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Authors: Vivian Liu

Proper citation: Vivian Liu 2015. RIPA lysis buffer (strong). protocols.io https://dx.doi.org/10.17504/protocols.io.dky4xv Copy   

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Authors: Sophie Adler, Kirstie Whitaker, Mira Semmelroch, Konrad Wagstyl
Summary: The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.Protocol 2 provides instructions on how to create FreeSurfer cortical segmentations.These instructions are based on the freely available protocols on the ENIGMA-epilepsy website http://enigma.ini.usc.eduWe are very grateful to Derrek Hibar, Neda Jahanshad, Roberto Toro, Jerod Rasmussen, Theo van Erp who wrote the orginal ENIGMA protocols and offered them with an unlimited license without warranty! The main changes are the paths, which are now directed to the meld folder.

Proper citation: Sophie Adler, Kirstie Whitaker, Mira Semmelroch, Konrad Wagstyl 2018. MELD Protocol 2 - Instructions for FreeSurfer Cortical Segmentations. protocols.io https://dx.doi.org/10.17504/protocols.io.n3edgje Copy   

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Authors: Ilse Verveer, Danielle Remmerswaal, Joran Jongerling, Frederik M. van der Veen, Ingmar H. A. Franken
Summary: The aim of the study was to explore the effects of repetitive tDCS on smoking behaviour by means of ecological momentary assessments (EMA) in a sample of ad libitum smokersParticipants recruited for this study were smokers between the age of 18 and 65 years who smoked 10 cigarettes or more a day and who had the ability to speak, read, and write in Dutch. Exclusion criteria were: 1) Current substance use disorder of a substance other than nicotine or caffeine; 2) History of neurological or psychiatric disorders; 3) Any contraindication for electrical brain stimulation procedures (i.e. electronic implants or metal implants); 4) Pregnancy or breast-feeding; 5) Intentions to actively try to quit smoking in the next three months. Participants were recruited via advertisement at Erasmus University Rotterdam from October 2016 until March 2018 and received either course credit or a financial compensation of 20 euroThe current study employed a double-blind, randomized, sham-controlled design in which subjects received a total of six tDCS sessions (active or sham) on three days in one week with at least one day in between. Participants were first randomly assigned to either sham or active tDCS. Then, before the tDCS sessions and at three months follow-up, participants completed the Fagerström Test of Nicotine Dependence (FTND; [28]). Breath carbon monoxide concentrations were also measured using a Micro+ Smokerlyzer (Bedfont Scientific Ltd., Rochester, UK) to objectively define smoking.To measure changes in smoking behaviour, participants were asked to keep track of their cigarette consumption, craving and affect in an application on their mobile phones (EMA). Questions in the application were presented at four random times a day for three weeks in total (random assessments; RA’s), starting the week before the first tDCS session. After three months, participants were asked to fill out the same four-time daily random assessments for one more week. In addition, participants were asked to start a session every time they smoked a cigarette (user-initiated smoking assessment; SA) for three months in total. An ‘end of the day’ assessment (EA) was also implemented for three months, which asked participants to fill out the total number of smoked cigarettes of that day.

Proper citation: Ilse Verveer, Danielle Remmerswaal, Joran Jongerling, Frederik M. van der Veen, Ingmar H. A. Franken 2020. Testing repetitive tDCS on daily smoking behaviour: A placebo controlled EMA study. protocols.io https://dx.doi.org/10.17504/protocols.io.bcgdits6 Copy   

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Authors: Gary Trubl, Natalie Solonenko
Group: Sullivan Lab
Summary: Resuspend viruses from soils and sediments

Proper citation: Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.hu3b6yn Copy   

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Authors: Sean Seaver
Summary: How to Make a 0.5M TCEP Stock Solution

Proper citation: Sean Seaver 2014. How to Make a 0.5M TCEP Stock Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.cizuf5 Copy   

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Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm 2017. Bacterial Cryopreservation. protocols.io https://dx.doi.org/10.17504/protocols.io.ihncb5e Copy   

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Authors: Kelsey Miller
Group: BioLegend

Proper citation: Kelsey Miller 2016. Intracellular Staining With True-Phos™ Perm Buffer in Cell Suspensions. protocols.io https://dx.doi.org/10.17504/protocols.io.e2fbgbn Copy   

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Authors: Brett Hanzlicek, Ben Abelson, Margot Damaser, Dennis Bourbeau
Group: SPARC
Summary: This protocol for cat surgery to expose the badder for inactive device insertion.

Proper citation: Brett Hanzlicek, Ben Abelson, Margot Damaser, Dennis Bourbeau 2021. SPARC Cat acute UroMOCA implantation surgery. protocols.io https://dx.doi.org/10.17504/protocols.io.bf2pjqdn Copy   

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Authors: Trina Knotts
Group: Mouse Metabolic Phenotyping Centers
Summary: Changes in fecal energy loss can result in differences in net energy balance and feed efficiency, and may result from, e.g., alterations in bile acid production, secretion or re-uptake, and changes in activities of enzymes involved in macronutrient digestion or uptake (e.g., pancreatic lipase). This assay will be coupled to food intake determinations and will involve fecal collection and feces weight measures for 48h, which can be coordinated with the meal pattern studies (catalog item D4003) or indirect calorimetry (catalog item D4007). Diet and fecal energy content will be measured by bomb calorimetry and the following reported: fecal energy density, total fecal energy loss/day, and fecal energy loss as a percent of energy intake. Alternatively, fecal samples and diet samples can be examined without food intake measurements. In this case, only diet and fecal energy density will be reported. Additional tests can be done through proximate analysis (D4005- Digestible Energy by Proximate Analysis) to determine protein or fat absorption.

