description: RT_200_5d_269_CLPR200_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 5, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

value: day/wk

value: 5, Units of Duration:day

tag: treatment time

tag: units of treatment time

value: hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_30_15d_243_Lung_CLPR30_RSTSRP805

status: Public on Oct 12 2012

type: RNA

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

country: USA

institute: CIIT Centers for Health Research

description: RT_30_15d_243_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing:
RMAExpress
Written by B. M. Bolstad <bmb@bmbolstad.com>
Version: 1.0.5 Release
http://rmaexpress.bmbolstad.com

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Lung tissue

label_protocol: standard Affymetrix protocol

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

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

value: RNAlater

value: adult

value: Pentobarbitol and exsanguination

value: Female

value: Weeks at start of exposure

value: Lung

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 15, Units of Duration:day

value: Air

value: inhalation


title: RT_200_5d_265_Lung_CLPR200_RSTSRP805

description: RT_200_5d_265_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods


title: RT_200_5d_267_Lung_CLPR200_RSTSRP805

description: RT_200_5d_267_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_200_5d_268_Lung_CLPR200_RSTSRP805

description: RT_200_5d_268_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: RT_30_15d_242_Lung_CLPR30_RSTSRP805

description: RT_30_15d_242_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods


title: RT_30_15d_241_Lung_CLPR30_RSTSRP805

description: RT_30_15d_241_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: Pfeiffer shNTC (10days)

city: Collegeville

first: Gopinath

last: Ganji

state: PA

address: 1250 South Collegeville Road

institute: GSK

description: Gene expression data from Pfeiffer cell line treated with non targeting shRNA for 10 days

hyb_protocol: According to manufacturer's instructions

data_processing: Data was analyzed using MAS (Microarray Suite) v. 5.0 algorithm using default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500

organism: Homo sapiens

source_name: Pfeiffer shNTC

growth_protocol: Cells were grown as recommended by ATCC or DSMZ.

extract_protocol: RNA extracted with Trizol reagent and purified per Trizol protocol; RNA further purified using RNeasy kit columns

treatment_protocol: Pfeiffer and KARPAS-422 cells plated in RPMI-1640 supplemented with 10% fetal bovine serum and 8 µg/ml polybrene were infected with lentiviral transduction particles (Sigma) containing shRNA specific for a non-mammalian control sequence or human EZH2. Sequences for the shRNA were as follows: shControl –   CCGGCAACAAGATGAAGAGCACCAACTCGAGTTGGTGCTCTTCATCTTGTTGTTTTT and shEZH2 – CCGGTATGATGGTTAACGGTGATCACTCGAGTGATCACCGTTAACCATCATATTTTTG. Two days after the addition of virus, cells were transferred to RPMI-1640 media supplemented with 10% fetal bovine serum and 1 µg/ml puromycin to select for infected cells. After 2 days of puromycin selection, cells were plated into 96 well plates.

tag: cell line

value: Pfeiffer

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment

value: Non targetting Control (10days)


title: RT_200_15d_279_Lung_CLPR200_RSTSRP805

description: RT_200_15d_279_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 200, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: Pfeiffer shEZH2 (10days)

description: Gene expression data from Pfeiffer cell line treated with shRNA against EZH2 for 10 days

scan_protocol: According to manufacturer's instructions

source_name: Pfeiffer shEZH2

tag: cell line

value: shEZH2 (10days)


title: KARPAS-422 shNTC (10days), biological rep2

description: Gene expression data from Karpas-422 cell line treated with non targeting shRNA for 10 days-replicate2

source_name: KARPAS-422 shNTC

label_protocol: According to manufacturer's instructions

tag: tissue type


title: KARPAS-422 shNTC (10days), biological rep 1

description: Gene expression data from Karpas-422 cell line treated with non targeting shRNA for 10 days - replicate1

tag: treatment


title: Toledo GSK126, biological rep 2

description:
Toledo_500nM_R6.11_T
Gene expression data from Toledo cell line treated with 500nM GSK126 treatment

data_processing: Data was analyzed using MAS (Microarray Suite) v. 5.0 algorithm using defulat settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500

treatment_protocol: 2x10^5 cells were seeded in 3 ml cell culture media into 6-well dishes and allowed to equilibrate overnight at 37 degrees Celcius and 5% CO2. The following day, DMSO or GSK126 were added to final concentrations of 0.1% DMSO and/or 500 nM GSK126. After 72 hours, cells were harvested by centrifugation, lysed with 750 ul Trizol reagent, and frozen at -80 degrees Celcius.

