|
| Status |
Public on Jun 01, 2020 |
| Title |
TGFB1_spheroids_1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian surface epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: m1102
cell type: Ovarian surface epithelial cells
treatment: 10ng/mL TGFB1
|
| Treatment protocol |
Spheroid Culture: TGFB1-treated cells were treated with 10ng/mL TGFB1 (R&D Systems) for 4 days prior to being cultured in low-attachment plates. Snail Overexpression: Cells were transduced with either a lentiviral vector control (WPI) or a Snail-overexpression construct. BRCA1 deletion: mOSE cells harvested from BRCA fl/fl mice were infected with an adenoviral vector expression either GFP (control) or Cre recominase. RNA was collected after confirming BRCA1 deletion.
|
| Growth protocol |
mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 4% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems). For spheroid cultures, cells were cultured on ultra low attachment plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using the RNeasy Kit (Qiagen)
Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
sphere_dge_results.csv
sphere_tpm_matrix.csv
|
| Data processing |
Pseudoalignment and transcript quantification performed with Kallisto (0.44.0) with -b 50
Differential expression analysis performed with Sleuth (0.30.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing TPM values for each gene across all samples
|
| |
|
| Submission date |
Nov 23, 2018 |
| Last update date |
Jun 01, 2020 |
| Contact name |
David Cook |
| E-mail(s) |
David.cook@uottawa.ca
|
| Organization name |
Ottawa Hospital Research Institute
|
| Department |
Cancer Therapeutics Program
|
| Street address |
501 Smyth Rd
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE122875 |
Transcriptional profile of stemness in the ovarian surface epithelium |
|
| Relations |
| BioSample |
SAMN10473197 |
| SRA |
SRX5058220 |
