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Authors: Arnav Moudgil, Rob Mitra
Group: Transposon Calling Cards
Summary: Here we present a computational pipeline for processing single cell calling card (scCC) data. These data will have been generated from single cell RNA-seq libraries following transfection/-duction of either undirected piggyBac transposase or your favorite transcription factor (YFTF) fused to piggyBac. This workflow demonstrates how to process scCC sequencing data derived from a 10x Chromium-based scCC library; the workflow can be parallelized on distributed computing architectures (e.g. slurm).

Proper citation: Arnav Moudgil, Rob Mitra 2019. Processing Single Cell Calling Card Sequencing Data. protocols.io https://dx.doi.org/10.17504/protocols.io.4phgvj6 Copy   

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Authors: Michiyo Tsuru
Group: Clinical Proteomics and Gene Therapy Laboratory
Summary: A 4-month-old male wild-type mouse swimming. The water temperature was 34 °C.

Proper citation: Michiyo Tsuru 2018. A 4-month-old male wild-type mouse swimming. Video 2.. protocols.io https://dx.doi.org/10.17504/protocols.io.j9ncr5e Copy   

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Authors: Yeonsoo Jang, Sang Hoon Ahn, Kyunghwa Lee, Jiyeon Lee, Jeong Hyun Kim
Summary: Purpose: The purpose of this study was to conduct a psychometric evaluation of the Korean version of the Hepatitis B Quality of Life Questionnaire (K-HBQOL), which is designed to assess the quality of life of patients with the hepatitis B virus (HBV).Methods: The K-HBQOL was developed by converting the original English version to Korean using a back-and-forth translation method. The translated questionnaire was distributed to 168 adults with HBV. Descriptive statistics were used to summarize the demographic characteristics of these participants. Confirmatory factor analysis and exploratory principal components analysis (CFA and PCA) were performed, applying varimax rotation and using Kaiser’s eigenvalue-greater-than-one rule to examine the factor structure. The minimum average partial rule was also used to identify the number of components.Results: The original factor model was not confirmed by CFA in this sample. Six components (Psychological Well-being, Stigmatization, Anticipation Anxiety, Weakness, Vitality, and Vulnerability) were extracted by PCA, with 69.11% of the total variance explained. In this process, one component present in the original factor model (Transmission) was not found, while another component (Weakness) was extracted.Conclusions: This study revealed the psychometric characteristics of the Korean version of the HBQOL for patients with hepatitis B. We suggest a study with a larger sample is needed to evaluate validity and reliability of the K-HBQOL for other Korean populations.

Proper citation: Yeonsoo Jang, Sang Hoon Ahn, Kyunghwa Lee, Jiyeon Lee, Jeong Hyun Kim 2019. Psychometric evaluation of the Korean version of the Hepatitis B Quality of Life Questionnaire. protocols.io https://dx.doi.org/10.17504/protocols.io.x32fqqe Copy   

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Authors: Isaac Núñez, Tamara Matute
Group: Laboratorio de Tecnologias Libres
Summary: Protocol to co-culture individual colonies of different strains (e.g. transformed with different vectors) on a LB agar plate in a distributed and random manner.This assay has been used for low cost and open source fluorescence imaging (please see https://osf.io/dy6p2/ for further information & data, https://github.com/SynBioUC/FluoPi for code and http://docubricks.com/viewer.jsp? for hardware assembly)

Proper citation: Isaac Núñez, Tamara Matute 2017. Colony mix assay. protocols.io https://dx.doi.org/10.17504/protocols.io.jsucnew Copy   

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Authors: Hiromu Okano, Takuya Mayumi, Yuki Kataoka, Masahiro Banno, Yasushi Tsujimoto, Akihiro Shiroshita, Shunsuke Taito, Joho Tokumine
Summary: BackgroundIntravascular catheterization procedures can cause lethal complication. An appropriate education should be needed for taking advantage of ultrasound guidance, which can realize successful catheterization and prevent mechanical complication. However, the previous review only analyzed central venous catheters, and multiple randomized controlled trials (RCTs) have been published since then. We will therefore conduct an update review of simulation education for all types of catheters.AimThe purpose of this systematic review is to assess whether simulation education for ultrasound-guided intravascular catheterization will improve the success rate of catheter insertion compared with no simulation educationMethods and analysisWe will conduct a systematic review of the relevant literature according to the Cochrane Handbook and the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. We will include RCTs assessing the effect of simulation education for ultrasound-guided intravascular catheterization.The primary outcomes are success rate and adverse events, and secondary outcomes are first-time puncture success rate in eligible patients and number of punctures to success. Two independent reviewers will extract the data and assess the risk of bias.Ethics and disseminationIn this systematic review, only data from previously conducted studies will be analyzed. We will publish this systematic review in peer-reviewed journals.

