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Sample GSM4075259 Query DataSets for GSM4075259
Status Public on Feb 12, 2020
Title EAE_rep2 [E11]
Sample type SRA
 
Source name EAE mouse
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype/variation: wild type
Sex: Male
age: P90
treatment: experimental autoimmune encephalomyelitis (EAE)
cell type: Flow cytometry sorted astrocytes
Treatment protocol Induction of EAE in mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse. ICV injection of 100 ng IL-1b and 50 ng TNFa. Cells were isolated 24 hours post-injection of IL1b/TNFa
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 the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description E11.CAGCGC
Data processing DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam.
Reads were aligned using GRCh38 mouse genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM
 
Submission date Sep 12, 2019
Last update date Feb 13, 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)
GSE130119 MAFG-driven astrocytes promote CNS inflammation
GSE137314 Genome-wide analysis of the transcriptional profile of IL1b/TNFa-treated and EAE astrocytes in B6 mice.
Relations
BioSample SAMN12735801
SRA SRX6835070

Supplementary file Size Download File type/resource
GSM4075259_E11-counts.txt.gz 2.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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