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| Status |
Public on Mar 01, 2017 |
| Title |
MCF7_Par_dup2_RNAseq |
| Sample type |
SRA |
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| Source name |
MCF7_Par_RNAseq
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
cell subtype: Parental
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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 |
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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
processed data file: MCF7_Parental_v_TAMresistant_raw_countmat.csv
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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 |
SAMN05736470 |
| SRA |
SRX2145572 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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