GSM2043612: villous_S15

  • Sam Buckberry (Creator)
  • Claire T. Roberts (Creator)



Source name - placental villous tissue
Organism - Homo sapiens
Characteristics -ercc spike-in pool: Mix_2
fetal sex: Female
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 (
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.
Date made available31 Aug 2016
PublisherGene Expression Omnibus (NCBI)

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