|
Status |
Public on Feb 25, 2022 |
Title |
Astrocytes CTRL2 Sick |
Sample type |
SRA |
|
|
Source name |
Astrocytes
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 disease state: undergoing EAE Sex: Female age: 10 weeks treatment: CTRL cell type: FACS Sorted Astrocytes 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 |
SAMN14655778 |
SRA |
SRX8151130 |