|
| Status |
Public on Sep 02, 2015 |
| Title |
MCF7_RNA-Seq_R2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 mammary gland/breast epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
atcc id: ATCC HTB-22
tissue derivation: breast
cell type: metastatic site derived
neoplasia type: adenocarcinoma
|
| Treatment protocol |
Cells were seeded at 1.5x10^6 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate-buffered saline (PBS) and stored in TRIzol 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 were grown in DMEM (Corning Mediatech 10-017). 10% Fetal Bovin Serum (Atlanta-S11550 lot#H1030) Pen/Strep (Life Technologies) and Glutamine (Life Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplification was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701). Illumina Barcodes used: MCF10A_sample1_AR002; MCF10A_sample2_AR004; MCF10A_sample3_AR001; MCF7_Sample1_AR002; MCF7_Sample2_AR004; MCF7_Sample2_AR005
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
MCF7 SAMPLE 2
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt
|
| Data processing |
Remove adapter reads (Cutadapt v1.6).
Trim low-quality base calls from both ends. Min score >= 15, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to a transcriptome and quantified using RSEM v1.2.7, genes with very low expression (<10 expected counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.4.5 package in R 3.1.0 using the mean value of gene-wise dispersion estimates.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: MCF7_MCF10A_RSEM_expectedcounts.txt: Tab-delimited table showing the expected counts from the RSEM quantification.
Supplementary_files_format_and_content: DeSeq2_MCF7_vs_MCF10A_foldchange.txt: Tab-delimited table showing the log2FC for all genes from DeSeq2 v1.4.5 analysis.
|
| |
|
| Submission date |
Aug 07, 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 (1) |
| GSE71862 |
Differential Gene Expression between MCF10A and MCF7 cells |
|
| Relations |
| SRA |
SRX1137251 |
| BioSample |
SAMN03979833 |
