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Sample GSM2285711 Query DataSets for GSM2285711
Status Public on Apr 17, 2017
Title MCF10A_R3
Sample type SRA
Source name mammary gland/breast epithelial cell
Organism Homo sapiens
Characteristics tissue: breast
cell type: luminal ductal cells
neoplasia type: fibrocystic disease
atcc id: ATCC CRL-10317
cell line: MCF10A
Treatment protocol Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and stored at -80C in TRIzol.
Growth protocol MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10A cells without growth factors were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + Pen/Strep (Life Technologies) and Glutamine (Life Technologies).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFiā„¢ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701).
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description growth factor+
Data processing Remove adapter reads (Cutadapt v1.6). Trim low quality base calls from both ends, Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v22). Genes with very low expression (<3 counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R 3.2.0.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.
Submission date Aug 19, 2016
Last update date May 15, 2019
Contact name Jonathan AR Gordon
Organization name University of Vermont
Department Biochemistry
Street address 89 Beaumont Ave Given E209
City Burlington
State/province VT
ZIP/Postal code 05405
Country USA
Platform ID GPL18460
Series (1)
GSE85857 Runx1 stabilizes the mammary epithelial cell phenotype and prevents epithelial to mesenchymal transition
BioSample SAMN05596816
SRA SRX2035765

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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