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Sample GSM1700388 Query DataSets for GSM1700388
Status Public on Feb 10, 2016
Title MCF7_input_R1
Sample type SRA
 
Source name MCF7_input
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: mammary gland/breast epithelial cell
neoplasia type: metastatic site derived
atcc id: adenocarcinoma; ATCC HTB-22
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 crosslinked with 0.8% formaldehyde (Thermo Scientific Cat no. 28908) in PBS for 10 minutes at room temperature with continuous shaking
Growth protocol MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271 or 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). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271 or SH30272 without phenol red) + 10% (v/v) FBS (Atlanta Biologicals).
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated using a modification of the Dignam method (Dignam et al Nucleic Acids Res. 1983) and pellets were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin ranging from 200-800 bp with an average peak size of 500 bp. For immunoprecipitation, 30 μg of sheared chromatin was incubated with 10 ug of anti H3K4me3 (Abcam, ab1012 lot#GR80367-1) or H3K4ac (Active Motif -39382 lot#29108001) overnight at 4°C and then incubated with 50 μl Protein-G Dynabeads (Life Technologies 10004D lot#123085320) for 4 h at 4°C.
Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range.
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 ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description MCF7 SAMPLE 5
genomic DNA control
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)
Concatenate replicates.
Align reads with STAR v2.4, splicing disabled with '--alignIntronMax 1'.
Call peaks and generate .bdg with MACS2, p-value e-5. (MACS2 v2.1.0.20140616)
Compare treatment bedgraph to input with MACS2 bdgcmp in logFE mode.
Convert logFE.bdg to bigwig with UCSC's bedGraphToBigWig v4
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of log fold enrichment over input from bdgcmp function of MACS2
 
Submission date May 29, 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)
GSE69377 Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes [ChIP-seq]
GSE75169 Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes
Relations
BioSample SAMN03743997
SRA SRX1043552

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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