title: delta sigZ 60 min after ethanol exposure (dZ0met60_2)

status: Public on May 11 2008

city: Wageningen

first: Menno

middle: van der

last: Voort

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

institute: Wageningen UR

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Loewess-normalisation, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus ATCC 14579

source_name: dZ 60

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total B. cereus RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

tag: delta sigZ 60 min after ethanol exposure.

source_name: dZ 0

tag: delta sigZ 0 min after ethanol exposure.


title: delta sigZ 30 min after ethanol exposure (dZ0met30_2)

type: RNA

country: Netherlands

description: No extra description.

molecule: total RNA

source_name: dZ 30

tag: delta sigZ 30 min after ethanol exposure.


title: Delta sigM 10 minutes after ethanol exposure (dM0met10_2)

description: No extra description.

source_name: dM 10

tag: Delta sigM 10 minutes after ethanol exposure.

source_name: dM 0

tag: Delta sigM 0 minutes after ethanol exposure.


title: delta sigZ 10 min after ethanol exposure (dZ0met10_2)

description: No extra description.

source_name: dZ 10

tag: delta sigZ 10 min after ethanol exposure.


title: delta sigZ 10 min after ethanol exposure (dZ0met10_1)

description: No extra description.

tag: delta sigZ 0 min after ethanol exposure


title: sigZ overexpression strain 90 min after induction with nisin (sigZover 2)

description: No extra description.

source_name: sigZ over 2

tag: sigZ overexpression strain 90 min after induction with nisin.

source_name: Empty 2

tag: Empty vector strain 90 min after induction with nisin.


title: delta sigZ 30 min after ethanol exposure (dZ0met30_1)

description: No extra description.


title: WT0.2 WT0.8 1 164605

description: No extra description

hyb_protocol: One microgram target was denatured by boiling for 3 min and immediate cooling on ice prior to hybridization. The target was mixed at 68 °C with Ambion slidehyb #1 hybridization buffer (Ambion Europe Ltd., Huntingdon, UK). Hybridization buffer with the target was applied to the slide by use of a Lifterslip. The slide and Lifterslip were incubated for 16 h at 49°C, after which it was washed at 20°C for 5 min with low stringency buffer (2x SSC and 0.5% SDS) and 5 min with high stringengy buffer (1x SSC and 0.25% SDS. The slide was dried by centrifugation at 1500 rpm for 1 min, prior to scanning.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 100% laser intensity, and 10 micron scan resolution.

source_name: Wild-type aerobe OD600 0.2

tag: Wild-type aerobe OD600 0.2

source_name: Wild-type aerobe OD600 0.8

tag: Wild-type aerobe OD600 0.8


title: delta sigZ 60 min after ethanol exposure (dZ0met60_1)

description: No extra description.


title: delta sigM after 30 min of ethanol exposure (dM0met30_2)

description: No extra description.

source_name: dM 30

tag: delta sigM after 30 min of ethanol exposure.

tag: delta sigM after 0 min of ethanol exposure.


title: WT0.2 WT0.8 2 164606

description: No extra description

source_name: Wildtype aerobe OD600 0.8

tag: Wildtype aerobe OD600 0.8

source_name: Wildtype aerobe OD600 0.2

tag: Wildtype aerobe OD600 0.2


title: Delta sigM after 30 min of exposure to ethanol (dM0met30_1)

description: No extra description.

tag: Delta sigM after 0 min of exposure to ethanol.

tag: Delta sigM after 30 min of exposure to ethanol.


title: delta sigM 60 min after ethanol (dM0met60_2)

description: No extra description.

source_name: dM 60

tag: delta sigM 60 min after ethanol .

tag: delta sigM 0 min after ethanol .


title: WT0.8 WT4 1 162784

description: No extra description

source_name: Wild-type aerobe OD600 4

tag: Wild-type aerobe OD600 4


title: WT0.8 WT4 2 162785 S01

description: No extra description

source_name: wild-type aerobe OD600 4

tag: wild-type aerobe OD600 4

source_name: wild-type aerobe OD600 0.8

tag: wild-type aerobe OD600 0.8


title: Wild-type 30 min after ethanol exposure. (WT0met30_2)

description: No extra description.

source_name: Wild-type 30

source_name: Wild-type 0

tag: Wild-type 0 min after ethanol exposure.


title: Overexpression strain sigZ, after 90 min nisin induction (sigZover1)

description: No extra description.

source_name: Empty 1

tag: Empty vector strain, after 90 min nisin induction.

source_name: sigZ over 1

tag: Overexpression strain sigZ, after 90 min nisin induction.


title: WT8(5) WT0.8(3) 1 164540

description: No extra description

source_name: Wildtype aerobe OD600 8

tag: Wildtype aerobe OD600 8


title: Anaer WT 2 164597

description: No extra description

source_name: Wildtype aerobe OD600 0.6

tag: Wildtype aerobe OD600 0.6

source_name: Wildtype anaerobe OD600 0.6

tag: Wildtype anaerobe OD600 0.6


title: Delta sigM 60 min after ethanol exposure (dM0met60_1)

description: No extra description.

source_name: dM 0

tag: Delta sigM 0 min after ethanol exposure.

tag: Delta sigM 60 min after ethanol exposure.


title: WTan0.4 WTan1.1 1 164471

description: No extra description

source_name: Wildtype anaerobe OD600 0.4

tag: Wildtype anaerobe OD600 0.4

source_name: WT anaerobe OD600 1.1

tag: WT anaerobe OD600 1.1


title: Anaer WT 1 164596

description: No extra description


title: Wild-type 30 min exposed to ethanol. (WT0met30_1)

description: No extra description.

tag: Wild-type 0 min exposed to ethanol.

tag: Wild-type 30 min exposed to ethanol.


title: Wild-type after 60 min of ethanol exposure. (WT0met60_2)

description: No extra description.

source_name: Wild-type 60

tag: Wild-type after 0 min of ethanol exposure.


title: Delta sigM 10 min after exposure to ethanol (dM0met10_1)

description: No extra description.

tag: Delta sigM 0 min after exposure to ethanol.

source_name: dM 10

tag: Delta sigM 10 min after exposure to ethanol.


title: Wild-type 60 minutes of exposure to ethanol. (WT0met60_1)

description: No extra description.

tag: Wild-type 0 min of exposure to ethanol.


title: WT8 WT0.8 2 164604

description: No extra description

source_name: Wildtype aerobe OD600 0.8

tag: Wildtype aerobe OD600 0.8


title: Wild-type 10 min after ethanol exposure. (WT0met10_2)

description: No extra description.

source_name: Wild-type 10

source_name: wild-type 0

tag: Wild-type 0 min after ethanol exposure.


title: WTan0.4 WTan0.2 2 164469

description: No extra description

source_name: Wild-type anaerobe OD600 0.2

tag: Wild-type anaerobe OD600 0.2

source_name: Wild-type anaerobe OD600 0.4

tag: Wild-type anaerobe OD600 0.4


title: WTan0.4 WTan0.2 1 164468

description: No extra description


title: Pi9_2W vs WT_2W_1-dye-swap

status: Public on May 10 2008

city: Davis

first: Ki-hong

last: Jung

state: CA

address: one shields

department: Plant pathology

country: USA

institute: UC DAVIS

description: Dye-swap of Biological replicate 1 of 2. Comparison of NBS2-pi9ox and TP309 without treatment using 2 weeks old leaf

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Genepix4000B and Genepix pro 4.0 software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed experimental signal/processed reference signal. We used LMGene Package

organism: Oryza sativa

source_name: background variety of NBS2-Pi9 overexpressed plant (TP309) without treatment

label_protocol: 0.5-1.0 µg of total RNAs were primed with 2 µl of 100 µM oligodT primer (20mer, invitrogen) at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Xanthomonas oryzae pv. oryzae (Xoo) isolate PXO99 was inoculated in leaf by clipping method. To do this, we grew the following plants for 8 weeks. NH1ox vs LG (WT), NRR1ox vs LG (WT), Xa21 vs TP309 (WT), GR978 vs IR64 (WT), spl17 vs IR64 (WT), spl11 vs IR64 (WT).  8 weeks old leaf tissues from these samples were collected at 1day after inoculation with Xoo and without treatment.  In addition, 8 weeks old leaf tissues from {OsCoi1ox and Nipponbare (WT)} and {OsNahG1ox and Nipponbare (WT)} were harvested.  In case of blast treatment (Magnaporthe grisea, MG), we grew the following plants for 2 weeks. NBS2-Pi9ox vs TP309 (WT), MPK5ox vs Nipponbare (WT), GR978 vs IR64 (WT), spl17 vs IR64 (WT), spl11 vs IR64 (WT). 2 weeks old leaf tissues from these samples were collected at 1day after inoculation with MG and without treatment.  In addition, 2 weeks old leaf tissues from OsCoi1ox and Nipponbare (WT) were harvested.

extract_protocol: 500ug total RNA extracted using Trizol following manufacturer's instructions. And then, 4-5ug mRNAs were isolated using Qiagen oligotex mRNA isolation midi kit. We used 0.5-1ug mRNAs for each hybridization

treatment_protocol: There are two types of comparisions: one is to compare pathogen treated leaves of 10 mutants and wild type control; and the other is to compare wound treated leaves of 10 mutants and wild type control.

