2)


title: Bladder tumor 1478-1 (60g1)


title: Bladder tumor 823-2 (35g1)


title: Bladder tumor 9923_S (13g2)


title: Bladder tumor 813 (52g2) F


title: Bladder tumor 822 (53g1) F


title: Bladder tumor 815 (19g2) F


title: Bladder tumor 813 (51g2) F


title: Bladder tumor 815 (20g2) F


title: Bladder tumor 815-1 (42g2)


title: Bladder tumor 812-1 (50g1)


title: Bladder tumor 01001T_E (45g2)


title: Bladder tumor 797-1 (34g2)


title: Bladder tumor 9286_S (64g1)


title: Bladder tumor 822 (54g1) F


title: Bladder tumor 823-2 (36G1)


title: Bladder tumor 812-1 (49g1)


title: Bladder tumor 9155_S (53g1)


title: Bladder tumor 794-3 (27g1)


title: Bladder tumor 795-13 (55g1)


title: Bladder tumor 794-3 (26g1)


title: Bladder tumor 815-1 (41g2)


title: Bladder tumor 795-13 (56g1)


title: Bladder tumor 793-1 (13g1)


title: Bladder tumor 775-1 (34g1)


title: Bladder tumor 797-1 (33g2)


title: Bladder tumor 763-1 (32g2)


title: Bladder tumor 763-1 (31g2)


title: Bladder tumor 760-1 (31g2)


title: Bladder tumor 747-7 (48g1)


title: Bladder tumor 793-1 (12g1)


title: Bladder tumor 747-7 (47g1)


title: Bladder tumor 735_UK (17g1)


title: Bladder tumor 712 (29g1) F


title: Bladder tumor 735_UK (16g1)


title: Bladder tumor 708 (8g2) F


title: Bladder tumor 746-1 (36g2)


title: Bladder tumor 746-1 (35g2)


title: Bladder tumor 745-1 (19g1) F


title: Bladder tumor 745-1 (20g1) F


title: Bladder tumor 703-1 (36g1)


title: Bladder tumor 703-1 (35g1)


title: Bladder tumor 712 (28g1) F


title: Bladder tumor 698_S (38g1)


title: Bladder tumor 698_S (52g1)


title: Bladder tumor 775-1 (33g1)


title: Bladder tumor 760-1 (30g2)


title: Bladder tumor 698-2 (38g1)


title: Bladder tumor 708 (7g2) F


title: Bladder tumor 698-2 (37g1)


title: Bladder tumor 679-2 (41g1)


title: Bladder tumor 682-2 (33g1)


title: Bladder tumor 692-1 (8g1) F


title: Bladder tumor 692-1 (39G1)


title: Bladder tumor 682-2 (34g1)


title: Bladder tumor 692-1 (40G1)


title: Bladder tumor 635_S (27g1)


title: Bladder tumor 677-1 (65g1) F


title: Bladder tumor 684-4 (34g2)


title: Bladder tumor 647-1 (40g1)


title: Bladder tumor 684-4 (33g2)


title: Bladder tumor 692-1 (7g1) F


title: Bladder tumor 647-1 (39g1)


title: Bladder tumor 637 (63g2) F


title: Bladder tumor 576-6 (40g2)


title: Bladder tumor 637 (64g2) F


title: Bladder tumor 679-2 (42g1)


title: Bladder tumor 576-6 (39g2)


title: Bladder tumor 546 (37g2) F


title: Bladder tumor 546 (38g2) F


title: Bladder tumor 677-1 (66g1) F


title: Bladder tumor 539-1 (31g1)