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| Status |
Public on Mar 01, 2017 |
| Title |
MCF7_E2_ER_ChIPseq |
| Sample type |
SRA |
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| Source name |
MCF7_E2_ER_ChIPseq
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
cell subtype: Wild Type
condition: White Medium + E2
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| Growth protocol |
MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
MacIntosh Grant Cornwell |
| E-mail(s) |
mcornwell1957@gmail.com
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| Organization name |
New York University
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| Department |
School of Medicine
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| Lab |
Ruggles Lab
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| Street address |
227 E 30th St.
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| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE86538 |
ChIP-seq of ER and RUNX2 in MCF7 breast cancer cell lines |
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| Relations |
| BioSample |
SAMN05736474 |
| SRA |
SRX2145563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2305313_MCF7_E2_peaks.bed.gz |
462.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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