tag: 2 weeks old leaf

source_name: NBS2-Pi9 over expressed plant without treatment


title: Pi9_2W vs WT_2W_1

description: Biological replicate 1 of 2. Comparison of NBS2-pi9ox and TP309 without treatment using 2 weeks old leaf


title: OsCoi1_8W vs WT_8W_1

description: Biological replicate 1 of 2. Comparison of OsCoi1ox and Nipponbare without treatment using 8 weeks old leaf

source_name: OsCoi1 overexpressed line without  treatment

tag: 8 weeks old leaf

source_name: background variety of OsCoi1 overexpressed plant (Nipponbare) without treatment


title: OsCoi1_8W vs WT_8W_2

description: Biological replicate 2 of 2. Comparison of OsCoi1ox and Nipponbare without treatment using 8 weeks old leaf


title: OsNahG1_8W vs WT_8W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 3. Comparison of OsNahG1ox and Nipponbare without treatment using 8 weeks old leaf

source_name: background variety of OsNahG1 overexpressed plant (Nipponbare) without treatment

source_name: OsNahG1 overexpressed line without  treatment


title: WTan0.4 WTan1 1 164466

description: No extra description

source_name: Wild-type anaerobe OD600 1.0

tag: Wild-type anaerobe OD600 1.0


title: OsCoi1_8W vs WT_8W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of OsCoi1ox and Nipponbare without treatment using 8 weeks old leaf


title: Pi9_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of NBS2-pi9ox and TP309 without treatment using 2 weeks old leaf


title: OsCoi1_8W vs WT_8W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 2. Comparison of OsCoi1ox and Nipponbare without treatment using 8 weeks old leaf


title: Pi9_2W vs WT_2W_2

description: Biological replicate 2 of 2. Comparison of NBS2-pi9ox and TP309 without treatment using 2 weeks old leaf


title: MPK5_2W vs WT_2W_3

description: Biological replicate 3 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf

source_name: MPK5 overexpressed line without  treatment

source_name: background variety of MPK5 overexpressed plant (Nipponbare) without treatment


title: WTan0.4 WTan1 2 164467

description: No extra description


title: OsNahG1_8W vs WT_8W_3

description: Biological replicate 3 of 3. Comparison of OsNahG1ox and Nipponbare without treatment using 8 weeks old leaf


title: OsNahG1_8W vs WT_8W_2

description: Biological replicate 2 of 3. Comparison of OsNahG1ox and Nipponbare without treatment using 8 weeks old leaf


title: Wild-type after 10 min of exposure to ethanol. (WT0met10_1)

description: No extra description.

source_name: Wild-type 0

tag: Wild-type after 0 min of exposure to ethanol.


title: OsNahG1_8W vs WT_8W_1

description: Biological replicate 1 of 3. Comparison of OsNahG1ox and Nipponbare without treatment using 8 weeks old leaf


title: MPK5_MG vs WT_MG_4

description: Biological replicate 4 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf

source_name: MPK5 overexpressed line treated with MG for 1 day

source_name: background variety of MPK5 overexpressed plant (Nipponbare) treated with MG for 1 day


title: MPK5_2W vs WT_2W_2

description: Biological replicate 2 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf


title: MPK5_2W vs WT_2W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf


title: MPK5_MG vs WT_MG_2

description: Biological replicate 2 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf


title: MPK5_2W vs WT_2W_1

description: Biological replicate 1 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf


title: SPL17_2W vs WT_2W_3

description: Biological replicate 3 of 3. Comparison of spl17 and IR64 without treatment using 2 weeks old leaf

source_name: spl17 line without treatment

source_name: background variety of spl17 plant (IR64) without treatment


title: SPL17_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 3. Comparison of spl17 and IR64 without treatment using 2 weeks old leaf


title: MPK5_MG vs WT_MG_3

description: Biological replicate 3 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf


title: MPK5_MG vs WT_MG_1

description: Biological replicate 1 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf


title: MPK5_MG vs WT_MG_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf


title: MPK5_MG vs WT_MG_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of MPK5ox and Nipponbare after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL17_2W vs WT_2W_2

description: Biological replicate 2 of 3. Comparison of spl17 and IR64 without treatment using 2 weeks old leaf


title: MPK5_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf


title: MPK5_2W vs WT_2W_4

description: Biological replicate 4 of 4. Comparison of MPK5ox and Nipponbare without treatment using 2 weeks old leaf


title: SPL17_2W vs WT_2W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 3. Comparison of spl17 and IR64 without treatment using 2 weeks old leaf


title: SPL17_2W vs WT_2W_1

description: Biological replicate 1 of 3. Comparison of spl17 and IR64 without treatment using 2 weeks old leaf


title: SPL17_MG vs WT_MG_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf

source_name: background variety of spl17 plant (IR64) treated with MG for 1 day

source_name: spl17 line treated with MG for 1 day


title: SPL17_MG vs WT_MG_3

description: Biological replicate 3 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL17_MG vs WT_MG_4

description: Biological replicate 4 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL17_MG vs WT_MG_1

description: Biological replicate 1 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL11_2W vs WT_2W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 2. Comparison of spl11 and IR64 without treatment using 2 weeks old leaf

source_name: background variety of spl11 plant (IR64) without treatment

source_name: spl11 line without treatment


title: SPL11_MG vs WT_MG_1

description: Biological replicate 1 of 2. Comparison of spl11 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf

source_name: spl11 line treated with MG for 1 day

source_name: background variety of spl11 plant (IR64) treated with MG for 1 day


title: SPL11_2W vs WT_2W_2

description: Biological replicate 2 of 2. Comparison of spl11 and IR64 without treatment using 2 weeks old leaf


title: SPL17_MG vs WT_MG_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL11_MG vs WT_MG_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of spl11 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL11_MG vs WT_MG_1-dye-swap

description: Dye-swap of Biological replicate 1 of 2. Comparison of spl11 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL11_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of spl11 and IR64 without treatment using 2 weeks old leaf


title: SPL17_MG vs WT_MG_2

description: Biological replicate 2 of 4. Comparison of spl17 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL11_MG vs WT_MG_2

description: Biological replicate 2 of 2. Comparison of spl11 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: GR978_2W vs WT_2W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf

source_name: background variety of GR978 plant (IR64) without treatment

source_name: GR978 line without treatment


title: GR978_2W vs WT_2W_3

description: Biological replicate 3 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf


title: GR978_2W vs WT_2W_2

description: Biological replicate 2 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf


title: SPL11_2W vs WT_2W_1

description: Biological replicate 1 of 2. Comparison of spl11 and IR64 without treatment using 2 weeks old leaf


title: GR978_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf


title: GR978_2W vs WT_2W_4

description: Biological replicate 4 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf


title: GR978_MG vs WT_MG_4

description: Biological replicate 4 of 4. Comparison of GR978 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf

source_name: GR978 line treated with MG for 1 day

source_name: background variety of GR978 plant (IR64) treated with MG for 1 day


title: GR978_2W vs WT_2W_1

description: Biological replicate 1 of 4. Comparison of GR978 and IR64 without treatment using 2 weeks old leaf


title: GR978_MG vs WT_MG_1

description: Biological replicate 1 of 4. Comparison of GR978 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: GR978_MG vs WT_MG_3

description: Biological replicate 3 of 4. Comparison of GR978 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL17_8W vs WT_8W_3

description: Biological replicate 3 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf


title: NRRox_Xoo vs WT_Xoo_1

description: Biological replicate 1 of 3. Comparison of NRR1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: NRR1over expressed plant treated with Xoo for 1day

source_name: background variety of NRR1 overexpressed plant (LG) treated with Xoo for 1 day


title: SPL17_8W vs WT_8W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf


title: NRRox_Xoo vs WT_Xoo_1-dye-swap

description: Dye-swap of Biological replicate 1 of 3. Comparison of NRR1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: NRR1over expressed plant treated with Xoo for 1 day


title: GR978_MG vs WT_MG_2

description: Biological replicate 2 of 4. Comparison of GR978 and IR64 after the inoculation with MG for 1 day using 2 weeks old leaf


title: SPL17_Xoo vs WT_Xoo_1

description: Biological replicate 1 of 4. Comparison of spl17 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: spl17 line treated with Xoo for 1 day

source_name: background variety of spl17 plant (IR64) treated with Xoo for 1day


title: SPL17_8W vs WT_8W_2

description: Biological replicate 2 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf

source_name: spl17 line without treatment


title: NRRox_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 3. Comparison of NRR1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: SPL17_Xoo vs WT_Xoo_4

description: Biological replicate 4 of 4. Comparison of spl17 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: SPL17_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 4. Comparison of spl17 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: SPL17_8W vs WT_8W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf

source_name: background variety of spl17 plant (IR64) without treatment


title: SPL11_8W vs WT_8W_2

description: Biological replicate 2 of 2. Comparison of spl11  and IR64 without treatment using 8 weeks old leaf


title: SPL17_Xoo vs WT_Xoo_3

description: Biological replicate 3 of 4. Comparison of spl17 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: SPL17_8W vs WT_8W_1

description: Biological replicate 1 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf


title: SPL17_8W vs WT_8W_4

description: Biological replicate 4 of 4. Comparison of spl17 and IR64 without treatment using 8 weeks old leaf


title: NRRox_Xoo vs WT_Xoo_3

description: Biological replicate 3 of 3. Comparison of NRR1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: SPL11_Xoo vs WT_Xoo_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of spl11 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: background variety of spl11 plant (IR64) treated with Xoo for 1 day

source_name: spl11 line treated with Xoo for 1 day


title: SPL11_Xoo vs WT_Xoo_1

description: Biological replicate 1 of 2. Comparison of spl11 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: GR978_8W vs WT_8W_2

description: Biological replicate 2 of 3. Comparison of GR978 and IR64 without treatment using 8 weeks old leaf


title: GR978_8W vs WT_8W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 3. Comparison of GR978 and IR64 without treatment using 8 weeks old leaf

source_name: GR978 lines without treatment


title: SPL11_8W vs WT_8W_1

description: Biological replicate 1 of 2. Comparison of spl11 and IR64 without treatment using 8 weeks old leaf

source_name: spl11 line without treatment

source_name: background variety of spl11 plant (IR64) without treatment


title: GR978_8W vs WT_8W_3-dye-swap

description: Biological replicate 3 of 3. Comparison of GR978 and IR64 without treatment using 8 weeks old leaf


