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Sample GSM1847015 Query DataSets for GSM1847015
Status Public on Sep 02, 2015
Title MCF10A_RNA-Seq_R1
Sample type SRA
 
Source name MCF10A mammary gland/breast epithelial cells
Organism Homo sapiens
Characteristics cell line: MCF10A
atcc id: ATCC CRL-10317
tissue derivation: breast
cell type: luminal ductal cells
neoplasia type: fibrocystic disease
Treatment protocol Cells were seeded at 1.5x10^6 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate-buffered saline (PBS) and stored in TRIzol at -80C.
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). MCF-7 cells were grown in DMEM (Corning Mediatech 10-017). 10% Fetal Bovin Serum (Atlanta-S11550 lot#H1030) 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 amplification was performed using KAPA HiFiā„¢ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701). Illumina Barcodes used: MCF10A_sample1_AR002; MCF10A_sample2_AR004; MCF10A_sample3_AR001; MCF7_Sample1_AR002; MCF7_Sample2_AR004; MCF7_Sample2_AR005
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description MCF10A SAMPLE 1
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt
Data processing Remove adapter reads (Cutadapt v1.6).
Trim low-quality base calls from both ends. Min score >= 15, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to a transcriptome and quantified using RSEM v1.2.7, genes with very low expression (<10 expected counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.4.5 package in R 3.1.0 using the mean value of gene-wise dispersion estimates.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: MCF7_MCF10A_RSEM_expectedcounts.txt: Tab-delimited table showing the expected counts from the RSEM quantification.
Supplementary_files_format_and_content: DeSeq2_MCF7_vs_MCF10A_foldchange.txt: Tab-delimited table showing the log2FC for all genes from DeSeq2 v1.4.5 analysis.
 
Submission date Aug 07, 2015
Last update date May 15, 2019
Contact name Jonathan AR Gordon
E-mail(s) Jonathan.A.Gordon@uvm.edu
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)
GSE71862 Differential Gene Expression between MCF10A and MCF7 cells
Relations
SRA SRX1137247
BioSample SAMN03979829

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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