Proper citation: Hiromu Okano, Takuya Mayumi, Yuki Kataoka, Masahiro Banno, Yasushi Tsujimoto, Akihiro Shiroshita, Shunsuke Taito, Joho Tokumine 2020. Efficacy of Simulation-Based Education for intravascular catheterization :protocol for a systematic review and meta- analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.biu6keze Copy   

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Authors: Joshua Welsh, Jennifer Jones
Group: Translational Nanobiology Section
Summary: This protocol outlines the steps required to collect data from light scatter reference materials for use with the FCMPASS software. This is one of a number of protocols in the pipeline for performing small particle calibration using the fcmpass software package.

Proper citation: Joshua Welsh, Jennifer Jones 2020. FCMPASS - Acquisition and gating of light scatter reference materials. protocols.io https://dx.doi.org/10.17504/protocols.io.bnhimb4e Copy   

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Authors: Bulent Arman Aksoy, Pınar Aksoy, Megan Wyatt, Chrystal M. Paulos, Jeff Hammerbacher
Group: Hammer Lab

Proper citation: Bulent Arman Aksoy, Pınar Aksoy, Megan Wyatt, Chrystal M. Paulos, Jeff Hammerbacher 2018. Human primary T cell culture media. protocols.io https://dx.doi.org/10.17504/protocols.io.qu5dwy6 Copy   

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Authors: John Tompkins, Jeffrey Ardell, Kalyanam Shivkumar

Proper citation: John Tompkins, Jeffrey Ardell, Kalyanam Shivkumar 2019. Mouse - Stellate Isolation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.2qegdte Copy   

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Authors: Melanie Bergmann , Stefan Riedinger , Ambra Stefani, Thomas Mitterling, Evi Holzknecht, Peter Grassmayr, Birgit Högl
Summary: This study evaluated the influence of a struck singing bowl on subjective and objective sleepiness during daytime compared to a relaxation period in a silent singing bowl. Subjective sleepiness was significantly lower after relaxation above a struck singing bowl. After gender stratification, the difference was still significant in women. Objective sleepiness was not different in both groups. Finally we can only speculate if women may be more susceptible to subjective improvements in case of sleepiness and show another perception of relaxation in a struck singing bowl compared to men.

Proper citation: Melanie Bergmann , Stefan Riedinger , Ambra Stefani, Thomas Mitterling, Evi Holzknecht, Peter Grassmayr, Birgit Högl 2020. Effects of singing bowl exposure on Karolinska sleepiness scale and pupillographic sleepiness test: A randomised crossover study.. protocols.io https://dx.doi.org/10.17504/protocols.io.bge9jth6 Copy   

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Authors: Yuzhalin AE, Lim SY, Gordon-Weeks AN, Roman Fischer, Kessler BM, Dihua Yu, Muschel RJ
Summary: Supporting Information 1. Raw results obtained from quantitative label-free proteomics analysis of decellularized and enriched tissues of the mouse intact liver (control) and MC38 mouse liver metastasis (tumor).

Proper citation: Yuzhalin AE, Lim SY, Gordon-Weeks AN, Roman Fischer, Kessler BM, Dihua Yu, Muschel RJ 2019. Supporting information 1 (Yuzhalin et al. 2019). protocols.io https://dx.doi.org/10.17504/protocols.io.7u2hnye Copy   

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Authors: Ryan Temel Lab
Group: Sangderk Lee lab

Proper citation: Ryan Temel Lab 2017. Extraction and analysis of liver lipids. protocols.io https://dx.doi.org/10.17504/protocols.io.iy7cfzn Copy   

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Authors: Stephanie Goya, Gabriel L. Rojo, Mercedes S. Nabaes Jordar, Laura E. Valinotto, Alicia S Mistchenko, Mariana Viegas
Summary: Here is a description of a protocol for whole genome sequencing of RSV from clinical samples (nasopharyngeal aspirates -NPA-). The protocol was tested with samples with viral loads as low as 10+03 viral copies/ml NPA.The RNA is amplified by RT-PCR in five overlapped fragments of around 2300-4500 nt in length by using specific primers which anneal in conserved regions of the genome. Briefly the protocol includes: viral RNA extraction from NPA done with silica membrane columns and fragment amplification performed in five independent reaction tubes with OneStep RT-PCR Kit (Qiagen). Each fragment size check performed in an agarose gel electrophoresis, clean-up step done with silica membrane columns and the quantification step performed by Qubit. Finally, amplicons pooled equimolarly and library prep done with Nextera XT Kit.

Proper citation: Stephanie Goya, Gabriel L. Rojo, Mercedes S. Nabaes Jordar, Laura E. Valinotto, Alicia S Mistchenko, Mariana Viegas 2018. Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load. protocols.io https://dx.doi.org/10.17504/protocols.io.qsedwbe Copy   

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Authors: Benjamin Istace, Anne Friedrich, Léo dAgata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury
Group: GigaScience Press
Summary: This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP006 protocol. It accompanies the GigaScience publication:Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience...

