|
| Status |
Public on Feb 25, 2022 |
| Title |
Microglia pGFAP-shEphB3 2 Sick |
| Sample type |
SRA |
| |
|
| Source name |
Microglia
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
disease state: undergoing EAE
Sex: Female
age: 10 weeks
treatment: pGFAP-shEphB3
cell type: FACS Sorted Microglia from CNS
|
| Treatment protocol |
Mice at day 7 after EAE induction where intrathecally injected with the lentiviral vector expressing a control vector (CTRL), a vector to knockdown EphB3 specifically in Astrocytes (pGFAP-shEphB3) or a vector to knock down EfnB3 in Microglia (pCD11b-shEfnB3)
|
| Growth protocol |
CNS was harvested and digested with papain and collagenase D, myelin removed by precol gradient and Astrocytes and Microglia were isolated by flow cytometry
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Arcturus® PicoPure®
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.7.2) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Feb 25, 2022 |
| Contact name |
Zhaorong Li |
| E-mail(s) |
zhaorong@bu.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Street address |
60 Fenwood Road
|
| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE149052 |
Eph Receptor B3/EphrinB3 signaling impact CNS pathology during EAE |
| GSE150858 |
Barcoded viral tracing of single-cell interactions in CNS inflammation |
|
| Relations |
| BioSample |
SAMN14655803 |
| SRA |
SRX8151147 |
