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Sample GSM4489447 Query DataSets for GSM4489447
Status Public on Feb 25, 2022
Title Astrocytes pGFAP-shEphB3 4GPSick
Sample type SRA
 
Source name Astrocytes
Organism Mus musculus
Characteristics strain: C57BL/6
disease state: undergoing EAE
Sex: Female
age: 10 weeks
treatment: pGFAP-shEphB3
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 SAMN14655771
SRA SRX8151137

Supplementary file Size Download File type/resource
GSM4489447_CCTAAGAC_AGGCTTAG.txt.gz 3.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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