Proper citation: Benjamin Istace, Anne Friedrich, Léo dAgata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury 2017. SQK-MAP006 protocol for library preparation for Nanopore sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.gvvbw66 Copy   

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Authors: Liz O'Brien, Connor Tsuchida
Group: The Center for Genome Editing and Recording
Summary: This protocol describes methods to express and purify PlmCasX plasmids.

Proper citation: Liz O'Brien, Connor Tsuchida 2019. 6L Live PlmCasX Expression & Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.8srhwd6 Copy   

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Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses.

Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Ascorbic Acid Antifade Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c87zzm Copy   

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Authors: Chunhua Li, Xianwei Yang, Libin Shao, Rui Zhang, QunLiu, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan
Summary: This protocol is used to clarity the process of stLFR library preparation for Bicolor Angelfish (Centropyge bicolor) genome.

Proper citation: Chunhua Li, Xianwei Yang, Libin Shao, Rui Zhang, QunLiu, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan 2020. stLFR library construction. protocols.io https://dx.doi.org/10.17504/protocols.io.bpwxmpfn Copy   

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Authors: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying
Group: Neurodegeneration Method Development Community

Proper citation: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying 2020. High-Performance Liquid Chromatography (HPLC). protocols.io https:// Copy   

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Authors: Kenji Ohgane
Summary: This protocol covers how to fit sigmoidal curve to data within Excel, and allows rapid estimation of EC50/IC50 values from experimental dose-response data. Although R or other specialized software is more suitable for detailed analyses, it is sometimes useful to perform sigmoidal fitting within Excel. Note that this is just a simplified version (only sigmoid fitting) of the protocol reported in Gerdi Kemmer & Sandro Keller (2010) Nat. Protocol 5: 267–281, and intended for routine laboratory use.

Proper citation: Kenji Ohgane 2019. Sigmoid fitting in Excel (Excel Solver Add-In). protocols.io https://dx.doi.org/10.17504/protocols.io.78ihrue Copy   

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Authors: Sunamita Lima

Proper citation: Sunamita Lima 2018. Protocol to accompany paper entitled "Pharmacological characterization of crotamine effects on mice hind limb paralysis employing both ex vivo and in vivo assays: insights into the involvement of voltage-gated ion channels in the crotamine action on skelet. protocols.io https://dx.doi.org/10.17504/protocols.io.p7wdrpe Copy   

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Authors: Prem Premsrirut, Ana Vasileva, Huiting Cheng
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing
Summary: OverviewAt the start of the Pandemic in the US, New York was hit with more cases of COVID-19 than any single country in the world. Although case numbers are finally at an all-time low, the question of how to safely reopen the economy, school and businesses still remains unclear. Today, SARS-CoV-2 detection via RT-PCR methods remains the gold standard to detect active infection and recommend isolation of individuals in order to prevent further spread. Unfortunately, the cost and bottlenecks created from repeated massive testing efforts have become unsustainable. As a way to address this issue, we have devised a strategy of pooling samples and testing entire populations together as one unit. This cuts the cost of testing dramatically and still enables the detection of a susceptible group that would need to undergo individual testing.To meet the COVID-19 testing demands, we created an organizational-based pooling strategy, whereby organizations can enroll in surveillance testing to monitor groups of people through pooled testing. By using organizational-based pooling, we avoid random pooling of samples. Instead, we pool groups of known contacts from a defined workplace, school or organization where people regularly interact. Therefore, a positive case would likely have an impact on the entire pooled population and the entire pooled population can be treated as an infected cohort until further individual testing, potentially, through a healthcare provider is recommended or offered.Method of Pooled TestingFor pooled surveillance testing to be effective and widely adopted, sample collection methods must also be simplified and non-invasive in order to achieve high compliance and enrollment into a surveillance program. The method of testing must also be highly sensitive to accurately detect one positive case in a large pool of negative samples. For these reasons, we developed a simple saliva collection method with a validated pooled saliva specimens using RT-PCR and an acceptable limit of detection, which will be the most sensitive diagnostic test to date. We established automated methods to pool up to 24 saliva specimens and if a positive case is detected, the pools can be further broken down to pools of 2 specimens. The remaining 2 individuals within a pool will be referred to or, potentially, offered further clinical diagnostic testing by a healthcare provider.

Proper citation: Prem Premsrirut, Ana Vasileva, Huiting Cheng 2020. Mirimus COVID-19 Pool Surveillance RT-PCR Testing. protocols.io https://dx.doi.org/10.17504/protocols.io.bkv3kw8n Copy   

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