tissue: bone marrow differentiated macrophages
genotype: Mkl1-/-, Apoe-/-
Treatment protocol
Mice were challenged with 1 mg/kg/min,1.44 mg/kg/day) by implantation of Alzet osmotic minipumps (Model 1004, Alzet, Cupertino, CA) for 7 days before bone marrow isolation. We in vitro differentiate cells to macropages for 7 days before RNA extraction for RNA-seq analysis.
Growth protocol
Bone morrow cells were cultured in standard differentiated medium for 7 days to differentiae to macrophages per standard protocol.
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.
Data processing
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCm38 + Gencode-M22 Annotation
Supplementary_files_format_and_content: Raw and normalized counts
Series (1)
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Supplementary data files not provided
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SRA Run Selector
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Raw data are available in SRA
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Processed data are available on Series record
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