Dataset

GSM2043601: villous_S4

The University of Western Australia
Sam Buckberry (Creator)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://research-repository.uwa.edu.au/en/datasets/fd84e6ab-166f-4678-9500-dba475ed3d63&rft.title=GSM2043601: villous_S4&rft.identifier=fd84e6ab-166f-4678-9500-dba475ed3d63&rft.publisher=Gene Expression Omnibus (NCBI)&rft.description= 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. &rft.creator=Roberts, Claire T. &rft.creator=Buckberry, Sam &rft.date=2016&rft.relation=https://research-repository.uwa.edu.au/en/publications/7ceadec3-9cef-48d5-91fb-098854109998&rft.type=dataset&rft.language=English Access the data

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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.

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Associated Persons
Claire T. Roberts ( Creator )

Issued: 2016-08-31

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  • global : fd84e6ab-166f-4678-9500-dba475ed3d63