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Name Authors DOI Group Summary Associated Publications RRIDs used Affiliations External URL Version Publication Date Proper Citation Record Last Update
Antibiotics solutions
 
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Diego Bonatto 10.17504/protocols.io.puednte Grupo de Estudos de Leveduras Cervejeiras 12Ampicillin100 mg/mL100 µg/mL3Bleocin5 mg/mL5 µg/mL4Carbenicillin*100 mg/mL100 µg/mL5Chloramphenicol25 mg/mL(dissolve in EtOH)25 µg/mL6Coumermycin25 mg/mL(dissolve in DMSO)25 µg/mL7Gentamycin10 mg/mL10 µg/mL8Kanamycin50 mg/mL50 µg/mL9Spectinomycin50 mg/mL50 µg/mL10Tetracycline10 mg/mL10 µg/mLNote: Unless otherwise indicated, the antibiotic powder can be dissolved in dH2O.*Note: Carbenicillin can be used in place of ampicillin. Carbenicillin is more stable, so it is potentially more effective at selecting only bacteria containing the plasmids of interest (for example, fewer satellite colonies will grow). However, it is also more expensive. Centro de Biotecnologia da UFRGS 2 2018 Diego Bonatto 2018. Antibiotics solutions. protocols.io dx.doi.org/10.17504/protocols.io.puednte 2021-03-29 03:10:09
Plumage pigments identification by High-performance liquid chromatography
 
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Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li 10.17504/protocols.io.sjtecnn GigaScience Press As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst’s pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds. Here we provide details of the protocols used for plumage pigments identification by High-performance liquid chromatography. The fat-soluble pigments (carotenoids) and oxidation products of melanins (TTCA and PTCA) can be qualitatively and quantificationally analyzed by HPLC with the corresponding standards, respectively. The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA., Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China. www.doi.org/10.5524/100486 1 2018 Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li 2018. Plumage pigments identification by High-performance liquid chromatography. protocols.io dx.doi.org/10.17504/protocols.io.sjtecnn 2021-03-29 03:10:10
A Randomized Trial of a Pilot Behavioral Support Intervention After Bariatric Surgery
 
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Michelle Lent 10.17504/protocols.io.2bagaie Bariatric surgery patients may experience significant psychosocial changes after surgery, but littlepsychological support is available beyond support groups postoperatively. We evaluated the feasibility of apostoperative support program targeting quality of life, psychosocial functioning and adherence to behavior change in bariatric surgery patients. This prospective, randomized pilot trial evaluated a comprehensive postoperative behavioral support intervention using a 4-month bi-weekly program in 24 bariatric surgery patients compared to 26 usual care patients that completed bariatric surgery within one year. Outcomes included feasibiilty and the difference in quality of life (as measured by the Short Form-36) between groups, as well as differences in psychosocial functioning (mood, eating behaviors) and adherence (diet, physical activity, appointments). Outcomes were assessed at baseline and treatment completion (4 months). The intervention focused on addressing psychosocial changes after surgery, strategies for postoperative diet and adherence, and preventing weight regain. Patients collaboratively set goals for diet, physical activity, adherence and other behavioral changes tailored to the needs of each participant. Intervention patients were asked to attend 8, one-hour bi-weekly treatment sessions in a 4-month time period. Lent MR, Campbell LK, Kelly MC, Lawson JL, Murakami JM, Gorrell S, Wood GC, Yohn MM, Ranck S, Petrick AT, Cunningham K, LaMotte ME, Still CD (2019) The feasibility of a behavioral group intervention after weight-loss surgery: A randomized pilot trial. PLoS ONE 14(10): e0223885. doi: 10.1371/journal.pone.0223885 Geisinger Health System, Philadelphia College of Osteopathic Medicine https://doi.org/10.1371/journal.pone.0223885 1 2019 Michelle Lent 2019. A Randomized Trial of a Pilot Behavioral Support Intervention After Bariatric Surgery. protocols.io dx.doi.org/10.17504/protocols.io.2bagaie 2021-03-29 03:10:10
DNA extraction for the Betta splendens genome
 
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Kailong Ma 10.17504/protocols.io.qvedw3e GigaScience Press, BGI This protocol is used to clarity the process of total DNA extraction for our Betta splendens genome. BGI-Shenzhen 1 2018 Kailong Ma 2018. DNA extraction for the Betta splendens genome. protocols.io dx.doi.org/10.17504/protocols.io.qvedw3e 2021-03-29 03:10:17
Use of Health Improvement Card by Chinese physical therapy students: A pilot study
 
