title: RT_100_13_4_DCBZ-100_Liver_07008

description: RT_100_13_4_DCBZ-100_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: ratio

value: Good

tag: sample preservation

value: weeks

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

value: per day

tag: treatment duration

tag: amount of vehicle

tag: units of amount of vehicle


title: RT_1000_13_252_TDPP_Mus_Liver

status: Public on Mar 01 2010

type: RNA

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

country: USA

institute: The Hamner Institutes for Health Sciences

description: RT_1000_13_252_TDPP_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Sample Type: tissue, Tissue: Liver, Tissue Harvest Methods: Tissue was excised from animal, minced, placed in RNA later, and stored at -80 degrees Centigrade, Harvest Time Point: 13, Units of Harvest Time Point: weeks

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: Tris(2,3-dibromopropyl)phosphate, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1000, Units of Dose or Concentration: ppm

value: ul

tag: dilution

tag: bioanalyzer results

value: RNA later

tag: strain or line

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

value: Female

tag: age

tag: units of age

tag: units of duration

tag: treatment time

tag: units of treatment time

value: days/wk

tag: vehicle for chemical

value: Rodent Chow

tag: route of exposure

value: Diet

tag: dose or concentration

tag: units of dose or concentration

value: ppm


title: RT_100_13_82r_BENZ_Mus_Li

description: RT_100_13_82r_BENZ_Mus_Li_Mouse430_2_RSTLRI601_1

treatment_protocol: in vivo Treatment: Benzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 100, Units of Dose or Concentration: mg/kg

tag: amount to core

tag: units of amount

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: in vivo treatment

value: Benzene

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: Corn Oil

tag: amount of vehicle

value: Gavage

tag: units of amount of vehicle

value: ml/kg

value: mg/kg


title: RT_20_13_145_TCPN-20_Liver_07008

description: RT_20_13_145_TCPN-20_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: 1,2,3-Trichloropropane, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 20, Units of Dose or Concentration: mg/kg

tag: dilution

tag: bioanalyzer results

value: Good

tag: strain or line

tag: individual

tag: developmental state

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: units of duration

tag: treatment time


title: RT_100_13_84_BENZ_Mus_Li

description: RT_100_13_84_BENZ_Mus_Li_Mouse430_2_RSTLRI601_1

tag: amount to core

tag: units of amount

tag: ratio

tag: rna integrity number

tag: sample preservation

value: weeks

tag: in vivo treatment

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_100_13_228_ETOX_Liver_07008

description: RT_100_13_228_ETOX_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: Ethylene Oxide, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

tag: dilution

tag: bioanalyzer results

tag: strain or line

tag: individual

tag: developmental state

tag: sacrifice method

value: Ethylene Oxide

tag: treatment repeat

tag: units of treatment repeat

value: hr/day

tag: treatment duration

value: Air

value: Inhalation


title: RT_1000_13_248_TDPP_Mus_Liver

description: RT_1000_13_248_TDPP_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

value: ul

tag: ratio

value: RNA later

value: Adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

tag: age

tag: units of age

tag: units of duration

tag: treatment time


title: RT_100_13_81_BENZ_Mus_Li

description: RT_100_13_81_BENZ_Mus_Li_Mouse430_2_RSTLRI601_1

tag: dilution

tag: rna integrity number

tag: sample preservation

value: Female

tag: in vivo treatment

value: per day

tag: units of treatment time

value: days/wk

tag: vehicle for chemical

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

tag: dose or concentration

tag: units of dose or concentration


title: RT_10000_13_12_NAAC_Mus_Li

description: RT_10000_13_12_NAAC_Mus_Li_Mouse430_2_RSTLRI601_1

treatment_protocol: in vivo Treatment: 4-Nitroanthranilic acid, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 10000, Units of Dose or Concentration: ppm

tag: amount to core

tag: units of amount

tag: ratio

tag: bioanalyzer results

tag: strain or line

tag: individual

tag: developmental state

tag: sacrifice method

value: 4-Nitroanthranilic acid

tag: treatment duration

value: Rodent Chow

value: Diet

value: ppm


title: RT_1000_13_254_TDPP_Mus_Liver

description: RT_1000_13_254_TDPP_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: dilution

tag: rna integrity number

value: Good

tag: sample preservation

tag: gender

tag: age

tag: units of age

tag: in vivo treatment

tag: units of duration

tag: treatment time


title: RT_100_13_230_ETOX_Liver_07008

description: RT_100_13_230_ETOX_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

value: weeks

tag: treatment repeat

tag: units of treatment repeat

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_100_13_180_MECL-100_Liver_07008

description: RT_100_13_180_MECL-100_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: Methylene Chloride, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 100, Units of Dose or Concentration: ppm

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: strain or line

tag: individual

tag: developmental state

tag: sacrifice method

value: Methylene Chloride

tag: treatment duration


title: RT_100_13_229_ETOX_Liver_07008

description: RT_100_13_229_ETOX_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: sample preservation

tag: gender

tag: age

tag: units of age

tag: in vivo treatment

value: Ethylene Oxide

value: hr/day

tag: units of duration

tag: treatment time


title: RT_100_13_88a_BENZ_MusLiver

description: RT_100_13_88a_BENZ_MusLiver_Mouse430_2_RSTLRI000

tag: ratio

tag: dilution

value: RNAlater

value: Benzene

tag: treatment repeat

tag: units of treatment repeat

tag: units of treatment time

tag: vehicle for chemical

value: Corn Oil

tag: amount of vehicle

tag: route of exposure

value: Gavage

tag: units of amount of vehicle

value: ml/kg

tag: dose or concentration

tag: units of dose or concentration

value: mg/kg


title: RT_100_13_227_ETOX_Liver_07008

description: RT_100_13_227_ETOX_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

value: ul

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: strain or line

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

value: Female

tag: treatment duration

value: Air

value: Inhalation


title: RT_100_13_2_DCBZ-100_Liver_07008

description: RT_100_13_2_DCBZ-100_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: 1,4-Dichlorobenzene, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 100, Units of Dose or Concentration: mg/kg

tag: ratio

tag: dilution

value: Good

tag: age

tag: units of age

value: weeks

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

value: per day

tag: units of duration

tag: treatment time

tag: units of treatment time

value: days/wk

tag: vehicle for chemical


title: RT_100_13_179_MECL-100_Liver_07008

description: RT_100_13_179_MECL-100_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

value: Methylene Chloride

value: hr/day

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration

value: ppm


title: RT_100_13_176_MECL-100_Liver_07008

description: RT_100_13_176_MECL-100_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: individual

tag: developmental state

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: treatment duration


title: RT_100_13_1_DCBZ-100_Liver_07008

description: RT_100_13_1_DCBZ-100_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: units of duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

value: Corn Oil

tag: amount of vehicle

value: Gavage

tag: units of amount of vehicle


title: RT_10_13_263_NPTH-10_Liver_07008

description: RT_10_13_263_NPTH-10_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

value: Naphthalene

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_10_13_264_NPTH-10_Liver_07008

description: RT_10_13_264_NPTH-10_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

value: ul

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration


title: RT_05_13_242_NPTH-05_Liver_07008

description: RT_05_13_242_NPTH-05_Liver_07008_Mouse430_2_RSTLRI000_2

treatment_protocol: in vivo Treatment: Naphthalene, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: strain or line

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_100_13_178_MECL-100_Liver_07008

description: RT_100_13_178_MECL-100_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

tag: gender

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_05_13_241_NPTH-05_Liver_07008

description: RT_05_13_241_NPTH-05_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration


title: RT_05_13_244_NPTH-05_Liver_07008

description: RT_05_13_244_NPTH-05_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line

value: Female

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_10_13_261_NPTH-10_Liver_07008

description: RT_10_13_261_NPTH-10_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: individual

tag: developmental state

tag: sacrifice method

tag: gender

value: Air

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_339_ACO1_Mus_Liver

description: RT_0_13_339_ACO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

treatment_protocol: in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: amount to core

tag: units of amount

tag: age

tag: units of age

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration

value: Inhalation


title: RT_0_13_341_ACO1_MusLiver

description: RT_0_13_341_ACO1_MusLiver_Mouse430_2_RT_HON06_MusLiver

tag: ratio

tag: dilution

tag: bioanalyzer results

value: Good

tag: sample preservation

tag: strain or line

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_98_CCO2_Mus_Li

description: RT_0_13_98_CCO2_Mus_Li_Mouse430_2_RSTLRI601_1

treatment_protocol: in vivo Treatment: Corn Oil, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Corn Oil, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: amount to core

tag: rna integrity number

tag: individual

tag: developmental state

tag: sacrifice method

tag: gender

value: weeks

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

value: ml/kg

tag: dose or concentration

tag: units of dose or concentration

value: mg/kg


title: RT_10_13_262_NPTH-10_Liver_07008

description: RT_10_13_262_NPTH-10_Liver_07008_Mouse430_2_RSTLRI000_2

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: age

tag: units of age

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration

value: days/wk


title: RT_0_13_94_CCO2_MusLiver

description: RT_0_13_94_CCO2_MusLiver_Mouse430_2_RSTLRI000

tag: amount to core

tag: ratio

tag: rna integrity number

tag: sample preservation

value: RNAlater

tag: strain or line

tag: individual

tag: developmental state

tag: sacrifice method

value: per day

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_55_CCO5_Liver_07008

description: RT_0_13_55_CCO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: gender

tag: age

tag: units of age

value: Corn Oil

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_96_CCO2_MusLiver

description: RT_0_13_96_CCO2_MusLiver_Mouse430_2_RSTLRI000

tag: amount to core

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration

value: Gavage


title: RT_0_13_53r_CCO5_Liver_07008

description: RT_0_13_53r_CCO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_54_CCO5_Liver_07008

description: RT_0_13_54_CCO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_340_ACO1_Mus_Liver

description: RT_0_13_340_ACO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

treatment_protocol: in vivo Treatment: Air, Treatment Repeat: 6, Units of Treatment Repeat: hr/day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Air, Route of Exposure: Inhalation, Units of Dose or Concentration: ppm

