SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
February 2014
Authors:
Michael A Quail, Miriam Smith, David Jackson, Steven Leonard, Thomas Skelly, Harold P Swerdlow, Yong Gu, and Peter Ellis
Info:
In this paper, scientists from the Wellcome Trust Sanger Institute and Frederick National Laboratory for Cancer Research describe Sample Assurance Spike-In sequencing, or SASI-Seq. The protocol adds uniquely barcoded amplicons to samples prior to library prep and sequencing; these barcodes allow users to deconvolute samples that get mixed up or to spot cross-contamination issues. They used Pippin Prep to test barcode robustness through the size selection process, finding that barcodes were not affected.
Citation:
BMC Genomics, 15:110
Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification
January 2014
Authors:
Peter Tessarz, Helena Santos-Rosa, Sam C. Robson, Kathrine B. Sylvestersen, Christopher J. Nelson1, Michael L. Nielsen and Tony Kouzarides
Info:
The authors describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A. The data suggests that this is the first histone epigenetic mark dedicated to a specific RNA polymerase. Pippin Prep was used to size select ChIP seq libraries prior to Illumina sequencing.
Citation:
Nature, 505 (23) January 2014
Clinical and pathological heterogeneity of a congenital disorder of glycosylation manifesting as a myasthenic/myopathic syndrome
January 2014
Authors:
Dorota M. Monies, Hindi N. Al-Hindi, Mohamed A. Al-Muhaizea, Dyala J. Jaroudi, Banan Al-Younes, Ewa A. Naim, Salma M. Wakil, Brian F. Meyer, Saeed Bohlega
Info:
Collaborators at the King Faisal Specialist Hospital and the Kink Abdulaziz City for Science and Technology, Saudi Arabia, identify an homozygous mutation of ALG2 that is related to congenital muscle weakness disorders. The Pippin Prep was used in sample prep for whole exome sequencing (TargetSeq) on the Ion Torrent Proton
Citation:
Neuromuscul Disord (2014)
Epigenetic Regulation of the DLK1-MEG3 MicroRNA Cluster in Human Type 2 Diabetic Islets
January 2014
Authors:
Vasumathi Kameswaran, Nuria C. Bramswig, Lindsay B. McKenna, Melinda Penn, Jonathan Schug, Nicholas J. Hand, Ying Chen, Inchan Choi, Anastassios Vourekas, Kyoung-Jae Won, Chengyang Liu, Kumar Vivek, Ali Naji, Joshua R. Friedman, and Klaus H. Kaestner
Info:
Researchers at the University of Pennsylvania and the Children’s Hospital of Philadelphia compared small RNAs from tissue samples taken from people with and without type 2 diabetes mellitus. They found evidence that a specific cluster of microRNAs was downregulated in diabetes patients, with the promoter of that locus hypermethylated. Pippin Prep was used to size-select microRNAs for sequencing.
Citation:
Cell Metabolism (2014)
Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
January 2014
Authors:
Glenn K. Fu, Weihong Xu, Julie Wilhelmy, Michael N. Mindrinos, Ronald W. Davis, Wenzhong Xiao, and Stephen P. A. Fodor
Info:
Scientists from Cellular Research and Stanford University describe a method for improving the use of RNA-seq for absolute quantification of gene expression by barcoding cDNA molecules. This molecular indexing method allowed the team to perform deep sampling and to quantify rare transcripts. Pippin Prep was used for sizing of the cDNA sample as well as for size selection in the digital PCR validation protocol.
Citation:
PNAS 2014 111 (5) 1891–1896