title: SPL11_8W vs WT_8W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 2. Comparison of spl11 and IR64 without treatment using 8 weeks old leaf


title: GR978_Xoo vs WT_Xoo_4

description: Biological replicate 4 of 4. Comparison of GR978 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: background variety of GR978 plant (IR64) treated with Xoo for 1 day

source_name: GR978 line treated with Xoo for 1 day


title: SPL11_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 2. Comparison of spl11 and IR64 after the inoculation with Xoo for 1 day  using 8 weeks old leaf


title: GR978_8W vs WT_8W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 3. Comparison of GR978 and IR64 without treatment using 8 weeks old leaf

source_name: background variety of GR978 plant (IR64) without treatment


title: GR978_Xoo vs WT_Xoo_2_dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of GR978 and IR64 after the inoculation with Xoo for 1 day  using 8 weeks old leaf

source_name: GR978 lines treated with Xoo for 1 day


title: SPL11_Xoo vs WT_Xoo_1-dye-swap

description: Dye-swap of Biological replicate 1 of 2. Comparison of spl11 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: GR978_Xoo vs WT_Xoo_3

description: Biological replicate 3 of 4. Comparison of GR978 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: GR978_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 4. Comparison of GR978 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: OsCoi1_2W vs WT_2W_2

description: Biological replicate 2 of 3. Comparison of OsCoi1ox and Nipponbare without treatment using 2 weeks old leaf

source_name: OsCoi1 overexpressed plant without treatment

source_name: background variety of OsCoi1 overexpressed plant (Nipponbare) without treatment


title: OsCoi1_2W vs WT_2W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 3. Comparison of OsCoi1ox and Nipponbare without treatment using 2 weeks old leaf


title: GR978_Xoo vs WT_Xoo_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of GR978 and IR64 after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: OsCoi1_2W vs WT_2W_3

description: Biological replicate 3 of 3. Comparison of OsCoi1ox and Nipponbare without treatment using 2 weeks old leaf


title: Xa21_Xoo vs WT_Xoo_3

description: Biological replicate 3 of 3. Comparison of Xa21 and TP309  after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: Xa21 expressed plant treated with Xoo for 1 day

source_name: background variety of Xa21 expressed plant (TP309) treated with Xoo for 1 day


title: OsCoi1_2W vs WT_2W_1

description: Biological replicate 1 of 3. Comparison of OsCoi1ox and Nipponbare without treatment using 2 weeks old leaf


title: GR978_8W vs WT_8W_1

description: Biological replicate 1 of 3. Comparison of GR978 and IR64 without treatment using 8 weeks old leaf

source_name: GR978 line without treatment


title: Xa21_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 3. Comparison of Xa21 and TP309  after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: Xa21_Xoo vs WT_Xoo_1

description: Biological replicate 1 of 3. Comparison of Xa21 and TP309 after the inoculation with Xoo for 1 day  using 8 weeks old leaf


title: Pi9_MG vs WT_MG_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of NBS2-pi9ox and TP309 after the inoculation with MG for 1 day  using 2 weeks old leaf

source_name: background variety of NBS2-pi9 overexpressed plant (TP309) treated with MG for 1 day

source_name: NBS2-Pi9 overexpressed plant treated with MG for 1 day


title: NRR1_8W vs WT_8W_4

description: Dye-swap  Biological replicate 4 of 4. Comparison of NRR1ox and LG without treatment using 8 weeks old leaf

source_name: background variety of NRR1 overexpressed plant (LG) without treatment

source_name: NRR1 overexpressed plant without treatment


title: Pi9_MG vs WT_MG_4

description: Dye-swap of Biological replicate 4 of 4. Comparison of NBS2-pi9ox and TP309 after the inoculation with MG for 1 day using 2 weeks old leaf


title: OsCoi1_2W vs WT_2W_1-dye-swap

description: Dye-swap Biological replicate 1 of 3. Comparison of OsCoi1ox and Nipponbare without treatment using 2 weeks old leaf


title: Pi9_MG vs WT_MG_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of NBS2-pi9ox and TP309  after the inoculation with MG for 1 day using 2 weeks old leaf


title: Pi9_MG vs WT_MG_2

description: Biological replicate 2 of 4. Comparison of NBS2-pi9ox and TP309 after the inoculation with MG for 1 day using 2 weeks old leaf


title: Pi9_MG vs WT_MG_3

description: Dye-swap of Biological replicate 3 of 4. Comparison of NBS2-pi9ox and TP309 after the inoculation with MG for 1 day using 2 weeks old leaf


title: NH1ox_8W vs WT_8W_3

description: Biological replicate 3 of 4. Comparison of NH1ox and LG without treatmentusing 8 weeks old leaf

source_name: NH1 overexpressed plant without treatment

source_name: background variety of NH1 overexpressed plant (LG) without treatment


title: NRR1_8W vs WT_8W_1

description: Biological replicate 1 of 4. Comparison of NRR1ox and LG without treatment using 8 weeks old leaf


title: NH1ox_8W vs WT_8W_2-dye-swap

description: Dye-swap of Biological replicate 2 of 4. Comparison of NH1ox and LG without treatment using 8 weeks old leaf


title: NRR1_8W vs WT_8W_3

description: Biological replicate 3 of 4. Comparison of NRR1ox and LG without treatment using 8 weeks old leaf


title: NRR1_8W vs WT_8W_2

description: Biological replicate 2 of 4. Comparison of NRR1ox and LG without treatment using 8 weeks old leaf


title: NH1ox_8W vs WT_8W_1-dye-swap

description: Dye-swap of Biological replicate 1 of 4. Comparison of NH1ox and LG without treatment using 8 weeks old leaf


title: Pi9_MG vs WT_MG_1

description: Biological replicate 1 of 4. Comparison of NBS2-pi9ox and TP309 after the inoculation with MG for 1 day using 2 weeks old leaf


title: NH1ox_8W vs WT_8W_2

description: Biological replicate 2 of 4. Comparison of NH1ox and LG without treatment using 8 weeks old leaf


title: NRR1_8W vs WT_8W_3-dye-swap

description: Dye-swap of Biological replicate 3 of 4. Comparison of NRR1ox and LG without treatment using 8 weeks old leaf


title: NH1ox_8W vs WT_8W_4

description: Biological replicate 4 of 4. Comparison of NH1ox and LG without treatment using 8 weeks old leaf


title: NH1ox_8W vs WT_8W_1

description: Biological replicate 1 of 4. Comparison of NH1ox and LG without treatment using 8 weeks old leaf


title: NH1ox_Xoo vs WT_Xoo_3

description: Biological replicate 3 of 3. Comparison of NH1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf

source_name: NH1 overexpressed plant treated with Xoo for 1 day

source_name: background variety of NH1 overexpressed plant (LG) treated with Xoo for 1 day


title: NH1ox_Xoo vs WT_Xoo_2-dye-swap

description: Dye-swap of Biological replicate 2 of 3. Comparison of NH1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: NH1ox_Xoo vs WT_Xoo_1

description: Biological replicate 1 of 3. Comparison of NH1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: NH1ox_Xoo vs WT_Xoo_1-dye-swap

description: Dye-swap of Biological replicate 1 of 3. Comparison of NH1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: NH1ox_Xoo vs WT_Xoo_2

description: Biological replicate 2 of 3. Comparison of NH1ox and LG after the inoculation with Xoo for 1 day using 8 weeks old leaf


title: Control sample 5_CONTROL; non-leukemic

status: Public on May 06 2008

type: genomic

city: London

first: Manu

last: Gupta

address: Charterhouse Sq.

department: Medical Oncology

country: United Kingdom

institute: Queen Mary University of London

description: SNP genotype data from non-leukemic controls

hyb_protocol: Affymetrix 10K 2.0 mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000-7G

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Not applicable

extract_protocol: DNA was prepared using standard proteinase K digestion and phenol/chloroform extraction

treatment_protocol: Mononuclear cells were harvested from peripheral blood or bone marrow of patients at presentation with AML and either cryopreserved in liquid nitrogen or used immediately for DNA extraction.

tag: no additional information


title: AML sample number AML10_401_REM; remission sample

description: SNP genotype data from AML patient at remission

source_name: AML blood/marrow cells

label_protocol: Affymetrix 10K 2.0 mapping assay protocol


title: AML sample number AML10_369_REM; remission sample


title: AML sample number AML10_400_REM; remission sample


title: Control sample 4_CONTROL; non-leukemic


title: Control sample 10_CONTROL; non-leukemic


title: Control sample 11_CONTROL; non-leukemic


title: AML sample number AML10_398_REM; remission sample


title: AML sample number AML10_364_REM; remission sample


title: Control sample 9_CONTROL; non-leukemic


title: AML sample number AML10_350_REM; remission sample


title: Control sample 6_CONTROL; non-leukemic


title: AML sample number AML10_379_REM; remission sample


title: AML sample number AML10_458; diagnostic sample

description: SNP genotype data from AML patient at diagnosis


title: Control sample 1_CONTROL; non-leukemic


title: Control sample 3_CONTROL; non-leukemic


title: Control sample 8_CONTROL; non-leukemic


title: Control sample 2_CONTROL; non-leukemic


title: AML sample number AML10_459; diagnostic sample


title: AML sample number AML10_456; diagnostic sample


title: AML sample number AML10_457; diagnostic sample


title: AML sample number AML10_385_REM; remission sample


title: AML sample number AML10_453; diagnostic sample


title: AML sample number AML10_452; diagnostic sample


title: AML sample number AML10_455; diagnostic sample


title: AML sample number AML10_454; diagnostic sample


title: AML sample number AML10_449; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 2/8