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Alice Jones, XB Wu, YW Bai, Jia Han, Elizabeth Dean 10.17504/protocols.io.54kg8uw This protocol describes the methods for a study aimed to investigate perceptions of Chinese physical therapy students on the use of the Health Improvement Care (HIC) as a clinical tool to assess lifestyle behaviors/attributes and provide lifestyle education advice to others. Title of the study: Use of Health Improvement Card by Chinese physical therapy students: A pilot study. Xubo Wu, Alice YM Jones, Yiwen Bai, Jia Han, Elizabeth Dean. Wu X, Jones AY, Bai Y, Han J, Dean E (2019) Use of the Health Improvement Card by Chinese physical therapy students: A pilot study. PLoS ONE 14(9): e0221630. doi: 10.1371/journal.pone.0221630 The University of Sydney, The University of Queensland, Shanghai University of Traditional Chinese Medicine, Department of Physical Therapy, Shanghai, China; Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Department of Rehabilitation Medicine, Shanghai, China, Shanghai University of Traditional Chinese Medicine, Department of Physical Therapy, Shanghai, China; Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Department of Rehabilitation Medicine, Shanghai, China, Shanghai University of Sports, Physiotherapy and Sports Rehabilitation Department, Shanghai, China; University of Canberra, Research Institute for Sport and Exercise, ACT, Australia; Swinburne University of Technology, Faculty of Health, Arts and Design, VIC, Australia, University of British Columbia, Department of Physical Therapy, Vancouver, Canada https://doi.org/10.1371/journal.pone.0221630 1 2019 Alice Jones, XB Wu, YW Bai, Jia Han, Elizabeth Dean 2019. Use of Health Improvement Card by Chinese physical therapy students: A pilot study. protocols.io dx.doi.org/10.17504/protocols.io.54kg8uw 2021-03-29 03:10:17
RT-free Nanopore direct RNA sequencing v1
 
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Miten Jain 10.17504/protocols.io.bpiimkce Reverse Transcription-free (RT-free) poly(A) RNA protocol for Nanopore Direct RNA SequencingThis protocol was developed as a collaboration between NASA Houston, Oxford Nanopore Technologies, and UC Santa Cruz to support direct RNA Nanopore sequencing on the International Space Station (ISS). Contributors: NASA JSC Houston: Sarah Stahl, Aaron S. Burton, Kristen K. John, Sarah L. Castro-WallaceOxford Nanopore Technologies: Daniel Jachimowicz, Daniel R. GaraldeUniversity of California Santa Cruz: Mark Akeson, Benedict Paten, Miten JainOxford Nanopore Technologies: Daniel Jachimowicz, Daniel R. GaraldeUniversity of California Santa Cruz: Mark Akeson, Benedict Paten, Miten Jain UC Santa Cruz 1 2020 Miten Jain 2020. RT-free Nanopore direct RNA sequencing v1. protocols.io dx.doi.org/10.17504/protocols.io.bpiimkce 2021-03-29 03:10:17
SSH Amazon EC2
 
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Mihai IONITA 10.17504/protocols.io.xjcfkiw University of Bucharest, Faculty of Biology https://eu-central-1.console.aws.amazon.com/ec2/v2/home?region=eu-central-1#Instances:sort=instanceId 2 2019 Mihai IONITA 2019. SSH Amazon EC2. protocols.io dx.doi.org/10.17504/protocols.io.xjcfkiw 2021-03-29 03:10:17
Extraction method B (FMS and CR)
 
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Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert 10.17504/protocols.io.im9cc96 GigaScience Press This protocol allows for adequate DNA extraction from fresh blood samples. Salleh FM, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP, An expanded mammal mitogenome dataset from Southeast Asia. GigaScience 6(8). doi: 10.1093/gigascience/gix053 Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark , Natural History Museum of Denmark, Copenhagen, Denmark https://doi.org/10.1093/gigascience/gix053 1 2017 Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert 2017. Extraction method B (FMS and CR). protocols.io dx.doi.org/10.17504/protocols.io.im9cc96 2021-03-29 03:10:17
Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hen's egg yolks.
 
