|
| Status |
Public on Apr 01, 2017 |
| Title |
IRJ43-MCF7_Y537N_WM_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
cell subtype - mutation: Y537N
condition: White Medium
treatment: none
|
| 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 |
ER_Mutants_Cufflinks_Gene_Counts.csv
|
| Data processing |
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
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
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 |
Feb 03, 2017 |
| 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) |
| GSE94493 |
ChIPseq and RNAseq of ER mutant breast cancer cell lines |
|
| Relations |
| BioSample |
SAMN06307745 |
| SRA |
SRX2539886 |