Proper citation: Trina Knotts 2019. UC Davis - Digestible Energy by Bomb Calorimetry. protocols.io https://dx.doi.org/10.17504/protocols.io.ygkftuw Copy   

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Authors: Boas Pucker
Group: High molecular weight DNA extraction from all kingdoms
Summary: Plant DNA extraction and preparation for ONT sequencingThis CTAB-based protocol is suitable for extraction of genomic DNA from a wide range of plant species. The DNA quality is sufficient for ONT sequencing after SRE enrichment of long fragments and removal of short fragments. Quality control steps are described as part of this protocol.Successful application for the genome sequencing of the following plant species:Arabidopsis species, Beta vulgaris (sugar beet), Brassica napus (rapeseed/canola), Dioscorea dumetorum (yams), Helichrysum umbraculigerum, mosses, Vitis vinifera (grapevine)References:Siadjeu C.*, Pucker B.*, Viehoever P., Albach D. and Weisshaar B. (2020). High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing. Genes. doi:10.3390/genes11030274.Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes. 2019. doi:10.3390/genes10090671.Photo provided by Hanna Schilbert (@HSchilbert).

Proper citation: Boas Pucker 2020. Plant DNA extraction and preparation for ONT sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.bcvyiw7w Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c53y8m Copy   

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Authors: Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg
Group: Human Cell Atlas Method Development Community

Proper citation: Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J.M Larsson, Omid R. Faridani, Rickard Sandberg 2020. Smart-seq3 Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bcq4ivyw Copy   

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Authors: Maci Heal

Proper citation: Maci Heal 2021. Converting microscopy image data and metadata with Microfile+. protocols.io https:// Copy   

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Authors: Lauren Smith, Lani Tieu, Olivier George
Group: George Lab

Proper citation: Lauren Smith, Lani Tieu, Olivier George 2020. Elevated Plus Maze. protocols.io https:// Copy   

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Authors: Rengin Yamur Akbiyik, Sevval Uysalcan
Summary: The protein expression is a process about synthesizing and modification for proteins in livingorganisms with using several laboratory techniques and devices. This technique is generallyused for obtaining protein from the competent cell that is used for carrying plasmids that possessthe protein that we want to express.Protein expression involves two general steps that;• Gene expression; which is continuum that converting DNA to the mRNA that can betranslate into protein.• Protein manufacturing; which is translation process.

Proper citation: Rengin Yamur Akbiyik, Sevval Uysalcan 2019. Protein Expression. protocols.io https://dx.doi.org/10.17504/protocols.io.sj2ecqe Copy   

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Authors: Sam Li
Group: BioLegend
Summary: Product description and procedure summary:The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc. Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Scale up volumes if using 14 mL tubes and Magnet, and place the tube in the magnet for 10 minutes.

Proper citation: Sam Li 2019. MojoSort™ Nanobeads Protocol - 2. protocols.io https://dx.doi.org/10.17504/protocols.io.7u7hnzn Copy   

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Authors: Sandra Rieger
Group: Diabetic Complications Consortium
Summary: To induce hyperglycemia in larval zebrafish, utilize a genetic β-cell ablation system involving the Tg(ins:NTR-mCherry) transgenic zebrafish strain (courtesy of Dr. Michael Parsons, Johns Hopkins University). This strain expresses the bacterial enzyme Nitroreductase (NTR), which is encoded by the nfsB gene, in β-cells of the pancreas starting around 24 hours post fertilization (hpf). Because NTR is genetically fused to the red fluorescent protein mCherry, β-cells expressing NTR can be visualized with fluorescence microscopy. Upon addition of the prodrug metronidazole (MTZ) to the embryo medium, NTR converts MTZ into a toxin, which selectively ablates NTR-expressing β-cells (Curado et al., Nature Protocols 3, 948-954 (2008). This can be monitored by the disappearance of the fluorescence under a confocal microscope. Diabetic Complication:

Proper citation: Sandra Rieger 2019. Ablation of ß-cells in Tg(ins:NTR-mCherry) transgenic zebrafish using metronidazole. protocols.io https://dx.doi.org/10.17504/protocols.io.8fkhtkw Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)

Proper citation: New England Biolabs 2015. E1202 Blunting Mixture. protocols.io https://dx.doi.org/10.17504/protocols.io.crqv5v Copy   

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Authors: Xiaohuan Sun, Yuehua Hu, Zewei Song
Summary: This protocol is used for bacteral 16S V4 and fungal ITS amplification following sequencing characterizaiton using DNBSEQ-G400 (previously known as BGISEQ-2000) sequencing platform.

Proper citation: Xiaohuan Sun, Yuehua Hu, Zewei Song 2021. High-throughput microbial metabarcoding amplification Protocol sequenced by DNBSEQ-G400. protocols.io https://dx.doi.org/10.17504/protocols.io.bn7rmhm6 Copy   

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Authors: Alex Rajewski
Summary: This describes a method to transform a plasmid into homemade DH5α cells.

Proper citation: Alex Rajewski 2018. E. coli Heat Shock Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.nwgdfbw Copy   

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