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Sample GSM1126125 Query DataSets for GSM1126125
Status Public on Jul 14, 2014
Title Epithelial CCH cells co-cultured with miR-132 overexpressing fibroblasts
Sample type RNA
 
Source name CCH cells cocultured with miR-132 overexpressing fibroblasts
Organism Homo sapiens
Characteristics cell type: Human mammary epithelial columnar cell hyperplasia cells
treatment: cocultured with fibroblasts transfected with miR-132 mimic
Treatment protocol Fibroblasts were transfected with 25nM miRNA mimic (Dharmacon) using Lipofectamine (Invitrogen) in Opti-MEM medium depleted from serum and penicillin-streptomycin. The medium was changed to serum-containing medium 6h after transfection. After 24 hours, cells were either harvested for total RNA extraction (miRNeasy from Qiagen) or put in coculture.
Growth protocol Fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Human mammary epithelial CCH cells were cultured in DMEM-F12 supplemented with 5% horse serum, cholera toxin (100 ng/ml), hydrocortisone (0.5 μg/ml), insulin (10 μg/ml), EGF (20 ng/ml) and 1% penicillin-streptomycin. All cells were maintained at 37C in a humified incubator (5% CO2).
Extracted molecule total RNA
Extraction protocol Transfection with miRNA mimics and total RNA extraction was perormed according to manufactures instructions.
Label biotin
Label protocol Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark). Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, Version 4, Affymetrix).
 
Hybridization protocol Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark). Following fragmentation, cDNA was hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays, followed by washing and staining using buffers from the GeneChip® Hybridization, Wash and Stain Kit.
Scan protocol Standard Affymetrix protocol performed by AROS Applied Biotechnology A/S (Aarhus, Denmark).
Description Gene expression from mammary epithelial columnar cell hyperplasia cells cocultured with fibroblasts transfected with miR-132 mimic
Data processing The data were analyzed with R, Bioconductor and Ingenuity Systems (Redwood City, CA). The RMA was used to normalise and summarise the expression values at the probeset level.
 
Submission date Apr 18, 2013
Last update date Jul 14, 2014
Contact name Sofie Björner
Organization name Lund University
Street address Jan Waldenströms gata 59
City Malmö
ZIP/Postal code 20502
Country Sweden
 
Platform ID GPL10739
Series (2)
GSE46197 Expression data from miR-132 overexpressing immortalized human mammary fibroblasts and from mammary epithelial columnar cell hyperplasia cells co-cultured with miR-132 overexpressing fibroblasts
GSE46199 Columnar cell hyperplasia

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
7892501 5.99122
7892502 5.52493
7892503 4.49879
7892504 10.39696
7892505 4.44896
7892506 5.81653
7892507 5.73594
7892508 6.69831
7892509 11.5803
7892510 5.14505
7892511 4.69133
7892512 7.3091
7892513 3.69319
7892514 11.394
7892515 10.15118
7892516 4.65739
7892517 6.38559
7892518 3.03095
7892519 6.14387
7892520 9.70613

Total number of rows: 257430

Table truncated, full table size 4021 Kbytes.




Supplementary file Size Download File type/resource
GSM1126125_epi_test.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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