value: Toledo

tag: genotype/variation

value: EZH2 wild type

tag: average gic50


title: RT_200_15d_277_Lung_CLPR200_RSTSRP805

description: RT_200_15d_277_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: tissue

tag: tissue harvest methods

value: day/wk

tag: treatment time

tag: units of treatment time

value: hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: KARPAS-422 shEZH2 (10days), biological rep 2

description: Gene expression data from Karpas-422 cell line treated with shRNA against EZH2 for 10 days-replicate2

source_name: KARPAS-422 shEZH2

tag: cell line

tag: tissue type

tag: treatment


title: KARPAS-422 shEZH2 (10days), biological rep 1

description: Gene expression data from Karpas-422 cell line treated with shRNA against EZH2 for 10 days-replicate1


title: Toledo vehicle, biological rep 1

description:
Toledo_veh_R6.7_S
Gene expression data from Toledo cell line treated with DMSO

tag: genotype/variation

tag: average gic50

value: DMSO (72h)


title: RT_200_15d_281_Lung_CLPR200_RSTSRP805

description: RT_200_15d_281_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

value: Female

tag: age

tag: units of age

value: Weeks at start of exposure

value: Lung

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 15, Units of Duration:day

value: Air


title: SU-DHL-4 GSK126, biological rep 2

description:
SU.DHL.4_500nM_R7.16_R
Gene expression data from SU-DHL-4 cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50 (nm)

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment


description: RT_200_15d_282_CLPR200_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

value: excellent

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: tissue

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

value: inhalation

tag: dose or concentration


title: RT_200_5d_266_Lung_CLPR200_RSTSRP805

description: RT_200_5d_266_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

value: RNAlater

value: adult

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 5, Units of Duration:day


title: SU-DHL-4 vehicle, biological rep 2

description:
SU.DHL.4_veh_R7.14_Q
Gene expression data from SU-DHL-4 cell line treated with DMSO

tag: cell line

tag: genotype/variation

tag: average gic50 (nm)

tag: tissue type

tag: treatment

value: DMSO (72h)


title: Toledo GSK126, biological rep 1

description:
Toledo_500nM_R6.8_T
Gene expression data from Toledo cell line treated with 500nM GSK126 treatment

value: Toledo

value: EZH2 wild type

tag: average gic50


title: RT_0_5d_206_Lung_ACO2_RSTSRP805

description: RT_0_5d_206_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

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

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Pentobarbitol and exsanguination

value: Female

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

value: Air Control

value: day/wk

tag: treatment time

tag: units of treatment time

value: hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_0_5d_203_Lung_ACO2_RSTSRP805

description: RT_0_5d_203_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

value: ul

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: Air


title: RT_200_15d_280_Lung_CLPR200_RSTSRP805

description: RT_200_15d_280_Lung_CLPR200_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

value: good

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: tissue

tag: tissue harvest methods

value: Chloroprene

value: 15, Units of Duration:day

value: inhalation


title: OCI-LY-19 GSK126, biological rep 1

description:
OCI.LY.19_500nM_R8.11_P
Gene expression data from OCI-LY-19 cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

tag: average gic50

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment


title: SU-DHL-4 GSK126, biological rep 1

description:
SU.DHL.4_500nM_R7.15_R
Gene expression data from SU-DHL-4 cell line treated with 500nM GSK126 treatment

value: EZH2 mutant

tag: average gic50 (nm)


title: Toledo vehicle, biological rep 2

description:
Toledo_veh_R6.10_S
Gene expression data from Toledo cell line treated with DMSO

value: Toledo

value: EZH2 wild type

value: DMSO (72h)


title: RT_0_15d_212_Lung_ACO2_RSTSRP805

description: RT_0_15d_212_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Air Control, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: array type

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNAlater

value: adult

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

value: Female

tag: age

tag: units of age

value: Weeks at start of exposure

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_0_5d_205_Lung_ACO2_RSTSRP805

description: RT_0_5d_205_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: tissue

value: Lung

tag: tissue harvest methods

value: Air Control

value: day/wk

value: 5, Units of Duration:day

value: hr/day


title: RT_0_5d_202_Lung_ACO2_RSTSRP805

description: RT_0_5d_202_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: Air

value: inhalation


title: RT_0_5d_201_Lung_ACO2_RSTSRP805

description: RT_0_5d_201_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: strain

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_0_15d_213_Lung_ACO2_RSTSRP805

description: RT_0_15d_213_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: tissue

tag: tissue harvest methods

value: 15, Units of Duration:day


title: OCI-LY-19 GSK126, biological rep 2

description:
OCI.LY.19_500nM_R8.12_P
Gene expression data from OCI-LY-19 cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

value: EZH2 wild type

tag: average gic50

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment


title: SU-DHL-4 vehicle, biological rep 1

description:
SU.DHL.4_veh_R7.13_Q
Gene expression data from SU-DHL-4 cell line treated with DMSO

value: EZH2 mutant

tag: average gic50 (nm)

value: DMSO (72h)


title: OCI-LY-19 vehicle, biological rep 1

description:
OCI.LY.19_veh_R8.9_O
Gene expression data from OCI-LY-19 cell line treated with DMSO