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: sacrifice method

tag: gender

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

value: hr/day

tag: treatment duration

tag: units of duration

value: ppm


title: RT_0_13_295_ACO5_Liver_07008

description: RT_0_13_295_ACO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

value: ul

tag: ratio

tag: rna integrity number

tag: sample preservation

value: RNA later

tag: strain or line

tag: individual

tag: age

tag: units of age

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_52_CCO5_Liver_07008

description: RT_0_13_52_CCO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_51r_CCO5_Liver_07008

description: RT_0_13_51r_CCO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

value: Female

tag: in vivo treatment

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: units of duration


title: RT_0_13_47a_FCO2_MusLiver

description: RT_0_13_47a_FCO2_MusLiver_Mouse430_2_RSTLRI000

treatment_protocol: in vivo Treatment: Rodent Chow, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 7, Units of Treatment Time: days/wk, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: sacrifice method

tag: gender

tag: age

tag: units of age

value: Rodent Chow

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

value: Diet


title: RT_0_13_338_ACO1_Mus_Liver

description: RT_0_13_338_ACO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: ratio

tag: rna integrity number

value: Good

tag: sample preservation

tag: strain or line

tag: individual

value: weeks

value: Air

tag: route of exposure

value: Inhalation

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_50_FCO2_Mus_Li

description: RT_0_13_50_FCO2_Mus_Li_Mouse430_2_RSTLRI601_1

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: in vivo treatment

tag: treatment duration

tag: units of duration

value: days/wk


title: RT_05_13_243_NPTH-05_Liver_07008

description: RT_05_13_243_NPTH-05_Liver_07008_Mouse430_2_RSTLRI000_2

tag: sacrifice method

tag: gender

tag: age

tag: units of age

value: Naphthalene

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_293_ACO5_Liver_07008

description: RT_0_13_293_ACO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: ratio

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_46_FCO2_Mus_Li

description: RT_0_13_46_FCO2_Mus_Li_Mouse430_2_RSTLRI601_1

tag: units of amount

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: sacrifice method

tag: gender

tag: in vivo treatment

tag: treatment duration

tag: units of duration


title: RT_0_13_48_FCO2_Mus_Li

description: RT_0_13_48_FCO2_Mus_Li_Mouse430_2_RSTLRI601_1

tag: amount to core

tag: ratio

tag: age

tag: units of age

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_97n_CCO2_Mus_Li

description: RT_0_13_97n_CCO2_Mus_Li_Mouse430_2_RSTLRI601_1

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

value: Corn Oil

tag: treatment repeat

tag: units of treatment repeat

value: per day

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle

value: ml/kg

tag: dose or concentration

tag: units of dose or concentration

value: mg/kg


title: RT_0_13_294_ACO5_Liver_07008

description: RT_0_13_294_ACO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: developmental state

tag: sacrifice method

tag: gender

tag: in vivo treatment

value: hr/day

tag: treatment duration

tag: units of duration

value: ppm


title: RT_0_13_292_ACO5_Liver_07008

description: RT_0_13_292_ACO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: rna integrity number

tag: sample preservation

value: RNA later

tag: strain or line

tag: individual

value: Adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_258_FCO1_Mus_Liver

description: RT_0_13_258_FCO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: developmental state

value: Female

value: Rodent Chow

tag: route of exposure

value: Diet

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_240_ACO4_Liver_07008

description: RT_0_13_240_ACO4_Liver_07008_Mouse430_2_RSTLRI000_2

tag: rna integrity number

value: Good

tag: sample preservation

tag: strain or line

tag: individual

tag: sacrifice method

tag: gender

value: weeks

tag: in vivo treatment

value: Air

tag: treatment duration

tag: units of duration


title: RT_0_13_237_ACO4_Liver_07008

description: RT_0_13_237_ACO4_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: age

tag: units of age

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

value: days/wk

tag: vehicle for chemical

value: Inhalation


title: RT_0_13_235r_CCO4_Mus_Liver

description: RT_0_13_235r_CCO4_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: developmental state

value: Corn Oil

value: per day

tag: amount of vehicle

tag: route of exposure

value: Gavage

tag: units of amount of vehicle

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_239_ACO4_Liver_07008

description: RT_0_13_239_ACO4_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

value: ul

tag: strain or line

tag: individual

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: in vivo treatment

tag: treatment duration

tag: units of duration


title: RT_0_13_173_CCO6_Liver_07008

description: RT_0_13_173_CCO6_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: developmental state

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

value: ml/kg

value: mg/kg


title: RT_0_13_259_FCO1_Mus_Liver

description: RT_0_13_259_FCO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

value: RNA later

tag: strain or line

tag: individual

tag: sacrifice method

tag: gender

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration

value: ppm


title: RT_0_13_132_CCO3_Mus_Li

description: RT_0_13_132_CCO3_Mus_Li_Mouse430_2_RSTLRI601_1

treatment_protocol: in vivo Treatment: Distilled Water, Treatment Repeat: 1, Units of Treatment Repeat: per day, Treatment Duration: 13, Units of Duration: weeks, Treatment Time: 5, Units of Treatment Time: days/wk, Vehicle for Chemical: Distilled water, Amount of Vehicle: 5, Route of Exposure: Gavage, Units of Amount of Vehicle: ml/kg, Dose or Concentration: 0, Units of Dose or Concentration: mg/kg

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: Adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

tag: in vivo treatment

value: Distilled Water

tag: treatment duration

tag: units of duration

value: Distilled water

tag: amount of vehicle

tag: units of amount of vehicle


title: RT_0_13_133_CCO3_Mus_Li

description: RT_0_13_133_CCO3_Mus_Li_Mouse430_2_RSTLRI601_1

tag: amount to core

tag: units of amount

value: Good

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

value: Female

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_0_13_236_ACO4_Liver_07008

description: RT_0_13_236_ACO4_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sacrifice method

tag: gender

tag: age

tag: units of age

value: weeks

value: Air

value: hr/day

tag: route of exposure

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_225r_CCO4_Mus_Liver

description: RT_0_13_225r_CCO4_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

tag: in vivo treatment

value: Corn Oil

tag: treatment duration

tag: units of duration

value: days/wk

tag: amount of vehicle

tag: units of amount of vehicle


title: B140H_A

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

description: Gene expression in an Ara-C-resistant AML cell line.

hyb_protocol: 15 micrograms labeled cRNA under standard conditions (Affymetrix, Santa Clara, CA).

scan_protocol: Standard (Affymetrix, Santa Clara, CA).

data_processing: Data generated using robust multiarray average (RMA).

source_name: B140H murine leukemia cell line derived from BXH-2 mice

label_protocol: MessageAmpTM III RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Passaged in ASM media in absence of Ara-C.

extract_protocol: RNeasy Midi Kit (QIAGEN, Valencia, CA).

treatment_protocol: Exposed to increasing concentrations of Ara-C.

tag: cell line

tag: cell type

value: murine leukemia cells

tag: ara-c sensitivity

value: resistant


title: RT_0_13_238_ACO4_Liver_07008

description: RT_0_13_238_ACO4_Liver_07008_Mouse430_2_RSTLRI000_2

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

value: Inhalation


title: RT_0_13_291_ACO5_Liver_07008

description: RT_0_13_291_ACO5_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: sample preservation

value: RNA later

tag: strain or line

tag: individual

tag: developmental state

tag: in vivo treatment

tag: treatment duration

tag: units of duration

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_175_CCO6_Liver_07008

description: RT_0_13_175_CCO6_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: sacrifice method

tag: gender

tag: age

tag: units of age

tag: treatment repeat

tag: units of treatment repeat

value: per day

tag: amount of vehicle

value: Gavage

tag: units of amount of vehicle

value: ml/kg

value: mg/kg


title: RT_0_13_262_FCO1_Mus_Liver

description: RT_0_13_262_FCO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

value: Adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Rodent Chow

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

value: Diet

value: ppm


title: RT_0_13_134_CCO3_Mus_Li

description: RT_0_13_134_CCO3_Mus_Li_Mouse430_2_RSTLRI601_1

tag: ratio

tag: dilution

tag: bioanalyzer results

value: Good

tag: sacrifice method

tag: gender

value: Female

tag: age

value: weeks

tag: in vivo treatment

value: Distilled Water

tag: treatment duration

tag: units of duration

value: Distilled water

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_266_FCO1_Mus_Liver

description: RT_0_13_266_FCO1_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: amount to core

tag: units of amount

value: ul

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: units of age

value: days/wk


title: RT_0_13_227r_CCO4_Mus_Liver

description: RT_0_13_227r_CCO4_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: ratio

tag: dilution

value: RNA later

tag: developmental state

value: Corn Oil

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle


title: RT_0_13_174_CCO6_Liver_07008

description: RT_0_13_174_CCO6_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: bioanalyzer results

tag: sacrifice method

tag: gender

tag: age

tag: in vivo treatment

value: per day

tag: treatment duration

tag: units of duration

value: Gavage

tag: dose or concentration

tag: units of dose or concentration


title: RT_0_13_230r_CCO4_Mus_Liver

description: RT_0_13_230r_CCO4_Mus_Liver_Mouse430_2_RT_HON06_MusLiver

tag: ratio

tag: dilution

tag: rna integrity number

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

tag: units of age

tag: treatment repeat

tag: units of treatment repeat

tag: treatment time

value: ml/kg

value: mg/kg


title: RT_0_13_172_CCO6_Liver_07008

description: RT_0_13_172_CCO6_Liver_07008_Mouse430_2_RSTLRI000_2

tag: amount to core

tag: units of amount

tag: bioanalyzer results

value: Adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: gender

tag: age

tag: units of treatment time

tag: vehicle for chemical

tag: amount of vehicle

tag: route of exposure

tag: units of amount of vehicle


title: B140H_C

tag: cell line

tag: cell type

value: murine leukemia cells

tag: ara-c sensitivity

value: resistant


title: RT_0_13_171_CCO6_Liver_07008

description: RT_0_13_171_CCO6_Liver_07008_Mouse430_2_RSTLRI000_2

tag: ratio

tag: dilution

tag: rna integrity number

value: Good

tag: sample preservation

tag: strain or line

tag: individual

tag: developmental state

tag: units of age

tag: in vivo treatment

tag: treatment repeat

tag: treatment duration

tag: units of duration

tag: dose or concentration

tag: units of dose or concentration


title: B140P_C

description: Gene expression in an Ara-C-sensitive AML cell line.

