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Sample GSM2683278 Query DataSets for GSM2683278
Status Public on Sep 13, 2017
Title RNA-seq for isolated mouse brain microglia, LPS group, replicate 3
Sample type SRA
Source name isolated brain microglia
Organism Mus musculus
Characteristics sample type: replicate 3
strain: C57BL/6
genotype/variation: WT
agent: LPS
tissue: brain
cell type: microglia
Treatment protocol To activate microglia, adult wildtype B6 mice received daily intraperitoneally injection of 1mg/Kg lipopolysaccharide (L4524, Sigma) or phosphate-buffered saline for 4 consecutive days before sacrifice.
Extracted molecule total RNA
Extraction protocol For Ptbp2-KO brain cortex RNA-seq, E18.5 mouse cortex RNA (three biological replicates) from Ptbp2-KO mice (Licatalosi et al., 2012) was prepared using Trizol (Ambion); ribosomal RNA was removed from 1 μg RNA using Ribo-Zero rRNA removal Kit (Illumina). For microglia isolation, mice were perfused with 30ml of heparinized PBS. Brains were excised, minced and two brains were placed into C tube and processed as per instructions for the Neural Tissue Dissociation Kit P (Miltenyi Biotec) using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, protocol 37_ABDK). Once digested, the debris and myelin was removed using the Debris Removal Solution (Miltenyi Biotec) followed by CD11b positive selection using Microglia CD11b beads (Miltenyi). Cells were counted, washed in PBS and pelleted prior to isolation of RNA. Total RNA from isolated microglia was prepared using Trizol (Ambion) and High Pure RNA Isolation Kit (Roche). The Total RNA was then further purified for polyadenylated RNA by using 150ng Total RNA in Dynabeads mRNA Purification Kit (Ambion).
RNA-seq libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) following manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Data processing RNA-seq mapping to mouse genome (mm10) was performed using STAR aligner (Dobin et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: txt files for read counts at gene level (Ensembl) generated by STAR aligner
Submission date Jun 26, 2017
Last update date May 15, 2019
Contact name Hun-Way Hwang
Organization name University of Pittsburgh
Department Department of Pathology
Lab S754 Scaife Hall
Street address 3550 Terrace Street
City Pittsburgh
State/province PA
ZIP/Postal code 15261
Country USA
Platform ID GPL16417
Series (1)
GSE94054 cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation
BioSample SAMN07276964
SRA SRX2955626

Supplementary file Size Download File type/resource 183.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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