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Authors: Brian Smith, [email protected] Micro.tucson
Proper citation: Brian Smith, [email protected] Micro.tucson 2019. Kings B Media (1L). protocols.io dx.doi.org/10.17504/protocols.io.xf4fjqw Copy
Authors: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao
Group: BGI
Summary: BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale.
Proper citation: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2020. BGISEQ-500 （DNBSEQ-G50） Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.bimzkc76 Copy
Authors: George Lykotrafitis
Summary: Centrifuge the whole blood in order to obtain the red blood cells.
Proper citation: George Lykotrafitis 2019. Centrifuge the whole blood to separate red blood cells. protocols.io dx.doi.org/10.17504/protocols.io.zzwf77e Copy
Authors: Luisa F. Jiménez Soto
Summary: This protocol was standarized in our lab based on the publication of Ahn T et al (2001): Polyacrylamide Gel Electrophoresis without a stacking Gel: Use of Amino Acids as Electrolytes. DOI:10.1006/abio.2001.5038
These gels run similar to a gradient gel: In a 6% gel you will be able to separate proteins ranging from 270 kDa to 25 kD an dhave them in the same gel.The adaptation to Stain-Free system was done based on the publication by Ladner CL et al (2004) : Visible fluorescent detection of proteins in polyacrylamide gels without staining. DOI:10.1016/j.ab.2003.10.047We have applied this protocol in the following publications: Zeitler AF, Gerrer KH, Haas R, Jiménez-Soto LF. Optimized semi-quantitative blot analysis in infection assays using the Stain-Free technology. J Microbiol Methods. 2016 Jul;126:38-41. doi: 10.1016/j.mimet.2016.04.016. PubMed PMID: 27150675.Jiménez-Soto LF, Haas R. The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated. Sci Rep. 2016 Mar 17;6:23227. doi: 10.1038/srep23227. PubMed PMID: 26983895; PubMed Central PMCID: PMC4794710.Jiménez-Soto LF, Clausen S, Sprenger A, Ertl C, Haas R. Dynamics of the Cag-type IV secretion system of Helicobacter pylori as studied by bacterial co-infections. Cell Microbiol. 2013 Nov;15(11):1924-37. doi: 10.1111/cmi.12166. PubMed PMID: 23844976.
Proper citation: Luisa F. Jiménez Soto 2016. Single Gel system based in Ahn T et al (2001). protocols.io dx.doi.org/10.17504/protocols.io.gipbudn Copy
Authors: Samir Parikh, John Shapiro, Brad Rovin
Group: KPMP
Summary: Recent advances in multi-scale interrogation of human tissue, including advanced imaging techniques and the powerful application of large dataset “omics”, have displayed significant promise toward identifying new and specific therapeutic targets, predicting disease progression, and individualizing treatment in participants with acute and chronic kidney disease. Our site, formed by the alliance of Indiana University and Ohio State University, will implement an unbiased tissue interrogation workflow for KPMP human kidney biopsies that integrates largescale 3D tissue imaging for quantitative supervised and unsupervised analysis/cytometry with sub-segmental “omics” data on the same kidney biopsy specimen. The sub-segmental “omics” pipeline will use fluorescence based Laser MicroDissection (LMD) to isolate specific nephron segments and interstitial/other targeted areas, for downstream analysis with transcriptomics and proteomics. The omics analysis will be eventually expanded to include bulk epigenetics. Acting harmoniously with other KPMP sites, our interrogation techniques are expected to facilitate back-mapping of key molecular pathways to the biopsy, which can subsequently identify foci of injury and/or regeneration that can undergo targeted sampling to generate further enriched omics. Therefore, in addition to a significant contribution to the human kidney atlas, our approach will complement other interrogation techniques within KPMP by providing tissue context and increasing spatial resolution for molecular signatures that arise in heterogeneous areas during kidney disease.
Proper citation: Samir Parikh, John Shapiro, Brad Rovin 2021. Laser Microdissection (LMD) for Regional Proteomics. protocols.io dx.doi.org/10.17504/protocols.io.brrqm55w Copy
Authors: Anna Martinez Casals, Cecilia Lindskog
Group: Human Protein Atlas
Summary: The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. All IHC staining in the Human Protein Atlas project are performed using the following standard protocol. The primary antibody dilution is based on titration optimization, the dilution suggested by the Human Protein Atlas can be found under antibody and antigen information for each antibody. When primary antibody originates from other host animals than rabbit, there are some modifications and different secondary antibody is used.
Proper citation: Anna Martinez Casals, Cecilia Lindskog 2019. Standardized immunohistochemical staining used in the Human Protein Atlas. protocols.io dx.doi.org/10.17504/protocols.io.yj8furw Copy
Authors: Deepak Nanjappa and Kathryn Coyne
Summary: This protocol was developed for transformation of Heterosigma akashiwo by electroporation. This species does not grow on solid medium, so transformants are grown "in bulk" and should not be considered clonal. We have had limited success with this protocol, which may need to be further optimized.
Proper citation: Deepak Nanjappa and Kathryn Coyne 2019. Electroporation of Heterosigma akashiwo. protocols.io dx.doi.org/10.17504/protocols.io.4qggvtw Copy
Authors: Mario Thomas, Jasmine Sollen, Natalia Ivanova, Michelle Feng, Reda Fayek, Heidi Abdilla, Stephanie Lim, Amanda Naaum
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, SANATA
Summary: This procedure outlines the protocol for testing for SARS-CoV-2 using a saliva sample collected from an individual. The purpose of this test is to detect low levels of SARS-CoV-2 antigen at a higher sensitivity. Precision Biomonitoring Inc. developed an ultra-rapid digital, disposable, highly-sensitive and inexpensive testing device used for screening purposes. The mobile app complementary to this medical device is connected through Bluetooth. Using this innovation, the user can be tested at point-of-care (POC) by a health care professional, and obtain qualitative results.