source_name: B140P murine leukemia cell line derived from BXH-2 mice

tag: cell line

value: sensitive


title: B140P_A

tag: cell type


title: B117P_C

source_name: B117P murine leukemia cell line derived from BXH-2 mice

tag: ara-c sensitivity


title: B117H_C

source_name: B117H murine leukemia cell line derived from BXH-2 mice


title: LKR13_Kras sh-4

city: Stanford

last: Sweet-Cordero

state: CA

address: CCSR-1215B, 269 Campus Dr

department: Pediatrics

institute: Stanford University

description: Cell lines derived from Kras-mutant mouse lung cancer model (KrasLA). Tyler Jacks lab (Johnson et al., 2001)

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara), using RMA algorithms.

label: biotinylation

source_name: LKR13, knockdown of K-ras by shRNA

label_protocol: Affymetrix protocol

extract_protocol: RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2 was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

treatment_protocol: LKR13 cells were infected with plko.1s vectors carrying one of two shRNAs against K-ras. 48 hours after infection, cells were selected with puromycin for 3 days. RNA was extracted 7 days post-infection.


title: LKR13_Control-1

label: Biotinylation

source_name: LKR13, knockdown of GFP by shRNA

treatment_protocol: LKR13 cells were infected with plko.1s vectors carrying an shRNA against GFP.  48 hours after infection, cells were selected with puromycin for 3 days.  RNA was extracted 7 days post-infection.


title: LKR13_Kras sh-3


title: B117P_A


title: LKR13_Control-3


title: LKR13_Control-4


title: hnoX rep3

city: Madison

first: Yanling

last: Wang

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

description: expression data from untreated hnoX- mutant

hyb_protocol: Following fragmentation, cDNA was labeled with biotin and hybridized to the Custom Vibrio fischeri GeneChip Array at 45℃ for 16 hours. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The array data were processed to generate CHP files by the GeneChip Operation Software (GCOS, Affymetrix). CHP files was normalized with GC-RMA method and further analyzed using the GeneSpring GX Software (Agilent), and the original CEL files were normalized using the RMAExpress v1.0 software with background adjustment, quantile normalization and the PLM summarization method.

organism: Aliivibrio fischeri

source_name: hnoX- mutant, untreated

label_protocol: Procedures for total RNA labeling were performed based on the protocols from the E. coli Genome Project at the University of Wisconsin-Madison.

growth_protocol: The wild-type and hnoX- mutant strains were freshly grown in LBS at 28 ℃ with shaking for 2-3 hours, until the OD600 reached 1.0. These pre-cultures were diluted 1:100 and grown in minimal-salts medium to early exponential phase (OD600 0.2-0.3).

extract_protocol: Thirty minutes after the NO treatment, cells from all the cultures were fixed with RNAprotect Bacteria Reagent (Qiagen, CA). Total RNA was isolated and purified using RNeasy Mini Kit (Qiagen, CA) according to the manufacturer’s instructions.

treatment_protocol: One half of each culture was exposed to 80 µM of the NO generator DEA-NONOate (half-life time, 16 min at 22-25 ℃; 1 M DEA-NONOate generates 1.5 M NO; Cayman Chemical, MI) and the other half was left untreated as a control.

tag: strain type

value: mutant

tag: treatment

value: untreated


title: hnoX rep2


title: hnoX rep1


title: hnoX+NO rep2

description: expression data from  hnoX- mutant treated with 80uM NO generator for 30 min

source_name: hnoX- mutant, treated with NO

value: NO treated


title: hnoX+NO rep3


title: wild-type +NO rep3

description: expression data from  wild-type treated with 80uM NO generator for 30 min

source_name: wild-type, treated with NO

value: wild-type


title: LKR13_Control-2


title: wild-type +NO rep2


title: wild-type +NO rep1


title: LKR13_Kras sh-1


title: LKR13_Wt1 sh-2

source_name: LKR13, knockdown of Wt1 by shRNA

treatment_protocol: LKR13 cells were infected with plko.1s vectors carrying one of two shRNAs against Wt1. 48 hours after infection, cells were selected with puromycin for 3 days.  RNA was extracted 7 days post-infection.


title: wild-type rep1

description: expression data from untreated wid-type

source_name: wild-type, untreated


title: wild-type rep2

description: experssion data from untreated wild-type


title: LKR13_Wt1 sh-1


title: LKR13_Kras sh-2


title: Wt1-null MEFs-2

description: Wt1f/f MEFs were infected with adenoviral Cre to knockout Wt1

hyb_protocol: Standard Affymetrix protocols were used.

data_processing: Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara) using RMA algorithms for normalization.

extract_protocol: RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

value: Mouse embryonic fibroblasts (MEFs)

tag: genome/variation


title: wild-type rep3


title: IMR-90-miR-29-KD(100nM)-1

city: BoSTON

first: jining

last: lu

address: 715 Albany street R304

institute: Boston University

hyb_protocol: standard Affymetrix hybridization

scan_protocol: standard Affymetrix scanning

data_processing: Affymetrix Expression Console software using RMA algorithm (log2 transformed)

label: standard Affymetrix labeling

organism: Homo sapiens

source_name: total RNA from IMR-90 cells 48hrs after transfection of 100 nM miR-29 LNA KD oligos

label_protocol: standard Affymetrix labeling

extract_protocol: Trizol (Invitrogen) was used for Total RNA isolation.

treatment_protocol: Transfection was carried out using Lipofectamine™ 2000 (Invitrogen)

value: fetal lung fibroblast


title: IMR-90-miR-29-KD(100nM)-3


title: IMR-90-SCR(100nM)-KD-2

source_name: total RNA from IMR-90 cells 48hrs after transfection of 100 nM Scrambled LNA oligos


title: IMR-90-miR-29-KD(50nM)-1

source_name: total RNA from IMR-90 cells 48hrs after transfection of 50 nM miR-29 LNA KD oligos


title: IMR-90-miR-29-KD(50nM)-3


title: IMR-90-SCR(100nM)-KD-3


title: IMR-90-SCR(100nM)-KD-1


title: hnoX+NO rep1


title: B117H_A

description: Gene expression in an Ara-C-resistant AML cell line.


title: IMR-90-miR-29-KD(50nM)-2


title: IMR-90-miR-29-KD(100nM)-2


title: EXP2_S5

city: Southampton

first: Patrick

last: Stephenson

address: Bassett Crescent East

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

hyb_protocol: Probe Precipitation Probe precipitation was carried out according to the manufacturer’s instructions. 3µl of linear acrylamide, 16µl of 3.3M Na Acetate (pH 5.2) and 400µl of 100% ethanol was added to each pooled cDNA mixture and the contents left to precipitate at -80°C for 1 h. Tubes were centrifuged at 4oC for 50 min in an Eppendorf 5417R centrifuge at 17,900g. The pellet was then washed with 500µl of 70% ethanol (v/v), and spun for an additional 10 minutes. The pellet was air dried at room temperature and resuspended in 18µl of nuclease-free water for 10 minutes in a 65°C heat block. Prewash Each slide was placed into a coplin jar containing 0.1% SDS (w/v) and mixed gently by inverting for 20 seconds, then left on the bench for 4 min 40 s. The buffer solution was replaced and the process repeated. The slides were then transferred to a coplin jar containing Milli-Q H2O, gently mixed by inverting for 20 seconds, and then left to sit on a bench for 1 min 40 s. The water was then replaced and the process repeated. The slides were then transferred to a slide rack, and the rack placed end down into 750 ml Milli-Q H2O at 95°C for 3 minutes. The slides were then transferred immediately to 50ml Falcon tubes containing tissue tightly packed at the bottom and centrifuged (without their caps) at room temperature for 3 min in a Sorvall Legend RT swing-out rotor centrifuge at 4,570g. N2 gas was blown gently over the slides to remove any dust, and finally placed into the hybridisation chambers. 1st Hybridisation and wash 2x SDS-based hybridisation buffer was wrapped in aluminium foil and thawed at room temperature for 15 min. The buffer was then vortexed thoroughly, centrifuged briefly and maintained in a water bath at 65°C for >15 min prior to use. Salmon sperm DNA was denatured at 95°C for 10 minutes, and then chilled on ice. A master mix was then prepared with 22.5µl of 2x SDS buffer, 4µl LNA dT blocker, and 0.5µl salmon sperm DNA per reaction and maintained at 65°C. 27µl of the hybridisation master mix was added to the 18µl of cDNA probe, and the contents gently vortexed and centrifuged briefly. The probes were then denatured in an 80°C heat block for 10 min before being transferred to a 65°C heat block. 20µl of Milli-Q H2O was added to each of the two wells on the hybridisation chamber to minimise probe evaporation. A single cDNA probe was then vortexed, centrifuged briefly and added in a straight line 5mm inwards from the long edge of the slide. The coverslip was then overlaid on the slide so that the hybridisation solution covered the entire printed area of the slide. The hybridisation chamber was then closed, and placed into a 60°C water bath to hybridise for 16 hours. The hybridisation chambers were removed from the 60°C water bath and the slides placed into a coplin jar containing 2x SSC (3M NaCl, 0.33M sodium citrate; pH 7.0) and 0.2% SDS (w/v) at room temperature for 5 minutes to allow the coverslips to slide off. Each slide was then transferred to a pre-warmed coplin jar containing 2x SSC/0.2% SDS and placed in a 65°C water bath without agitation for 15 minutes. Each slide was then transferred to a coplin jar containing 2x SSC at room temperature. The jar was inverted for 30 seconds, then left to sit for 4 min 30 s, and the process repeated twice more in 2xSSC and three times in 0.2x SSC. The slides were then transferred immediately to 50ml Falcon tubes containing tissue tightly packed at the bottom and centrifuged (without their caps) at room temperature for 3 min in a Sorvall Legend RT swing-out rotor centrifuge at 4,570g. N2 gas was blown gently over the slides to remove any dust, and finally placed into the hybridisation chambers. 2nd Hybridisation and wash 2x SDS-based hybridisation buffer and 3DNA Array 350 capture reagent were wrapped in aluminium foil and thawed at room temperature for 15 min. These solutions were then mixed briefly, incubated in a 65°C and 55°C, respectively, for 15 min and then vortexed, centrifuged briefly and maintained at 65°C. The master mix was then prepared with 22.5µl of 2x SDS buffer, 17.5µl nuclease-free water, and 2.5µl of each Cy3 and Cy5 dendrimer per reaction. This master mix was denatured at 80°C for 10 min, and maintained at 65°C. 20µl of Milli-Q H2O was added to both wells on the hybridisation chamber. A single dendrimer probe was vortexed, centrifuged briefly and added to each slide in a line 5mm inwards from the long edge. A coverslip was added so that the hybridisation solution covered the entire printed area of the slide. The hybridisation chamber was closed and placed in a 60°C water bath to hybridise for 3 hours. The same wash procedure as for the 1st hybridisation wash was repeated, and, after drying, the slides were ready for scanning.

