| Summary: | 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 a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS. Cells were then incubated for a further 4 days in alpha+ MEM /10% FCS containing 12ng/ml CSF1. 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: C2_R3 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 ...
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