Data

GSM2043598: villous_S1

The University of Western Australia
Buckberry, Sam ; Roberts, Claire T.
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/a93ef1e2-e74a-492d-9700-719aa490794f&rft.title=GSM2043598: villous_S1&rft.identifier=a93ef1e2-e74a-492d-9700-719aa490794f&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=Buckberry, Sam &rft.creator=Roberts, Claire T. &rft.date=2016&rft.relation=http://research-repository.uwa.edu.au/en/publications/7ceadec3-9cef-48d5-91fb-098854109998&rft.type=dataset&rft.language=English Access the data
Cite Saved to MyRDA Save to MyRDA

Access:

Open

Full 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.

Notes

External Organisations
University of Adelaide
Associated Persons
Claire T. Roberts (Creator)

Issued: 2016-08-31

This dataset is part of a larger collection

Click to explore relationships graph
Help

Related Publications

Related Data

Related Organisations

Related People

Related Websites

User Contributed Tags    

Login to tag this record with meaningful keywords to make it easier to discover

Identifiers
  • global : a93ef1e2-e74a-492d-9700-719aa490794f