C3_R1_Mature macrophage_mouse1

• Other Authors: David Joyce (Creator), Fiona Pixley (Creator), Julie Proudfoot (Creator), School of Biomedical Sciences (isManagedBy)
• Format: Dataset
• Language: unknown
• Published: The University of Western Australia
• Subjects: Greenland
• Online Access: https://researchdata.edu.au/c3r1mature-macrophagemouse1/1445894

Associated Persons Michael Murrey (Creator); Eloise Greenland (Creator)James Steer (Creator) Sample type: SRA Source name: bone marrow derived Organism: Mus musculus Characteristics strain: C57BL/6 Sex: male age: 8 to 10 weeks Growth protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS, non-adherent cells were incubated for two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% FCS. Extracted molecule: total RNA Extraction protocol: mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column. 1 ug of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Ion Torrent protocols Library strategy: RNA-Seq Library source: transcriptomic Library selection: cDNA Instrument model: Ion Torrent Proton Description: C3_R1 C1_C2_C3_allprobes_reads.txt C1_C2_C3_allprobes_log2_RPM.txt Data processing: Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence- returning a fastq file (raw data) Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner. The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60 The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files) Ampliseq Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Returning a fastq file (raw data) of reads associated with each of the 16000 barcoded primer pairs. Reads were then mapped to the GRCm38.p6 genome using the open ...