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Sample GSM272841 Query DataSets for GSM272841
Status Public on Mar 13, 2008
Title HEEC_BPA-exposed_replicate 1
Sample type RNA
 
Channel 1
Source name Primary culture HEEC, obtained in proliferative phase, individual 1, BPA exposed 24 h
Organism Homo sapiens
Characteristics Female of fertile age
Tissue: endometrium
Cells: endothelial cells
Menstrual cycle phase: proliferative
Biomaterial provider Uppsala University Hospital
Treatment protocol At subconfluency in passage 2, HEEC in four culture flasks per culture (biological replicate) were exposed to 50 µM BPA for 24h. Control HEEC in four culture flasks per culture were exposed to fresh culture medium containing 0.21% DMSO.
Growth protocol HEEC were kept in 25 cm2 culture flasks (Fischer Scientific GTF, Västra Frölunda, Sweden) and grown in Microvascular Endothelial Cell Medium-2 (EGM™-2MV Bulletkit®; In vitro Sweden AB, Stockholm, Sweden) at 37ºC in an atmosphere of 5% CO2 in humidified air. Four culture flask per treatment alternative and culture (biological replicate) were used.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Mini Kit spin protocol (Qiagen AB, Solna, Sweden) and QiaShredder homogenizers (Qiagen AB, Solna, Sweden) according to manufacturer's instructions.
Label Cy5
Label protocol For each treatment and biological replicate, 500 ng isolated RNA was amplified and labelled using the Low RNA Input Linear Amplification Kit PLUS, Two-colour (Agilent Technologies Sweden AB, Kista, Sweden) and then purified using the RNeasy MinElute Cleanup Kit (Qiagen AB, Solna, Sweden). The amplification and labelling reactions were performed using the polymerase chain reaction (PCR) instrument model PTC-100 (MJ Research Inc, Waltham, MA, USA). Dye swaps were performed between the individuals to avoid dye bias between RNA from BPA treated and untreated HEEC. After the labelling reaction, the Nanodrop ND-1000 Spectrophotometer was used to measure the incorporation of Cy dye.
 
Channel 2
Source name Primary culture HEEC, obtained in proliferative phase, individual 1, control exposed 24 h
Organism Homo sapiens
Characteristics Female of fertile age
Tissue: endometrium
Cells: endothelial cells
Menstrual cycle phase: proliferative
Biomaterial provider Uppsala University Hospital
Treatment protocol At subconfluency in passage 2, HEEC in four culture flasks per culture (biological replicate) were exposed to 50 µM BPA for 24h. Control HEEC in four culture flasks per culture were exposed to fresh culture medium containing 0.21% DMSO.
Growth protocol HEEC were kept in 25 cm2 culture flasks (Fischer Scientific GTF, Västra Frölunda, Sweden) and grown in Microvascular Endothelial Cell Medium-2 (EGM™-2MV Bulletkit®; In vitro Sweden AB, Stockholm, Sweden) at 37ºC in an atmosphere of 5% CO2 in humidified air. Four culture flask per treatment alternative and culture (biological replicate) were used.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Mini Kit spin protocol (Qiagen AB, Solna, Sweden) and QiaShredder homogenizers (Qiagen AB, Solna, Sweden) according to manufacturer's instructions.
Label Cy3
Label protocol For each treatment and biological replicate, 500 ng isolated RNA was amplified and labelled using the Low RNA Input Linear Amplification Kit PLUS, Two-colour (Agilent Technologies Sweden AB, Kista, Sweden) and then purified using the RNeasy MinElute Cleanup Kit (Qiagen AB, Solna, Sweden). The amplification and labelling reactions were performed using the polymerase chain reaction (PCR) instrument model PTC-100 (MJ Research Inc, Waltham, MA, USA). Dye swaps were performed between the individuals to avoid dye bias between RNA from BPA treated and untreated HEEC. After the labelling reaction, the Nanodrop ND-1000 Spectrophotometer was used to measure the incorporation of Cy dye.
 
 
Hybridization protocol Pre-hybridization buffer (5 x sodium chloride sodium citrate [SSC, VWR International AB, Stockholm, Sweden], 5 x Denhardt’s solution [Sigma-Aldrich Sweden AB, Stockholm, Sweden], 0.02 µg/µl tRNA [Invitrogen AB, Lidingö, Sweden], 0.5% sodiumdodecylsulfate [SDS, VWR International AB, Stockholm, Sweden] and 50% formamide [Sigma-Aldrich Sweden AB, Stockholm, Sweden]) was applied to each array under a hybrislip (22 x 60 mm, Sigma-Aldrich Sweden AB, Stockholm, Sweden). Incubation was performed in an Hybridization Cassette ArrayIt™ (TeleChem International Inc ArrayIt, Sunnyvale, CA, USA) at 42°C for 45 min at 100% humidity in a Heating Circulator model 8201 (PolyScience, Niles, Il, USA). Each array was then transferred to a 50 ml centrifugation tube containing double distilled water. The arrays were washed five times by repeatedly turning the tubes upside down for 30 seconds each time. Hybridization and post-hybridization washes of the slides were performed using the Pronto! Hybridization Kit (Corning Life Sciences, Noricon AB, Helsingborg, Sweden). The Hybridization Cassette ArrayIt™ and Erie Scientific Lifterslip (25 x 60 mm, Histolab, Västra Frölunda, Sweden) were used for hybridization of the slides at 42°C for 18-20 hours. After hybridization, the slides were washed in the three wash buffers described in the Pronto! Hybridization Kit.
Scan protocol The slides were scanned in a ScanArray Express HT microarray scanner ([Packard BioScience] Perkin Elmer Life Sciences Inc, Boston, MA, USA). The scanning was performed at two different voltage values for the photo multiplier tube to get a wide dynamic range of signals (high or low). The laser value default was 99%. The tiff files from the scanned arrays were gridded using the software Spotreader v 1.3.1 (Niles Scientific, Portola Valley, CA, USA).
Description Biological replicate 1 of 5. BPA exposed HEEC vs control HEEC, harvested after passage 2.
Data processing The BioArray Software Environment BASE (Saal et al., 2002) and the Linnaeus Center of Bioinformatics Data Warehouse (LCB-DWH) (Ameur et al., 2006) were used for microarray data storage and analysis. Data was normalized within arrays using the print-tip lowess method (Yang et al., 2002).
 
Submission date Mar 12, 2008
Last update date Mar 12, 2008
Contact name Carolina Bredhult
Organization name Uppsala University
Department Women's and Children's Health
Street address Uppsala University Hospital
City Uppsala
ZIP/Postal code 75185
Country Sweden
 
Platform ID GPL5886
Series (1)
GSE10802 Gene Expression Analysis of Human Endometrial Endothelial Cells Exposed to Bisphenol A

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Treated/untreated control)

Data table
ID_REF VALUE
1 -0.03075476
2 -0.07237024
3 0.01092299
4 -0.08893051
5 0.10109849
6 -0.10213931
7 0.01087662
8 -0.35534631
9 0.05995973
10 -0.05214500
11 -0.02352378
12 -0.14734172
13 0.33217989
14 -0.25422664
15 -0.13573807
16 -0.02564367
17 -0.15132190
18 -0.01486144
19 -0.00842597
20 -0.19550934

Total number of rows: 30000

Table truncated, full table size 501 Kbytes.




Supplementary file Size Download File type/resource
GSM272841.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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