Protocols   Select Another Resource Report Type

Authors: Shuangshuang Li

Proper citation: Shuangshuang Li 2018. Cell proliferation assay. protocols.io https://dx.doi.org/10.17504/protocols.io.h4kb8uw Copy   

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Authors: Brian Aevermann, Richard Scheuermann
Group: Human Cell Atlas Method Development Community
Summary: NS-Forest is an alogrithm that determines the minimum set of genes that are necessary and sufficient to define a cell type cluster derived from single cell RNAseq expression data. Development and stable releases can be found at : https://github.com/JCVenterInstitute/NSForest

Proper citation: Brian Aevermann, Richard Scheuermann 2018. NS-Forest version 2. protocols.io https://dx.doi.org/10.17504/protocols.io.un7evhn Copy   

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Authors: Fabio Grati, Martina Scanu, Luca Bolognini
Summary: These protocols refer to a study having the aim to identify and test at field artificial structures suitable as collectors for common cuttlefish Sepia officinalis eggs in wild condition for restocking purpose.During the same study, three different protocols were tested and compared. The 'seagrass' collector, the 'longline' collector and the 'trap' collector.This work was supported by the project “Protection, improvement and integrated management of the sea environment and of cross-border natural resources – ECOSEA”, funded by EU Adriatic IPA Cross-border Cooperation 2007-2013 (2°ord./0236/0).

Proper citation: Fabio Grati, Martina Scanu, Luca Bolognini 2018. Artificial eggs collector for common cuttlefish. protocols.io https://dx.doi.org/10.17504/protocols.io.sipecdn Copy   

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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community, PATH
Summary: This is Part 5 of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Study Vaccine (Part 5 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5zkq76 Copy   

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Authors: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa

Proper citation: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa 2019. Virus titration. protocols.io https://dx.doi.org/10.17504/protocols.io.7zhhp36 Copy   

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Authors: Diep Ganguly, Timothy Rhodes, Nay Chi Khin, Estee E Tee, Kai Xun Chan
Group: Pogson Genomics Group
Summary: Protocol for recombinant protein expression in E. coli for protein purification and subsequent enzyme assays, protein crystallography etc.

Proper citation: Diep Ganguly, Timothy Rhodes, Nay Chi Khin, Estee E Tee, Kai Xun Chan 2020. Heterologous protein expression in E. coli. protocols.io https://dx.doi.org/10.17504/protocols.io.bdjti4nn Copy   

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Authors: Martin Thomas Jahn
Group: hostmicrobeprotocols
Summary: Protocoll to create a fixed suspension of sponge associated prokaryotes (SAP) from sponge tissue.This can serve as the basis for Fluorescence in situ hybridisation and/or cell sorting.This protocol was tested for different sponge species but might also be adapted to other organisms (let others know)The protocol was modified from :Fieseler L, Horn M, Wagner M, Hentschel U. (2006) Discovery of the novel candidate phylum "Potibactetia" in marine sponges (vol 70, pg 3724, 2004). Applied and Environmental Microbiology;72(8):5677-.PMID:15184179 DOI:10.1128/AEM.70.6.3724-3732.2004

Proper citation: Martin Thomas Jahn 2019. Isolate prokaryotes from sponge tissue (SAP). protocols.io https://dx.doi.org/10.17504/protocols.io.u8vezw6 Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. Stacking gel buffer (4X). protocols.io https://dx.doi.org/10.17504/protocols.io.eq4bdyw Copy   

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Authors: Charlotte Herzeel
Summary: Instructions for recreating the elPrep4.0.0 WGS benchmarks used in the following paper:Herzeel C, Costanza P, Decap D, Fostier J, Verachtert W. elPrep: A multithreaded framework for sequence analysis. BioRxv https://doi.org/10.1101/492249

Proper citation: Charlotte Herzeel 2019. Instructions for recreating elPrep 4.0.0 WGS benchmarks. protocols.io https://dx.doi.org/10.17504/protocols.io.w35fgq6 Copy   

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Authors: Michael Lloyd Strack
Summary: This protocol describes a method of sampling groundwater from bore-holes. The method was used in my PhD research on aquifer microbial ecology over two weeks at the Wellington Research Station in New South Wales, Australia. With a little practise, the method can probably be carried out solo by most people, although additional assistance would certainly speed things up. I managed to consistently sample and process groundwater from eight bores a day using this method; your mileage may vary depending on number of workers, distance between bores, and so on.The sampling protocol describes the use of an inertia pump for bores with an internal diameter of approximately 5 cm and a sampled depth of less than 60 m. It includes the measurement of bore information - such as depth and water table - as well as the use of water meters to measure the pH, dissolved oxygen, temperature and conductivity of groundwater, and of course the collection of the groundwater sample itself.Separete protocols will be provided for sampling narrow-diameter bores, sampling stygofauna, sampling surface soils, conducting colorimetric analysis of ferrous and sulphide anion concentrations, and further post-processing and analyses of the groundwater samples collected in this protocol.

