Citations

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

March 2018

Authors:
Seyed Yahya Anvar, Guy Allard, Elizabeth Tseng, Gloria Sheynkman, et al.

Info:
Researchers from Leiden University Medical Center and other institutions studied the relationships between transcription initiation and splicing and polyadenylation events in breast cancer cells and several types of human tissue. They found that there are still unresolved mechanisms governing transcription. The team used SageELF to create size-based fractions for cDNA libraries prior to sequencing with PacBio.

Citation:
Genome Biology 2018 19:46
doi: 10.1186/s13059-018-1418-0

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Transmission of microRNA antimiRs to mouse offspring via the maternal-placental-fetal unit

March 2018

Authors:
Jonas Hönig, Ivana Mižíková, Claudio Nardiello, David Emanuel Surate Solaligue, et al.

Info:

In Germany, researchers delivered microRNA inhibitors to pregnant mice, finding that the antimiRs were then detectable in offspring, where they caused fewer off-target effects compared to direct injection of antimiRs into mouse pups. This approach could make it easier to study the effects of microRNAs during pregnancy and early postnatal development. For this project, the team used PippinHT to size-select RNA pools with a target size of 154 bp.

Citation:
RNA
http://rnajournal.cshlp.org/content/early/2018/03/14/rna.063206.117.abstract

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Improving saliva shotgun metagenomics by chemical host DNA depletion

February 2018

Authors:
Clarisse Marotz, Jon Sanders, Cristal Zuniga, Livia Zaramela, Rob Knight, and Karsten Zengler

Info:
Scientists from the University of California, San Diego, developed and evaluated a new protocol for enriching microbial DNA collected from fresh and frozen human saliva samples. Compared to commercially available kits, their method is “cost-effective, rapid, and robust,” the team concludes. They used PippinHT to remove primer dimers and target 300 bp to 800 bp DNA fragments prior to sequencing.

Citation:
Microbiome. 2018; 6: 42.
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0426-3

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Study protocol: rationale and design of the community-based prospective cohort study of kidney function and diabetes in rural New Mexico, the COMPASS study

February 2018

Authors:
Antonin Jaros, Hafiz Sroya, Venita Wolfe, Vikas Ghai, et al.


Info:

Scientists report design and launch of the COMPASS study, a prospective, longitudinal cohort in rural New Mexico aimed at better understanding diabetic chronic kidney disease and related biomarkers. They believe focusing on a high-risk area will help address disparities in kidney disease research. For miRNA biomarker discovery, they are using PippinHT to select purified PCR products ranging from 127 bp to 156 bp.

Citation:
BMC Nephrology
doi: 10.1186/s12882-018-0842-4

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Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

February 2018

Authors:
Emily Fowler, Irina Mohorianu, Damian Smith, Tamas Dalmay, Tracey Chapman

Info:

Scientists present a method for removing highly abundant rRNAs for improved analysis of small RNAs in RNA interference studies. Results showed increased resolution of sRNAs, even those seen at low frequency. For this work, the team cited BluePippin as a commonly used size selection tool for preparing sRNA-seq libraries.

Citation:
PLoS One
doi: 10.1371/journal.pone.0191966

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