status: Public on May 07 2008

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

hyb_protocol: Samples were hybridized by NimbleGen Systems, Reykjavik, Iceland

scan_protocol: Arrays were scanned by NimbleGen Systems, Reykjavik, Iceland

data_processing: The log2-ratio of Dam-Fusion signal over Dam-only signal was calculated. Subsequently, normalization was applied within arrays using loess. All 16 arrays were median and variance normalized on the basis of the common 9731 probes on all 16 arrays. Replicate samples in reverse dye orientation were averaged. Finally, the median over the entire array set was subtracted from the data. 8 data files are included which give the final normalized values (GPLxxx_norm_value.tsv)

source_name: Tig3 Human fibroblast cells, expressing LaminB1-Dam

label_protocol: Samples were labeled by NimbleGen Systems, Reykjavik, Iceland

growth_protocol: see Nat Protoc. 2007;2(6):1467-78. for detailed growth, treatment, and extraction protocols. In short: lentivirus is transfected in, and harvested from 293Tcells, grown in DMEM + 10% FCS + Pen/Strep

extract_protocol: gDNA is isolated using the Dneasy Tissuekit

treatment_protocol: Tig3 cells are transducted with the lentiviruses. gDNA is harvested after 3 days incubation

tag: LaminB1-Dam (EXPERIMENTAL)

source_name: Tig3 Human fibroblast cells, expressing Dam

tag: Dam (REFERENCE)


title: AML sample number AML10_443; diagnostic sample


title: AML sample number AML10_446; diagnostic sample


title: AML sample number AML10_450; diagnostic sample


title: AML sample number AML10_445; diagnostic sample


title: AML sample number AML10_442; diagnostic sample


title: AML sample number AML10_451; diagnostic sample


title: AML sample number AML10_444; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 5/8


title: AML sample number AML10_448; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 4/8


title: AML sample number AML10_447; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 8/8


title: AML sample number AML10_436; diagnostic sample


title: AML sample number AML10_440; diagnostic sample


title: AML sample number AML10_437; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 3/8


title: AML sample number AML10_439; diagnostic sample


title: AML sample number AML10_441; diagnostic sample


title: AML sample number AML10_438; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 6/8


title: Tig3 human fibroblast cells, Emerin DamID, platform chr4

source_name: Tig3 Human fibroblast cells, expressing Emerin-Dam

tag: Emerin-Dam (EXPERIMENTAL)


