P-GSE44831-3 - P-GSE44831-3

Type
feature_extraction
Description
Illumina Genome Analyzer II GA2 HiSeq and CASAVA 1.8.2 for base calling Additional quality control was applied to the datasets by clipping or removing poor quality reads and N's by ea-utils toolkit (
), with -p 10 and -q 7 settings, then mapped to P. yoelii YM strain reference genome using tophat version 1.4.1 with default parameters The differential transcript abundances between samples were measured in Fragments per kilobase of transcript per million mapped fragments (FPKM) using Cufflinks and Cuffdiff by a protocol from Trapnell C. et al. (2012) Nature. RNA-Seq differential analysis was visualized by CummeRbund Transcripts with P values of less than 0.01 and at least 4-fold difference in expression (i.e., log fold > 2) were selected to identify the most differentially regulated genes. Coverage plots were generated to examine the RNA distribution of reads across selected genes-of-interest by comparing the number of unique reads present at each nucleotide position Genome_build: Mus musculus UCSC version mm10 Supplementary_files_format_and_content: tab-delimited text files (cuffdiff gene_exp.diff) include gene differential FPKM values for each Sample
Links
Experiment E-GEOD-44831