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Sample GSM2498468 Query DataSets for GSM2498468
Status Public on Oct 16, 2017
Title 7hr Control (Water), 2
Sample type RNA
 
Channel 1
Source name TK6 lymphoblastoid cell line
Organism Homo sapiens
Characteristics agent: 1,2,4-benzenetriol
time: 7hr
concentration: 0
Treatment protocol TK6 cells were exposed to 3 concentrations of the test chemical as follows: 15, 20 and 30 µg/ml, in addition to vehicle and positive controls (water (+S9), and BaP(+S9), respectively). Cells were co-exposed to each chemical (+S9) for four hours, then the media was replaced and cells were collected 3 to 4 hours later. All exposures were done in the presence of 2% aroclor-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The cells were then re-suspended in 3 ml of media and re-incubated for an additional 3 to 4 hours before being harvested for RNA extraction. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.
Growth protocol TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that compound requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 2% Aroclor 1254-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.
Extracted molecule total RNA
Extraction protocol Following chemical exposures, total RNA was isolated from treated and control TK6 cells between 7 and 8 hours post-exposure. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.0 to 10 and A260/280 absorbance ratios ≥2.0 were used for gene expression analysis.
Label Cy5,Cy3
Label protocol Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on the 7-8 hour time points from the definitive studies (n=3 per concentration and time point), along with the corresponding vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).
 
Channel 2
Source name TK6 lymphoblastoid cell line
Organism Homo sapiens
Characteristics time: 7hr
reference: DMSO (Pool)
Treatment protocol TK6 cells were exposed to 3 concentrations of the test chemical as follows: 15, 20 and 30 µg/ml, in addition to vehicle and positive controls (water (+S9), and BaP(+S9), respectively). Cells were co-exposed to each chemical (+S9) for four hours, then the media was replaced and cells were collected 3 to 4 hours later. All exposures were done in the presence of 2% aroclor-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The cells were then re-suspended in 3 ml of media and re-incubated for an additional 3 to 4 hours before being harvested for RNA extraction. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.
Growth protocol TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that compound requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 2% Aroclor 1254-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.
Extracted molecule total RNA
Extraction protocol Following chemical exposures, total RNA was isolated from treated and control TK6 cells between 7 and 8 hours post-exposure. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.0 to 10 and A260/280 absorbance ratios ≥2.0 were used for gene expression analysis.
Label Cy3,Cy5
Label protocol Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on the 7-8 hour time points from the definitive studies (n=3 per concentration and time point), along with the corresponding vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).
 
 
Hybridization protocol Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A or B, Agilent Microarray Design ID: 028004 or 039494; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.
Scan protocol Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.
Description Co-hybridized with negative vehicle control pool (DMSO +S9)
Data processing The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R. After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.
 
Submission date Feb 22, 2017
Last update date Oct 17, 2017
Contact name Julie Buick
E-mail(s) julie.buick@canada.ca
Phone 613-960-1599
Organization name Health Canada
Department Mechanistic Studies Division
Lab Genomics Lab
Street address 50 Colombine Driveway
City Ottawa
State/province Ontario
ZIP/Postal code K1A 0K9
Country Canada
 
Platform ID GPL17077
Series (2)
GSE95188 Application of the TGx-28.65 genomic biomarker to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human cells [BT]
GSE95192 Application of the TGx-28.65 genomic biomarker to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human cells

Data table header descriptions
ID_REF
VALUE Sample represents the lowess normalized, dye swapped log2 ratio's of the treatment relative to the vehicle control.

Data table
ID_REF VALUE
A_19_P00315452 0.172506729
A_19_P00315459 -0.181045664
A_19_P00315482 0.022881273
A_19_P00315492 0.031894969
A_19_P00315493 0.109867471
A_19_P00315502 0.043518904
A_19_P00315506 -0.010010231
A_19_P00315518 -0.143261305
A_19_P00315519 -0.144606525
A_19_P00315524 0.163902825
A_19_P00315528 0.117560353
A_19_P00315529 0.103603289
A_19_P00315538 0.051349371
A_19_P00315541 0.058159417
A_19_P00315543 0.048874623
A_19_P00315550 -0.146264322
A_19_P00315551 0.091767849
A_19_P00315554 0.034487958
A_19_P00315581 -0.033188459
A_19_P00315583 0.045664724

Total number of rows: 50599

Table truncated, full table size 1280 Kbytes.




Supplementary file Size Download File type/resource
GSM2498468_253949421551_201505050945_S01_GE2_1100_Jul11_1_1.txt.gz 5.7 Mb (ftp)(http) TXT
GSM2498468_253949421551_201505050945_S01_GE2_1100_Jul11_2_1.txt.gz 5.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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