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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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DNA extraction from plants Resource Report Resource Website |
Remco Stam | Technical University of Munich | 1 | 2020 | Remco Stam 2020. DNA extraction from plants. protocols.io https:// | 2021-04-15 09:15:21 | ||||||
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Case Processing SOP (Spleen) Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bbcuiiww | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure is to outline procedures for processing and storing spleen received for HuBMAP consortium assay and analysis. | University of Florida | 2 | 2020 | Marda Jorgensen 2020. Case Processing SOP (Spleen). protocols.io https://dx.doi.org/10.17504/protocols.io.bbcuiiww | 2021-04-15 09:15:21 | |||
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Hybridization of DNA oligos Resource Report Resource Website |
Laura Sánchez | DOI:10.17504/protocols.io.8guhtww | AEGIS - Madrid iGEM 2019 | This protocol is used to hibridate two complementary DNA chains. | AEGIS - Madrid iGEM Team 2019 | 1 | 2019 | Laura Sánchez 2019. Hybridization of DNA oligos. protocols.io https://dx.doi.org/10.17504/protocols.io.8guhtww | 2021-04-15 09:15:21 | |||
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RNA to cDNA and RT-PCR protocol Resource Report Resource Website |
Heather Robeson, Jing Jin, Mohammed S. Orloff | DOI:10.17504/protocols.io.bpatmien | Used applied biosystems high-capacity RNA-to-cDNA kit and fast SYBR green master mix protocol | Jin J, Robeson H, Fagan P, Orloff MS (2020) Association of PARP1-specific polymorphisms and haplotypes with non-small cell lung cancer subtypes. PLoS ONE 15(12): e0243509. doi: 10.1371/journal.pone.0243509 | University of Arkansas for Medical Sciences, University of Arkansas for Medical Sciences, University of Arkansas for Medical Sciences | https://doi.org/10.1371/journal.pone.0243509 | 1 | 2020 | Heather Robeson, Jing Jin, Mohammed S. Orloff 2020. RNA to cDNA and RT-PCR protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bpatmien | 2021-04-15 09:15:21 | ||
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Protocol for the detection of rare alleles in bulk seed samples Resource Report Resource Website |
Anthony Brusa, Eric Patterson | DOI:10.17504/protocols.io.brtam6ie | This protocol was developed for the detection of Amaranthus palmeriseeds in mixed pools with other Amaranthus sp. seeds. This is a bulk testing protocol; each pool of seeds generates one data point, the presence or absence of A. palmeri in that sample. Testing pools should be assembled based on the relevant information (e.g. location, population, seed lot, seed supplier, etc.). Controls are extremely important for KASP based assays; this protocol requires positive, negative, and no-template controls. We strongly recommend running 8 controls for the rare allele being detected (e.g. A. palmeri) to aid in data analysis.The protocols may be extended to any species for which appropriate species-specific KASP markers have been developed. DNA extraction protocols were performed using the MPBio FastDNA Plant Kit, but other methods may be substituted. | University of Minnesota - Twin Cities, Michigan State University | 2 | 2021 | Anthony Brusa, Eric Patterson 2021. Protocol for the detection of rare alleles in bulk seed samples. protocols.io https://dx.doi.org/10.17504/protocols.io.brtam6ie | 2021-04-15 09:15:21 | ||||
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Adult mouse lung cell dissociation (on ice) Resource Report Resource Website |
Andrew Potter | DOI:10.17504/protocols.io.q6bdzan | Human Cell Atlas Method Development Community | This protocol was used to dissociate adult (8-10 wk) mouse lung tissue. The entire procedure is carried out on ice (to reduce artifact gene expression changes) and takes about half an hour. The yield was 16,240 non-RBC/mg tissue with 87% viability. | University of Cincinnati | 1 | 2018 | Andrew Potter 2018. Adult mouse lung cell dissociation (on ice). protocols.io https://dx.doi.org/10.17504/protocols.io.q6bdzan | 2021-04-15 09:15:47 | |||
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Routine Cell Culture Resource Report Resource Website |
Sean Misek | DOI:10.17504/protocols.io.q2jdycn | Neubig_Lab | Michigan State University | 1 | 2018 | Sean Misek 2018. Routine Cell Culture. protocols.io https://dx.doi.org/10.17504/protocols.io.q2jdycn | 2021-04-15 09:15:47 | ||||
