Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA321741: Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neural Stem Cell Model Systems

Source: NCBI / GSE81475
Submission Date: May 16 2016
Release Date: Sep 06 2016
Update Date: May 15 2019

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.

GEN Datasets:
GEND000206
Strategy:
Species:
Tissue:
Healthy Condition:
Protocol
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
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
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
Publications
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia.
Cell reports . 2016-08-24 [PMID: 27568284]