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Sample GSM2738313 Query DataSets for GSM2738313
Status Public on Aug 01, 2020
Title MCF10A_gc10bza_R4
Sample type SRA
 
Source name mammary gland/breast epithelial cell
Organism Homo sapiens
Characteristics cell line: MCF10A
cell type: mammary gland/breast epithelial cell
neoplasia type: luminal ductal cells
atcc id: fibrocystic disease;ATCC CRL-10317
treatment: gc10bza
Treatment protocol Prior to treatment cells were plated in serum containing media for 24hrs to establish a monolayer. Media was removed and replaced with 2% charcoal-stripped serum for 48hrs prior to 24hr treatment with each pharmaceutical agent. Cells were harvested for ChIP-seq analysis 24 hrs post-treatment as previously described (Messier, et al. Oncotarget 2016).
Growth protocol MCF10A cells were grown in DMEM: F12 (Hyclone-SH30272 without phenol red), 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). MCF7 were grown in DMEM: F12 (Hyclone-SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals). ) Prior to treatment cells were plated in serum containing media for 24hrs to establish a monolayer. Media was removed and replaced with 2% charcoal-stripped serum for 48hrs prior to 24hr treatment with each pharmaceutical agent. Cells were harvested for ChIP-seq analysis 24 hrs post-treatment as previously described (Messier, et al. Oncotarget 2016).
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.
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
 
Description MCF10A_gc10bza_merged_norm_pos.bw
MCF10A_gc10bza_merged_norm_neg.bw
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 (< 10 counts) were removed from the analysis.
Strand specific read depth normalized bigwigs created by UCSC's genomeCoverageBed (specifying scale 10^6/readcount and strand) and bedGraphToBigWig
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the normalized counts from the HTSeq-count quantification. Bigwig tracks, strand specific and normalized for read depth (UCSC's genomeCoverageBed -bg -split -scale 10^6/$read_count -strand + or -).
 
Submission date Aug 09, 2017
Last update date Aug 01, 2020
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)
GSE102469 Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines (RNA-seq)
GSE102472 Epigenetic and Expression Profiling of Tissue Selective Estrogen Compounds in Breast Epithelial Cell Lines
Relations
BioSample SAMN07488178
SRA SRX3083308

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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