|
| Status |
Public on Oct 31, 2018 |
| Title |
Column_1 _Control |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian surface epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: EtOH (vehicle control)
cell type: Ovarian surface epithelial cells
|
| Treatment protocol |
Cells were seeded and allowed to normalize to hormone-free media consisting of 5% charcoal-stripped FBS in phenol red-free DMEM-F12 media (Sigma) for 48 hours before treating with 100nM E2 (Sigma). An equivalent volume of 100% EtOH (vehicle) was added to control dishes for a final concentration of 0.0002% EtOH. Media was refreshed every 3-4 days and cells were collected for scRNA-seq after 15 days in culture.
|
| Growth protocol |
mOSE cells were cultured in media consisting of a-Minimum Essential Medium (Corning) supplemented with 5% FBS, 0.01mg/mL ITSS (Roche), 2ug/mL EGF (R&D Systems).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspensions of control and E2-treated mOSE were processed using the Fluidigm HT 3' scRNA-seq protocol. The left cell inlet of the integrated fluidics circuit (IFC; leading to columns 1-10 of the plate) were loaded with control cells, while E2-treated cells were loaded into the right inlet (columns 11-20 of the IFC plate)
Library were constructed using the standard protocol described for the Fluidigm HT 3' scRNA-seq. Libraries were sequenced on a NextSeq500 high-out 26x75bp run
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files for each column of the IFC were further demultiplexed using Fluidigm's API for demultiplexing, resulting in a single fastq file for each cell capture site (40 sites per column).
Pseudoalignment and transcript quantification of each fastq file was performed with Kallisto (0.44.0)
Capture sites with zero or >1 cell, those with apoptotic cells, and those that led to poor-quality data (low number of sequencing reads, high mitochondrial proportion) were all filtered
Expression counts were normalized using scaling factors calculated using scran. Normalized values were imputed using MAGIC.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files containing raw counts, imputed logged expression, and metadata for each cell
|
| |
|
| Submission date |
Oct 30, 2018 |
| Last update date |
Oct 31, 2018 |
| 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 |
GPL19057 |
| Series (1) |
| GSE121957 |
Single-cell RNA sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium |
|
| Relations |
| BioSample |
SAMN10345574 |
| SRA |
SRX4954306 |
