NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4041822 Query DataSets for GSM4041822
Status Public on May 26, 2021
Title BMDMs, WT-LPS_1
Sample type SRA
 
Source name CK_LPS-vs-WT_LPS
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
age: 7-week-old
genotype: WT
agent: LPS
tissue: Bone marrow
cell type: BMDMs
Treatment protocol LPS stimulation for 4 hour
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.
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
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
 
Submission date Aug 21, 2019
Last update date May 26, 2021
Contact name Li-Chung Hsu
E-mail(s) lichunghsu@ntu.edu.tw
Phone +886-2-23123456
Organization name National Taiwan University
Department Graduate institute of Molecular Medicine
Street address No.7, ChungShan S. Rd., ZhongZheng Dist.
City Taipei
ZIP/Postal code 10002
Country Taiwan
 
Platform ID GPL21273
Series (1)
GSE136161 Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation
Relations
BioSample SAMN12617972
SRA SRX6749752

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap