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Sample GSM1944515 Query DataSets for GSM1944515
Status Public on Feb 10, 2016
Title RNA-Seq_MCF10A_R1
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
cell line: MCF10A
Biomaterial provider ATCC CRL-10317
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 pellets stored 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 and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271) + 10% (v/v) FBS (Atlanta Biologicals) Pen/Strep (Life Technologies) Glutamine (Life Technologies) .
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy Plus Mini kit (Qiagen #74134).
RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina #RS-122-2301). 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
 
Data processing Remove adapter reads (Cutadapt v1.6)
Trim 10bp from 5'end. (FASTQ Trimmer 1.0.0)
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 (v21). Genes with very low expression (<3 counts) were removed from the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.
 
Submission date Nov 18, 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 (2)
GSE75168 Histone H3 lysine 4 acetylation-methylation dynamics define breast cancer subtypes [RNA-seq]
GSE75169 Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes
Relations
BioSample SAMN04277120
SRA SRX1438068

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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