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PD-L1 22C3 LDT on VENTANA BenchMark ULTRA automate Resource Report Resource Website |
Marius Ilié, Paul Hofman | DOI:10.17504/protocols.io.ixacfie | Optimised VENTANA BenchMark ULTRA protocol for PD-L1 assay using the concentrate 22C3 antibody.For the purpose of protocol development 95% of clinical specimens consisted of surgical resection specimens and the remaining 5% were bronchial biopsies and transbronchial mediastinal lymph node biopsies. | Ilie M, Khambata-Ford S, Copie-Bergman C, Huang L, Juco J, Hofman V, Hofman P (2017) Use of the 22C3 anti–PD-L1 antibody to determine PD-L1 expression in multiple automated immunohistochemistry platforms. PLoS ONE 12(8): e0183023. doi: 10.1371/journal.pone.0183023 | Université Côte d'Azur, University Hospital Federation OncoAge, Laboratory of Clinical and Experimental Pathology, Hôpital Pasteur, Nice, France, Université Côte d'Azur, University Hospital Federation OncoAge, Laboratory of Clinical and Experimental Pathology, Hôpital Pasteur, Nice, France | https://doi.org/10.1371/journal.pone.0183023 | 1 | 2017 | Marius Ilié, Paul Hofman 2017. PD-L1 22C3 LDT on VENTANA BenchMark ULTRA automate. protocols.io https://dx.doi.org/10.17504/protocols.io.ixacfie | 2021-04-15 09:15:21 | ||
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Total DNA "Midi" CTAB prep. for Zymoseptoria tritici Resource Report Resource Website |
Bruce Mcdonald | DOI:10.17504/protocols.io.s2wegfe | Zymoseptoria community protocols (STBnet) | Bruce McDonald 1990 modified from Murray and Thompson | ETHZ - ETH Zurich | 1 | 2018 | Bruce Mcdonald 2018. Total DNA "Midi" CTAB prep. for Zymoseptoria tritici. protocols.io https://dx.doi.org/10.17504/protocols.io.s2wegfe | 2021-04-15 09:15:21 | |||
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Phosphate-buffered Saline (PBS) Resource Report Resource Website |
Katy Monteith | DOI:10.17504/protocols.io.p4rdqv6 | Vale Lab | This protocol describes how to make 1 L of PBS to a final concentration of 1x or 10x solution. The solution can be made RNase free with the addition of DEPC (diethyl pyrocarbonate) as in step 5. | University of Edinburgh | 1 | 2018 | Katy Monteith 2018. Phosphate-buffered Saline (PBS). protocols.io https://dx.doi.org/10.17504/protocols.io.p4rdqv6 | 2021-04-15 09:15:21 | |||
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Cell Surface Immunofluorescence Staining Protocol Resource Report Resource Website |
Kelsey Knight | DOI:10.17504/protocols.io.tihekb6 | BioLegend | BioLegend | http://www.biolegend.com/media_assets/support_protocol/BioLegend_Surface_Staining_Flow_Protocol_060215.pdf | 3 | 2018 | Kelsey Knight 2018. Cell Surface Immunofluorescence Staining Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.tihekb6 | 2021-04-15 09:15:21 | |||
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General preparation of liposomes using probe-tip sonication Resource Report Resource Website |
Monica Rieth, Andrew Lozano, Jordan Grant | DOI:10.17504/protocols.io.3tdgni6 | Labyrieth | This method outlines a general approach for preparing liposomes using probe-tip sonication. The method has been optimized for the preparation of pure DPPC liposomes on a 25-mg scale and may require modifications as the quantity of lipid is altered or upon addition of other lipids and small molecules. | Southern Illinois University-Edwardsville, Southern Illinois University-Edwardsville, Southern Illinois University-Edwardsville | 1 | 2020 | Monica Rieth, Andrew Lozano, Jordan Grant 2020. General preparation of liposomes using probe-tip sonication. protocols.io https://dx.doi.org/10.17504/protocols.io.3tdgni6 | 2021-04-15 09:15:21 | |||
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Nuclei Isolation Prep and Protocol Resource Report Resource Website |
Emmy Li, Rene Sit | DOI:10.17504/protocols.io.6m8hc9w | Chan Zuckerberg Biohub | UCSF, CZ Biohub | 1 | 2019 | Emmy Li, Rene Sit 2019. Nuclei Isolation Prep and Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.6m8hc9w | 2021-04-15 09:15:21 | ||||
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Bacterial transformation Resource Report Resource Website |
Stephen Floor | DOI:10.17504/protocols.io.mnwc5fe | Stephen Floor Lab | Standard protocol to transform bacteria with a plasmid using chemically competent E. coli and antibiotic resistance. | UCSF | 2 | 2018 | Stephen Floor 2018. Bacterial transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.mnwc5fe | 2021-04-15 09:15:21 | |||
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S. cerevisiae Δpho84 complementation: metal toxicity Resource Report Resource Website |
