Libraries were sequenced on the Illumina Hi-Seq 2500. Basecalls were performed with CASAVA version 1.8.Sequence adapters were trimmed using AdapterRemoval with options --trimns, --minlength 20. Trimmed RNA-Seq reads were aligned to known UCSC hg19 genes and the hg19 genome using Bowtie 2 v2.1.0 and TopHat v2.0.9 with options --library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180. UCSC hg19 reference genome and transcriptome was obtained through Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).Aligned RNA-Seq reads were summarised using the summarizeOverlaps algorithm with the UCSC known genes hg19 GTF file using the the options overlapMode=``Union'', ignoreStrand=FALSE, singleEnd=FALSE, fragments=TRUE to generate a table of unique read counts per gene for each sample.Genome_build: hg19Supplementary_files_format_and_content: A count table of uniquely mapped read pairs overlapping genes.
|Date made available||31 Aug 2016|
|Publisher||Gene Expression Omnibus (NCBI)|
Buckberry, S. (Creator), Roberts, C. T. (Creator)(31 Aug 2016). GSM2043601: villous_S4. Gene Expression Omnibus (NCBI).