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Sample GSM2305325 Query DataSets for GSM2305325
Status Public on Mar 01, 2017
Title MCF7_RUNX2_DOX_dup1_RNAseq
Sample type SRA
Source name MCF7_RUNX2_DOX_RNAseq
Organism Homo sapiens
Characteristics cell type: MCF7
cell subtype: RUNX2 DOX inducible model
condition: Full Medium + Doxycycline
Growth protocol MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.
Extracted molecule total RNA
Extraction protocol Cell lines were extracted using the Rneasy (Qiagen # 74104) kit with the substitution of Trizol instead of Buffer RLT. Preparation for sequaencing is done using the Illumina Truseq RNAseq v2 kit (15025063)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description processed data file: MCF7_RUNX2_NoDOX_v_DOX_raw_countmat.csv
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:
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
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
BioSample SAMN05736462
SRA SRX2145575

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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