NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM985631 Query DataSets for GSM985631
Status Public on Feb 20, 2013
Title HepG2-2NF control-72h rep1
Sample type RNA
 
Source name HepG2 cell line
Organism Homo sapiens
Characteristics replicate: 1
cell line: HepG2
treatment: 2NF control
Treatment protocol The exposure to the selected chemicals was done for a period of 72h at IC10 concentrations.
Growth protocol Hepatocytes were isolated by using a two-step collagenase perfusion technique . The viability was assessed by trypan blue exclusion and the cells (≥85% viability) were cultured as a monolayer at a density of 0.57x105 cells/cm2 in William’s E medium supplemented with 10%v/v fetal bovine serum, 292mg/ml L-glutamine, 7ng/ml glucagon and antibiotics (7.33IU/ml benzylpenicillin sodium, 50µg/ml kanamycin monosulphate, 50µg/ml streptomycin sulphate, and 10µg/ml ampicillin sodium) in an incubator at 37°C (5% CO2 and 95% air, 100% humidity). After 4 hours, the medium was renewed with serum-free culture medium, supplemented with 25µg/ml hydrocortisone hemisuccinate and 1mg/ml bovine insulin. The hES-Hep cells were derived, cultured and characterized from the human embryonic stem cell (hESC) line SA002 (Cellartis AB, Sweden), as previously described, with an additional step of enzymatic passaging for further expansion before the onset of hepatic differentiation (Heins et al. 2006). The differentiation of SA002 cells into hepatocyte-like cells was achieved by the sequential exposure to growth factors, such as human growth factor and differentiation-promoting factors, including hydrocortisone and insulin (Brolen et al. 2010). The hepatocellular carcinoma-derived HepG2 cell line (Rockville, USA) was cultured and handled as previously described (Tolosa et al. 2011). Human hepatoma HepaRG cells (Biopredic International, France) were cultivated as previously described (Gripon et al. 2002; Guillouzo et al. 2007). At day 13 of cultivation, low DMSO-containing medium was added for a period of 7 days.
Extracted molecule total RNA
Extraction protocol Samples for RNA isolation were collected after 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.
Label biotin
Label protocol We used standard Affymetrix labeling protocols
 
Hybridization protocol We used standard Affymetrix hybridisation rotocols
Scan protocol We used standard Affymetrix scanning parameters
Description Control (2NF1)
Data processing The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip). All samples were further normalized by GC-RMA algorithm. In the hES-Heps 2NF, BaP, MAN, MPH, NIF, PIPB, SDF and SPB shared one control whereas AFB, CND, TPA, TOL, WYE and CYCLO shared another control. In the HepaRG system several compounds shared also one control. The groups were divided as follows: 1) 2NF, BaP, MPH, NIF, PIPB and SPB; 2) WYE, AFB, CND, CYCLO, TPA and TOL; 3) MAN and SDF; 4) NNK. In the HepG2 system there were shared control among several compounds also. 2NF, BaP, NIF, PIPB and SPB shared one control, AFB, CND, CYCLO, TPA, TOL and WYE shared another control. The third group was MAN, MPH and SDF which had their own control whereas NNK had its own control. In the HepsC and the HepsT systems there were also several groups of compounds having the same control.The compounds were separated as follows: 1)2NF, NIF and PIPB sharing one control; 2)NNK, MAN, SDF and SPB sharing one control; 3)AFB, CND, CYCLO, TPA, TOL and WYE sharing one control; 4) BaP and MPH sharing one control.
 
Submission date Aug 14, 2012
Last update date Feb 20, 2013
Contact name Tatyana Doktorova
Organization name VUB
Department FAFY
Street address Laarbeeklaan 103, building G
City Brussels
State/province Belgium
ZIP/Postal code 1090
Country Belgium
 
Platform ID GPL13916
Series (1)
GSE40117 Analyses of transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models
Relations
Reanalyzed by GSM985652
Reanalyzed by GSM985688
Reanalyzed by GSM985695
Reanalyzed by GSM985707

Data table header descriptions
ID_REF
VALUE GC-RMA signal

Data table
ID_REF VALUE
ENSG00000000003_at 1277.572
ENSG00000000005_at 3.548
ENSG00000000419_at 3111.779
ENSG00000000457_at 21.993
ENSG00000000460_at 34.76
ENSG00000000938_at 4.322
ENSG00000000971_at 2.778
ENSG00000001036_at 878.512
ENSG00000001084_at 242.957
ENSG00000001167_at 17.119
ENSG00000001460_at 4.786
ENSG00000001461_at 6.362
ENSG00000001497_at 27.569
ENSG00000001561_at 39.507
ENSG00000001617_at 15.991
ENSG00000001626_at 2.925
ENSG00000001629_at 298.589
ENSG00000001631_at 11.019
ENSG00000002016_at 5.976
ENSG00000002330_at 5.758

Total number of rows: 18919

Table truncated, full table size 473 Kbytes.




Supplementary file Size Download File type/resource
GSM985631_HUL-H-DMO-72-R-1-2.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap