Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 78
Release date: Feb 1 2018
Last update date: Nov 29 2018
Access: Public
Taxon: Homo sapiens
Dataset link Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

Experimental Protocol


The Universal Human Reference RNA (Agilent) was diluted to 500 ng/ul in 200ul of RNase-free water and 3.94ul of the Spike-in RNA Variant Control E2 Mix (Lexogen) were added. The sample was split into two aliquots, one of which was then heated at 94° C for 1 hour and 27 minutes. 1ul of ERCC RNA Spike-In Mix 1 was added to both the intact and degraded samples. The final intact and degraded RNA samples were then diluted to 25 ng/uL and were distributed to each of the ten genomics core facilities (members of ABRF) for ribo-depletion and library preparation following vendor protocol. Each site prepared between one and four library types. Indices were assigned by the group to prevent overlapping among libraries. Libraries were pooled at an equimolar concentration from each kit using site-specific quantification and pooling SOPs and return each pool along with individual un-pooled libraries to the designated sequencing site. The sequencing site quantified each pool, multiplexed and sequenced over three high output paired-end 75bp runs on the Illumina NextSeq 500. contributor: The Association of Biomolecular Resource Facilities (ABRF) DNA Sequencing Research Group (DSRG) members

Repositories


GEO

GSE100127

ENA

SRP109549

BioProject

PRJNA390766

Download


Contact


Jyothi Thimmapuram