title: OCI-LY-19 vehicle, biological rep 2

description:
OCI.LY.19_veh_R8.10_O
Gene expression data from OCI-LY-19 cell line treated with DMSO


title: RT_0_15d_209_Lung_ACO2_RSTSRP805

description: RT_0_15d_209_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

value: RNAlater

tag: strain

value: adult

value: Pentobarbitol and exsanguination

value: Female

tag: units of age

value: Weeks at start of exposure

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: DB GSK126, biological rep 2

description:
DB_500nM_R7.4_N
Gene expression data from DB cell line treated with 500nM GSK126 treatment

tag: cell line

value: DB

tag: genotype/variation

tag: average gic50

tag: tissue type

tag: treatment


title: RT_0_15d_210_Lung_ACO2_RSTSRP805

description: RT_0_15d_210_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: tissue

value: Lung

tag: tissue harvest methods

value: Air Control

value: day/wk

value: hr/day


title: DB GSK126, biological rep 1

description:
DB_500nM_R7.3_N
Gene expression data from DB cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

tag: average gic50

tag: tissue type

tag: treatment


title: DB vehicle, biological rep 2

description:
DB_veh_R7.2_M
Gene expression data from DB cell line treated with DMSO


title: RT_0_15d_211_Lung_ACO2_RSTSRP805

description: RT_0_15d_211_Lung_ACO2_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

value: excellent

tag: strain

tag: units of age

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: SU-DHL-6 GSK126, biological rep 2

description:
SU.DHL.6_500nM_R8.24_L
Gene expression data from SU-DHL-6 cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment


title: SU-DHL-6 GSK126, biological rep 1

description:
SU.DHL.6_500nM_R8.23_L
Gene expression data from SU-DHL-6 cell line treated with 500nM GSK126 treatment


title: DB vehicle, biological rep 1

description:
DB_veh_R7.1_M
Gene expression data from DB cell line treated with DMSO

value: DMSO (72h)


title: SU-DHL-6 vehicle, biological rep 2

description:
SU.DHL.6_veh_R8.22_K
Gene expression data from SU-DHL-6 cell line treated with DMSO


title: cbp1∆_rep1

city: Chestnut Hill

first: Hugh

middle: P

last: Cam

state: MA

address: Higgins Hall Room 355, 140 Commonwealth Avenue

department: Biology

institute: Boston College

description: expression profiling of cbp1∆ vs. wildtype cells

hyb_protocol: 150 ng each of labeled mutant and wildtype cDNA were combined with 2X Hi-RPM Hybridization Buffer and 10X GE Blocking Reagent from the Agilent Gene Expression Hybridization Kit. Combined samples were hybridized to Agilent 4x44k array slides in an Agilent SureHyb chamber at 65° C, 20 RPM for 24 hours. Slides were washed once with 6X SSPE. (Invitrogen)/0.005% N-Lauroylsarcosine (Sigma L7414), once with 0.06X SSPE/0.005%  N-Lauroylsarcosine, and once with Agilent Stabilization and Drying solution according to Agilent protocols.

scan_protocol: Slides were scanned using an Agilent G2565CA Scanner.

data_processing: Scanned slides were processed using Agilent Feature Extraction Software (v.10.5.1.1), extraction protocol GE2_105_Jul10. Red and green channel spot and background intensities from Feature Extraction files were processed using the R/Bioconductor limma package (v.3.10.2) using the read.maimages function (source=agilent). log2 fold-changes of mutant vs. wildtype were determined with the normalizeWithinArrays function using the loess normalization method.

label: Alexa Fluor 647

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells

label_protocol: 20 ug of total RNA was reverse transcribed using anchored oligo-dT and labeled with Alexa Fluor 647 (mutant) or Alexa Fluor 555 (wildtype) using the Superscript III Indirect cDNA Labeling Kit (Invitrogen) according to the manufacturer's instructions.

growth_protocol: Logarithmically growing cultures were grown 18 hours to mid-exponential phase (A595 ~ 0.5) in standard rich media (YEA) shaking at 250 RPM. For the cbp1∆ experiments, both mutant and wildtype cells were cultured at 30° C. For the clr3∆ clr6-1 experiments, both mutant and wildtype cells were cultured at 26° C.

extract_protocol: 10 mL cultures were harvested by centrifuging 2000 RPM for 2 minutes at room temperature, decanted, then snap frozen in liquid nitrogen. RNA was extracted using a hot acid phenol method (Lyne et al., 2003), then purified with Qiagen RNEasy spin columns according to the manufacturer's protocol.

