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Sample GSM2936669 Query DataSets for GSM2936669
Status Public on Sep 25, 2018
Title Control rep3
Sample type SRA
 
Source name adult microglia
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: cerebrum
treatment: none
age: 6-8 weeks
Treatment protocol Primary microglia treated with or without Pam3CSK4 (100 ng/ml) for 24 h and followed with IFN-γ (20 ng/ml) for 24 h.
Growth protocol Adult microglia were prepared from 6-8 weeks old mice. Microglia were plated onto 24-well plates at a density of 1×10^5 cells per well with DMEM/F12 supplemented with 10% heat-inactivated FBS, 2 mM glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 ng/ml recombination TGF-β1 (Miltenyi, Germany), and 10 ng/ml Recombinant Mouse M-CSF Protein (R&D, USA). Half of the medium was changed every 3 days, for a total of 10-14 days. Cultures were incubated at 37 °C in a humidified atmosphere of 5% CO2/95%.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100. Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description 3
Data processing Illumina Casava1.7 software used for basecalling.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
used Tophat v2.1.0 to map the cleaned reads to the mouse mm10 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM, count
 
Submission date Jan 17, 2018
Last update date Sep 25, 2018
Contact name Jiawen Qian
E-mail(s) qjw@fudan.edu.cn
Organization name Fudan University
Department Immunology
Lab Chu Lab
Street address 130 Dong'an Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (1)
GSE109297 The Effect of TLR2 Activation on Transcriptome of IFN-induced Microglia
Relations
BioSample SAMN08369983
SRA SRX3586845

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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