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Sample GSM5394559 Query DataSets for GSM5394559
Status Public on Sep 08, 2022
Title microglia_069MG_BRC2251_1
Sample type SRA
 
Source name Human Developing brain
Organism Homo sapiens
Characteristics conditioned media type: MediaType_microglia
conditioned media origin: ConditionedMedia_069MG
treated stem cells: Cells_BRC2251
sequencing lane: Lane_1
Treatment protocol MG vs GSC CM 48 hours
Growth protocol GSCs, primary microglia and human developing brian cultures were 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), at a plating density 35,000 cells per cm2 and media volume 250ul per cm2. Conditioned media was harvested from these cultures after 48 hours, mixed 50:50 with fresh media and applied to cultures for 48 hours prior to harvesting cells for RNA extraction.
Extracted molecule total RNA
Extraction protocol Extraction using Rneasy micro Plus kit according to manufacturer's instructions.
NEB Ultra II
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Sample13.s_1
Data processing Quality checks were performed using FastQC (v0.11.2), summarised with MultiQC (v1.8). Fastq files were randomly subsampled to 25M reads. 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)
GSE178620 Stem Cell transcriptional response to Microglia-Conditioned Media
GSE178623 Microglia regulate Zika virus infection in human developing brain and glioma; Stem Cell transcriptional response to Microglia-Conditioned Media
Relations
BioSample SAMN19800475
SRA SRX11190671

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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