David Milner | DOI:10.17504/protocols.io.re4d3gw | Richards Lab | Testing for metal toxicity as a result of addition of a putative phosphate transporter to a S. cerevisiae Δpho84 strain | University of Exeter | 1 | 2018 | David Milner 2018. S. cerevisiae Δpho84 complementation: metal toxicity. protocols.io https://dx.doi.org/10.17504/protocols.io.re4d3gw | 2021-04-15 09:15:48 | |||
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Wastewater Concentration by Adsorption and Direct Extraction for SARS-CoV-2 RNA Detection and Quantification using RT-ddPCR Resource Report Resource Website |
Aaron Bivins, Warish Ahmed, Devin North, Kyle Bibby | DOI:10.17504/protocols.io.bhiuj4ew | Coronavirus Method Development Community, 2019-nCoV Wastewater Epidemiology | The following protocol describes the GERM Lab workflow for processing wastewater for SARS-CoV-2 via pH adjustment, MCE filtration, extraction, and assay by droplet digital PCR (ddPCR). It is synonymous to method A as described in Ahmed et al. 2020 (the referenced manuscript) with modifications to the consumables and PCR format. It is intended for use in a BSL2+ lab with extra precautions for processing environmental specimens for SARS-CoV-2 as described in the CDC Interim Laboratory Biosafety Guidelines. | University of Notre Dame, CSIRO, University of Notre Dame, University of Notre Dame | https://www.sciencedirect.com/science/article/pii/S004896972033480X | 2 | 2020 | Aaron Bivins, Warish Ahmed, Devin North, Kyle Bibby 2020. Wastewater Concentration by Adsorption and Direct Extraction for SARS-CoV-2 RNA Detection and Quantification using RT-ddPCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bhiuj4ew | 2021-04-15 09:15:24 | ||
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School environmental contamination of methicillin-sensitive Staphylococcus aureus as an independent risk factor for nasal colonization in schoolchildren: an observational, cross-sectional study protocol Resource Report Resource Website |
Jialing Lin, Zhenjiang Yao | DOI:10.17504/protocols.io.wqvfdw6 | A cross-sectional study was conducted in eight elementary schools in Guangzhou, China. Nasal swabs from students and environmental swabs from school environments were collected. Univariate and multivariate logistic regression analyses under a multistage stratified cluster cross-sectional survey design were performed to access the prevalence relationship and influencing factors, respectively. Phenotypic and molecular characterizations of MSSA isolates were conducted using the Kirby-Bauer disk diffusion method and polymerase chain reaction assays, respectively. | University of New South Wales, Guangdong Pharmaceutical University | https://doi.org/10.1371/journal.pone.0208183 | 2 | 2019 | Jialing Lin, Zhenjiang Yao 2019. School environmental contamination of methicillin-sensitive Staphylococcus aureus as an independent risk factor for nasal colonization in schoolchildren: an observational, cross-sectional study protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.wqvfdw6 | 2021-04-15 09:15:24 | |||
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Optogenetically stimulating enteric neurons in the murine large intestine. Resource Report Resource Website |
Dante Heredia, Thomas Gould | DOI:10.17504/protocols.io.bgr9jv96 | Protocol for optogenetically stimulating neuronal subtypes in murine colonic myenteric plexus. | Department of Physiology and Cell Biology, University of Nevada Reno School of Medicine, Department of Physiology and Cell Biology, University of Nevada Reno School of Medicine | 1 | 2020 | Dante Heredia, Thomas Gould 2020. Optogenetically stimulating enteric neurons in the murine large intestine.. protocols.io https://dx.doi.org/10.17504/protocols.io.bgr9jv96 | 2021-04-15 09:15:48 | ||||
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DASH Protocol v2.5 Resource Report Resource Website |
Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman | DOI:10.17504/protocols.io.y9gfz3w | Chan Zuckerberg Biohub | This protocol is for performing Depletion of Abundant Sequences by Hybridization (DASH) after preparing sequencing libraries and pooling together.DASH is most useful for RNA-seq of human metagenomic samples, where abundant species such as human mitochondrial ribosomal RNAs (rRNAs) occupy a majority of the sequencing space available, leaving a minor fraction for regions of interest. DASH treatment is performed after ligation of adapters and unique barcoding of the RNA-seq library. It employs CRISPR-Cas9 complexed to a set of guide RNAs (gRNAs) targeted to the abundant regions to be depleted in a given library. These abundant regions in the library are then cleaved, leaving only the fragments with intact adapters on both ends to be further amplified and sequenced. | CZ Biohub, CZ Biohub, CZ Biohub, UCSF, CZ Biohub | 1 | 2019 | Amy Lyden, Emily Crawford, Jenai Quan, Saharai Caldera, David Dynerman 2019. DASH Protocol v2.5. protocols.io https://dx.doi.org/10.17504/protocols.io.y9gfz3w | 2021-04-15 09:15:24 | |||
