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| Status |
Public on Oct 25, 2019 |
| Title |
BCSCs 3 |
| Sample type |
SRA |
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| Source name |
MCF7 cell line
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| Organism |
Homo sapiens |
| Characteristics |
signature: CD44high/CD24low
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| Treatment protocol |
The population of PKH26+ cells was used as qBCSCs in this study. The labeled cells were cultured under tumorspheres formation conditions (described above) for 2 weeks, and the medium was changed every 2 days. After two weeks’ incubation, the tumorspheres were dissociated by accutase (Gibco; A1110501), then the single cell suspension was washed by HBSS and subjected to FACS Vantage (BD). Cells with the signal of PKH26 (Ex:551nm, Em:567nm) were harvested. For activation of qBCSCs obtained above, FACS-sorted qBCSCs were plated in 6-well ultra-low-attachment plates (Corning; 3471) and cultured in tumorspheres formation conditions (described above) plus 50 ng/ml exosomes that has been isolated form MCF7 cells culture supernatants by cell medium exosome isolation kit (Life technology; 4478359) according to the manufacturer’s instructions for 20 hrs, which is the time that just before one cell dividing into two cells.
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| Growth protocol |
BCSCs (either BCSCs, qBCSCs or activated qBCSCs) were plated at a density of 4000-8000 cells/well in the 6-well ultra-low-attachment plates and cultured in tumorspheres formation conditions (DMEM/F12 (Corning; 10-092-cv) supplemented with 10% serum replacement (SR; Thermo Fisher Scientific; 10828028), human recombinant epidermal growth factor (EGF 20 ng/ml), heparin sodium of 5 ng/ml (MedChemExpress; 9041-08-1), human recombinant basic fibroblast growth factor of bFGF (20 ng/ml) (PeproTech; 96-100-18B-500) at 37℃ in a humidified 5% CO2 incubator). The medium was replaced every 2 days. After culturing for two weeks, tumorspheres could be visualized using an inverted phase-contrast microscope.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNAs of bulk cells (either BCSCs, qBCSCs or activated qBCSCs) were extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
BCSCs
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| Data processing |
The library of each samples was sequenced on an Illumina Hiseq PE150 platform with a 150 bp paired-end module
Clean reads were aligned to the reference genome using Bowtie2 (v2.2.9) and TopHat (v2.1.1).
Cuffdiff (v2.2.1) was used to calculate FPKMs for coding genes in each sample
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Dec 13, 2018 |
| Last update date |
Oct 25, 2019 |
| Contact name |
sen ye |
| E-mail(s) |
[email protected]
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| Phone |
+8657188206365
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| Organization name |
Zhejiang University
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| Street address |
866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE123810 |
The list of differential gene expression between BCSCs, qBCSC and activated qBCSCs |
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| Relations |
| BioSample |
SAMN10589667 |
| SRA |
SRX5128426 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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