|Public on Oct 01, 2018
|Homo sapiens; Mus musculus
|cell line: human breast cancer cell line MCF-7
cell type: mouse MSC cells
growth protocol: MCF-7 cells cocultured with MSCs in 3D culture
reporter gene: Firefly Luciferase (MCF-7)
|2E5/well MCF-7 cells are cultured in DMEM with 10% FBS and then cocultured with 2E5/well mouse MSC in serum-free DMEM/F12 media in 6-well low attachment plates, treated with 5uM Arsenic trioxide or PBS (Vehicle) for <48h
|After centrifuge, total RNA were extracted by Direct-zol RNA miniprep kit. . The first and second strand cDNA were prepared by SuperScript III First-Strand Synthesis System and NEBNext mRNA Second Strand Synthesis Module from at least 200ng total RNA for each sample. Illumina Nextera XT DNA Sample Prep Kit was used with 1 ng of dsDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using nextera Illumina protocols
|Illumina NextSeq 500
|Illumina Nextseq 500 automatically used bcl2fastq2 (version 2.17) for basecalling. FASTQ files were downloaded from BaseSpace.
RNA-seq NGS reads derived from cocultures containing a mixture of human and mouse reads were separated using Xenome (version 1.0.1).
RNA-seq NGS reads were mapped using STAR RNA-seq aligner (version 2.4.1d).
RSEM (version 1.2.28) was used to quantify gene and isoform expression.
DEseq2 R package is used to normalize the gene/isoform expression matrix.
Genome_build: GRCh38.83 and GRCm38.83
Supplementary_files_format_and_content: CoAs.RData (includes RSEM read counts and DESeq2 normalized gene expression values) and CoAs.csv (includes only the DESeq2 normalized gene expression values).
|Aug 22, 2018
|Last update date
|Oct 01, 2018
|Roswell Park Cancer Institute
|Molecular and Cellular Biology
|Elm and Carlton Streets, MRC 328
|ATO treatment on mesenchymal stem cells (MSCs) interacting breast cancer cells