value: cbp1∆ cells

tag: cell growth temperature

value: 30° C

label: Alexa Fluor 555

value: wildtype cells


title: clr3∆_clr6-1_rep1

description: expression profiling of clr3∆ clr6-1 vs. wildtype cells

tag: strain

value: clr3∆ clr6-1 cells

value: 26 °C


title: clr3∆_clr6-1_rep2


title: cbp1∆_rep2


title: SU-DHL-6 vehicle, biological rep 1

description:
SU.DHL.6_veh_R8.21_K
Gene expression data from SU-DHL-6 cell line treated with DMSO


title: HT GSK126, biological rep 2

description:
HT _500nM_R7.28_J
Gene expression data from HT cell line treated with 500nM GSK126 treatment

value: HT

value: EZH2 wild type


title: HT GSK126, biological rep 1

description:
HT _500nM_R7.27_J
Gene expression data from HT cell line treated with 500nM GSK126 treatment


title: Primary Plasma Cell Leukemia PCL-035 Expression

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-035

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions were summarized as median value for each sample.

source_name: Primary Plasma Cell Leukemia PCL-035

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: cell type

value: plasma cell

tag: disease state

value: plasma cell leukemia

tag: genome variation

value: translocation t(11;14)


title: Primary Plasma Cell Leukemia PCL-026 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-026

source_name: Primary Plasma Cell Leukemia PCL-026

value: translocation t(14,16)


title: Primary Plasma Cell Leukemia PCL-028 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-028

source_name: Primary Plasma Cell Leukemia PCL-028


title: SU-DHL-10 GSK126, biological rep 2

description:
SU.DHL.10_500nM_R7.36_H
Gene expression data from SU-DHL-10 cell line treated with 500nM GSK126 treatment


title: HT vehicle, biological rep 1

description:
HT _veh_R7.25_I
Gene expression data from HT cell line treated with DMSO


title: HT vehicle, biological rep 2

description:
HT _veh_R7.26_I
Gene expression data from HT cell line treated with DMSO


title: Primary Plasma Cell Leukemia PCL-027 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-027

source_name: Primary Plasma Cell Leukemia PCL-027


title: Primary Plasma Cell Leukemia PCL-034 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-034

source_name: Primary Plasma Cell Leukemia PCL-034

value: translocation t(4;14)


title: Primary Plasma Cell Leukemia PCL-032 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-032

source_name: Primary Plasma Cell Leukemia PCL-032


title: Primary Plasma Cell Leukemia PCL-036 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-036

source_name: Primary Plasma Cell Leukemia PCL-036


title: Primary Plasma Cell Leukemia PCL-030 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-030

source_name: Primary Plasma Cell Leukemia PCL-030

value: translocation t(14,20)


title: Primary Plasma Cell Leukemia PCL-022 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-022

source_name: Primary Plasma Cell Leukemia PCL-022


title: RT_03_15d_129_Lung_CLPR03_RSTSRP805

description: RT_03_15d_129_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

organism: Mus musculus

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0.3, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: days/week

value: 15, Units of Duration:days

value: 6 hr/day

value: Air

value: inhalation


title: Primary Plasma Cell Leukemia PCL-029 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-029

source_name: Primary Plasma Cell Leukemia PCL-029

tag: cell type

value: plasma cell

tag: disease state

value: plasma cell leukemia

tag: genome variation

value: translocation t(14,16)


title: RT_03_5d_117_Lung_CLPR-03_RSTSRP805

description: RT_03_5d_117_Lung_CLPR-03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 0.3, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: strain

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: Primary Plasma Cell Leukemia PCL-021 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-021

source_name: Primary Plasma Cell Leukemia PCL-021

value: translocation t(4;14)


title: SU-DHL-10 vehicle, biological rep 1

description:
SU.DHL.10_veh_R7.33_G
Gene expression data from SU-DHL-10 cell line treated with DMSO

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment

value: DMSO (72h)


title: SU-DHL-10 GSK126, biological rep 1

description:
SU.DHL.10_500nM_R7.35_H
Gene expression data from SU-DHL-10 cell line treated with 500nM GSK126 treatment


title: Primary Plasma Cell Leukemia PCL-019 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-019

source_name: Primary Plasma Cell Leukemia PCL-019

tag: cell type

tag: disease state

tag: genome variation


title: Primary Plasma Cell Leukemia PCL-017 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-017

source_name: Primary Plasma Cell Leukemia PCL-017


title: Primary Plasma Cell Leukemia PCL-020 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-020

source_name: Primary Plasma Cell Leukemia PCL-020

value: translocation none


title: Primary Plasma Cell Leukemia PCL-014 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-014

source_name: Primary Plasma Cell Leukemia PCL-014

value: translocation t(11;14)


title: Primary Plasma Cell Leukemia PCL-023 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-023

source_name: Primary Plasma Cell Leukemia PCL-023


title: Primary Plasma Cell Leukemia PCL-015 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-015

source_name: Primary Plasma Cell Leukemia PCL-015


title: Primary Plasma Cell Leukemia PCL-018 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-018

source_name: Primary Plasma Cell Leukemia PCL-018


title: Primary Plasma Cell Leukemia PCL-010 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-010

source_name: Primary Plasma Cell Leukemia PCL-010


title: KARPAS-422 vehicle, biological rep 2

description:
Karpas.422_veh_R6.40_E
Gene expression data from KARPAS-422 cell line treated with DMSO


