|
| Status |
Public on Oct 12, 2018 |
| Title |
Single-cell-derived spheroid 8 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
sample type: Single-cell-derived spheroid
|
| Treatment protocol |
NA
|
| Growth protocol |
The single-cell (MDA-MB-231, obtained from the American Type Culture Collection) suspension was obtained by trypsinization. Cells were seeded in an ultra-low attachment 96-well plate (Corning, one cell per well). The cells were maintained in serum-free Dulbecco's Modified Eagle Medium/Nutrient Mixture F12 (DMEM /F12) (Gibco) supplemented with B27 (Invitrogen), 20 ng/mL epidermal growth factor (EGF) (Sigma), 20 ng/mL basic fibroblast growth factor (bFGF) (BD Biosciences). Only wells that contained a single cell initially were used for subsequent studies. For spheroid passage, the single-cell-derived spheroid was sucked up by a micro-pipette and dissociated with a small amount of trypsin-Ethylene Diamine Tetraacetic Acid (EDTA) and mechanically dispersed. The resulting single cells were then re-suspended in serum-free medium. The spheroids were passed every 7-10 days, and only spheroids bigger than 50μm in size were included in the analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Discover-sc WTA Kit (Vazyme, Cat. N711-01).
TruePrep DNA library Prep Kit V2 for Illumina (Vazyme cat. TD-503).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
C8
RNA sequencing
mRNA
processed data file: All_FPKM_table.txt
|
| Data processing |
Sequencing was performed on Illumina HiseqXten with paired-end reads of 150bp.
The quality of sequencing data was assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Mapping to the reference of hg19 Human Genome was conducted by TopHat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Gene-level expression abundance were obtained from the Cufflinks package (http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All_FPKM_table.txt: Tab-delimited text file including gene-level expression abundance (fragments per kilobase of exon per million fragments mapped) for all samples.
|
| |
|
| Submission date |
Jun 22, 2018 |
| Last update date |
Oct 12, 2018 |
| Contact name |
Meng ying Tong |
| Organization name |
Dalian Medical University
|
| Street address |
Longtou Street
|
| City |
Dalian |
| State/province |
Liaoning |
| ZIP/Postal code |
116041 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE116180 |
Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells |
|
| Relations |
| BioSample |
SAMN09474240 |
| SRA |
SRX4285329 |
