Deep RNA sequencing of the human placental transcriptome
Transcriptomics Dataset
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General Information
AccessionGSE77085
TitleDeep RNA sequencing of the human placental transcriptome
DescriptionThe goal of this study was to conduct an in-depth analysis of the human placental transcriptome. RNA was extracted from 16 placental samples using TRIzol following the manufacturers protocol. All samples were spiked with 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. 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. All samples were processed in the same way, with all sequencing libraries created in the same batch and sequenced together.
Landing Pagehttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77085
RepositoryGene Expression Omnibus
Tools used to analyze the dataset
Dataset Accession
Clustergrammer
Published October 2017
Web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable heatmaps
4645
ARCHS4
Published September 2017
ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO ...
4645
Canned Analyses generated with the dataset
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Dataset Accession
Tool Name
Interactive heatmap visualization of RNA-seq dataset GSE77085
ARCHS4, Clustergrammer
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
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