title: KARPAS-422 GSK126, biological rep 1

description:
Karpas.422_500nM_R6.38_F
Gene expression data from KARPAS-422 cell line treated with 500nM GSK126 treatment


title: RT_03_15d_125_Lung_CLPR03_RSTSRP805

description: RT_03_15d_125_Lung_CLPR03_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat


title: RT_90_5d_168_Lung_CLPR-90_RSTSRP805

description: RT_90_5d_168_Lung_CLPR-90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 90, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: rna integrity number

tag: strain

value: days/week

tag: treatment duration

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: KARPAS-422 vehicle, biological rep 1

description:
Karpas.422_veh_R6.37_E
Gene expression data from KARPAS-422 cell line treated with DMSO

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50

tag: tissue type

tag: treatment


title: WSU-DLCL2 GSK126, biological rep 1

description:
WSU.DLCL2_500nM_R7.7_D
Gene expression data from WSU-DLCL2cell line treated with 500nM GSK126 treatment

value: DLBCL (diffuse large B-cell lymphoma)


title: WSU-DLCL2 GSK126, biological rep 2

description:
WSU.DLCL2_500nM_R7.8_D
Gene expression data from WSU-DLCL2 cell line treated with 500nM GSK126 treatment


title: VS0016_GEP

description: legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

source_name: Human multiple myeloma patient VS0016

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: vh status

value: mut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: VC0142_GEP

source_name: Human multiple myeloma patient VC0142


title: VB0013_GEP

source_name: Human multiple myeloma patient VB0013


title: KARPAS-422 GSK126, biological rep 2

description:
Karpas.422_500nM_R6.41_F
Gene expression data from KARPAS-422cell line treated with 500nM GSK126 treatment


title: VP0089_GEP

source_name: Human multiple myeloma patient VP0089


title: Primary Plasma Cell Leukemia PCL-016 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-016

source_name: Primary Plasma Cell Leukemia PCL-016

tag: cell type

value: plasma cell

value: plasma cell leukemia

tag: genome variation

value: translocation t(14,16)


title: VS0140_GEP

source_name: Human multiple myeloma patient VS0140


title: VD0026_GEP

source_name: Human multiple myeloma patient VD0026


title: VG0442_GEP

source_name: Human multiple myeloma patient VG0442

value: unmut


title: TL0397_GEP

source_name: Human multiple myeloma patient TL0397


title: WSU-DLCL2 vehicle, biological rep 2

description:
WSU.DLCL2_veh_R7.6_C
Gene expression data from WSU-DLCL2 cell line treated with DMSO

value: DMSO (72h)


title: RT_90_5d_169_Lung_CLPR-90_RSTSRP805

description: RT_90_5d_169_Lung_CLPR-90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

value: Lung

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 5, Units of Duration:days


title: WSU-DLCL2 vehicle, biological rep 1

description:
WSU.DLCL2_veh_R7.5_C
Gene expression data from WSU-DLCL2 cell line treated with DMSO

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50

value: 134 nM nM

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment


title: VD0354_GEP

source_name: Human multiple myeloma patient VD0354

tag: vh status

value: mut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: RT_90_5d_167_Lung_CLPR90_RSTSRP805

description: RT_90_5d_167_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

value: days/week

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: SL0083_GEP

source_name: Human multiple myeloma patient SL0083

tag: vh status

value: unmut

tag: disease state

tag: sample type

tag: patient


title: SF0098_GEP

source_name: Human multiple myeloma patient SF0098


title: SG0168_GEP

source_name: Human multiple myeloma patient SG0168


title: RT_90_5d_166_Lung_CLPR-90_RSTSRP805

description: RT_90_5d_166_Lung_CLPR-90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

value: RNAlater

value: adult

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: units of age

value: Weeks at start of exposure

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: SG0114_GEP

source_name: Human multiple myeloma patient SG0114

tag: vh status

tag: disease state


title: SV0046_GEP

source_name: Human multiple myeloma patient SV0046

value: mut

tag: sample type

tag: patient


title: Primary Plasma Cell Leukemia PCL-037 Expression

description:
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-037

source_name: Primary Plasma Cell Leukemia PCL-037

tag: cell type

value: plasma cell

value: plasma cell leukemia

tag: genome variation

value: translocation t(11;14)


title: SU-DHL-10 vehicle, biological rep 2

description:
SU.DHL.10_veh_R7.34_G
Gene expression data from SU-DHL-10 cell line treated with DMSO

tag: cell line

tag: genotype/variation

value: EZH2 mutant

tag: average gic50

tag: tissue type

value: DLBCL (diffuse large B-cell lymphoma)

tag: treatment

value: DMSO (72h)


title: Pfeiffer vehicle, biological rep 2

description:
Pfeiffer_veh_R6.4_A
Gene expression data from Pfeiffer cell line treated with DMSO

value: Pfeiffer

value: 28 nM


title: RT_90_5d_165_Lung_CLPR-90_RSTSRP805

description: RT_90_5d_165_Lung_CLPR-90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Lung