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Angel Justiz-Vaillant 10.17504/protocols.io.bjj3kkqn University of the West Indies, [email protected] Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hens was a reproducible and feseable test used to meassure IgY development after vaccination. University of The West Indies. St. Augustine. Trinidad and Tobago. 1 2020 Angel Justiz-Vaillant 2020. Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hen's egg yolks.. protocols.io dx.doi.org/10.17504/protocols.io.bjj3kkqn 2021-03-29 03:10:16
Assessment of cell death
 
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karen maciel de oliveira 10.17504/protocols.io.ruhd6t6 This assay is used to measure cell viability. Dead cells have damage membranes. The ethidium homodimer-1 enters damaged cells and is fluorescent when bound to nucleic acids, producing a bright red fluorescence in damaged or dead cells. Oliveira KM, Binda NS, Lavor MSL, Silva CMO, Rosado IR, Gabellini ELA, Silva JFD, Oliveira CM, Melo MM, Gomez MV, Melo EG (2018) Conotoxin MVIIA improves cell viability and antioxidant system after spinal cord injury in rats. PLoS ONE 13(10): e0204948. doi: 10.1371/journal.pone.0204948 Universidade Federal de Minas Gerais https://doi.org/10.1371/journal.pone.0204948 1 2018 karen maciel de oliveira 2018. Assessment of cell death. protocols.io dx.doi.org/10.17504/protocols.io.ruhd6t6 2021-03-29 03:10:16
Transformation using Electroporation
 
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Alba Balletbó 10.17504/protocols.io.7jzhkp6 iGEM Wageningen 2019 Wageningen University 1 2019 Alba Balletbó 2019. Transformation using Electroporation. protocols.io dx.doi.org/10.17504/protocols.io.7jzhkp6 2021-03-29 03:10:16
Striga hermonthica germination assay
 
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Emily Bellis, Elizabeth Kelly 10.17504/protocols.io.2wdgfa6 This protocol describes a standard germination assay for Striga hermonthica carried out in the Penn State quarantine facility. The Pennsylvania State University, The Pennsylvania State University 1 2019 Emily Bellis, Elizabeth Kelly 2019. Striga hermonthica germination assay. protocols.io dx.doi.org/10.17504/protocols.io.2wdgfa6 2021-03-29 03:10:16
Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride
 
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David Dunigan and Irina Agarkova 10.17504/protocols.io.eq7bdzn VERVE Net University of Nebraska-Lincoln 1 2016 David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride. protocols.io dx.doi.org/10.17504/protocols.io.eq7bdzn 2021-03-29 03:10:16
Electroporation of Euplotes crassus: conditions that allow for the uptake of DAPI.
 
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Lawrence A. Klobutcher 10.17504/protocols.io.gwmbxc6 Protist Research to Optimize Tools in Genetics (PROT-G) The electroporation procedure and conditions described allow for the entry of DAPI into the cell, resulting in nuclear staining. We have not yet been successful in using these conditions for transformation of Euplotes crassus, but only a couple of constructs have been tried to date. University of Connecticut Health Center 1 2017 Lawrence A. Klobutcher 2017. Electroporation of Euplotes crassus: conditions that allow for the uptake of DAPI.. protocols.io dx.doi.org/10.17504/protocols.io.gwmbxc6 2021-03-29 03:10:17
CRISPR/Cas9 based knockout generation in Aurantiochytrium limacinum (ATCC MYA-1381)
 
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Anbarasu Karthikaichamy, Jackie Collier 10.17504/protocols.io.baeyibfw Collier Lab Transformation protocol for electroporation of CRISPR/Cas9 ribonucleoprotein (RNP) complex in urantiochytrium limacinum (ATCC MYA-1381; Stramenopile/ Heterokont, Thraustochytrid). State University of New York at Stony Brook, State University of New York at Stony Brook 1 2019 Anbarasu Karthikaichamy, Jackie Collier 2019. CRISPR/Cas9 based knockout generation in Aurantiochytrium limacinum (ATCC MYA-1381). protocols.io dx.doi.org/10.17504/protocols.io.baeyibfw 2021-03-29 03:10:16
Oral versus intravenous methylprednisolone for treatment of relapses in multiple sclerosis?a meta-analysis of randomized controlled trials.
 
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Shuo Liu 10.17504/protocols.io.j5hcq36 Liu S, Liu X, Chen S, Xiao Y, Zhuang W (2017) Oral versus intravenous methylprednisolone for the treatment of multiple sclerosis relapses: A meta-analysis of randomized controlled trials. PLoS ONE 12(11): e0188644. doi: 10.1371/journal.pone.0188644 first affiliated hospital of Shantou University Medical College https://doi.org/10.1371/journal.pone.0188644 1 2017 Shuo Liu 2017. Oral versus intravenous methylprednisolone for treatment of relapses in multiple sclerosis?a meta-analysis of randomized controlled trials.. protocols.io dx.doi.org/10.17504/protocols.io.j5hcq36 2021-03-29 03:10:16
Experimental procedure of Household Activities and Physical Activity
 
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Kenji Tsuchiya 10.17504/protocols.io.jatcien Tsuchiya K, Mitsui S, Fukuyama R, Yamaya N, Fujita T, Shimoda K, Tozato F, An acute bout of housework activities has beneficial effects on executive function. Neuropsychiatric Disease and Treatment doi: 10.2147/NDT.S153813 https://doi.org/10.2147/NDT.S153813 1 2018 Kenji Tsuchiya 2018. Experimental procedure of Household Activities and Physical Activity. protocols.io dx.doi.org/10.17504/protocols.io.jatcien 2021-03-29 03:10:19
ELISA for quantification of IL-6 in human serum or plasma.
 
