|
|
GEO help: Mouse over screen elements for information. |
|
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 |
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 |
SAMN08369979 |
SRA |
SRX3586850 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|