title: AML sample number AML10_434; diagnostic sample


title: AML sample number AML10_435; diagnostic sample


title: AML sample number AML10_430; diagnostic sample


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 7/8


title: Tig3 human fibroblast cells, LaminB1 DamID, platform chr4


title: Tig3 human fibroblast cells, LaminB1 DamID, platform 1/8


title: AML sample number AML10_432; diagnostic sample


title: AML sample number AML10_431; diagnostic sample


title: AML sample number AML10_426; diagnostic sample


title: AML sample number AML10_427; diagnostic sample


title: AML sample number AML10_425; diagnostic sample


title: AML sample number AML10_415; diagnostic sample


title: AML sample number AML10_420; diagnostic sample


title: AML sample number AML10_411; diagnostic sample


title: AML sample number AML10_410; diagnostic sample


title: AML sample number AML10_416; diagnostic sample


title: AML sample number AML10_421; diagnostic sample


title: AML sample number AML10_405; diagnostic sample


title: AML sample number AML10_406; diagnostic sample


title: AML sample number AML10_417; diagnostic sample


title: AML sample number AML10_412; diagnostic sample


title: AML sample number AML10_407; diagnostic sample


title: AML sample number AML10_428; diagnostic sample


title: AML sample number AML10_433; diagnostic sample


title: AML sample number AML10_422; diagnostic sample


title: AML sample number AML10_429; diagnostic sample


title: AML sample number AML10_423; diagnostic sample


title: AML sample number AML10_414; diagnostic sample


title: AML sample number AML10_419; diagnostic sample


title: AML sample number AML10_424; diagnostic sample


title: AML sample number AML10_404; diagnostic sample


title: AML sample number AML10_413; diagnostic sample


title: AML sample number AML10_403; diagnostic sample


title: AML sample number AML10_418; diagnostic sample


title: AML sample number AML10_409; diagnostic sample


title: AML sample number AML10_408; diagnostic sample


title: AML sample number AML10_401; diagnostic sample


title: AML sample number AML10_402; diagnostic sample


title: AML sample number AML10_392; diagnostic sample


title: AML sample number AML10_397; diagnostic sample


title: AML sample number AML10_393; diagnostic sample


title: AML sample number AML10_395; diagnostic sample


title: AML sample number AML10_400; diagnostic sample


title: AML sample number AML10_398; diagnostic sample


title: AML sample number AML10_394; diagnostic sample


title: AML sample number AML10_399; diagnostic sample


title: AML sample number AML10_389; diagnostic sample


title: AML sample number AML10_381; diagnostic sample


title: AML sample number AML10_376; diagnostic sample


title: AML sample number AML10_380; diagnostic sample


title: AML sample number AML10_391; diagnostic sample


title: AML sample number AML10_377; diagnostic sample


title: AML sample number AML10_388; diagnostic sample


title: AML sample number AML10_396; diagnostic sample


title: AML sample number AML10_383; diagnostic sample


title: AML sample number AML10_387; diagnostic sample


title: AML sample number AML10_373; diagnostic sample


title: AML sample number AML10_385; diagnostic sample


title: AML sample number AML10_382; diagnostic sample


title: AML sample number AML10_390; diagnostic sample


title: AML sample number AML10_378; diagnostic sample


title: AML sample number AML10_374; diagnostic sample


title: AML sample number AML10_379; diagnostic sample


title: AML sample number AML10_384; diagnostic sample


title: AML sample number AML10_371; diagnostic sample


title: AML sample number AML10_372; diagnostic sample


title: AML sample number AML10_375; diagnostic sample


title: AML sample number AML10_386; diagnostic sample


title: AML sample number AML10_369; diagnostic sample


title: AML sample number AML10_370; diagnostic sample


title: AML sample number AML10_367; diagnostic sample


title: AML sample number AML10_362; diagnostic sample


title: AML sample number AML10_359; diagnostic sample


title: AML sample number AML10_365; diagnostic sample


title: AML sample number AML10_360; diagnostic sample


title: AML sample number AML10_364; diagnostic sample


title: AML sample number AML10_352; diagnostic sample


title: AML sample number AML10_354; diagnostic sample


title: AML sample number AML10_349; diagnostic sample


title: AML sample number AML10_368; diagnostic sample


title: AML sample number AML10_363; diagnostic sample


title: AML sample number AML10_358; diagnostic sample


title: AML sample number AML10_341; diagnostic sample


title: AML sample number AML10_353; diagnostic sample


title: AML sample number AML10_347; diagnostic sample


title: AML sample number AML10_346; diagnostic sample


title: AML sample number AML10_345; diagnostic sample


title: AML sample number AML10_348; diagnostic sample


title: AML sample number AML10_350; diagnostic sample


title: AML sample number AML10_355; diagnostic sample


title: AML sample number AML10_351; diagnostic sample


title: AML sample number AML10_356; diagnostic sample


title: AML sample number AML10_361; diagnostic sample


title: AML sample number AML10_342; diagnostic sample


title: AML sample number AML10_340; diagnostic sample


title: AML sample number AML10_343; diagnostic sample


title: AML sample number AML10_366; diagnostic sample


title: AML sample number AML10_338; diagnostic sample


title: AML sample number AML10_339; diagnostic sample


title: AML sample number AML10_335; diagnostic sample


title: AML sample number AML10_337; diagnostic sample


title: AML sample number AML10_333; diagnostic sample


title: AML sample number AML10_332; diagnostic sample


title: AML sample number AML10_330; diagnostic sample


title: AML sample number AML10_357; diagnostic sample


title: AML sample number AML10_334; diagnostic sample


title: AML sample number AML10_329; diagnostic sample


title: AML sample number AML10_325; diagnostic sample


title: AML sample number AML10_327; diagnostic sample


title: AML sample number AML10_320; diagnostic sample


title: AML sample number AML10_322; diagnostic sample


title: AML sample number AML10_336; diagnostic sample


title: AML sample number AML10_324; diagnostic sample


title: AML sample number AML10_328; diagnostic sample


title: AML sample number AML10_326; diagnostic sample


title: AML sample number AML10_323; diagnostic sample


title: AML sample number AML10_313; diagnostic sample


title: AML sample number AML10_318; diagnostic sample


title: AML sample number AML10_321; diagnostic sample


title: AML sample number AML10_316; diagnostic sample


title: AML sample number AML10_331; diagnostic sample


title: AML sample number AML10_344; diagnostic sample


title: AML sample number AML10_317; diagnostic sample


title: AML sample number AML10_319; diagnostic sample


title: AML sample number AML10_314; diagnostic sample


title: AML sample number AML10_311; diagnostic sample


title: AML sample number AML10_315; diagnostic sample


title: AML sample number AML10_306; diagnostic sample


title: AML sample number AML10_301; diagnostic sample


title: AML sample number AML10_312; diagnostic sample


title: AML sample number AML10_309; diagnostic sample


title: AML sample number AML10_302; diagnostic sample


title: AML sample number AML10_299; diagnostic sample


title: AML sample number AML10_304; diagnostic sample


title: AML sample number AML10_307; diagnostic sample


title: AML sample number AML10_305; diagnostic sample


title: AML sample number AML10_298; diagnostic sample


title: AML sample number AML10_295; diagnostic sample


title: AML sample number AML10_288; diagnostic sample


title: AML sample number AML10_289; diagnostic sample


title: AML sample number AML10_294; diagnostic sample


title: AML sample number AML10_285; diagnostic sample


title: AML sample number AML10_292; diagnostic sample


title: AML sample number AML10_300; diagnostic sample


title: AML sample number AML10_310; diagnostic sample


title: AML sample number AML10_303; diagnostic sample


title: AML sample number AML10_308; diagnostic sample


title: AML sample number AML10_297; diagnostic sample


title: AML sample number AML10_286; diagnostic sample


title: AML sample number AML10_296; diagnostic sample


title: AML sample number AML10_283; diagnostic sample


title: AML sample number AML10_293; diagnostic sample


title: AML sample number AML10_290; diagnostic sample


title: AML sample number AML10_282; diagnostic sample


title: AML sample number AML10_291; diagnostic sample


title: AML sample number AML10_284; diagnostic sample


title: AML sample number AML10_278; diagnostic sample


title: AML sample number AML10_277; diagnostic sample


title: AML sample number AML10_287; diagnostic sample


title: AML sample number AML10_281; diagnostic sample


title: AML sample number AML10_276; diagnostic sample


title: AML sample number AML10_280; diagnostic sample


title: AML sample number AML10_279; diagnostic sample


title: AML sample number AML10_274; diagnostic sample


title: AML sample number AML10_269; diagnostic sample


title: AML sample number AML10_271; diagnostic sample


title: AML sample number AML10_275; diagnostic sample


title: AML sample number AML10_268; diagnostic sample


title: AML sample number AML10_273; diagnostic sample


title: AML sample number AML10_270; diagnostic sample


title: AML sample number AML10_265; diagnostic sample


title: AML sample number AML10_267; diagnostic sample


title: AML sample number AML10_272; diagnostic sample


title: AML sample number AML10_266; diagnostic sample


title: AML sample number AML10_260; diagnostic sample


title: AML sample number AML10_262; diagnostic sample


title: AML sample number AML10_257; diagnostic sample


title: AML sample number AML10_256; diagnostic sample


title: AML sample number AML10_258; diagnostic sample


title: AML sample number AML10_263; diagnostic sample


title: AML sample number AML10_261; diagnostic sample


title: AML sample number AML10_245; diagnostic sample


title: AML sample number AML10_250; diagnostic sample


title: AML sample number AML10_255; diagnostic sample


title: AML sample number AML10_253; diagnostic sample


title: AML sample number AML10_246; diagnostic sample


title: AML sample number AML10_249; diagnostic sample


title: AML sample number AML10_254; diagnostic sample


title: AML sample number AML10_248; diagnostic sample


title: AML sample number AML10_259; diagnostic sample


title: AML sample number AML10_264; diagnostic sample


title: AML sample number AML10_247; diagnostic sample


title: AML sample number AML10_242; diagnostic sample


title: AML sample number AML10_252; diagnostic sample


title: AML sample number AML10_240; diagnostic sample


title: AML sample number AML10_238; diagnostic sample


title: AML sample number AML10_244; diagnostic sample


title: AML sample number AML10_235; diagnostic sample


title: AML sample number AML10_241; diagnostic sample


title: AML sample number AML10_236; diagnostic sample


title: AML sample number AML10_237; diagnostic sample


title: AML sample number AML10_251; diagnostic sample


title: AML sample number AML10_243; diagnostic sample


title: AML sample number AML10_239; diagnostic sample


title: AML sample number AML10_234; diagnostic sample


title: AML sample number AML10_232; diagnostic sample


title: AML sample number AML10_233; diagnostic sample


title: AML sample number AML10_229; diagnostic sample


title: AML sample number AML10_231; diagnostic sample


title: AML sample number AML10_230; diagnostic sample


title: AML sample number AML10_226; diagnostic sample


title: AML sample number AML10_221; diagnostic sample


title: AML sample number AML10_227; diagnostic sample


title: AML sample number AML10_208; diagnostic sample


title: AML sample number AML10_217; diagnostic sample


title: AML sample number AML10_209; diagnostic sample


title: AML sample number AML10_214; diagnostic sample


title: AML sample number AML10_223; diagnostic sample


title: AML sample number AML10_225; diagnostic sample


title: AML sample number AML10_216; diagnostic sample


title: AML sample number AML10_224; diagnostic sample


title: AML sample number AML10_211; diagnostic sample


title: AML sample number AML10_219; diagnostic sample


title: AML sample number AML10_218; diagnostic sample


title: AML sample number AML10_207; diagnostic sample


title: AML sample number AML10_212; diagnostic sample


title: AML sample number AML10_222; diagnostic sample


title: AML sample number AML10_213; diagnostic sample


title: AML sample number AML10_215; diagnostic sample


title: AML sample number AML10_220; diagnostic sample


title: AML sample number AML10_206; diagnostic sample


title: AML sample number AML10_205; diagnostic sample


title: AML sample number AML10_203; diagnostic sample


title: AML sample number AML10_210; diagnostic sample


title: AML sample number AML10_200; diagnostic sample


title: AML sample number AML10_199; diagnostic sample


title: AML sample number AML10_204; diagnostic sample


title: AML sample number AML10_202; diagnostic sample


title: AML sample number AML10_198; diagnostic sample


title: AML sample number AML10_193; diagnostic sample


title: AML sample number AML10_194; diagnostic sample


title: AML sample number AML10_197; diagnostic sample


title: AML sample number AML10_191; diagnostic sample


title: AML sample number AML10_182; diagnostic sample


title: AML sample number AML10_190; diagnostic sample


title: AML sample number AML10_184; diagnostic sample


title: AML sample number AML10_180; diagnostic sample


title: AML sample number AML10_195; diagnostic sample


title: AML sample number AML10_228; diagnostic sample


title: AML sample number AML10_185; diagnostic sample


title: AML sample number AML10_188; diagnostic sample


title: AML sample number AML10_196; diagnostic sample


title: AML sample number AML10_187; diagnostic sample


title: AML sample number AML10_186; diagnostic sample


title: AML sample number AML10_189; diagnostic sample


title: AML sample number AML10_179; diagnostic sample


title: AML sample number AML10_192; diagnostic sample


title: AML sample number AML10_181; diagnostic sample


title: AML sample number AML10_183; diagnostic sample


title: AML sample number AML10_178; diagnostic sample


title: AML sample number AML10_172; diagnostic sample


title: AML sample number AML10_176; diagnostic sample


title: AML sample number AML10_174; diagnostic sample


title: AML sample number AML10_175; diagnostic sample


title: AML sample number AML10_170; diagnostic sample


title: AML sample number AML10_177; diagnostic sample


title: AML sample number AML10_171; diagnostic sample


title: AML sample number AML10_173; diagnostic sample


title: AML sample number AML10_166; diagnostic sample


