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Sample GSM2305320 Query DataSets for GSM2305320
Status Public on Mar 01, 2017
Title PE1B_ER_ChIPseq
Sample type SRA
 
Source name patient derived Pleaural Effusion
Organism Homo sapiens
Characteristics cell type: Patient
cell subtype: Pleural Effusion
condition: N/A
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
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq: ChIP-seq reads were aligned using bowtie
ChIP-seq: Peaks were called using MACS2 with default parameters, including a q value < 0.001
ChIP-seq: bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
ChIP-seq: A binding intensity matrix was generated using bamliquidator
ChIP-seq: Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
RNA-seq: RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
RNA-seq: Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
RNA-seq: Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
RNA-seq: Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
RNA-seq: All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
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 Sep 07, 2016
Last update date May 15, 2019
Contact name MacIntosh Grant Cornwell
E-mail(s) mcornwell1957@gmail.com
Organization name New York University
Department School of Medicine
Lab Ruggles Lab
Street address 227 E 30th St.
City New York City
State/province NY
ZIP/Postal code 10016
Country USA
 
Platform ID GPL18573
Series (1)
GSE86538 ChIP-seq of ER and RUNX2 in MCF7 breast cancer cell lines
Relations
BioSample SAMN05736476
SRA SRX2145570

Supplementary file Size Download File type/resource
GSM2305320_PE1B_peaks.bed.gz 296.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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