|
| Status |
Public on Oct 01, 2018 |
| Title |
Co_veh_rep1 |
| 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 |
| E-mail(s) |
hai.wang@roswellpark.org
|
| 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 |
|
| Relations |
| BioSample |
SAMN09881625 |
| SRA |
SRX4597243 |
