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Sample GSM5394585 Query DataSets for GSM5394585
Status Public on Sep 08, 2022
Title Embryo.48h.n.2215
Sample type SRA
 
Source name Human Developing Brain
Organism Homo sapiens
Characteristics tissue: Type_Embryo
infection time: Hours_48
zika mcherry reporter status: PosNeg_n
sample id: ID_2215
Treatment protocol mCherry MOI 1 48 hours (embryo); MOI 3 72 hours (GBM)
Growth protocol Primary patient GBM and human developing brain cultures were generated by dissociation of primary tissue samples and plated in standard adherent serum-free culture conditions supplemented with laminin, EGF and FGF (10ng/ml ea) according to published protocols (Pollard et al., Cell Stem Cell 2009), but with precoating of plastics with 1:20 laminin to improve attachment. Representative wells were dissociated for counting the day after plating, then infections performed using Zika-mCherry reporter virus at MOI 10 for 1 hour. Infected cultures were dissociated for FACS sorting and analydsasis at 48 hours or 72 hours as indicated.
Extracted molecule total RNA
Extraction protocol Zika mCherry positive and negative fractions were sorted by FACS directly into Buffer RLT Plus, followed by extraction using Rneasy micro Plus kit according to manufacturer's instructions.
Takara Clontech Smartseq pico V2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 7- BRC2215 48hr negative
Data processing Quality checks were performed using FastQC (v0.11.2), summarised with MultiQC (v1.8). Fastq files were randomly subsampled to 50M reads and read trimming of the first 3 nucleotides (due to poor quality) was performed using TrimGalore (v0.6.4_dev). Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (STAR_2.5.2a) with default parameters. Density plots, violin plots, MA plots, Jaccard similarity index, dendrograms and PCA were performed as further quality checks
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433). Differential expression analysiss was performed using edgeR (v3.28.1) and DESeq2 (1.30.0).
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.8).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Csv of raw and normalised abundances. Rows represent features and columns represent samples. Values are raw in the first instance, and normalised with noise removed in the second.
 
Submission date Jun 21, 2021
Last update date Sep 08, 2022
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24676
Series (2)
GSE178621 Microglia regulate Zika virus infection in human developing brain and glioma
GSE178623 Microglia regulate Zika virus infection in human developing brain and glioma; Stem Cell transcriptional response to Microglia-Conditioned Media
Relations
BioSample SAMN19800546
SRA SRX11190629

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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