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Angel Justiz-Vaillant 10.17504/protocols.io.bjy7kpzn University of the West Indies, [email protected] Interleukin-10 is a pleiotropic cytokine playing a critical role as a regulator of myeloid and lymphoid cell function. Due to the ability of IL-10 to blocking cytokine synthesis and many accessory cell functions of antigen-presenting cells such as macrophages this cytokine is a potent suppressor of the effector functions of macrophages, T-cells and NK cells. IL-10 also participates in regulating proliferation and differentiation of B-lymphocytes, mast cells and thymocytes [1]. Reference1. Ouyang W, O'Garra A. IL-10 Family Cytokines IL-10 and IL-22: from Basic Science to Clinical Translation.Immunity. 2019;50(4):871-891. doi:10.1016/j.immuni.2019.03.020 University of the West Indies St. Augustine 1 2020 Angel Justiz-Vaillant 2020. ELISA for quantification of IL-6 in human serum or plasma.. protocols.io dx.doi.org/10.17504/protocols.io.bjy7kpzn 2021-03-29 03:10:15
Lysate Preparation from Viruses in Mammalian Tissue
 
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Bioline 10.17504/protocols.io.f5gbq3w Bioline The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases.This protocol describes the isolation of viral RNA from small amounts of tissue (up to 20 mg for most types of tissue). http://www.bioline.com/us/downloads/dl/file/id/3789/isolate_ii_biofluids_rna_kit_product_manual.pdf 1 2016 Bioline 2016. Lysate Preparation from Viruses in Mammalian Tissue. protocols.io dx.doi.org/10.17504/protocols.io.f5gbq3w 2021-03-29 03:10:14
A method for isolating RNA from canine bone 
 
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Rebecca Nance, Payal Agarwal, Maninder Sandey, Dmytro Starenki, Jey Koehler, Abdul Mohin Sajib, Bruce F Smith 10.17504/protocols.io.be86jhze Extracting sufficient quantity and quality RNA from bone is essential for downstream application, such as transcriptomic sequencing, to evaluate gene expression. Isolation of RNA from bone presents a unique challenge owing to the hypocellular, brittle and mineralized matrix, which makes homogenizing the tissue difficult and provides little RNA to work with. Removal of contaminating tissue, such as bone marrow and connective tissue, is essential for isolating RNA that is unique to osteoblasts, osteoclasts and osteocytes. This protocol establishes a method to effectively isolate RNA from normal canine bone cells using the second phalanx, without contamination from other tissue types, for downstream transcriptomic analysis.This method combines physical manipulation to remove exterior tissue, washing and centrifugation to remove cells and fat within the diaphysis, homogenization using a mortar and pestle on dry ice prior to bead dissociation, followed by acid guanidinium thiocyanate-phenol-chloroform extraction and column purification to yield sufficiant quantity and quality RNA from canine phalanges. The second phalanx was chosen due to its size small enough to fit into a 1.7 mL microfuge tube, but large enough to provide enough RNA. Mean RNA obtained using this protocol was 14.7 ug of RNA per gram of frozen bone. Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine , Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine, Department of Pathobiology, Auburn University College of Veterinary Medicine, Hudson Alpha Institute for Biotechnology, Huntsville AL , Department of Pathobiology, Auburn University College of Veterinary Medicine, Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine, Scott-Ritchey Research Center, Auburn University College of Veterinary Medicine https://www.future-science.com/doi/10.2144/btn-2019-0153?fbclid=IwAR1AdUnM10wOsts2pwp5AYhi_UkxRibNLK4ZjWFpwuusnqA6_IyRxiIFeGg 1 2020 Rebecca Nance, Payal Agarwal, Maninder Sandey, Dmytro Starenki, Jey Koehler, Abdul Mohin Sajib, Bruce F Smith 2020. A method for isolating RNA from canine bone . protocols.io dx.doi.org/10.17504/protocols.io.be86jhze 2021-03-29 03:10:14

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