title: AML sample number AML10_160; diagnostic sample


title: AML sample number AML10_158; diagnostic sample


title: AML sample number AML10_154; diagnostic sample


title: AML sample number AML10_167; diagnostic sample


title: AML sample number AML10_162; diagnostic sample


title: AML sample number AML10_155; diagnostic sample


title: AML sample number AML10_156; diagnostic sample


title: AML sample number AML10_153; diagnostic sample


title: AML sample number AML10_163; diagnostic sample


title: AML sample number AML10_159; diagnostic sample


title: AML sample number AML10_169; diagnostic sample


title: AML sample number AML10_165; diagnostic sample


title: AML sample number AML10_168; diagnostic sample


title: AML sample number AML10_152; diagnostic sample


title: AML sample number AML10_157; diagnostic sample


title: AML sample number AML10_149; diagnostic sample


title: AML sample number AML10_145; diagnostic sample


title: AML sample number AML10_161; diagnostic sample


title: AML sample number AML10_148; diagnostic sample


title: AML sample number AML10_151; diagnostic sample


title: AML sample number AML10_147; diagnostic sample


title: AML sample number AML10_150; diagnostic sample


title: AML sample number AML10_144; diagnostic sample


title: AML sample number AML10_141; diagnostic sample


title: AML sample number AML10_146; diagnostic sample


title: AML sample number AML10_143; diagnostic sample


title: AML sample number AML10_142; diagnostic sample


title: AML sample number AML10_164; diagnostic sample


title: AML sample number AML10_139; diagnostic sample


title: AML sample number AML10_132; diagnostic sample


title: AML sample number AML10_138; diagnostic sample


title: AML sample number AML10_134; diagnostic sample


title: AML sample number AML10_137; diagnostic sample


title: AML sample number AML10_133; diagnostic sample


title: AML sample number AML10_124; diagnostic sample


title: AML sample number AML10_118; diagnostic sample


title: AML sample number AML10_129; diagnostic sample


title: AML sample number AML10_127; diagnostic sample


title: AML sample number AML10_125; diagnostic sample


title: AML sample number AML10_122; diagnostic sample


title: AML sample number AML10_119; diagnostic sample


title: AML sample number AML10_140; diagnostic sample


title: AML sample number AML10_123; diagnostic sample


title: AML sample number AML10_131; diagnostic sample


title: AML sample number AML10_130; diagnostic sample


title: AML sample number AML10_135; diagnostic sample


title: AML sample number AML10_126; diagnostic sample


title: AML sample number AML10_117; diagnostic sample


title: AML sample number AML10_112; diagnostic sample


title: AML sample number AML10_113; diagnostic sample


title: AML sample number AML10_121; diagnostic sample


title: AML sample number AML10_136; diagnostic sample


title: AML sample number AML10_114; diagnostic sample


title: AML sample number AML10_120; diagnostic sample


title: AML sample number AML10_116; diagnostic sample


title: AML sample number AML10_110; diagnostic sample


title: AML sample number AML10_111; diagnostic sample


title: AML sample number AML10_109; diagnostic sample


title: AML sample number AML10_105; diagnostic sample


title: AML sample number AML10_115; diagnostic sample


title: AML sample number AML10_108; diagnostic sample


title: AML sample number AML10_107; diagnostic sample


title: AML sample number AML10_102; diagnostic sample


title: AML sample number AML10_106; diagnostic sample


title: AML sample number AML10_100; diagnostic sample


title: AML sample number AML10_101; diagnostic sample


title: AML sample number AML10_99; diagnostic sample


title: AML sample number AML10_96; diagnostic sample


title: AML sample number AML10_128; diagnostic sample


title: AML sample number AML10_104; diagnostic sample


title: AML sample number AML10_103; diagnostic sample


title: AML sample number AML10_92; diagnostic sample


title: AML sample number AML10_98; diagnostic sample


title: AML sample number AML10_94; diagnostic sample


title: AML sample number AML10_89; diagnostic sample


title: AML sample number AML10_90; diagnostic sample


title: AML sample number AML10_97; diagnostic sample


title: AML sample number AML10_93; diagnostic sample


title: AML sample number AML10_84; diagnostic sample


title: AML sample number AML10_85; diagnostic sample


title: AML sample number AML10_83; diagnostic sample


title: AML sample number AML10_79; diagnostic sample


title: AML sample number AML10_82; diagnostic sample


title: AML sample number AML10_91; diagnostic sample


title: AML sample number AML10_86; diagnostic sample


title: AML sample number AML10_88; diagnostic sample


title: AML sample number AML10_78; diagnostic sample


title: AML sample number AML10_81; diagnostic sample


title: AML sample number AML10_95; diagnostic sample


title: AML sample number AML10_80; diagnostic sample


title: AML sample number AML10_87; diagnostic sample


title: AML sample number AML10_72; diagnostic sample


title: AML sample number AML10_74; diagnostic sample


title: AML sample number AML10_75; diagnostic sample


title: AML sample number AML10_71; diagnostic sample


title: AML sample number AML10_69; diagnostic sample


title: AML sample number AML10_66; diagnostic sample


title: AML sample number AML10_64; diagnostic sample


title: AML sample number AML10_62; diagnostic sample


title: AML sample number AML10_65; diagnostic sample


title: AML sample number AML10_63; diagnostic sample


title: AML sample number AML10_76; diagnostic sample


title: AML sample number AML10_60; diagnostic sample


title: AML sample number AML10_56; diagnostic sample


title: AML sample number AML10_70; diagnostic sample


title: AML sample number AML10_51; diagnostic sample


title: AML sample number AML10_59; diagnostic sample


title: AML sample number AML10_73; diagnostic sample


title: AML sample number AML10_54; diagnostic sample


title: AML sample number AML10_55; diagnostic sample


title: AML sample number AML10_57; diagnostic sample


title: AML sample number AML10_58; diagnostic sample


title: AML sample number AML10_49; diagnostic sample


title: AML sample number AML10_53; diagnostic sample


title: AML sample number AML10_52; diagnostic sample


title: AML sample number AML10_48; diagnostic sample


title: AML sample number AML10_67; diagnostic sample


title: AML sample number AML10_47; diagnostic sample


title: AML sample number AML10_45; diagnostic sample


title: AML sample number AML10_50; diagnostic sample


title: AML sample number AML10_46; diagnostic sample


title: AML sample number AML10_68; diagnostic sample


title: AML sample number AML10_44; diagnostic sample


title: AML sample number AML10_61; diagnostic sample


title: AML sample number AML10_43; diagnostic sample


title: AML sample number AML10_41; diagnostic sample


title: AML sample number AML10_42; diagnostic sample


title: AML sample number AML10_39; diagnostic sample


title: dksA::aphA3 mutant of 81176 (Campylobacter_dksAmutantvswildtype_slide280)

city: Ames

first: Byeonghwa

last: Jeon

state: IA

address: 1113 Vet Med

institute: ISU

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts (120 pmol of label) of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 3 min. The hybridization mixture was loaded onto a microarray slide (OciChipTM, Ocimum Biosolutions, Indianapolis, IN) and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as per the manufacture’s recommendations and dried by centrifugation.  Briefly, the slides the slides were washed three times in wash buffer 1 (2X SSC + 0.1% SDS) for 5 minutes at 32 C.  They were then washed three times in wash buffer 2 (1X SSC) at 32 C ofr 5 minutes and finally three times in wash buffer 3 (0.1X SSC) for 5 minutes at 32 C.  The slides were dried in a conical bottom tube centrifuges at 400g for 3 minutes.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings.  Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength and the spot-specific background median of each spot.  Using the R statistical package (Version 2.0.1, The R Foundation for Statistical Computing) a background-subtracted value for each spot of each of the three scans was obtained by subtracting the spot-specific background median from the spot-specific signal mean.  The natural log of each value was obtained and each of the same array by dye combinations was median centered to a common median by addition of a constant.  Following median centering the median of the three adjusted-log-background subtracted spot signals was determined and this value was used as spot signal for all further calculations.  As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni subsp. jejuni 81-176

source_name: Campylobacter jejuni dksA::aphA3 mutant of 81176

label_protocol: cDNA was synthesized using aminoallyl-dNTP with the ChipShotTM indirect cDNA Labeling System (Promega) according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with CyTMDye Post-labeling Reactive Pack (Amersham Bioscience, Piscataway, NJ).

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: Strain

value: Campylobacter jejuni dksA::aphA3 strain 81176

tag: Growth conditions

value: Grown in mueller hinton broth at 37 C, 120 rpm for 6 hours


title: AML sample number AML10_38; diagnostic sample


title: AML sample number AML10_40; diagnostic sample


title: Wildtype grown for 6 hours (Campy_dksAmutantvswildtype_Slide25)

source_name: C. jejuni wildtype grown for 6 hours

value: Campylobacter jejuni wildtype strain 81176


title: Wildtype strain 81176 (Campylobacter_dksAmutantvswildtype_slide28)

source_name: Campylobacter jejuni wildtype strain 81176


title: dksA::aphA3 mutant of 81176 (Campylobacter_dksAmutantvswildtype_slide30)


title: Wildtypre strain 81176 (Campylobacter_dksAmutantvswildtype_slide27)

source_name: Campylobacter wildtypre strain 81176


title: dksA::aphA3 mutant of 81176 (Campylobacter_dksAmutantvswildtype_slide31)


title: AML sample number AML10_37; diagnostic sample


title: Wildtype strain 81176 (Campylobacter_dksAmutantvswildtype_slide31)


title: Wildtype strain 81176 (Campylobacter_dksAmutantvswildtype_slide30)


title: Wildtype strain 81176 (Campylobacter_dksAmutantvswildtype_slide280)


title: dksA::aphA3 grown for 6 hours (Campy_dksAmutantvswildtype_Slide25)

source_name: C. jejuni dksA::aphA3 grown for 6 hours


title: AML sample number AML10_36; diagnostic sample


title: AML sample number AML10_31; diagnostic sample


title: dksA::aphA3 mutant of strain 81176 (Campylobacter_dksAmutantvswildtype_slide27)

source_name: Campylobacter dksA::aphA3 mutant of strain 81176


title: AML sample number AML10_33; diagnostic sample


title: AML sample number AML10_14; diagnostic sample


title: AML sample number AML10_13; diagnostic sample


title: AML sample number AML10_26; diagnostic sample


title: dksA::aphA3 mutant of 81176 (Campylobacter_dksAmutantvswildtype_slide28)

source_name: Campylobacter dksA::aphA3 mutant of 81176


title: AML sample number AML10_29; diagnostic sample


title: AML sample number AML10_19; diagnostic sample


title: AML sample number AML10_32; diagnostic sample


title: AML sample number AML10_21; diagnostic sample


title: AML sample number AML10_16; diagnostic sample


title: AML sample number AML10_22; diagnostic sample


title: AML sample number AML10_23; diagnostic sample


title: AML sample number AML10_11; diagnostic sample


title: AML sample number AML10_15; diagnostic sample


title: AML sample number AML10_17; diagnostic sample


title: AML sample number AML10_12; diagnostic sample


title: AML sample number AML10_10; diagnostic sample


title: AML sample number AML10_5; diagnostic sample


title: AML sample number AML10_7; diagnostic sample


title: AML sample number AML10_6; diagnostic sample


title: AML sample number AML10_8; diagnostic sample


title: AML sample number AML10_1; diagnostic sample


title: AML sample number AML10_3; diagnostic sample


title: AML sample number AML10_4; diagnostic sample


title: whole_larvae_rep3

status: Public on May 01 2008

city: St. Augustine

first: Marco

middle: V.

last: Neira

state: FL

address: 9505 Oceanshore Blvd.

department: The Whitney Laboratory

institute: University of Florida

description: Sample represents pooled material from 200 individuals

hyb_protocol: The biotin-labeled cRNA was fragmented and hybridized for 16 hours to the Affymetrix GeneChip® Plasmodium/Anopheles Genome Array according to the manufactures’ protocols.  The arrays were then washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450

scan_protocol: Hybridized chips were scanned on a GeneChip Scanner 3000 (Affymetrix, Inc) using default values to generate signal intensities

data_processing: GeneSifter™ (VizX Labs, Seattle, WA, USA) software was used to perform all statistical analyses. Expression values were background-adjusted, normalized, and log2-transformed by applying the robust multiarray average (RMA) algorithm (Irizarry et al., 2003).

organism: Anopheles gambiae

source_name: Whole 4th. instar An. gambiae larvae

label_protocol: cDNA was synthesized from 5ug of total RNA using the One-Cycle Eukaryotic Target Labeling reagents (Affymetrix, Inc.).  The cDNA was used as a template for in vitro transcription (IVT) in the presence of T7 RNA Polymerase and a biotinytlated nucleotide/ribonucleotide mix for cRNA amplification and biotin labeling using the IVT labeling kit (Affymetrix, Inc).

growth_protocol: Eggs of the G3 strain of An. gambiae were obtained from the Centers for Disease Control and Prevention (CDC; Atlanta, Georgia). Mosquito larvae were reared in distilled water at 28C, 12h: 12h light: darkness cycle, and provided with a mixture of baker’s yeast and ground Tetramin® flakes as food.

extract_protocol: Total RNA was extracted using the RNAeasy-Mini Kit™ (Qiagen®, Chatsworth, CA, USA) following the manufacturer’s recommendations

treatment_protocol: For each biological repeat, 50-200 fourth-instar larvae were anesthetized on ice and dissected in RNAse-free 70% ETOH. Their salivary glands were extracted and stored at -20C in 70% ETOH until RNA extraction. Three biological repeats were performed in order to obtain statistical significance.

tag: Larval instar


title: AML sample number AML10_2; diagnostic sample


title: AML sample number AML10_9; diagnostic sample


title: SmutansTW1_TVglu_rep2

city: Gainesville

first: Robert

middle: A

last: Burne

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

description: Streptococcus mutans ccpA mutant

hyb_protocol: Hybridizations were carried out in a Maui 4-chamber hybridization system (BioMicro Systems, Salt Lake City, Utah) for 17 h at 42ºC. The slides were then washed according to TIGR protocols (SOT# M008, version 2.1, 11/06).

scan_protocol: The slides were scanned using a GenePix Scanner (Axon Instruments Inc., Union City, CA).

