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| Status |
Public on Sep 08, 2022 |
| Title |
control_G334_G322_2 |
| Sample type |
SRA |
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| Source name |
Cell Line
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| Organism |
Homo sapiens |
| Characteristics |
conditioned media type: MediaType_control
conditioned media origin: ConditionedMedia_G334
treated stem cells: Cells_G322
sequencing lane: Lane_2
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| Treatment protocol |
MG vs GSC CM 48 hours
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction using Rneasy micro Plus kit according to manufacturer's instructions.
NEB Ultra II
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample5.s_2
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| 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.
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| Submission date |
Jun 21, 2021 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
Wellcome-MRC Cambridge Stem Cell Institute
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| Street address |
Puddicombe Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| BioSample |
SAMN19800494 |
| SRA |
SRX11190656 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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