Summary: Conclusions: We successfully established the NCX-NES cell culture as an experimental system for the study of neural stem cells and used it to study ZIKV infection
Overall Design: Single cell RNA-seq of over 1;000 cells of NCX-NES cell culture and fetal brain. All of the cells in this dataset are non-ZIKV-infected.
Strategy: |
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Species: |
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Tissue: |
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Healthy Condition: |
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Growth Protocol: | Cells were resuspended in DMEM/F12 with addition of B27 supplement (1:1000), N2 supplement (1:100), 20 ng/ml FGF-2, 20 ng/ml EGF, 1.6 g/l glucose, 20 ?g/ml insulin and 5 ng/ml BDNF. 10 ?M rock inhibitor (Y-27632, Stemgent 04-0012) was added to increase cell viability. The cells were then plated into dishes coated with poly-L-ornithine (0.01%, Sigma P4957), laminin (5 ?g/ml, Invitrogen 23017-015) and fibronectin (1μg/ml, Corning, 354008,). Medium was changed 12 hr after plating and the cells were passaged using 0.25% trypsin within 3 d and replated to obtain a monolayer of cells at a density of 4–5 × 104 cells/cm2. Half of the media was changed every 2–3 d to allow culture conditioning." |
Treatment Protocol: | - |
Extract Protocol: | RNA was extracted after single cell capture using C1 single cell auto prep system, with manufacturer protocol. |
Library Construction Protocol: | RNA libraries were prepared for sequencing using with Illumina NEXTERA XT kit |
Molecule Type: | poly(A)+ RNA |
Library Source: | |
Library Layout: | SINGLE |
Library Strand: | - |
Platform: | ILLUMINA |
Instrument Model: | Illumina HiSeq 2000 |
Strand-Specific: | Unspecific |
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 |
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