Dataset

GSM2043610: villous_S13

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/68a16ab6-eae7-4b59-a8a0-55fbed24a7f5&rft.title=GSM2043610: villous_S13&rft.identifier=68a16ab6-eae7-4b59-a8a0-55fbed24a7f5&rft.publisher=Gene Expression Omnibus (NCBI)&rft.description= Source name placental villous tissue Organism Homo sapiens Characteristics ercc spike-in pool: Mix_1 fetal sex: Male gestational age (weeks): 39.86 tissue: placental villous tissue Treatment protocol Placenta samples were collected and dissected post-delivery and incubated in RNAlater solution at 4 degrees celcius for 24 hours before being stored at -80 degrees celcius. Extracted molecule total RNA Extraction protocol RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with mix 1 or mix 2 of the 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts. Ribosomal RNAs were depleted from samples using Ribo-Zero Gold. and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol at the Australian Cancer Genomics Facility in Adelaide. Library strategy RNA-Seq Library source transcriptomic Library selection cDNA Instrument model Illumina HiSeq 2500 Data processing 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: hg19 Supplementary_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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Source name placental villous tissue
Organism Homo sapiens
Characteristics ercc spike-in pool: Mix_1
fetal sex: Male
gestational age (weeks): 39.86
tissue: placental villous tissue
Treatment protocol Placenta samples were collected and dissected post-delivery and incubated in RNAlater solution at 4 degrees celcius for 24 hours before being stored at -80 degrees celcius.
Extracted molecule total RNA
Extraction protocol RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with mix 1 or mix 2 of the 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts.
Ribosomal RNAs were depleted from samples using Ribo-Zero Gold. and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol at the Australian Cancer Genomics Facility in Adelaide.

Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500

Data processing 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: hg19
Supplementary_files_format_and_content: A count table of uniquely mapped read pairs overlapping genes.

Notes

Associated Persons
Claire T. Roberts ( Creator )

Issued: 2016-08-31

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Identifiers
  • global : 68a16ab6-eae7-4b59-a8a0-55fbed24a7f5