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Sample GSM2609732 Query DataSets for GSM2609732
Status Public on May 09, 2017
Title mRNA_348_NDf_4
Sample type RNA
 
Source name mRNA, patient 348, pre-adipocyte, replicate 4
Organism Homo sapiens
Characteristics patient id: 348
cell type: Pre-adipocyte
treatment: None
concentration: 0
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 white subcutaneous pre-adipocytes
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 13.24442151
5 9.57303568
9 14.48767084
10 8.664299126
11 6.06391933
12 10.21066673
13 6.164487965
17 6.828489135
18 7.139302639
19 9.264621786
20 11.68784039
22 7.686305976
24 5.467265893
26 9.122765096
28 10.24857825
32 10.55748697
36 6.532572384
37 9.661023405
40 8.343441445
41 9.087665411

Total number of rows: 28972

Table truncated, full table size 500 Kbytes.




Supplementary file Size Download File type/resource
GSM2609732_SG11464137_253949439061_S001_GE1_107_Sep09_1_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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