Proper citation: Mario Thomas, Jasmine Sollen, Natalia Ivanova, Michelle Feng, Reda Fayek, Heidi Abdilla, Stephanie Lim, Amanda Naaum 2020. XPRIZE SANATA Protocol for Saliva LFIA Test. protocols.io dx.doi.org/10.17504/protocols.io.bqfrmtm6 Copy
Authors: Angel Justiz-Vaillant
Group: Carbon
Summary: This ELISA was used to study the interactions between protein-LAG (PLAG) and staphylococcal protein-A (SpA) with different immunoglobulin preparations of mammalian and avian species.
Proper citation: Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Staphylococcal Protein A sandwich ELISA. protocols.io dx.doi.org/10.17504/protocols.io.btbbniin Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines how to generate tables to analyze CRISPR interactions. Based on methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R16: CRISPR Analysis. protocols.io dx.doi.org/10.17504/protocols.io.ejqbcmw Copy
Authors: Natalie Solonenko, Marie Burris
Group: Sullivan Lab, Temperton Lab
Summary: This protocol is intended for extraction of HMW DNA from bacterial or viral samples.
Proper citation: Natalie Solonenko, Marie Burris 2019. DNA extraction for HMW DNA. protocols.io dx.doi.org/10.17504/protocols.io.6cbhasn Copy
Authors: Jing Xu
Summary: The superoxide radical scavenging effects were examined [11]. Briefly, extract (1 ml) was added to 1 ml of 50 μM NBT solution and 1 ml of 468 μMNADH, and a 1ml aliquot of 60 μM PMS reaction mixture. After 5min, absorbance was read at 560 nm. The inhibition percent and IC50 valueswere calculated.
Proper citation: Jing Xu 2020. Superoxide Radical-scavenging Activity. protocols.io dx.doi.org/10.17504/protocols.io.bdaxi2fn Copy
Authors: Diogo Provete
Proper citation: Diogo Provete 2016. 0.1 M Millonig's phosphate buffer (pH=7.2). protocols.io dx.doi.org/10.17504/protocols.io.e3vbgn6 Copy
Authors: Elisabetta Caselli, Elisabetta Caselli
Summary: Testing antibacterial activity of bacteriophages on hard surfaces
Proper citation: Elisabetta Caselli, Elisabetta Caselli 2018. Testing antibacterial activity of bacteriophages on hard surfaces. protocols.io dx.doi.org/10.17504/protocols.io.nwmdfc6 Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Phenol extraction of Chlorella cells. protocols.io dx.doi.org/10.17504/protocols.io.eshbeb6 Copy
Authors: Rob A B Oostendorp
Summary: Appendix 2.Overview of 9 Steps of Clinical Reasoning Process including the Variables of Quality Indicators for Physiotherapy Care Process of Patients with Whiplash-Associated Disorders (WAD) for Analysis
Proper citation: Rob A B Oostendorp 2018. 2. Steps of Clinical Reasoning Process and Variables of Quality Indicators for Physiotherapy Care Process of Patients with WAD for Analysis. protocols.io dx.doi.org/10.17504/protocols.io.utgewjw Copy
Authors: Ruth Polachek, doreen
Group: XPRIZE Rapid Covid Testing
Summary: LessTests SARS-CoV2 general diagnosis protocol, using LessTests software solution.The LessTests method is agnostic to the labware, and has already been demonstrated as successful using multiple device and kit combinations.
Proper citation: Ruth Polachek, doreen 2020. LessTests. protocols.io dx.doi.org/10.17504/protocols.io.bkiakuae Copy
Authors: Alexandre Paix
Group: Genetics
Proper citation: Alexandre Paix 2015. Seamless editing of sgRNAs cloning mixture. protocols.io dx.doi.org/10.17504/protocols.io.dxb7im Copy
Authors: Nicola O'Reilly, Svend Kjaer, Maria Greco
Group: Coronavirus Method Development Community, Crick COVID-19 Consortium
Summary: Purpose of examination / Clinical relevanceAt the end of 2019, several pneumonia cases were reported in Wuhan, China and the pathogen was confirmed as a new viral strain. World Health organization has named the newly identified coronavirus as 2019-nCoV, also known as COVID19. The disease developed into a dangerous pandemic, posing major challenges to the NHS. Although more research is necessary to better understand the virus, in response to the emergency, simple and rapid testing is essential to identify the virus in infected individuals. This will aid the implementation of efficient interventions to contain the spread, and distinguish healthcare workers who have been infected, and are required to self-isolate, from those showing similar symptoms but which are not 2019-nCoV associated. The latter category may continue to work, alleviating stress on hard-pressed healthcare resources. 2019-nCoV is an RNA virus, and the diagnostic tests detect viral RNA in swabs from patient airways using a reverse transcriptase PCR assay. Samples are submitted to HSL, an accredited reporting laboratory, and transferred to FCI for testing.Principles of ExaminationThis procedure involves the preparation of binding buffer for the RNA extraction protocol.
Proper citation: Nicola O'Reilly, Svend Kjaer, Maria Greco 2020. Preparation of Binding Buffer (BB). protocols.io dx.doi.org/10.17504/protocols.io.bfd2ji8e Copy
Authors: Frank Aylward
Proper citation: Frank Aylward 2019. SYSB 3036 W01: Introduction to Unix. protocols.io dx.doi.org/10.17504/protocols.io.xhffj3n Copy
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