Identification of Circular RNAs using RNA Sequencing
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
Authors: Sekar, Shobana; Geiger, Philipp; Cuyugan, Lori; Boyle, Annalee; Serrano, Geidy; Beach, Thomas G.; Liang, Winnie S.
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs involved in functions including micro-RNA (miRNA) regulation, mediation of protein-protein interactions, and regulation of parental gene transcription. In classical next generation RNA sequencing (RNA-seq), circRNAs are typically overlooked as a result of poly-A selection during construction of mRNA libraries, or are found at very low abundance, and are therefore difficult to isolate and detect. Here, a circRNA library construction protocol was optimized by comparing library preparation kits, pre-treatment options and various total RNA input amounts. Two commercially available whole transcriptome library preparation kits, with and without RNase R pre-treatment, and using variable amounts of total RNA input (1 to 4 mu g), were tested. Lastly, multiple tissue types; including liver, lung, lymph node, and pancreas; as well as multiple brain regions; including the cerebellum, inferior parietal lobe, middle temporal gyrus, occipital cortex, and superior frontal gyrus; were compared to evaluate circRNA abundance across tissue types. Analysis of the generated RNA-seq data using six different circRNA detection tools (find_circ, CIRI, Mapsplice, KNIFE, DCC, and CIRCexplorer) revealed that a stranded total RNA library preparation kit with RNase R pre-treatment and 4 mu g RNA input is the optimal method for identifying the highest relative number of circRNAs. Consistent with previous findings, the highest enrichment of circRNAs was observed in brain tissues compared to other tissue types.
Physiological-based cord clamping in very preterm infants - Randomised controlled trial on effectiveness of stabilisation
RESUSCITATION
Authors: Knol, Ronny; Brouwer, Emma; van den Akker, Thomas; DeKoninck, Philip; van Geloven, Nan; Polglase, Graeme R.; Lopriore, Enrico; Herkert, Ellen; Reiss, Irwin K. M.; Hooper, Stuart B.; Te Pas, Arjan B.
Abstract
Aim: To test whether stabilising very preterm infants while performing physiological-based cord clamping (PBCC) is at least as effective as the standard approach of time-based delayed cord clamping (DCC). Methods: A randomised controlled non-inferiority study was performed in two centres from May until November 2018, including preterm infants born below 32 weeks of gestational age. Infants were allocated to PBCC or standard DCC. Infants receiving PBCC were stabilised on a purpose-built resuscitation table with an intact umbilical cord. The cord was clamped when the infant had regular spontaneous breathing, heart rate >= 100 bpm and SpO(2) 90% while using FiO(2) 0.40. In infants receiving DCC, the cord was clamped at 30 60 seconds after birth before they were transferred to the standard resuscitation table for further treatment and stabilisation. Primary outcome was time to reach respiratory stability. Results: Thirty-seven infants (mean gestational age 29+0 weeks) were included. Mean cord clamping time was 5:49 +/- 2:37 min in the PBCC (n = 20) and 1:02 +/- 0:30 min in the DCC group (n = 17). Infants receiving PBCC needed less time to reach respiratory stability (PBCC 5:54 +/- 2:27 min; DCC 7:07 +/- 2:54 min; mean difference corrected for gestational age 1:19 min, 95 degrees 6 CI [3:04 0:27]), showing non-inferiority with the pre-defined limit of 1:15 min. No significant differences between the groups were found for maternal blood loss, postpartum haemorrhage, infant temperature at admission or short-term neonatal outcomes. Conclusion: Stabilisation of very preterm infants with physiological-based cord clamping is at least as effective as with standard DCC.