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

value: days/week

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: Pfeiffer GSK126, biological rep 2

description:
Pfeiffer_500nM_R6.5_B
Gene expression data from Pfeiffer cell line treated with 500nM GSK126 treatment

tag: cell line

tag: genotype/variation

tag: average gic50

tag: tissue type

tag: treatment


title: SA0021_GEP

source_name: Human multiple myeloma patient SA0021

tag: vh status

value: mut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: Donor7_control

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the manufacturer's instructions.

scan_protocol: BeadArrays were  scanned using an Illumina BeadArray Reader. Scanner settings were set at a default for DirectHyb.

data_processing: Raw data were extracted using Illumina Genometudio Gene Expression Module v1.1. The data were transformed using variance stabilizing transformation (vst), normalised using robust spline normalisation with Bioconductor package lumi in R and adjusted for batch effect using ComBat (http://statistics.byu.edu/johnson/ComBat/Usage.html). Genes that were not expressed in any of the samples were removed prior to the identification of differentially expressed genes.

label_protocol: Total RNA (100-200 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer.

tag: cell type

value: primary CD4+ T cells

tag: batch


title: RM0400_GEP

source_name: Human multiple myeloma patient RM0400


title: SA0093_GEP

source_name: Human multiple myeloma patient SA0093

value: unmut


title: RR0157_GEP

source_name: Human multiple myeloma patient RR0157


title: Pfeiffer GSK126, biological rep 1

description:
Pfeiffer_500nM_R6.2_B
Gene expression data from Pfeiffer cell line treated with 500nM GSK126 treatment

value: EZH2 mutant

value: DLBCL (diffuse large B-cell lymphoma)


title: RG0443_GEP

source_name: Human multiple myeloma patient RG0443


title: RT_90_15d_180_Lung_CLPR90_RSTSRP805

description: RT_90_15d_180_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 90, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 15, Units of Duration:days


title: Pfeiffer vehicle, biological rep 1

description:
Pfeiffer_veh_R6.1_A
Gene expression data from Pfeiffer cell line treated with DMSO

tag: cell line

value: Pfeiffer

tag: genotype/variation

tag: average gic50

value: 28 nM

tag: tissue type

tag: treatment

value: DMSO (72h)


title: RT_90_15d_177_Lung_CLPR90_RSTSRP805

description: RT_90_15d_177_Lung_CLPR90_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

value: Lung

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

value: days/week

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: Donor4_SAHA

tag: cell type

value: primary CD4+ T cells

tag: batch


title: RB0040_GEP

description: legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

source_name: Human multiple myeloma patient RB0040

tag: vh status

value: mut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: Donor9_control


title: RB0087_GEP

source_name: Human multiple myeloma patient RB0087

value: unmut


title: Donor6_control


title: RG0077_GEP

source_name: Human multiple myeloma patient RG0077


title: RG0045_GEP

source_name: Human multiple myeloma patient RG0045


title: RA0023_GEP

source_name: Human multiple myeloma patient RA0023


title: Donor5_control


title: PR0084_GEP

source_name: Human multiple myeloma patient PR0084


title: PS0044_GEP

source_name: Human multiple myeloma patient PS0044


title: RT_2_5d_137_Lung_CLPR-2_RSTSRP805

description: RT_2_5d_137_Lung_CLPR-2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 2, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

value: good

value: RNAlater

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbital (5.2 mg/kg) and exsanguination

tag: age

tag: units of age

value: Weeks at start of exposure

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 5, Units of Duration:days


title: PM0340_GEP

source_name: Human multiple myeloma patient PM0340

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: RT_2_5d_135_Lung_CLPR-2_RSTSRP805

description: RT_2_5d_135_Lung_CLPR-2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

value: Lung

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: Chloroprene

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: Donor5_SAHA

tag: cell type

tag: batch


title: RT_2_5d_136_Lung_CLPR2_RSTSRP805

description: RT_2_5d_136_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: dilution

tag: rna integrity number

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

value: 6 hr/day

value: Air

value: inhalation


title: RT_2_5d_134_Lung_CLPR-2_RSTSRP805

description: RT_2_5d_134_Lung_CLPR-2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure


title: PG0065_GEP

source_name: Human multiple myeloma patient PG0065

tag: vh status

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: PI0172_GEP

source_name: Human multiple myeloma patient PI0172

value: unmut


title: PP0195_GEP

source_name: Human multiple myeloma patient PP0195


title: Donor9_SAHA

tag: cell type

value: primary CD4+ T cells

tag: batch


title: TG0139_GEP

source_name: Human multiple myeloma patient TG0139


title: PM0117_GEP

source_name: Human multiple myeloma patient PM0117

value: mut


title: PD0164_GEP

source_name: Human multiple myeloma patient PD0164


title: Donor6_SAHA


title: RT_2_15d_145_Lung_CLPR2_RSTSRP805

description: RT_2_15d_145_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 2, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

