Computational protocol: Characterisation of CDKL5 Transcript Isoforms in Human and Mouse

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Protocol publication

[…] The following RNA-seq datasets were analysed in this study: human brain GEO sample ID GSM1173806 []; human testis GEO sample ID GSM759517 and ENCODE sample ID ENCSR693GGB [, ]; mouse brain GEO sample ID’s GSM1020640, GSM1020649 and GSM1020657 []; mouse testis GEO sample ID’s GSM1020648, GSM1020656 and GSM1020665 []. Mapping RNA-seq reads to the human and mouse genomes was carried out using the STAR read aligner, version 2.4.2a []. To generate STAR genome indices for each species, the following command line was run in each case: STAR --runMode genomeGenerate --genomeDir --genomeFastaFiles --sjdbGTFfile where is the directory into which the index files were written, were FASTA-formatted files containing sequences from the primary assembly of the respective species' genome (Ensembl v80), and was a GTF-formatted genome annotation file for the respective species (also Ensembl v80). To map a particular set of RNA-seq reads to a species' genome, the following command line was run: STAR --genomeDir --readFilesIn --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate where was the directory into which the species' index files were written, and and enumerated the FASTQ-formatted files containing paired-end RNA-seq reads for the dataset. STAR was run in two-pass mapping mode to give the most sensitive detection of reads mapping across novel splice junctions. RNA-seq output images were generated using the Integrative Genomics Viewer (IGV) and Sashimi plots [–]. […]

Pipeline specifications

Software tools STAR, IGV, Sashimi plots
Applications RNA-seq analysis, Transcriptome data visualization
Organisms Mus musculus, Homo sapiens
Diseases Spasms, Infantile