NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2609764 Query DataSets for GSM2609764
Status Public on May 09, 2017
Title mRNA_986_A10nM_2
Sample type RNA
 
Source name mRNA, patient 986, bisphenol A 10nM, replicate 2
Organism Homo sapiens
Characteristics patient id: 986
cell type: Adipocyte
treatment: BPA
concentration: 10nM
Treatment protocol They were induced to differentiate into adipocytes with either vehicle (DMSO) or the selected chemical (BPA, BPF, BPS) at 10nM or 10µM.
Growth protocol Primary human white subcutaneous pre-adipocytes were cultured in PBM-2 medium. Confluent pre-adipocytes were induced to differentiate with PBM-2 medium supplemented with insulin, dexamethasone, IBMX and indomethacin (all supplied by Lonza) for ten days according to the instructions of the manufacturer.
Extracted molecule total RNA
Extraction protocol Specific kits (Kit Small & Large RNA; Macherey Nagel) were used to extract all species of RNAs. The RNA concentration was determined by absorbance at 260 nm (A260), and the purity was estimated by determining the A260/A230 ratio with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). RNA Integrity Number (RIN) was assessed with a Bioanalyzer (Agilent). This kit allowed the extraction of small and large RNAs with no degradation (RIN>9).
Label Cy3
Label protocol 100 ng of total RNA per sample were dephosphorylated by incubation with a calf intestinal phosphatase at 37 °C for 30 min and denatured with 100% DMSO at 100 °C for 7 min. They were then labeled with Cyanine 3-pCp at 16°C for 2 hours, with a T4 ligase. Micro Bio-Spin 6 chromatography columns (Bio-Rad Laboratories, Hercules, CA) were used to purify the labeled RNA. The efficiency of the labeling procedure was verified with the Agilent miRNA Spike-in Kit.
 
Hybridization protocol For mRNA samples, a total of 600 ng of cRNA was fragmented and hybridized overnight at 65 °C. The purified labeled miRNAs were prepared with 10 × Blocking Agent and 2 × Hi-RPM hybridization buffer and incubated with the array in hybridization chambers (Agilent) for 20 hours at 55 °C. The slides were then washed as described in the protocol. The efficiency of the hybridization procedure was verified with the Agilent miRNA Spike-in Kit.
Scan protocol Microarrays were run on a SureScan microarray scanner (Agilent Technologies). Raw data were acquired with Feature Extraction Software (ver. 10.7.3.1). Calculation of the total gene signal for each miRNA replicated probe subtracted background signals.
Description mRNA profiling of human primary adipocytes atfer 10 days of diffenciation with 10nM of bisphenol A
Data processing After a preliminary between-array normalization, unexpressed probes were filtered out according to detection pvalues. Expression values were normalized with housekeeping genes for mRNA and estimated using a linear model to take into account the probe affinity over the 30 probes characterizing each one of the miRNA. All analyses were performed using R (packages Limma and AgiMicroRna).
 
Submission date May 08, 2017
Last update date Jan 23, 2018
Contact name Odile Poulain-Godefroy
Organization name Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille
Department Center for Infection and Immunity of Lille (CIIL)
Lab UMR8204
Street address 1, rue du Pr Calmette
City Lille
ZIP/Postal code 59000
Country France
 
Platform ID GPL16699
Series (2)
GSE98680 mRNA/miRNA expression profiles of human primary adipocytes exposed to low doses of bisphenols A, F and S [mRNA]
GSE98682 mRNA/miRNA expression profiles of human primary adipocytes exposed to low doses of bisphenols A, F and S

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 13.60565635
5 9.47840449
9 11.53049101
10 9.133490104
11 6.394164931
12 10.62205904
13 6.64275371
17 6.362735309
18 6.491630441
19 8.659277437
20 12.53502641
22 7.459488542
24 5.584440598
26 9.055781402
28 9.980675132
32 9.754301799
36 7.263334414
37 9.803862037
40 7.880857333
41 7.786678034

Total number of rows: 28972

Table truncated, full table size 501 Kbytes.




Supplementary file Size Download File type/resource
GSM2609764_SG11464137_253949439064_S001_GE1_107_Sep09_1_4.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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