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Manual dissection of the Schistosoma mansoni esophagus and back end for proteomic analysis Resource Report Resource Website |
Leandro Xavier Neves, R. Alan Wilson, William de Castro Borges | DOI:10.17504/protocols.io.tq2emye | Schistosomes are intravenous parasites with ability to survive in the mammalian host for decades, using its blood as a source of nutrients. The feeding process is multistep and takes place along the worm’s alimentary tract, which comprises an (i) oral cavity opening to a short (ii) esophagus that is connected to the (iii) the gut caecum. The ultrastructureal morphology of Schistosoma mansoni and S. japonicum has revealed the existence of two secretory cell masses surrounding the esophagus tube, referred to as the anterior and posterior esophageal glands (antESO and postESO, respectively). We recently established that the esophageal glands have a pivotal role in the first steps of blood processing. For instance, erythrocytes and leucocytes are quickly processed along the esophagus before they are propelled to the lower parts of the intestines for further digestion nutrient uptake. We propose that incorrect functioning of alimentary tract is associated with worms death by starvation. This was first observed in the self-cure response of Rhesus macaque (Macaca mulatta), one of few known vertebrate hosts capable of combating the disease through worm elimination once the infection is stablished. Classical immunoproteomics (2D-PAGE and Western blotting) has revealed potential targets in both exposed tegument and secreted gut proteins. Recently, a more detailed investigation using S. japonicum in the Rhesus model shed light on the possible operating mechanisms that prevent parasite feeding on blood. In addition, ultrastructural studies and immunocytochemistry on surviving worms indicated the esophageal lumen and the gland secretions as the primary targets of a potent and protective humoral immune response that ultimately disrupts the esophageal functions. Therefore, the molecular characterisation of the esophageal gland constituents is imperative if one intends to emulate the Rhesus self-cure response for therapeutic purposes. However, this is not a trivial task as challenges are multiple. Perhaps, the most important caveat is that both anterior and posterior parts of the oesophageal gland represent a minor fraction of the whole parasite body (or even of its head), meaning that dominant constituents, such as those derived from muscle tissues, suppress the identification of a unique set of gland products. Indeed, our recent investigation on the soluble protein composition of a S. mansoni preparation failed to detect the presence of gland products attesting for their low abundance in the whole worm. Although optimized protocols for chemical/enzymatic dissection are reported for isolation of testes and ovary of adult worms, no method has proved feasible for gastrodermal epithelium and the esophageal gland cells. We tackled these challenges by developing a dissection technique on worms preserved in RNAlater solution aided by an essential set of scissors and tweezers that delivers adequate precision during the procedure. The method herein described is compatible with downstream proteomic analyses using mass spectrometry and has permitted a large-scale characterisation of proteins expressed in the S. mansoni esophagus and gastrodermis. This methodology can be applied in the molecular characterisation of other schistosome organs and tissues that present a well-defined anatomic location. | Laboratório Nacional de Biociências, LNBio/CNPEM, University of York, Universidade Federal de Ouro Preto | 1 | 2019 | Leandro Xavier Neves, R. Alan Wilson, William de Castro Borges 2019. Manual dissection of the Schistosoma mansoni esophagus and back end for proteomic analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.tq2emye | 2021-04-15 09:15:48 |
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