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Sample GSM3732384 Query DataSets for GSM3732384
Status Public on Feb 12, 2020
Title M3_Naive_Parenchyma_rep1
Sample type SRA
 
Source name Naive_Parenchyma
Organism Mus musculus
Characteristics Sex: Female
disease: Naive
region: Parenchyma
molecule subtype: immunoprecipitated mRNA via HA-tagged Rpl22 ribosomal subunit
Treatment protocol Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
Extracted molecule total RNA
Extraction protocol Protocol largely derived from Sanz et al. 2009, PNAS. Each CNS region was microdissected and homogenized in supplemented homogenization buffer (HB-S). Debris was pelleted, and supernatant was immunoprecipitated with an anti-HA antibody (Sigma, #H9658, 1:150) overnight. Following washes, RNA was purifiied using a Qiagen RNeasy purification kit (Qiagen, #74106). mRNA was then isolated using mRNA DIRECT kit (Thermo Fisher, #61012).
Libraries were prepared using a similar protocol as MARS-seq (Jaitin et al. Science 2014).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The right reads were trimmed using fastx (v0.0.13) fastx_trimmer.
Sequencing reads was aligned against the mm10 genome using STAR with default parameters and --quantMode geneCounts to count unique reads mapped
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene counts generated from STAR geneCounts
 
Submission date Apr 22, 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)
GSE130118 Genome-wide analysis of the transcriptional profile of astrocytes across EAE by CNS region in Gfap-Cre;Ribotag(f/f) mice uisng Ribotag immunoprecipitation.
GSE130119 MAFG-driven astrocytes promote CNS inflammation
Relations
BioSample SAMN11475531
SRA SRX5717477

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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