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| Status |
Public on Mar 07, 2019 |
| Title |
with LPS and AG, 2 |
| Sample type |
SRA |
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| Source name |
RAW264.7
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| Organism |
Mus musculus |
| Characteristics |
tissue: macropahge
agent: with LPS and AG
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| Treatment protocol |
Macrophage (RAW264.7) with vector, with 0.5 mg/mL LPS alone or combined 1 μM arctigenin treatment.
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| Growth protocol |
Cells were cultured in 1640 medium containing 10% foetal bovine serum (FBS), 100 unit/mL penicillin, and 100 g/mL streptomycin. The cells were maintained at 37°C under 5% CO2 (v/v) in a humidified incubator
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from cells using an RNA extraction kit (Qiagen K.K., Tokyo, Japan). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA.Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Sample 5
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| Data processing |
Illumina HiSeq X Ten system for next-generation sequencing by OE Biotech. Co., Ltd. (Shanghai, China)
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq R package functions estimateSizeFactors and nbinomTest.
Genome_build: mm9
Supplementary_files_format_and_content: mRNA_counts.xls include raw read for each Sample ...
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| Submission date |
Mar 06, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Lu Lu |
| E-mail(s) |
coinland@gzucm.edu.cn
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| Organization name |
Guangzhou University of Chinese Medicine
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| Street address |
No.12,Airport Road,Baiyun District
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| City |
Guangzhou |
| ZIP/Postal code |
510407 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE127902 |
Next Generation Sequencing Facilitates Quantitative Analysis of Macrophage (RAW264.7) with and without arctigenin treatment |
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| Relations |
| BioSample |
SAMN11074130 |
| SRA |
SRX5472755 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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