|
| Status |
Public on Feb 10, 2016 |
| Title |
RNA-Seq_MDA-MB-231_R3 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland/breast epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell type: metastatic site derived
neoplasia type: adenocarcinoma
cell line: MDA-MB-231
|
| Biomaterial provider |
ATCC HTB-26
|
| Treatment protocol |
Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and pellets stored at -80C.
|
| Growth protocol |
MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells and MDA-MB-231 were grown in DMEM: F12 (Hyclone-SH30271) + 10% (v/v) FBS (Atlanta Biologicals) Pen/Strep (Life Technologies) Glutamine (Life Technologies) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plus Mini kit (Qiagen #74134).
RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina #RS-122-2301). Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Remove adapter reads (Cutadapt v1.6)
Trim 10bp from 5'end. (FASTQ Trimmer 1.0.0)
Trim low quality base calls from both ends. Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0)
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v21). Genes with very low expression (<3 counts) were removed from the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.
|
| |
|
| Submission date |
Nov 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan AR Gordon |
| E-mail(s) |
Jonathan.A.Gordon@uvm.edu
|
| Organization name |
University of Vermont
|
| Department |
Biochemistry
|
| Street address |
89 Beaumont Ave Given E209
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (2) |
| GSE75168 |
Histone H3 lysine 4 acetylation-methylation dynamics define breast cancer subtypes [RNA-seq] |
| GSE75169 |
Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes |
|
| Relations |
| BioSample |
SAMN04277128 |
| SRA |
SRX1438076 |
