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Sample GSM2936674 Query DataSets for GSM2936674
Status Public on Sep 25, 2018
Title IFN-g rep3
Sample type SRA
Source name adult microglia
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: cerebrum
treatment: IFN-gamma
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 9
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
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
BioSample SAMN08369979
SRA SRX3586850

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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