scan_protocol: The arrays from experiment one were scanned using a Scan Array Express Packard Bioscience scanner (PerkinElmer, MA, USA). Lasers one (633nm) and three (543nm) were set to 90% power by default. Partial scans were conducted for each slide to determine optimal scanning conditions, at a resolution of 10μm, and the photomultiplier tube (PMT) gain adjusted during the scans to increase or decrease the amount of fluorescence captured. Several small scans were completed across the slide to obtain suitable PMT values. A full scan was then completed. The output files were saved as TIFF (tagged image file format) images ready for processing.

data_processing: Image processing was completed to measure the signal intensity (background and foreground) of each spot on the array. Arrays were processed using ImaGene software (BioDiscovery, CA, USA) where a grid is overlaid on each array to help with spot location, and allowed the program to identify each individual spot. The results were saved as text files ready for quality control evaluation and analysis. Normalisation was completed for channel, array and clone effects, and then an r-script was used to determine the level of correlation between sample density and gene expression. The normalisation included a print-tip LOWESS, which checks for consistency between print-tip groups (i.e. array subgrids), and a scaled normalisation between arrays. The normalised files were then analysed using GeneSpring Version 7.3 (Agilent Technologies, CA, USA). Data was normalised to the median intensity and to control spots prior to data collection.

organism: Picea sitchensis

source_name: Sitka spruce cambial tissue - high Density

label_protocol: Hybridizations were performed using the Genisphere Array300 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. 40 micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.5 M NaOH / 0.05 M EDTA at 65ºC for 15 min followed by neutralization in 2.875 M Tris-HCl (pH 8.0).

extract_protocol:
The RNA extraction protocol used was a modified version of that described by Chang et al. (Chang et al. 1993). For each sample CTAB extraction buffer (2% CTAB (w/v), 2% PVP (w/v), 100mM Tris-HCl (pH 8.0), 25mM EDTA, 2M NaCl) was warmed to 65oC, and 0.8% 2-ME (v/v) added with 500 µg ground xylem tissue. Samples were vortexed thoroughly for 15s and the suspension incubated for 10min at 65oC. 0.25 volume chlorophorm:isoamyl alcohol (24:1, v/v) was added and the tubes centrifuged for 20min at room temperature in a Sorvall Legend RT swing-out rotor (Thermo Fisher Scientific, MA, USA) at 4,500g. The upper phase was transferred to a new tube with 0.25 volume chlorophorm:isoamyl alcohol (24:1, v/v) and re-centrifuged. The upper phase was again transferred to a new tube containing 0.25 volume 10M lithium chloride, and left to precipitate overnight at 4oC.
Following incubation, tubes were centrifuged at 4oC for 30min in a Sorvall Legend RT swing-out rotor at 4,500g. The supernatant was removed, and the pellet re-suspended in SSTE buffer (1M NaCl, 0.5% SDS (w/v), 10mM Tris-HCl (pH 8.0), 1mM EDTA) at 60oC. Resuspended samples were transferred to an Eppendorf tube and incubated for 5min at 60oC. One volume chloroform:isoamyl alcohol (24:1, v/v) were then added and the tubes centrifuged at room temperature for 10min in an Eppendorf 5417R centrifuge (Eppendorf, Hamburg, Germany) at 17,900g. The upper phase was transferred to a new tube containing 2 volumes 100% ethanol and left to precipitate at -80oC for 1h. The precipitate was then centrifuged at 4oC for 10min in an Eppendorf 5417R centrifuge at 17,900g. The pellet was washed 70% ethanol (v/v) by centrifuging at 4oC for 5min in an Eppendorf 5417R centrifuge at 17,900g. The pellet was then left at room temperature to air dry and re-suspended in RNase free MQ H2O.
The RNA was quantified using a NanoDrop© ND-1000 Spectrophotometer (Thermo Scientific, DE, USA) and analysed using the Agilent 2100 Bioanalyzer RNA chip (Agilent Technologies, CA, USA) to assess RNA contamination and degradation.

tag: tissue

value: Cambial tissue

tag: age

value: 15 year old

tag: density

value: high density tree (C20133-630)

tag: collection time

value: summer 2004

source_name: Sitka spruce cambial tissue - low Density

tag: tissue type

value: low density tree (C20166-126)


title: EXP3_S4

value: low density tree (C20163-610)

value: high density tree (C20135-649)


title: EXP2_S1

value: low density tree (C20166-713)

value: high density tree (C20133-64)


title: EXP2_S6

value: low density tree (C20166-534)

value: high density tree (C20133-127)


title: EXP3_S1

value: high density tree (C20132-731)

value: low density tree (C20149-475)


title: EXP1_S8

value: low density tree (C20124-344)


title: EXP2_S4

value: high density tree (C20133-172)

value: low density tree (C20166-458)


title: EXP1_S7

value: low density tree (C20150-590)

value: high density tree (C20132-625)


title: EXP2_S2

value: Cambial tissue

value: 15 year old

value: high density tree (C20133-478)

value: low density tree (C20166-95)


title: EXP2_S3

value: high density tree (C20133-551)

value: summer 2004

value: low density tree (C20166-152)


title: EXP1_S9

value: low density tree (C20149-55)


title: EXP1_S6

value: high density tree (C20160-153)

value: low density tree (C20150-144)


title: EXP1_S4

value: low density tree (C20163-541)

value: high density tree (C20132-659)


title: EXP1_S5

value: low density tree (C20135-324)

value: high density tree (C20135-683)


title: EXP3_S3

value: low density tree (C20163-154)


title: F001-s-m-3

type: genomic

city: St Lucia

first: Daniel

last: Aguirre de Carcer

state: QLD

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

description: Patient F001, male, sigmoid colon, replicate3

hyb_protocol: The previously spiked, labelled and fragmented cRNA samples were hybridised in quadruplicate to CustomArray 4 X 2K Microarrays  fabricated by CombiMatrix (Mukilteo WA, USA), as specified by the manufacturer.

scan_protocol: The hybridised microarray slides were scanned using an Axon Genepix 4000A microarray scanner (Axon Instruments, Union City CA, USA). The images obtained were analysed using GenePix Pro 6.0 software (Axon Instruments), and probe signals were recorded as 635nm foreground – 635nm background intensities.

data_processing: The raw signal data was first processed using the Genespring GX10 software (Agilent Technologies, Santa Clara, CA). Intensity values were transformed to log 2. To avoid the generation of biased profiles during the normalization step, hybridisations showing abnormal-looking intensity distributions  were discarded prior to normalization using the quantile normalization method (based on the normalization of intensity distributions). Probes with signal values lower than the highest negative control signals were removed from further analysis.

molecule: genomic DNA

organism: Bacteria

source_name: Sigmoid colon mucosal biopsy

label_protocol: Aliquots (500ng) of the cRNA samples were spiked with 7ng of the control mitochondrial cRNA, then labeled and fragmented using the Label IT uArray Cy5 labeling Kit (Mirus, Madison WI, USA).

extract_protocol:
The mucosal biopsies were snap frozen in liquid N2 and stored at -80°C until processing. The DNA was extracted and purified from the frozen biopsies using the AllPrep DNA/RNA Mini Kit (Qiagen Pty Ltd, Hilden, Germany), according to the manufacturer’s instructions and stored at 4°C until processing.
total DNA (100-500 ng) extracted from the biopsy samples were used for the PCR amplification of the Archaea and Bacteria rrs-genes. As an internal standard, the mitochondrial rrs gene was also PCR amplified using human DNA. All PCR reactions were performed in triplicate for each sample, then pooled and purified using the Minielute PCR purification kit (Qiagen Inc., Valencia CA, USA). Where necessary, the amplicons were concentrated using Pellet Paint (Novagen, Madison WI, USA).
Single stranded cRNA was then produced from 500 ng aliquots of the pooled PCR products, using the MEGAScript T7 In Vitro transcription kit (Ambion, Austin TX, USA) as specified by the manufacturer. The resulting cRNA samples were purified using the MEGAclear Kit (Ambion), and the size and purity of the products obtained at each step was assessed by agarose gel electrophoresis and with a ND-1000 spectrophotometer (NanoDrop Technologies).