value: ul

tag: dilution

tag: rna integrity number

value: RNAlater

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 15, Units of Duration:days

tag: dose or concentration


title: PF0024_GEP

source_name: Human multiple myeloma patient PF0024

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: RT_2_5d_133_Lung_CLPR-2_RSTSRP805

description: RT_2_5d_133_Lung_CLPR-2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure


title: PG0028_GEP

source_name: Human multiple myeloma patient PG0028


title: Donor8_SAHA

tag: cell type

tag: batch


title: RT_2_15d_144_Lung_CLPR2_RSTSRP805

description: RT_2_15d_144_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: ratio

tag: rna integrity number

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

tag: dose or concentration


title: PA0351_GEP

source_name: Human multiple myeloma patient PA0351

tag: vh status

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

tag: patient


title: PA0146_GEP

source_name: Human multiple myeloma patient PA0146

value: peripheral blood mononuclear cells


title: Donor7_SAHA

tag: cell type

tag: batch


title: PA0145_GEP

source_name: Human multiple myeloma patient PA0145

value: unmut


title: Donor8_control

value: primary CD4+ T cells


title: Donor4_control


title: NS0060_GEP

source_name: Human multiple myeloma patient NS0060


title: OV0127_GEP

source_name: Human multiple myeloma patient OV0127

value: mut


title: OM0201_GEP

source_name: Human multiple myeloma patient OM0201


title: RT_2_15d_142_Lung_CLPR2_RSTSRP805

description: RT_2_15d_142_Lung_CLPR2_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation


title: RT_13_5d_154_Lung_CLPR13_RSTSRP805

description: RT_13_5d_154_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

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

value: good

value: RNAlater

value: adult

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: dose or concentration


title: PA0058_GEP

source_name: Human multiple myeloma patient PA0058

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: Donor3_control

tag: cell type

tag: batch


title: NM0156_GEP

source_name: Human multiple myeloma patient NM0156


title: NG0068_GEP

source_name: Human multiple myeloma patient NG0068


title: Donor2_control


title: MS0115_GEP

source_name: Human multiple myeloma patient MS0115


title: RT_13_5d_153_Lung_CLPR-13_RSTSRP805

description: RT_13_5d_153_Lung_CLPR-13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure


title: RT_13_5d_151_Lung_CLPR-13_RSTSRP805

description: RT_13_5d_151_Lung_CLPR-13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: dose or concentration


title: MS0189_GEP

source_name: Human multiple myeloma patient MS0189

tag: vh status

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: MS0357_GEP

source_name: Human multiple myeloma patient MS0357


title: MM0097_GEP

source_name: Human multiple myeloma patient MM0097

value: unmut


title: Donor3_SAHA

tag: cell type

value: primary CD4+ T cells

tag: batch


title: MN0167_GEP

source_name: Human multiple myeloma patient MN0167

value: mut


title: MP0137_GEP

source_name: Human multiple myeloma patient MP0137


title: MO0174_GEP

source_name: Human multiple myeloma patient MO0174


title: MG0449_GEP

source_name: Human multiple myeloma patient MG0449


title: NB0333_GEP

source_name: Human multiple myeloma patient NB0333


title: Donor2_SAHA


title: RT_13_5d_149_Lung_CLPR-13_RSTSRP805

description: RT_13_5d_149_Lung_CLPR-13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: days/week

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

tag: route of exposure


title: Donor1_SAHA

tag: cell type

tag: batch


title: MG0170_GEP

source_name: Human multiple myeloma patient MG0170

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: MF0048_GEP

source_name: Human multiple myeloma patient MF0048


title: Donor1_control


title: MF0379_GEP

source_name: Human multiple myeloma patient MF0379


title: PEO4_rep3

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

hyb_protocol: Lawrence Berkeley National Laboratory service

data_processing: RMA implementation provided in Affy package  (v1.28.0) of Bioconductor was used to obtain normalised (log2) intensity values for set of arrays.

growth_protocol: 3E6 cells were seeded in 10mls RPMI1640 (10% FCS, pen, strep, L-glutamine)

tag: cell line

value: ovarian cancer cells

tag: platinum sensitivity

value: resistant


title: RT_13_5d_152_Lung_CLPR-13_RSTSRP805

description: RT_13_5d_152_Lung_CLPR-13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

value: adult

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: Air

value: inhalation

tag: dose or concentration


title: RT_13_15d_161_Lung_CLPR13_RSTSRP805

description: RT_13_15d_161_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: days/week, Treatment Duration: 15, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: 6 hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 13, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: Lung

