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Sample GSM2476815 Query DataSets for GSM2476815
Status Public on Apr 01, 2017
Title Y537N-E2-NN7-MP2497
Sample type SRA
 
Source name MCF7
Organism Homo sapiens
Characteristics cell type: MCF7
cell subtype - mutation: Y537N
condition: White Medium
treatment: E2
Growth protocol MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Cell lines before ChIP were then either introduced to White Medium DMEM with or without supplemental E2 or Doxycycline, Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit. All of the ChIP-seq performed was done using a combination of Estrogen Receptor ab-10/Thermo Scientific/# MS315PABX and Estrogen Receptor HC-20/Santa Cruz Biotechnolofy/sc-543.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq reads were aligned using bowtie
Peaks were called using MACS2 with default parameters, including a q value < 0.001
bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
A binding intensity matrix was generated using bamliquidator
Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ER ChIP
Supplementary_files_format_and_content: Count Matrix Files for two separate experiments, one for MCF7 Parental and Tamoxifen Resistant lines, and anotherr for RUNX2 with and without DOX
 
Submission date Feb 03, 2017
Last update date May 15, 2019
Contact name MacIntosh Grant Cornwell
E-mail(s) mcornwell1957@gmail.com
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Brown Lab
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL18573
Series (1)
GSE94493 ChIPseq and RNAseq of ER mutant breast cancer cell lines
Relations
BioSample SAMN06307702
SRA SRX2539920

Supplementary file Size Download File type/resource
GSM2476815_PN2-Y537N-DOX-N7-RJ2274-peaks.bed.gz 481.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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