tag: source


title: F001-t-m-1

description: Patient F001, male, transverse colon, replicate1

source_name: Transverse colon mucosal biopsy


title: F001-t-m-3

description: Patient F001, male, transverse colon, replicate3


title: F001-s-m-2

description: Patient F001, male, sigmoid colon, replicate2


title: F001-s-m-1

description: Patient F001, male, sigmoid colon, replicate1


title: CG542-t-f-2

description: Patient CG542, female, transverse colon, replicate2


title: F001-t-m-2

description: Patient F001, male, transverse colon, replicate2


title: F001-r-m-1

description: Patient F001, male, rectum, replicate1

source_name: Rectum mucosal biopsy

value: Patient F001, male, rectum, replicate1


title: F001-r-m-3

description: Patient F001, male, rectum, replicate3

value: Patient F001, male, rectum, replicate3


title: EXP1_S3

value: Cambial tissue

value: high density tree (C20124-641)

value: low density tree (C20150-485)


title: CG542-t-f-1

description: Patient CG542, female, transverse colon, replicate1


title: EXP1_S2

value: 15 year old

value: high density tree (C20133-478)

value: low density tree (C20166-713)


title: F001-c-m-3

description: Patient F001, male, cecum, replicate3

source_name: Cecum mucosal biopsy

value: Patient F001, male, cecum, replicate3


title: EXP3_S2

value: low density tree (C20149-327)

value: summer 2004

value: high density tree (C20132-98)


title: F001-c-m-2

description: Patient F001, male, cecum, replicate2

value: Patient F001, male, cecum, replicate2


title: DNMT3B

city: Columbus

first: Samson

middle: T.

last: Jacob

state: OH

address: 420 W. 12th Ave

institute: Ohio State University

hyb_protocol: Cy5-labeled pulldown material was hybridized to a microarray printed on aminosilane-coated slides,  using an Affymetrix/GMS 417 arrayer. This microarray contained 8640 CpG island genomic fragments (on average 500-bp). Post-hybridization washing step was carried out at 5o˚C with 1X SSC, 0.1% SDS followed by an additional wash in the same solution at room temperature and a last wash with 0.2X SSC at room temperature. Slides were dried by centrifugation.

scan_protocol: Hybridized slides were scanned with a GenePix 4000A scanner (Axon Instruments, Foster City, CA), and the acquired images were analyzed with the software GENE PIX PRO 3.0. Each spot was localized using a grid and the repeat-containing CpG loci were excluded from further analysis.

data_processing: Both DNMT3B Ab and DNMT3B_control rabbit IgG were labeled with the same fluorophor, no dye effect correction was needed. As the same amount of DNA was used for each hybridization, no signal normalization was performed prior to signal comparison between  Cy5 signal intensities at 635 nm from both slides.

source_name: DNMT3B IP of RKO cells

label_protocol: Incorporation of amino-allyl dUTP (aa-dUTP, Sigma) into pulldown DNA and control rabbit-IgG antibody DNA was conducted by using the Bioprime DNA-labeling system protocol (Life Technologies, Grand Island, NY). Cy5 fluorescent dye was coupled to aa-dUTP-labeled pulldown DNA and control no-antibody DNA, and hybridized to two identically prepared CpG island microarrays.

growth_protocol: RKO cells from ATCC were grown according to supplier's protocol at 37oC in a humidified incubator at 5% CO2.

extract_protocol: Exponentially growing RKO cells were treated with 1% formaldehyde at 37oC for 10 minutes, followed by treatment with 50 mM glycine, wash 3 times with ice cold PBS. Cells were extracted with lysis buffer (Tris, pH81., 50 mM, EDTA , pH 8.0, 50 mM and 1% SDS containing protease inhibitor cocktail and soluble chroamtin was made by sonication.  The crosslinked chromatin (DNA fragmented to ~600bp size by sonication) from 100 million RKO cells was pre-cleared with pre-immune IgG and protein A beads followed by immunoprecipitation with affinity purified antibody against DNMT3B or rabbit IgG.  The precipitated DNA was dissolved in RIPA buffer and subjected to a second round of immunoprecipitation with the same antibody to minimize pull down of false positive targets. This DNA was then separated on an agarose gel and DNA from 0.5 to 3kb in size was purified by using Gel Extraction kit (Qiagen) and subjected to microarray analysis.

value: RKO

tag: ip antibody


title: DNMT3B_noAb

source_name: noAb control of RKO cells

value: rabbit IgG


title: EXP1_S1

value: high density tree (C20160-744)

value: low density tree (C20149-475)


title: GTL-16_Doxycycline_Rep2

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: GTL-16 cells transduced with a lentiviral vector encoding for an inducible MET shRNA and treated with doxycycline (1mg/ml) for 48h to induce the shRNA.

hyb_protocol: 750 ng of cRNA was hybridized on human-8 V2 for 16-20 hours. Array washing was performed using wash buffer; a high stringency temperature wash was performed at 55C for 10 minutes. Arrays were stained with SA-Cy3.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan scanner and analyzed by Illumina's BeadStudio version 1.5.1.3.

data_processing:
Data were summarized and rank-invariant normalized using the Illumina Beadstudio software (ver. 1.5.1.3).

Non-normalized data is available in the 'GSE19043_non-normalized.txt' file, which is linked to the GSE19043 Series record as a supplementary file.

source_name: GTL-16, Met shRNA induced doxycycline, 48h

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit starting from 500ng of total RNA.

growth_protocol: Standard growth conditions.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: (i) DiFi cells: treatment with PHA-665752 (24h, 1uM) or Gefitinib (24h, 1uM), or an equivalent volume of DMSO as a control. (ii) GTL-16 cells: transduction with a lentivirus encoding for a doxycycline-inducible MET shRNA, followed by treatment with doxycycline (48h, 1ug/ml) or PHA-665752 (24h, 1uM) or Gefitinib (24h, 1uM), or an equivalent volume of DMSO as a control.

value: gastric cancer

tag: molecular profile

value: MET amplification, KRAS wt

tag: transduction

value: doxycycline

tag: treatment time


title: F001-c-m-1

description: Patient F001, male, cecum, replicate1

value: Patient F001, male, cecum, replicate1


title: GTL-16_Doxycycline_Rep3

value: lentivirus encoding for a doxycycline-inducible MET shRNA


title: GTL-16_Doxycycline_Rep1


title: CG569-t-f-3

description: Patient CG569, female, transverse colon, replicate3


title: GTL-16_Gefitinib_Rep2

description: GTL-16 cells transduced with a lentiviral vector encoding for an inducible MET shRNA and treated with the EGFR inhibitor Gefitinib (1uM) for 24h.

source_name: GTL-16, EGFR inhibition Gefitinib, 24h

value: Gefitinib


title: CG569-s-f-3

description: Patient CG569, female, sigmoid colon, replicate3


title: CG569-t-f-4

description: Patient CG569, female, transverse colon, replicate4


title: CG569-t-f-2

description: Patient CG569, female, transverse colon, replicate2


title: CG569-s-f-2

description: Patient CG569, female, sigmoid colon, replicate2


title: CG569-r-f-4

description: Patient CG569, female, rectum, replicate4


title: CG569-s-f-1

description: Patient CG569, female, sigmoid colon, replicate1


title: CG569-r-f-5

description: Patient CG569, female, rectum, replicate5


title: CG569-t-f-1

description: Patient CG569, female, transverse colon, replicate1


title: CG569-r-f-2

description: Patient CG569, female, rectum, replicate2


title: CG569-r-f-1

description: Patient CG569, female, rectum, replicate1


title: GTL-16_Gefitinib_Rep3


title: GTL-16_PHA-665752_Rep2

description: GTL-16 cells transduced with a lentiviral vector encoding for an inducible MET shRNA and treated with the Met inhibitor PHA-665752 (1uM) for 24h.

source_name: GTL-16, Met inhibition PHA-665752, 24h


title: GTL-16_Gefitinib_Rep1


title: GTL-16_DMSO_Rep1

description: GTL-16 cells transduced with a lentiviral vector encoding for an inducible MET shRNA and treated with DMSO (1:1000) for 24h.

source_name: GTL-16, control DMSO, 24h

value: DMSO


title: GTL-16_PHA-665752_Rep3


title: GTL-16_DMSO_Rep3


title: DiFi_Gefitinib_Rep3

description: DiFi cells treated with the EGFR inhibitor Gefitinib (1uM) for 24h.

source_name: DiFi, EGFR inhibition Gefitinib, 24h

value: DiFi

value: colon cancer

value: EGFR amplification, KRAS wt


title: CG569-r-f-3

description: Patient CG569, female, rectum, replicate3


title: GTL-16_DMSO_Rep2


title: DiFi_Gefitinib_Rep2


title: F001-r-m-2

description: Patient F001, male, rectum, replicate2

value: Patient F001, male, rectum, replicate2


title: CG569-c-f-3

description: Patient CG566, female, cecum, replicate3


title: CG569-c-f-4

description: Patient CG566, female, cecum, replicate4


title: DiFi_Gefitinib_Rep1


title: DiFi_PHA-665752_Rep3

description: DiFi cells treated with the Met inhibitor PHA-665752 (1uM) for 24h.

source_name: DiFi, Met inhibition PHA-665752, 24h


title: DiFi_PHA-665752_Rep2


title: CG566-t-m-3

description: Patient CG566, male, transverse colon, replicate3


title: CG566-t-m-2

description: Patient CG566, male, transverse colon, replicate2


title: DiFi_DMSO_Rep2

description: DiFi cells treated with DMSO (1:1000) for 24h.