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

value: 15, Units of Duration:days

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure


title: RT_13_15d_160_Lung_CLPR13_RSTSRP805

description: RT_13_15d_160_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

value: Chloroprene


title: MC0105_GEP

source_name: Human multiple myeloma patient MC0105

tag: vh status

value: unmut

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: PEO4_rep2

scan_protocol: Lawrence Berkeley National Laboratory service

tag: cell line

tag: cell type

tag: platinum sensitivity


title: RT_13_15d_159_Lung_CLPR13_RSTSRP805

description: RT_13_15d_159_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

value: days/week

tag: treatment duration

tag: treatment time

tag: units of treatment time

value: 6 hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: PEO4_rep4

label_protocol: Lawrence Berkeley National Laboratory service

tag: cell line

tag: cell type

value: ovarian cancer cells

tag: platinum sensitivity

value: resistant


title: MG0110_GEP

description: legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

source_name: Human multiple myeloma patient MG0110

tag: vh status

value: mut

tag: disease state

tag: sample type

tag: patient


title: MB0065_GEP

source_name: Human multiple myeloma patient MB0065


title: MC0134_GEP

source_name: Human multiple myeloma patient MC0134


title: MC0055_GEP

source_name: Human multiple myeloma patient MC0055


title: PEO1_rep4

extract_protocol: Lawrence Berkeley National Laboratory service

value: sensitive


title: RT_13_15d_158_Lung_CLPR13_RSTSRP805

description: RT_13_15d_158_Lung_CLPR13_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: Air

value: inhalation


title: LL0130_GEP

source_name: Human multiple myeloma patient LL0130

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: LP0364_GEP

source_name: Human multiple myeloma patient LP0364


title: MA0088_GEP

source_name: Human multiple myeloma patient MA0088


title: PEO1_rep3

tag: cell line

tag: cell type

tag: platinum sensitivity


title: MA0151_GEP

source_name: Human multiple myeloma patient MA0151


title: LM0150_GEP

source_name: Human multiple myeloma patient LM0150


title: LV0118_GEP

source_name: Human multiple myeloma patient LV0118


title: PEO1_rep2


title: RT_0_5d_104_Lung_ACO1_RSTSRP805

description: RT_0_5d_104_Lung_ACO1_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

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

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: Lung

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Air Control

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 5, Units of Duration:days

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: PEO1_rep1

tag: cell line

tag: cell type

tag: platinum sensitivity


title: LG0337_GEP

source_name: Human multiple myeloma patient LG0337

tag: vh status

tag: disease state

value: B-cell chronic lymphocytic leukemia

tag: sample type

value: peripheral blood mononuclear cells

tag: patient


title: RT_0_5d_103_Lung_ACO1_RSTSRP805

description: RT_0_5d_103_Lung_ACO1_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: days/week

value: 6 hr/day


title: RT_0_5d_102_Lung_ACO1_RSTSRP805

description: RT_0_5d_102_Lung_ACO1_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: LI0133_GEP

source_name: Human multiple myeloma patient LI0133

tag: vh status

value: mut

tag: disease state

tag: sample type

tag: patient


title: IA0025_GEP

source_name: Human multiple myeloma patient IA0025


title: HG0135_GEP

source_name: Human multiple myeloma patient HG0135

value: unmut


title: LP0076_GEP

source_name: Human multiple myeloma patient LP0076


title: IL0066_GEP

source_name: Human multiple myeloma patient IL0066


title: LG0038_GEP

source_name: Human multiple myeloma patient LG0038


title: PEO4_rep1

tag: cell line

tag: cell type

value: ovarian cancer cells

tag: platinum sensitivity

value: resistant


title: GR0092_GEP

source_name: Human multiple myeloma patient GR0092


title: GP0171_GEP

source_name: Human multiple myeloma patient GP0171


title: LF0102_GEP

source_name: Human multiple myeloma patient LF0102


title: RT_0_5d_101_Lung_ACO1_RSTSRP805

description: RT_0_5d_101_Lung_ACO1_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

source_name: Lung tissue

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

value: Air


title: GR0169_GEP

source_name: Human multiple myeloma patient GR0169

tag: vh status

tag: disease state

tag: sample type

tag: patient


title: RT_0_5d_105_Lung_ACO1_RSTSRP805

description: RT_0_5d_105_Lung_ACO1_RSTSRP805_Mouse430_2_RSTSRP805_1: Female mice (B6C3F1/Crl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 0.3, 2, 13, or 90 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Mouse 430_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

value: Pentobarbital (5.2 mg/kg) and exsanguination

value: Weeks at start of exposure

value: Lung

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

value: inhalation

tag: dose or concentration


title: GN0095_GEP

source_name: Human multiple myeloma patient GN0095

tag: vh status

value: B-cell chronic lymphocytic leukemia


title: GR0033_GEP

source_name: Human multiple myeloma patient GR0033

tag: disease state

value: peripheral blood mononuclear cells


title: GM0041_GEP

source_name: Human multiple myeloma patient GM0041

tag: sample type