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Sample GSM2043604 Query DataSets for GSM2043604
Status Public on Aug 31, 2016
Title villous_S7
Sample type SRA
 
Source name placental villous tissue
Organism Homo sapiens
Characteristics ercc spike-in pool: Mix_2
fetal sex: Male
gestational age (weeks): 41.29
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.
 
Submission date Jan 21, 2016
Last update date May 15, 2019
Contact name Sam Buckberry
E-mail sam.buckberry@uwa.edu.au
Organization name The University of Western Australia
Street address 35 Stirling Highway, Crawley
City Perth
State/province WA
ZIP/Postal code 6009
Country Australia
 
Platform ID GPL16791
Series (1)
GSE77085 Deep RNA sequencing of the human placental transcriptome
Relations
BioSample SAMN04432823
SRA SRX1539766

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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