source_name: DiFi, control DMSO, 24h


title: CG569-c-f-2

description: Patient CG566, female, cecum, replicate2


title: CG566-s-m-1

description: Patient CG566, male, sigmoid colon, replicate1


title: GTL-16_PHA-665752_Rep1


title: CG566-s-m-2

description: Patient CG566, male, sigmoid colon, replicate2


title: CG566-r-m-3

description: Patient CG566, male, rectum, replicate3

value: Patient CG566, male, rectum, replicate3


title: CG566-r-m-2

description: Patient CG566, male, rectum, replicate2

value: Patient CG566, male, rectum, replicate2


title: CG566-c-m-2

description: Patient CG566, male, cecum, replicate2

value: Patient CG566, male, cecum, replicate2


title: CG566-c-m-1

description: Patient CG566, male, cecum, replicate1

value: Patient CG566, male, cecum, replicate1


title: CG569-c-f-1

description: Patient CG566, female, cecum, replicate1


title: CG563-t-m-1

description: Patient CG563, male, transverse colon, replicate1


title: CG563-t-m-2

description: Patient CG563, male, transverse colon, replicate2


title: CG563-s-m-2

description: Patient CG563, male, sigmoid colon, replicate2


title: CG563-s-m-1

description: Patient CG563, male, sigmoid colon, replicate1


title: CG563-r-m-2

description: Patient CG563, male, rectum, replicate2

value: Patient CG563, male, rectum, replicate2


title: CG566-r-m-1

description: Patient CG566, male, rectum, replicate1

value: Patient CG566, male, rectum, replicate1


title: CG563-r-m-1

description: Patient CG563, male, rectum, replicate1

value: Patient CG563, male, rectum, replicate1


title: DiFi_PHA-665752_Rep1


title: CG563-c-m-2

description: Patient CG563, male, cecum, replicate2

value: Patient CG563, male, cecum, replicate2


title: DiFi_DMSO_Rep3


title: CG563-c-m-1

description: Patient CG563, male, cecum, replicate1

value: Patient CG563, male, cecum, replicate1


title: CG550-t-m-3

description: Patient CG550, male, transverse colon, replicate3


title: CG566-c-m-3

description: Patient CG566, male, cecum, replicate3

value: Patient CG566, male, cecum, replicate3


title: CG550-t-m-1

description: Patient CG550, male, transverse colon, replicate1


title: CG550-r-m-2

description: Patient CG550, male, rectum, replicate2

value: Patient CG550, male, rectum, replicate2


title: CG550-s-m-3

description: Patient CG550, male, sigmoid colon, replicate3


title: CG550-r-m-1

description: Patient CG550, male, rectum, replicate1

value: Patient CG550, male, rectum, replicate1


title: CG550-s-m-1

description: Patient CG550, male, sigmoid colon, replicate1


title: CG550-t-m-2

description: Patient CG550, male, transverse colon, replicate2


title: CG550-s-m-2

description: Patient CG550, male, sigmoid colon, replicate2


title: DiFi_DMSO_Rep1

value: DMSO


title: CG550-c-m-3

description: Patient CG550, male, cecum, replicate3

scan_protocol: The hybridised microarray slides were scanned using an Axon Genepix 4000A microarray scanner (Axon Instruments, Union City CA, USA). The images obtained were analysed using GenePix Pro 6.0 software (Axon Instruments), and probe signals were recorded as 635nm foreground – 635nm background intensities

value: Patient CG550, male, cecum, replicate3


title: CG550-c-m-2

description: Patient CG550, male, cecum, replicate2

value: Patient CG550, male, cecum, replicate2


title: CG544-t-f-3

description: Patient CG544, female, transverse colon, replicate3


title: CG550-r-m-3

description: Patient CG550, male, rectum, replicate3

value: Patient CG550, male, rectum, replicate3


title: CG550-c-m-1

description: Patient CG550, male, cecum, replicate1

value: Patient CG550, male, cecum, replicate1


title: Menadione treated 6h sample - summary of normalized experimental data (flop)

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

country: Hungary

institute: University of Debrecen

description: Primary unprocessed experimental data are  provided as supplementary files

hyb_protocol: We hybridized the control and experimental samples to the arrays at 62 °C overnight. Than we washed the slide in: -2XSSC, 0.1%SDS at RT 10min -0.2XSSC, 0.1%SDS at 60°C 10min -0.2XSSC, 0.1%SDS at 60°C 10min -0.2XSSC rinse -0.05XSSC rinse -Air-dry

scan_protocol: Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software.

data_processing: Gene expression ratios were subjected to LOESS-type block-by-block normalization using SAS for Windows, version 8. (SAS Institute Inc., Cary, NC, USA.) software.

organism: Aspergillus nidulans

source_name: Menadione treated

label_protocol: Gene expression ratios were estimated according to the protocol adapted from Biotechniques 29(3) Sept 2000, 548-562.

growth_protocol: Emericella nidulans FGSC 26 was grown in shake flasks (500 ml) containing 100 ml minimal-nitrate medium, pH 6.5 supplemented with 0.5 % yeast extract. Culture media were inoculated with 1x108 spores and were incubated for 18 h at 37 °C and 3.3 Hz shaking frequency. Mycelia were separated by filtration on sintered glass and were transferred immediately into pre-incubated 100 ml aliquots of minimal-nitrate medium, pH 6.5 supplemented with stress-inducing agents (stress-exposed cultures).

extract_protocol: Mycellium were frozen at -70 °C and, subsequently, were vacuum-dried overnight at room temperature. Total RNA was extracted from approximately 100 mg quantities of dried mycelial mats using TRISOL reagent (Invitrogen).

treatment_protocol: Late exponential phase (18 h) Emericella nidulans mycelia were treated in minimal media with 0.8 mM menadione (sodium bisulfite addition compound) for 6 h.

tag: Emericella nidulans FGSC 26 (biA1, veA1).

source_name: Untreated control

growth_protocol: Emericella nidulans FGSC 26 was grown in shake flasks (500 ml) containing 100 ml minimal-nitrate medium, pH 6.5 supplemented with 0.5 % yeast extract. Culture media were inoculated with 1x108 spores and were incubated for 18 h at 37 °C and 3.3 Hz shaking frequency. Mycelia were separated by filtration on sintered glass and were transferred immediately into pre-incubated 100 ml aliquots of minimal-nitrate medium, pH 6.5 left untreated.

extract_protocol: Mycellium were frozen at -70°C and, subsequently, were vacuum-dried overnight at room temperature. Total RNA was extracted from approximately 100 mg quantities of dried mycelial mats using TRISOL reagent (Invitrogen).

treatment_protocol: Late exponential phase (18 h) Emericella nidulans mycelia were transfered to minimal media for 6 h.


title: CG544-t-f-1

description: Patient CG544, female, transverse colon, replicate1


title: Menadione treated 6h sample - summary of normalized experimental data (flip)

description: Primary unprocessed experimental data are provided as supplementary files


