|
| Status |
Public on Mar 15, 2018 |
| Title |
Control Microglia A |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CD1
tissue: Microglia
treatment: Control
|
| Treatment protocol |
EVs were isolated by serial centrifugation from primary NSCs cultured from the subventricular zone of CD1 mice. Cultured microglia were then subjected to control or EV treatments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Extraction RNA library preparation with polyA selection.
NEBNext Ultra RNA Library Preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner. The RNA-seq aligner is executed using a splice aligner which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step. Unique exon hit counts were calculated using Feature counts from the Subread package. After mapping and unique exon hit count calculations, downstream differential expression analysis was performed using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include number of mapped reads.
|
| |
|
| Submission date |
Feb 20, 2018 |
| Last update date |
Mar 16, 2018 |
| Contact name |
David Matthew Feliciano |
| E-mail(s) |
dfelici@clemson.edu
|
| Phone |
8644821296
|
| Organization name |
Clemson University
|
| Department |
Biological Sciences
|
| Lab |
Neurogenesis and Neurogenetics
|
| Street address |
132 Long Hall
|
| City |
Clemson |
| State/province |
South Carolina |
| ZIP/Postal code |
29634-0314 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE110892 |
Neural Stem Cell Extracellular Vesicle-Treated Microglia and Transcriptional Response |
|
| Relations |
| BioSample |
SAMN08569849 |
| SRA |
SRX3729222 |
