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Authors: David Eccles
Summary: This protocol is for a semi-manual method for read demultiplexing, as used after my presentation Sequencing DNA with Linux Cores and Nanopores to work out the number of reads captured by different barcodes.Input: reads as a FASTQ file, barcode sequences as a FASTA fileOutput: reads split into single FASTQ files per target [barcode]Note: barcode / adapter sequences are not trimmed by this protocol
Proper citation: David Eccles 2019. Demultiplexing Nanopore reads with LAST. protocols.io dx.doi.org/10.17504/protocols.io.7vmhn46 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the PCR protocol for Phusion® High-Fidelity DNA Polymerase (M0530)
Proper citation: New England Biolabs 2017. PCR Protocol for Phusion® High-Fidelity DNA Polymerase (M0530). protocols.io dx.doi.org/10.17504/protocols.io.irrcd56 Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: Quick Ligation products may be transformed by many different methods. The following protocol is recommended by New England Biolabs.
Proper citation: New England Biolabs 2015. Transformation Protocol. protocols.io dx.doi.org/10.17504/protocols.io.cpxvpm Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Summary: For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
Proper citation: David Dunigan and Irina Agarkova 2016. CviJI Buffer A. protocols.io dx.doi.org/10.17504/protocols.io.esibece Copy
Authors: Fan Rao, Wen-long Li, Zhou-ping Yin
Proper citation: Fan Rao, Wen-long Li, Zhou-ping Yin 2018. Non-rigid point cloud registration based lung motion estimation using tangent-plane distance. protocols.io dx.doi.org/10.17504/protocols.io.qrhdv36 Copy
Authors: Payam Amiri
Proper citation: Payam Amiri 2017. Agar Plates. protocols.io dx.doi.org/10.17504/protocols.io.hpab5ie Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.dep3dm Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol to generate Nextera libraries using 0.2x reagents in a 96-well PCR plate using the Formulatrix Mantis instrument.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Proper citation: Allen Institute for Brain Science 2021. Nextera XT at 0.2X On the Mantis. protocols.io dx.doi.org/10.17504/protocols.io.brdjm24n Copy
Authors: Alice Pawlowski
Summary: This protocol can be used to hybridize small RNAs (50 - 200 nt) - either from total RNA isolates or from in vitro transcripts - with digoxigenein-labeled probes, followed by detection with chemiluminescence using CDP-star. The protocol follows mainly the instructions given in the DIG Northern Starter Kit, Version 8.0 (Roche). It is adjusted to Northern Blots with membrane size of around 9 x 10 cm2 .
Proper citation: Alice Pawlowski 2020. Hybridization and detection of small RNA samples with DIG-labeled probes. protocols.io dx.doi.org/10.17504/protocols.io.us6ewhe Copy
Authors: Institute of Medical Biotechnology
Group: Optical Clearing of Tissue
Summary: Protocol for preparing a 3.7% Paraformaldehyde (PFA) solution. 3.7% PFA solution can be used to fix tissues.
Proper citation: Institute of Medical Biotechnology 2020. 3.7% Paraformaldehyde solution. protocols.io dx.doi.org/10.17504/protocols.io.bcfpitmn Copy
Authors: Tereza Blassova
Proper citation: Tereza Blassova 2019. General Immunohistochemical Protocol for formalin-fixed, paraffin-embedded tissue sections. protocols.io dx.doi.org/10.17504/protocols.io.7uxhnxn Copy
Authors: Anna Behle, Nicolas Schmelling
Group: Axmann Lab, iGEM Duesseldorf 2018
Summary: Protocol for seamless, scarless, homology-based cloning of vectors using an enzyme-free technique. The method was published by Zurbriggen et al., 2015, doi: 10.1371/journal.pone.0137652It relies on the endogenous homologous recombination machinery of E. coli lab strains.
Proper citation: Anna Behle, Nicolas Schmelling 2016. AQUA cloning. protocols.io dx.doi.org/10.17504/protocols.io.gs9bwh6 Copy
Authors: Cancer Research UK / Wellcome Gurdon Institute media kitchen
Summary: Prepare NGM plates without peptone. Peptone is necessary for bacterial growth and thus by not adding peptone, one can control for the number of bacteria present on an NGM plate by seeding a known number of bacteria.
Proper citation: Cancer Research UK / Wellcome Gurdon Institute media kitchen 2019. Prepare NGM no peptone plates. protocols.io dx.doi.org/10.17504/protocols.io.5sng6de Copy
Authors: Tina Lasisi
Summary: This protocol describes how to prepare hair fibers for cross-sectional microscopy.
Proper citation: Tina Lasisi 2020. Sample preparation protocol for cross-sectional microscopy of hair fibers. protocols.io dx.doi.org/10.17504/protocols.io.bbwcipaw Copy
Authors: Benjamin Tully
Group: Center for Dark Energy Biosphere Investigations
Summary: Method used to perform quality control on Illumina sequences - includes adapter/primer removal and quality trimmingGoal: Remove low quality sequences to increase average quality score of reads above 28
Proper citation: Benjamin Tully 2015. Basic Illumina Sequence Quality Control. protocols.io dx.doi.org/10.17504/protocols.io.d4e8td Copy
Authors: Elizabeth Allen
Summary: Nile Red is prepared in acetone to make a working concentration of 1000 ug/mL. It should be stored at 4°C in the dark.
Proper citation: Elizabeth Allen 2016. Nile Red prepared in acetone. protocols.io dx.doi.org/10.17504/protocols.io.fdpbi5n Copy
Authors: LeinU01 BRAIN grant
Group: BICCN, Allen Institute for Brain Science
Summary: Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for RNA-seq analysis.
Proper citation: LeinU01 BRAIN grant 2019. Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform. protocols.io dx.doi.org/10.17504/protocols.io.y6rfzd6 Copy
Authors: Jernej Turnsek
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Map and nucleotide sequence of the conjugation episome used to generate a TpSIl3p-EGFP expressing T. pseudonana strain reported in Faktorová D. et al.
Proper citation: Jernej Turnsek 2019. pTpPuc3_TpSil3p-eGFP. protocols.io dx.doi.org/10.17504/protocols.io.7ghhjt6 Copy
Authors: Ryan Paerl
Summary: Charcoal treatment of seawater for removal of organics. This is an updated approach to that used by Carlucci & Silbernagiel, 1970. The approach was used in Paerl et al., 2015 Limnology and Oceanography; DOI: 10.1002/lno.10009
Proper citation: Ryan Paerl 2016. Charcoal treatment of seawater to remove organics (esp. vitamins).. protocols.io dx.doi.org/10.17504/protocols.io.ehgbb3w Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: Glucose tolerance test measures systemic clearance of glucose following an intraperitoneal bolus injection of 20% dextrose. This experiment measures insulin sensitivity in awake mice assuming that there are no alterations in the animal’s pancreatic -cell function and insulin secretion. Insulin sensitivity is altered in obese mice.
Proper citation: Jason Kim 2019. U Mass - Glucose Tolerance Test. protocols.io dx.doi.org/10.17504/protocols.io.xxafpie Copy
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