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Sample GSM3351302 Query DataSets for GSM3351302
Status Public on Oct 01, 2018
Title Co_veh_rep2
Sample type SRA
Source name MCF7-MSC organoids
Organisms Homo sapiens; Mus musculus
Characteristics 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
passage: P140-P142
reporter gene: Firefly Luciferase (MCF-7)
treatment: control
Growth protocol 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
Extracted molecule total RNA
Extraction protocol 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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing 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).
Submission date Aug 22, 2018
Last update date Oct 01, 2018
Contact name Hai Wang
Organization name Roswell Park Cancer Institute
Department Molecular and Cellular Biology
Lab Hai Wang
Street address Elm and Carlton Streets, MRC 328
City Buffalo
State/province NY
ZIP/Postal code 14263
Country USA
Platform ID GPL19415
Series (1)
GSE118923 ATO treatment on mesenchymal stem cells (MSCs) interacting breast cancer cells
BioSample SAMN09881624
SRA SRX4597244

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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