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Sample GSM3721910 Query DataSets for GSM3721910
Status Public on Feb 12, 2020
Title WT_rep1
Sample type SRA
 
Source name WT_flow cytometry sorted astrocytes
Organism Mus musculus
Characteristics strain background: C57Bl/6
genotype/variation: littermate control willd type
Sex: male
age: P84
cell type: Flow cytometry sorted astrocytes
Treatment protocol Induction of EAE in mice. EAE was induced by injecting 200 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
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 Illumina NextSeq 500
 
Description *_HMW5KBGX9.*.AAGAGGCA_TATGCAGT
Data processing Reads were aligned against the GRCm38 mouse genome using STAR (v.2.5.3) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were marked for duplicates using Picard (v.2.7.1)
Reads were removed for duplicates, mapping quality below 30, unmapped reads, mate unmapped, and multi-mapped.
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 13, 2019
Last update date Feb 12, 2020
Contact name Michael Wheeler
E-mail(s) mwheeler0@bwh.harvard.edu
Organization name Brigham and Women's Hospital
Department Neurology
Street address 60 Fenwood Rd.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (2)
GSE129773 Genome-wide analysis of the transcriptional profile of WT and CSF2RB astrocyte conditional KO during EAE in B6 mice [Csf2rb RNA-seq]
GSE130119 MAFG-driven astrocytes promote CNS inflammation
Relations
BioSample SAMN11413292
SRA SRX5679300

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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