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software and overlayed. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, then the intensity values of each spot were measured. Data was normalized using Microarray data analysis software (MIDAS), by using LOWESS and Iterative Log Mean Centering with default settings.

organism: Streptococcus mutans

source_name: S. mutans TW1 grown in TV+0.5% glucose

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Purified cDNAs were coupled with indocarbocyanine (Cy3)-dUTP

growth_protocol:
Growth Media: Tryptone-Vitamin broth with 0.5% glucose added
OD600: 0.5

extract_protocol: RNA from S. mutans was isolated from 50 ml cultures that were grown under the desired conditions and harvested by centrifugation at 4ºC. Pelleted cells were resuspended in 400 ml of DEPC-treated water, 800 ml of RNA protect reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were incubated at room temperature for 5 min with vortexing for 10 s at one minute intervals. Cells were then pelleted, resuspended in 500 ml Tris-EDTA (50:10) buffer and transferred to 1.5 ml screw cap tubes containing sterile glass beads (0.1 mm avg. diam.; Biospec, Bartlesville, OK), 100 ml of 1% SDS and 650 ml of acid phenol:chloroform (5:1). The mixture was homogenized in a Bead Beater twice for 40 s and chilled on ice for 2 min between cycles. Samples were centrifuged for 30 min at maximum speed at 4ºC. Two additional hot acid phenol:chloroform extractions were performed followed by one extraction with chloroform:isoamyl-alcohol (24:1). RNA was precipitated in the presence of isopropanol and sodium acetate, pH 5, at -20ºC for 1 h, followed by multiple washes with 70% ethanol, one wash with 99% ethanol, and drying in vacuo. RNA was resuspended in DEPC-treated water and digested with DNAseI (Ambion, Austin, TX). The RNA was re-purified and treated on-column with DNaseI using the RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA), as recommended by the supplier.

tag: Strain TW1

value: knockout of the ccpA homolog via insertion of a kanamycin cassette

source_name: S. mutans UA159 grown in BHI

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Reference cDNA was coupled with indodicarbocyanine (Cy5)-dUTP (Amersham Biosciences, Piscataway, NJ).

growth_protocol:
Growth Media: Brain Heart Infusion
OD600: 0.5

tag: Strain UA159


title: SmutansTW1_TVglu_rep1

description: Streptococcus mutans ccpA mutant


title: larval_salivary_gland_rep3

description: Sample represents pooled material from 50 dissected individuals

source_name: Salivary glands of 4th. instar An. gambiae larvae


title: AML sample number AML10_77; diagnostic sample


title: SmutansUA159_TVglu_rep4

description: Streptococcus mutans ccpA wildtype

source_name: S. mutans UA159 grown in TV+0.5% glucose


title: whole_larvae_rep1


title: whole_larvae_rep2


title: SmutansUA159_TVglu_rep3

description: Streptococcus mutans ccpA wildtype


title: SmutansTW1_TVglu_rep3

description: Streptococcus mutans ccpA mutant


title: larval_salivary_gland_rep1


title: SmutansTW1_TVglu_rep4

description: Streptococcus mutans ccpA mutant


title: larval_salivary_gland_rep2


title: IAP-flanking region vs whole genome (promoters in C3H)

status: Public on May 03 2008

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: See above.

hyb_protocol: Hybridization and post hybridization wash were carried out essentially according to the manufacturers’ protocol (version 2) for oligonucleotide array-based CGH for genomic DNA analysis (Agilent).

scan_protocol: Hybridized arrays were scanned using the Axon 4000B scanner (Axon Instruments, Burlingame, CA) and processed using GenePix Pro 5.1 software (Axon Instruments).

data_processing: Fluorescence ratios were normalized so that the mean of the ratio of medians of all of the features is equal to 1.

organism: Mus musculus

source_name: IAP-flanking C3H genomic DNA fragments

label_protocol: Affinity-purified DNA fragments containing the LTR sequence were digested by Rsa I and AluI, and then labeled fluorescently by Cy3. Clean-up of digested or fluorescently-labeled DNA was carried out with QIAprep Spin Miniprep Kit (Qiagen) or Microcon YM-30 filters (Millipore, Billerica, MA), respectively.

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction. Two methods were employed in the generation of genomic DNA fragments containing a common sequence at both ends; the degenerate oligonucleotide-primed PCR (DOP-PCR) method and the digestion by restriction enzymes followed by linker ligation. The digestion by restriction enzymes was carried out with the following three enzymes; Bam HI, Bgl II and Fba I.  One μg of genomic DNA was digested by these enzymes independently, or in combination with another enzyme (double digestions).  Subsequently, all restricted fragments were mixed, purified by using a QIAquick PCR Purification Kit and ligated to a linker. DNA fragments containing the contiguous sequences covering the LTR region of IAP element and its flanking region were purified using the affinity with the biotin labeled oligonucleotides which had highly conserved sequences within LTR.

tag: C3H/He female tale

source_name: C3H genomic DNA fragments

label_protocol: Genomic DNA was digested by Rsa I and AluI, and labeled fluorescently by Cy5. Clean-up of digested or fluorescently-labeled DNA was carried out with QIAprep Spin Miniprep Kit (Qiagen) or Microcon YM-30 filters (Millipore, Billerica, MA), respectively.


title: SmutansUA159_TVglu_rep2

description: Streptococcus mutans ccpA wildtype


title: IAP-flanking region vs whole genome (promoters in C57BL, 2 of 2)

description: See above.

source_name: IAP-flanking C57BL/6J genomic DNA fragments

tag: C57BL/6J female tale

source_name: C57BL/6J genomic DNA fragments

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction


title: SmutansTW1_TVgal_rep3

description: Streptococcus mutans ccpA mutant

hyb_protocol: Hybridizations were carried out in a Maui 4-chamber hybridization system (BioMicro Systems, Salt Lake City, Utah) for 17 h at 42ºC.  The slides were then washed according to TIGR protocols (SOT# M008, version 2.1, 11/06).

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software and overlayed.  A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, then the intensity values of each spot were measured.  Data was normalized using Microarray data analysis software (MIDAS), by using LOWESS and Iterative Log Mean Centering with default settings.

source_name: S. mutans TW1 grown in TV+0.5% galactose

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications.  The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2.  SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields.  Purified cDNAs were coupled with indocarbocyanine (Cy3)-dUTP

growth_protocol:
Growth Media:  Tryptone-Vitamin broth with 0.5% galactose added
OD600: 0.5

extract_protocol: RNA from S. mutans was isolated from 50 ml cultures that were grown under the desired conditions and harvested by centrifugation at 4ºC.  Pelleted cells were resuspended in 400 ml of DEPC-treated water, 800 ml of RNA protect reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were incubated at room temperature for 5 min with vortexing for 10 s at one minute intervals.  Cells were then pelleted, resuspended in 500 ml Tris-EDTA (50:10) buffer and transferred to 1.5 ml screw cap tubes containing sterile glass beads (0.1 mm avg. diam.; Biospec, Bartlesville, OK), 100 ml of 1% SDS and 650 ml of acid phenol:chloroform (5:1).  The mixture was homogenized in a Bead Beater twice for 40 s and chilled on ice for 2 min between cycles.  Samples were centrifuged for 30 min at maximum speed at 4ºC.  Two additional hot acid phenol:chloroform extractions were performed followed by one extraction with chloroform:isoamyl-alcohol (24:1).  RNA was precipitated in the presence of isopropanol and sodium acetate, pH 5, at -20ºC for 1 h, followed by multiple washes with 70% ethanol, one wash with 99% ethanol, and drying in vacuo.  RNA was resuspended in DEPC-treated water and digested with DNAseI (Ambion, Austin, TX). The RNA was re-purified and treated on-column with DNaseI using the RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA), as recommended by the supplier.

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications.  The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2.  SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields.  Reference cDNA was coupled with indodicarbocyanine (Cy5)-dUTP (Amersham Biosciences, Piscataway, NJ).

growth_protocol:
Growth Media:  Brain Heart Infusion
OD600:  0.5


title: SmutansTW1_TVgal_rep4

description: Streptococcus mutans ccpA mutant


title: SmutansUA159_TVgal_rep1

description: Streptococcus mutans ccpA wildtype

source_name: S. mutans UA159 grown in TV+0.5% galactose


title: IAP-flanking region vs whole genome (promoters in C3H, 2 of 2)

description: See above.

tag: C3H female tale


title: SmutansUA159_TVglu_rep1

description: Streptococcus mutans ccpA wildtype


title: SmutansUA159_TVgal_rep3

description: Streptococcus mutans ccpA wildtype


title: IAP-flanking region vs whole genome (AML)

description: See above.

source_name: IAP-flanking genomic DNA fragments of AML

tag: a leukemic C3H/He male mouse, acute myeloid leukemia

source_name: C3H/He male tale

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction.

tag: C3H male tale


title: SmutansUA159_TVgal_rep4

description: Streptococcus mutans ccpA wildtype


title: IAP-flanking region vs whole genome (promoters in C57BL)

description: See above.

source_name: C57BL/6J female tale


title: SmutansTW1_TVgal_rep2

description: Streptococcus mutans ccpA mutant


title: SmutansUA159_TVgal_rep2

description: Streptococcus mutans ccpA wildtype


title: IAP-flanking region vs whole genome (C3H/He normal cell)

description: See above.

source_name: IAP-flanking C3H/He genomic DNA fragments

tag: C3H/He male tale

source_name: C3H/He genomic DNA fragments


title: SmutansTW1_TVgal_rep1

description: Streptococcus mutans ccpA mutant


title: Beige control stomach antrum RNA replicate 1

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 44 Binney St.

institute: Dana-Farber Cancer Institute

description: This study looks at gastric cell lineages with respect to FOXQ1 to compare stomach antrum from three different strains of mice, BL6, Satin and Beige.

