|
| Status |
Public on Mar 01, 2024 |
| Title |
As-500D-03 |
| Sample type |
SRA |
| |
|
| Source name |
Rat fetal neural stem cell-derived Astrocyte
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Rat fetal neural stem cell-derived Astrocyte
treatment: 100 µg/ml 500nm polystyrene microspheres
|
| Treatment protocol |
NSC-derived astrocytes were treated with non-fluorescent microspheres (Polybead®) 0-100 ug/ml for 7 days, with new microbeads in fresh media every 2-3 days.
|
| Growth protocol |
Rat fetal neural stem cells (NSCs) were cultured in KnockOut DMEM/F12 supplemented with StemPro NSC SFM (2%), b-FGF and EGF (20ng/mL) (Peprotech, NJ, USA), GlutaMAX-1 (2mM) and 1% penicillin/streptomycin. These cells were culture on poly-L-ornithine (MilliporeSigma, ON, Canada) or Geltrex (ThermoFisher, ON, Canada) coated culture dishes. NSCs were differentiated into astrocytes with differentiation media consisting of D-MEM Medium with N-2 supplement (1%), 2mM GlutaMAX-1 supplement and 1% FBS, while plated on Geltrex coated plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell culture samples using Qiagen miRNeasy kits. Subsequent steps were followed as per manufacture's instructions.
Polystyrene microsphere-treated astrocyte cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DifferentialExpression_MicroPlastics_Astrocytes_Gill_500.tsv
|
| Data processing |
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0) -p -Q=12 -C -t exon -g gene_id
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2
|
| |
|
| Submission date |
Feb 19, 2024 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Santokh Gill |
| E-mail(s) |
santokh.gill@hc-sc.gc.ca
|
| Organization name |
Health Canada
|
| Department |
251 Sir Frederick Banting Driveway
|
| Street address |
251 SIR FREDERICK BANTING
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE256038 |
Polystyrene nano- and microplastic particles induce an inflammatory gene expression profile in neural stem cell-derived astrocytes |
|
| Relations |
| BioSample |
SAMN39986504 |
| SRA |
SRX23658678 |
