Gene Expression
Nebulas
Gene Expression NebulasSummary: Single human primary prostate epithelial cells grown as a monolayer (2D) or as organoids (3D) were separated, collected and prepped for RNA-seq using the 10x Genomics Chromium Genome Reagent kit v2 Chemistry. 3,500-5,000 cells were collected from each sample and sequenced at a depth of ~45,000 genes per cells on a 2x150nt lane in a HiSeq 4000. CellRanger alignment was performed to produce the RAW data files.
Overall Design: Two samples: monolayer cells and organoid cells
| Strategy: |
|
| Species: |
|
| Tissue: |
|
| Healthy Condition: |
|
| Cell Type: |
|
| Growth Protocol: | Human prostate PrE cells were grown from collagenase digested patient tissue onto a cell culture dish until ~70 confluent. Cells were collected and frozen into aliquots. A aliquot was thawed into PrEGM media (lonza) and grown to 70% confluent and a second aliquot was thawed into 50% matrigel grown in KSFM media supplemente with DHT and charcoal stripped FBS to form organoids. |
| Treatment Protocol: | - |
| Extract Protocol: | Organoids were collected from Matrigel by dispase and digested to single cells using TryPLE. Monolayer cells were picked up from the cell culture plate using TryPLE. Single cells were separated using 10x genomics technology. |
| Library Construction Protocol: | Chromium Genome Reagent Kit (v2 Chemistry) |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 4000 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
|---|