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

scan_protocol: excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis

data_processing: dChip

label: biotinylated complementary RNA (cRNA)

source_name: control mouse stomach antrum from the Beige strain

label_protocol: standard approach

extract_protocol: trizol extraction

tag: approximately 4 month old mouse with the Beige mutation (disrupting the LYST gene)


title: IAP-flanking region vs whole genome (C3H)

description: See above.


title: K11-5 #2

city: Atlanta

first: Hideharu

last: Hashimoto

state: GA

address: 1510 Clifton

department: Biochemistry

institute: Emory University

description: Study to compare gene expression in wild type, K11 and K11-5 cells

hyb_protocol: Following Affymetrix protocols

scan_protocol: Using Affymetrix scanner and mannuals

data_processing: Affymetrix CHP files including row data were generated with GCOS

label: Used Affymetrix one cycle labeling Kit

organism: Gallus gallus

source_name: H1 complete null chicken B-cell derived DT40 cells

label_protocol: Following Affymetrix one cycle labeling Kit mannuals

growth_protocol: Cells were cultured in RPMI1640, 10% FCS, 1% chicken serum, 2 mM L-glutamin, 50 micro-M of 2-Mercaptoethanol, and 100 nM of Z-VAD-FMK at 39.5C

extract_protocol: From exponately growing DT40 cells, Total RNAs were extracted with Sepasol I (Nakarai) and RNeasy (QIAGEN) as vender's mannuals

treatment_protocol: Apoptosis is induced in H1 null cells, we culture DT40 cells to inhibit apoptosis with pan-caspase inhibitor, 100 nM of Z-VAD-FMK.

tag: In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804] but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities(Hashimoto et al., DNA repair (2007) [17613284], so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Then we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analyzed those gene expression pattern in wild-type, K11, and K11-5 cells.


title: wild-type #2

source_name: wild type chicken B-cell derived DT40 cells

extract_protocol: From exponately growing DT40 cells, Total RNAs were extracted with Sepasol I (Nakarai) and RNeasy (QIAGEN) as vendor's mannuals


title: K11 #2

source_name: Endogenous H1 knock out chicken B-cell derived DT40 cells


title: IAP-flanking region vs whole genome (C57BL)

description: See above.


title: Satin stomach antrum RNA replicate 1

source_name: Satin stomach antrum RNA replicate 1

tag: Satin stomach antrum RNA replicate 1, RNA from a mouse of the Satin strain, containing a mutation in the Foxq1 locus


title: K11-5 #1


title: K11 #1


title: C57/BL6 control stomach antrum RNA replicate 1

source_name: BL6 control mouse stomach antrum RNA

tag: approximately 4 months old


title: Satin stomach antrum RNA replicate 2

source_name: Satin stomach antrum RNA replicate 2

tag: Satin stomach antrum RNA replicate 2, from a mouse containing a mutation in the foxq1 locus


title: wild type #1


title: C57/BL6 control stomach antrum RNA replicate 2

tag: C57/BL6 control stomach antrum RNA from 4 month old mouse


title: Beige control stomach antrum RNA replicate 2

source_name: control mouse stomach antrum from the Beige strain replicate 2

tag: RNA array from sample taken from Beige mouse antrum (which has a mutation in the LYST gene)


title: ZHBTc4(Tc+), 96hr, #2

status: Public on Apr 24 2008

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: ZHBTc4(Tc+), 96hr

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: ZHBTc4(Tc+), 96hr

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: see Niwa et al. nature genetics, 24(2000) 372-376.

treatment_protocol: The sample were treated with ROSA-TET system, Tet inducible system, as described in [An efficient system to establish multiple embryonic stem cell lines carrying an inducible expression unit], Nucleic Acids Res. 2005; 33(4): e43.  Specifically, 5 ug of circular plasmid DNA of Tcl1 exchange vector (pZhC-Tcl1), which have only cds region of Tcl1 gene, and pCAGGS-Cre were co-transfected into EBRTcH3 ES cells. ES cells were cultured in regular medium within 18 ug/ml zeocin, and then, the clones of ES cells were isolated. Tet is present in the culture medium.

tag: embryonic stem cell

tag: Strain

tag: Gender

value: male

tag: Genetic modification

value: gene knock in

tag: Individual Identifier

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: ZHBTc4(Tc+), 72hr, #3

description: ZHBTc4(Tc+), 72hr

source_name: ZHBTc4(Tc+), 72hr


title: ZHBTc4(Tc+), 96hr, #3

description: ZHBTc4(Tc+), 96hr


title: ZHBTc4(Tc+), 120hr, #2

description: ZHBTc4(Tc+), 120hr

source_name: ZHBTc4(Tc+), 120hr


title: Glioblastoma GBM_250_acgh

status: Public on Apr 29 2008

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

description: comparative genomic hybridization of human glioblastoma vs. normal genomic DNA

hyb_protocol: Genomic DNA hybridization to Agilent CGH arrays were performed as per manufacturer’s protocol

scan_protocol: Scanning was performed as per manufacturer's protocol

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: human glioblastoma tumor

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Total DNA extracted using PureGene kit following manufacturer's instructions (Gentra Systems).

tag: Human glioblastoma tumor

source_name: universal human male genomic DNA

tag: normal human male genomic DNA


title: ZHBTc4(Tc+), 120hr, #3

description: ZHBTc4(Tc+), 120hr


title: Glioblastoma GBM_204_acgh


title: ZHBTc4(Tc+), 120hr, #1

description: ZHBTc4(Tc+), 120hr


title: ZHBTc4(Tc+), 72hr, #2

description: ZHBTc4(Tc+), 72hr


title: ZHBTc4(Tc+), 96hr, #1

description: ZHBTc4(Tc+), 96hr


title: Nanog/EF1#6  LIF-

description: Nanog transfectants

source_name: Nanog transfectants

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.

value: Nanog cloned in pEF6/IRES neo plasmid


title: Oct4KO_24hr_rep2

description: Oct3/4 KO,  24hr

source_name: Oct3/4 KO,  24hr

extract_protocol: TROZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used. 1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using a glass-Teflon? or power homogenizer (Polytron, or Tekmar's TISSUMIZER? or equivalent). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at 15 to 30?C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30?C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8?C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30?C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8?C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8?C. 6. REDISSOLVING THE RNA At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes). Do not dry the RNA by centrifugation under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60?C. (Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70?C. (See Bracete, et.al. (1998) Focus 20:3 p 82).

value: Transgenic and Knock down

source_name: Universal Mouse Reference Cell Line Pool


title: Glioblastoma GBM_219_acgh


title: Oct4KO_24hr_rep1

description: Oct3/4 KO,  24hr


title: ZHBTc4(Tc+), 72hr, #1

description: ZHBTc4(Tc+), 72hr


title: Nanog/EF1#6  LIF+

description: Nanog transfectants


title: Oct4KO_12hr_rep2

description: Oct3/4 KO,  12hr

source_name: Oct3/4 KO,  12hr


title: Glioblastoma GBM_183_acgh


title: Glioblastoma GBM_147_acgh


title: Glioblastoma GBM_121_acgh


title: Nanog/EF1#6  LIF+,RA

description: Nanog transfectants


title: Nanog episomal  LIF+RA

description: Nanog transfectants

value: Episomal pPYFloxed vector


title: ZHBTc4(Tc+), 48hr, #2

description: ZHBTc4(Tc+), 48hr

source_name: ZHBTc4(Tc+), 48hr


title: Glioblastoma GBM_172_acgh


title: Glioblastoma GBM_120_acgh


title: Glioblastoma GBM_149_acgh


title: Oct4KO_12hr_rep1

description: Oct3/4 KO,  12hr


title: Nanog episomal   LIF-

description: Nanog transfectants


title: Oct4KO_6hr_rep1

description: Oct3/4 KO,  6hr

source_name: Oct3/4 KO,  6hr


title: Oct4KO_6hr_rep2

description: Oct3/4 KO,  6hr


title: Nanog episomal #3  LIF+

description: Nanog transfectants


title: ZHBTc4(Tc+), 48hr, #1

description: ZHBTc4(Tc+), 48hr


title: Oct4KO_3hr_rep2

description: Oct3/4 KO,  3hr

source_name: Oct3/4 KO,  3hr


title: ZHBTc4(Tc+), 24hr, #1

description: ZHBTc4(Tc+), 24hr

source_name: ZHBTc4(Tc+), 24hr


title: ZHBTc4(Tc+), 24hr, #2

description: ZHBTc4(Tc+), 24hr


title: ZHBTc4(Tc+), 0hr, #3

description: ZHBTc4(Tc+), 0hr

source_name: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 0hr, #2

description: ZHBTc4(Tc+), 0hr


title: Oct4KO_0hr_rep2

description: Oct3/4 KO, 0 hr

source_name: Oct3/4 KO, 0 hr


title: Oct4KO_0hr_rep1

description: Oct3/4 KO, 0 hr


title: Oct4KO_3hr_rep1

description: Oct3/4 KO,  3hr


title: Glioblastoma GBM_253_acgh