title: CG544-t-f-2

description: Patient CG544, female, transverse colon, replicate2


title: CG544-r-f-1

description: Patient CG544, female, rectum, replicate1


title: CG544-r-f-3

description: Patient CG544, female, rectum, replicate3


title: CG544-r-f-2

description: Patient CG544, female, rectum, replicate2


title: CG544-s-f-3

description: Patient CG544, female, sigmoid colon, replicate3


title: CG544-r-f-4

description: Patient CG544, female, rectum, replicate4


title: CG544-c-f-1

description: Patient CG544, female, cecum, replicate1

organism:
Bacteria
Archaea


title: CG544-s-f-1

description: Patient CG544, female, sigmoid colon, replicate1


title: CG544-c-f-4

description: Patient CG544, female, cecum, replicate4


title: CG544-c-f-3

description: Patient CG544, female, cecum, replicate3


title: CG544-c-f-2

description: Patient CG544, female, cecum, replicate2


title: CG542-c-f-3

description: Patient CG542, female, cecum, replicate3


title: CG542-s-f-1

description: Patient CG542, female, sigmoid colon, replicate1


title: CG544-s-f-2

description: Patient CG544, female, sigmoid colon, replicate2


title: CG542-s-f-3

description: Patient CG542, female, sigmoid colon, replicate3


title: CG542-s-f-2

description: Patient CG542, female, sigmoid colon, replicate2


title: CG542-r-f-2

description: Patient CG542, female, rectum, replicate2


title: CG541-t-f-2

description: Patient CG541, female, transverse colon, replicate2


title: CG542-r-f-1

description: Patient CG542, female, rectum, replicate1


title: CG542-c-f-2

description: Patient CG542, female, cecum, replicate2


title: CG541-t-f-4

description: Patient CG541, female, transverse colon, replicate4


title: CG542-c-f-1

description: Patient CG542, female, cecum, replicate1


title: CG541-t-f-1

description: Patient CG541, female, transverse colon, replicate1


title: CG541-t-f-3

description: Patient CG541, female, transverse colon, replicate3


title: CG541-r-f-3

description: Patient CG541, female, rectum, replicate3


title: CG517-t-f-1

description: Patient CG517, female, transverse colon, replicate1


title: CG517-s-f-2

description: Patient CG517, female, sigmoid colon, replicate2


title: CG541-s-f-4

description: Patient CG541, female, sigmoid colon, replicate4


title: CG541-s-f-3

description: Patient CG541, female, sigmoid colon, replicate3


title: CG541-r-f-2

description: Patient CG541, female, rectum, replicate2


title: CG517-t-f-2

description: Patient CG517, female, transverse colon, replicate2


title: CG541-r-f-4

description: Patient CG541, female, rectum, replicate4


title: CG517-c-f-3

description: Patient CG517, female, cecum, replicate3


title: CG517-r-f-3

description: Patient CG517, female, rectum, replicate3


title: CG541-r-f-1

description: Patient CG541, female, rectum, replicate1


title: CG517-r-f-1

description: Patient CG517, female, rectum, replicate1


title: CG507-t-m-2

description: Patient CG507, male, transverse colon, replicate2


title: CG541-s-f-1

description: Patient CG541, female, sigmoid colon, replicate1


title: CG507-s-m-1

description: Patient CG507, male, sigmoid colon, replicate1


title: CG517-s-f-1

description: Patient CG517, female, sigmoid colon, replicate1


title: CG541-s-f-2

description: Patient CG541, female, sigmoid colon, replicate2


title: CG507-c-m-3

description: Patient CG507,male, cecum, replicate3

value: Patient CG507,male, cecum, replicate3


title: CG507-t-m-1

description: Patient CG507, male, transverse colon, replicate1


title: CG517-c-f-1

description: Patient CG517, female, cecum, replicate1


title: CG507-c-m-1

description: Patient CG507, male, cecum, replicate1

value: Patient CG507, male, cecum, replicate1


title: CG517-c-f-2

description: Patient CG517, female, cecum, replicate2


title: CG517-s-f-3

description: Patient CG517, female, sigmoid colon, replicate3


title: CG507-r-m-2

description: Patient CG507, male, rectum, replicate2

value: Patient CG507, male, rectum, replicate2


title: CG507-r-m-3

description: Patient CG507, male, rectum, replicate3

value: Patient CG507, male, rectum, replicate3


title: CG507-r-m-1

description: Patient CG507, male, rectum, replicate1

value: Patient CG507, male, rectum, replicate1


title: CG517-r-f-2

description: Patient CG517, female, rectum, replicate2


title: CG507-c-m-2

description: Patient CG507, male, cecum, replicate2

value: Patient CG507, male, cecum, replicate2


title: CG507-s-m-2

description: Patient CG507, male, sigmoid colon, replicate2


title: HYB109

status: Public on Feb 28 2010

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

hyb_protocol: according to manufacturer's protocol

scan_protocol: using Agilent Feature Extraction 8.5 Software

data_processing: Subtraction background correction and loess normalisation were applied to the data. Scan-date dependent biases were corrected by subtracting systematic noise across all arrays for each scan date

label_protocol: according to manufacturer's protocol

extract_protocol: genomic DNA isolated using proteinase-K treatment and phenol chloroform purification

tag: sample type

value: cell line

tag: tissue origin

value: ovarian

source_name: male pool

value: tissue


title: HYB105


title: HYB99

source_name: OVTOKO


title: HYB97


title: HYB110


title: HYB100


title: HYB94

value: tumour

value: Post-treatment (Paclitaxel)

tag: patient number


title: HYB96

value: breast


title: HYB89


title: HYB93


title: HYB101


title: HYB88


title: HYB103


title: HYB104


title: HYB87


title: HYB102


title: HYB108


title: HYB83

value: Pre-treatment


title: HYB86


title: HYB107


title: HYB95

value: Post-treatment (Paclitaxel & Carboplatin)


title: HYB85


title: HYB98

source_name: OVMANA


title: HYB92


title: HYB82


title: HYB84


title: HYB90


title: HYB79


title: HYB77


title: HYB76

value: Post-treatment (Carboplatin)


title: HYB81


title: HYB73


title: HYB78


title: HYB71

source_name: OCUBF


title: HYB66


title: HYB67


title: HYB80


title: HYB75


title: HYB56


title: HYB64


title: HYB54


title: HYB60


title: HYB57


title: HYB55


title: HYB52


title: HYB65


title: HYB68


title: HYB70


title: HYB62


title: HYB51


title: HYB63


title: HYB74


title: HYB72


title: HYB53


title: HYB69


title: HYB47


title: HYB49


title: HYB50


title: HYB48


title: Favorable Histology Wilms Tumor_WT15

city: Chicago

first: Elizabeth

middle: J

last: Perlman

state: IL

address: 2373 North Lincoln Avenue, Room A.204

department: Pathology

institute: Northwestern University/Children's Memorial Hospital

description: Favorable Histology Wilms Tumor

hyb_protocol: Hybridization: The labeled, fragmented cRNA was hybridized to the Affymetrix HG - U133A oligonucleotide array for 16 hours at 45°C according to Affymetrix protocol. Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols. Washing, staining, and scanning: The hybridized microarrays were washed using pre-programmed Affymetrix protocols and individual reagents purchased from Sigma. The arrays were stained with streptavidin-phycoerythrin (SAPE, Molecular Probes, Eugene, OR) and the signal amplified using an antibody solution containing 0.1 mg/ml normal goat IgG (Sigma), and 3 µg/ml biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA). Staining was done in the GeneChip Fluidics Station using pre-programmed Affymetrix protocols. The arrays were scanned in an HP GeneArray Scanner at the excitation wavelength of 488 nm. The amount of light emitted at 570 nm is proportional to the bound target at each location on the microarray.

scan_protocol: The arrays were scanned in an HP GeneArray Scanner.

data_processing: Positional-dependent-nearest-neighbor model (PDNN) software was used to translate the scanned images into expression analysis files and to normalize the data across all arrays (http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/).  The normalized value of each probeset for each tumor is provided in the attached excel spreadsheet All Normalized Data.

source_name: Favorable Histology Wilms Tumor, Pretreatment tumor tissue

label_protocol:
cDNA synthesis:
cDNA synthesis was performed by SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen). The manufacturer’s protocol was modified by the use of an HPLC- purified T7-(dT)24 primer (GenSet Oligos, Proligo, Boulder, CO) and incubation at 42°C. The double-stranded cDNA product was purified by phenol/chloroform extraction using Phase Lock Gels (Eppendorf Scientific, Westbury, NY) followed by ethanol precipitation. The resulting pellet was washed twice in 80% ethanol, dried, and re-suspended in 22 µl of RNAse-free water.
Biotin-labeled cRNA synthesis:
22 µl of purified cDNA underwent an in vitro transcription (IVT) using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY).  The resulting biotin-labeled cRNA was purified using RNeasy Mini Kit (Qiagen) and quantified using a GeneQuant DNA/RNA calculator (Amersham Biosciences).  Labeled cRNA (17 µg) was fragmented according to Affymetrix protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen, Carlsbad, CA) extraction and treated with DNase I (Roche, Indianapolis, IN).   The RNA was purified by RNeasy Mini Kit (Qiagen, Valencia, CA) and the concentration determined by optical density as measured by a GeneQuant DNA/RNA calculator (Amersham Biosciences, Piscataway, NJ).  Samples with A260/A280 of less than 1.8 were excluded. The quality of the RNA was further assessed by electrophoresis on a 1% agarose gel and samples rejected if significant RNA degradation was observed.

