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| Status |
Public on May 26, 2021 |
| Title |
BMDMs, KO-Ctrl_1 |
| Sample type |
SRA |
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| Source name |
CK_ctrl-vs-WT_ctrl
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
age: 7-week-old
genotype: Tut7-/-
agent: Ctrl
tissue: Bone marrow
cell type: BMDMs
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| Treatment protocol |
LPS stimulation for 4 hour
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| Growth protocol |
Bone marrow-derived macrophages (BMDMs) were prepared from femurs and tibia bones of 7-week old mice and bone marrow was flushed out with DMEM medium using a 25-gauge syringe. The bone marrow progenitor cells were harvested, and differentiated in high-glucose DMEM medium containing 20% L929 cell-conditioned medium for 7 days. Adherent BMDMs were collected and cultured in DMEM containing 10 ng/ml M-CSF overnight for further experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of BMDMs were harvested using Trizol reagent.
cDNA 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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| Data processing |
Basecalls performed using Illumina HiSeq PE150
Total of 4.45-11.8 million clean reads (Reads Per Kilo bases per Million reads, RPKMs) were obtained from each sample. RPKMs were compared to mouse RefSeq-RNA mm10 and quantitated using FANSe3 (Fast and Accurate mapping algorithm for Next-generation Sequencing, the 3rd generation (Rajkumar, A.P. et al., 2015 and Zhang, G. et al., 2012)).
The differential genes expression of each stimulation (including control and LPS) of each genotype was quantified using edgeR (Robinson, M.D., McCarthy, D.J. & Smyth, G.K., 2010) and FANSe3.
Genome_build: mm10
Supplementary_files_format_and_content: DiffExprAnalysis includes CK_ctrl-vs-WT_ctrl, CK_LPS-vs-WT_LPS, WT_LPS-vs-WT_ctrl and venn.
Supplementary_files_format_and_content: RC_RPKM.xlsx
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| Submission date |
Aug 21, 2019 |
| Last update date |
May 26, 2021 |
| Contact name |
Li-Chung Hsu |
| E-mail(s) |
lichunghsu@ntu.edu.tw
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| Phone |
+886-2-23123456
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| Organization name |
National Taiwan University
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| Department |
Graduate institute of Molecular Medicine
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| Street address |
No.7, ChungShan S. Rd., ZhongZheng Dist.
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| City |
Taipei |
| ZIP/Postal code |
10002 |
| Country |
Taiwan |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE136161 |
Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation |
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| Relations |
| BioSample |
SAMN12617970 |
| SRA |
SRX6749754 |
| 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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