tag: Favorable Histology Wilms Tumor


title: HYB46

tag: treatment


title: Favorable Histology Wilms Tumor_WT10

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT14

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT13

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT12

description: Favorable Histology Wilms Tumor


title: HYB44


title: Favorable Histology Wilms Tumor_WT6

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT11

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT3

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT8

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT2

description: Favorable Histology Wilms Tumor


title: HYB43


title: HYB42


title: Favorable Histology Wilms Tumor_WT4

description: Favorable Histology Wilms Tumor


title: Favorable Histology Wilms Tumor_WT7

description: Favorable Histology Wilms Tumor


title: HYB39


title: Rhabdoid Tumor_RT9

description: Rhabdoid Tumor

source_name: Rhabdoid Tumor, Pretreatment tumor tissue

tag: Rhabdoid Tumor


title: Favorable Histology Wilms Tumor_WT1

description: Favorable Histology Wilms Tumor


title: HYB40


title: Rhabdoid Tumor_RT8

description: Rhabdoid Tumor


title: HYB45


title: HYB41


title: Favorable Histology Wilms Tumor_WT5

description: Favorable Histology Wilms Tumor


title: Rhabdoid Tumor_RT5

description: Rhabdoid Tumor


title: Rhabdoid Tumor_RT7

description: Rhabdoid Tumor


title: Rhabdoid Tumor_RT3

description: Rhabdoid Tumor


title: HYB37


title: Rhabdoid Tumor_RT15

description: Rhabdoid Tumor


title: Clear Cell Sarcoma of the Kidney_CCSK12

description: Clear Cell Sarcoma of the Kidney

source_name: Clear Cell Sarcoma of the Kidney, Pretreatment tumor tissue

tag: Clear Cell Sarcoma of the Kidney


title: Rhabdoid Tumor_RT14

description: Rhabdoid Tumor


title: Clear Cell Sarcoma of the Kidney_CCSK17

description: Clear Cell Sarcoma of the Kidney


title: Rhabdoid Tumor_RT12

description: Rhabdoid Tumor


title: HYB36


title: HYB34


title: HYB38


title: HYB33


title: Clear Cell Sarcoma of the Kidney_CCSK14

description: Clear Cell Sarcoma of the Kidney


title: Rhabdoid Tumor_RT10

description: Rhabdoid Tumor


title: Clear Cell Sarcoma of the Kidney_CCSK16

description: Clear Cell Sarcoma of the Kidney


title: HYB32


title: Clear Cell Sarcoma of the Kidney_CCSK18

description: Clear Cell Sarcoma of the Kidney


title: Rhabdoid Tumor_RT1

description: Rhabdoid Tumor


title: Clear Cell Sarcoma of the Kidney_CCSK9

description: Clear Cell Sarcoma of the Kidney


title: HYB30


title: Clear Cell Sarcoma of the Kidney_CCSK10

description: Clear Cell Sarcoma of the Kidney


title: HYB35


title: HYB31


title: Clear Cell Sarcoma of the Kidney_CCSK11

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK8

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK6

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK7

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK1

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK2

description: Clear Cell Sarcoma of the Kidney


title: Cellular Mesoblastic Nephroma_CMN13

description: Cellular Mesoblastic Nephroma

source_name: Cellular Mesoblastic Nephroma, Pretreatment tumor tissue

tag: Cellular Mesoblastic Nephroma


title: HYB28


title: Clear Cell Sarcoma of the Kidney_CCSK3

description: Clear Cell Sarcoma of the Kidney


title: Clear Cell Sarcoma of the Kidney_CCSK4

description: Clear Cell Sarcoma of the Kidney


title: Cellular Mesoblastic Nephroma_CMN8

description: Cellular Mesoblastic Nephroma


title: Favorable Histology Wilms Tumor_WT9

description: Favorable Histology Wilms Tumor


title: Cellular Mesoblastic Nephroma_CMN12

description: Cellular Mesoblastic Nephroma


title: Cellular Mesoblastic Nephroma_CMN7

description: Cellular Mesoblastic Nephroma


title: Cellular Mesoblastic Nephroma_CMN9

description: Cellular Mesoblastic Nephroma


title: HYB24


title: Clear Cell Sarcoma of the Kidney_CCSK5

description: Clear Cell Sarcoma of the Kidney


title: Cellular Mesoblastic Nephroma_CMN5

description: Cellular Mesoblastic Nephroma


title: HYB23


title: Cellular Mesoblastic Nephroma_CMN4

description: Cellular Mesoblastic Nephroma


title: HYB27


title: Cellular Mesoblastic Nephroma_CMN6

description: Cellular Mesoblastic Nephroma


title: HYB21


title: HYB25


title: Cellular Mesoblastic Nephroma_CMN11

description: Cellular Mesoblastic Nephroma


title: HYB26


title: HYB22


title: HYB20


title: HYB19


title: HYB29


title: Cellular Mesoblastic Nephroma_CMN1

description: Cellular Mesoblastic Nephroma


title: Cellular Mesoblastic Nephroma_CMN3

description: Cellular Mesoblastic Nephroma


title: HYB10


title: HYB14


city: Rio de Janeiro

first: Marcelo

last: Ribeiro-Alves

state: RJ

address: Avenida Brasil 4365. Manguinhos.

department: Centro de Desenvolvimento Tecnológico em Saúde

country: Brazil

institute: Fundação Oswaldo Cruz

description: Biological replicate 3 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

hyb_protocol: Hybridization of 15 h followed by washing was performed in an automated slide processor (ASP, Amersham Biosciences).

scan_protocol: The slides were scanned in a Generation III laser scanner (Amersham Biosciences).

data_processing: print-tip LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Bioconductor/R limma package was used.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 3

label_protocol: The cDNA complex probes were prepared by reverse transcription using 10 µg of total RNA from controls or CD49e silenced TECs which were labeled using CyScribe post-labeling kit (Amersham Biosciences, England), and oligo dT12–18 as a primer.

growth_protocol: TEC cells were cultured in 10% fetal bovine serum-supplemented RPMI 1640 medium at 37oC in a 5% CO2 atmosphere.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: We transfected two siRNAs (Qiagen, Hilden, Germany), one scramble, this siRNA is not complementary to any gene in mammals, other siRNA, was designed to specifically silence the expression of integrin alpha5 subunit, CD49e-siRNA. Semi-confluent cultures of human TECs cell line were transiently transfected with 2.5 nM of CD49e-siRNA or scramble siRNA using Hiperfect reagent (Qiagen) in 24 well plates, following manufacturer’s instructions.Forty-eight hours after transfection we made RNA extraction for cDNA microarray.

tag: cell line

value: thymic epithelial cell line transfected with siRNA complementar to CD49e

value: We transfected CD49e siRNA (Qiagen, Hilden, Germany), designed to specifically silence the expression of integrin alpha5 subunit, CD49e-siRNA. Semi-confluent cultures of human TECs cell line were transiently transfected with 2.5 nM of CD49e-siRNA using Hiperfect reagent (Qiagen) in 24 well plates, following manufacturer’s instructions. Forty-eight hours after transfection we made RNA extraction for cDNA microarray.

source_name: Jurkat, Hela, Hep-2 and U343

value: Jurkat, Hela, Hep-2 and U343 mix


description: Biological replicate 1 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 1


title: HYB9


description: Biological replicate 2 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 2


title: HYB13


title: HYB15


title: HYB18


title: HYB7


title: HYB5


title: HYB8


title: HYB12


title: HYB16


title: HYB4


title: Cellular Mesoblastic Nephroma_CMN2

description: Cellular Mesoblastic Nephroma


title: HYB6


description: Biological replicate 6 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 6

value: thymic epithelial cell line transfected with scramble siRNA

value: We transfected scramble siRNA (Qiagen, Hilden, Germany), this siRNA is not complementary to any gene in mammals. Semi-confluent cultures of human TECs cell line were transiently transfected with 2.5 nM of scramble siRNA using Hiperfect reagent (Qiagen) in 24 well plates, following manufacturer’s instructions. Forty-eight hours after transfection we made RNA extraction for cDNA microarray.


title: HYB11

source_name: OVSAHO


title: HYB17


description: Biological replicate 4 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 4


description: Biological replicate 5 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 5


description: Biological replicate 6 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 6


title: HYB1

source_name: male pool


description: Biological replicate 5 of 6. Control thymic epithelial cell, transfected with siRNA complementar to CD49e.

source_name: TEC_ch1 = CD49e siRNA transfected thymic epithelial cell replicate 5


description: Biological replicate 4 of 6. Control thymic epithelial cell, untreated.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 4

value: thymic epithelial cell line

value: no treatment


description: Biological replicate 1 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 1


title: TMP- JCW28_37 repeat 1

status: Public on Feb 16 2010

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: In vivo TMP photobinding of genomic DNA from JCW28 strain at 37ºC. Replicate 1

hyb_protocol: The arrays were pre-hybridized with 10 ml UltraHyb solution (Ambion) in a roller oven during 1 h at 46ºC. 33P-dCTP labeled DNA (5x106 dpm/ml) was then added and the hybridization conducted during 16 h at 46ºC. Arrays were washed at 65ºC, once in 2xSSC plus 0.1% SDS for 20 min, and twice in 0.2xSSC plus 0.1% SDS for 30 min.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager

data_processing: Raw image quantization background subtracted.

organism: Saccharomyces cerevisiae

source_name: JCW28 S. cerevisiae strain

label_protocol: Exonuclease resistant DNA chains were subjected to random priming with the Strip-EZ DNA kit (Ambion), which incorporates a modified dCTP nucleotide that produces easily strippable chains.

growth_protocol: Exponential growth in YPD at 30ºC. Then 10 min at 37ºC

extract_protocol: Yeast cells were disrupted using the Fast-Prep apparatus and total DNA was fragmented down to a 2 kb average size by using a Branson Sonifier. Following proteinase K and RNAse I incubations, DNA fragments were extracted twice with phenol and once with phenol-chloroform, precipitated with EtOH, washed with 70% EtOH, and resuspended in 100 µl of water. Genomic DNA fragments were incubated with TMP (0.4 µg/ml) and irradiated (360 nm, at a dose of 1.2 kJ/m2/min during 120 seconds) to produce an amount of crosslinks comparable to that obtained in vivo (1 crosslink/10 kb). Crosslinked fragments were selected by exonuclease digestions: DNA samples were boiled for 2 min, chilled on ice, and then digested with excess Exonuclease I (NE BioLabs) during 4 hours. Undigested DNA was recovered with a GFX filtration kit (Amersham) in 50 µl of water and further digested with excess Exonuclease (NE BioLabs) during 6 hours. The reaction terminated by inactivation of the enzyme at 80ºC during 10 min.

tag: strain

value: JCW28 (top1 top2ts strain)


title: TMP- JCW28_37 repeat 3

description: In vivo TMP photobinding of genomic DNA from JCW28 strain at 37ºC. Replicate 3

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.


description: Biological replicate 2 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 2


description: Biological replicate 1 of 6. Control thymic epithelial cell, untreated.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 1


description: Biological replicate 3 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 3


description: Biological replicate 3 of 6. Control thymic epithelial cell, untreated.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 3


description: Biological replicate 4 of 6. Control thymic epithelial cell, transfected with scramble siRNA.

source_name: TEC_ch1 = Scramble siRNA transfected thymic epithelial cell replicate 4

source_name: Jurkat, Hela, Hep-2 and U343


title: TMP- JCW25_37 repeat 3

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 37ºC. Replicate 3

source_name: JCW25 S. cerevisiae strain

label_protocol: Exonuclease resistant DNA chains were subjected to random priming with the Strip-EZ DNA kit (Ambion), which incorporates a modified dCTP nucleotide that produces easily strippable chains

value: JCW25 (wt)


title: TMP- JCW28_37 repeat 2

description: In vivo TMP photobinding of genomic DNA from JCW28 strain at 37ºC. Replicate 2


title: TMP- JCW25_37 repeat 1

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 37ºC. Replicate 1


description: Biological replicate 6 of 6. Control thymic epithelial cell, untreated.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 6


title: TMP-Genomic DNA repeat 3

description: In vitro TMP photobinding of genomic DNA from JCW25 strain. Replicate 3

source_name: JCW25 genomic DNA

growth_protocol: Exponential growth in YPD


title: TMP-Genomic DNA repeat 1

description: In vitro TMP photobinding of genomic DNA from JCW25 strain. Replicate 1

label_protocol: Exonuclease resistant DNA chains were subjected to random priming with the Strip-EZ DNA kit (Ambion), which incorporates a modified dCTP nucleotide that produces easily strippable chain


title: TMP- JCW25_30 repeat 2

description: In vivo TMP photobinding of genomic DNA from JCW25 strain at 30ºC. Replicate 2

growth_protocol: Exponential growth in YPD at 30ºC


title: TMP-Genomic DNA repeat 2

description: In vitro TMP photobinding of genomic DNA from JCW25 strain. Replicate 2


description: Biological replicate 2 of 6. Control thymic epithelial cell, untreated.

source_name: TEC_ch1 = Control untransfected thymic epithelial cell replicate 2