Proper citation: Michael Lloyd Strack 2017. Groundwater sampling from bores ~5 cm wide and < 60 m sampled depth. protocols.io https://dx.doi.org/10.17504/protocols.io.jvxcn7n 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 - 1. protocols.io https://dx.doi.org/10.17504/protocols.io.7u5hny6 Copy   

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Authors: Sam Li
Group: BioLegend
Summary: Buyer is solely responsible for determining whether Buyer has all intellectual property rights that are necessary for Buyer's intended uses of the BioLegend TotalSeq™ products. For example, for any technology platform Buyer uses with TotalSeq™, it is Buyer's sole responsibility to determine whether it has all necessary third party intellectual property rights to use that platform and TotalSeq™ with that platform.  TotalSeq™-B antibodies are designed to be used with 10x Single Cell 3’ Reagent Kit v3 with Feature Barcoding. The adjusted protocol below is for customers who are utilizing TotalSeq™-A antibodies with the v3 kit instead. Note: Step 4 from the 10x Genomics user guide document number CG000185, Rev B only applies to the cDNA library and NOT to the TotalSeq™-A library.  Please read the entire protocol below and the 10x Genomics user guide for the Chromium Single Cell 3ʹ Reagent Kits v3 with Feature Barcoding technology for Cell Surface Protein before starting the experiments. 10x Genomics user guide document number CG000185, Rev B. Commonly used abbreviations:ADT: Antibody derived tags, the oligo sequence conjugated to regular TotalSeq™-A antibodiesHTO: Hashtag oligonucleotides, the oligo sequence conjugated to TotalSeq™-A Hashtag antibodies

Proper citation: Sam Li 2019. TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.8aahsae Copy   

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Authors: Kelsey Miller
Group: BioLegend
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: For Human CD4 Nanobeads, please refer to the protocol found on the product webpage for MojoSort™ Human CD4 Nanobeads (Cat. No. 480013/480014).

Proper citation: Kelsey Miller 2016. MojoSort™ Nanobeads Regular Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.e2sbgee Copy   

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Authors: Carmen M Galvez-Sanchez, Pablo de la Coba, José M. Colmenero, Gustavo A. Reyes del Paso, Stefan Duschek
Summary: Concentration difficulties, forgetfulness and mental slownessare common in fibromyalgia syndrome (FMS); initial findings suggest that rheumatoid arthritis (RA) may also be accompanied by cognitive impairments. This study aimed to compare attentional performance between patients with FMS and RA. Attention was quantified in the domains of alerting, orienting and executive control using the Attentional Network Test – Interaction (ANT-I) in 56 women with FMS, 41 women with RA and 50 healthy women. Pain severity was statistically controlled in the group comparison. While FMS patients exhibited longer reaction times and made more errors on the ANT-I than RA patients and healthy women, performance did not differ between RA patients and healthy women. The magnitude of group differences did not vary by the experimental conditions of the ANT-I, suggesting a general attentional deficit in FMS rather than specific impairments in the domains of alerting, orienting and executive control. Differences between patient groups may relate to the different pathogenetic mechanisms involved in the disorders, i.e. inflammatory processes in RA and central nervous sensitization in FMS. In FMS, heightened activity in the pain neuromatrix may interfere with attention, because it requires enhanced neural resources in brain areas that are involved in both pain and attentional processing. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Carmen M Galvez-Sanchez, Pablo de la Coba, José M. Colmenero, Gustavo A. Reyes del Paso, Stefan Duschek 2021. Attentional function in fibromyalgia and rheumatoid arthritis. protocols.io https://dx.doi.org/10.17504/protocols.io.bq2zmyf6 Copy   

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Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology

Proper citation: André M. Comeau and Rachel T. Noble 2016. FLV tracer assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dzu76v Copy   

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Authors: Antibodies Online Gmbh
Group: antibodies-online
Summary: CUT&RUN (Cleavage Under Targets and Release Using Nuclease) offers a novel approach to pursue epigenetics. The method is designed to map genome wide transcription factor binding sites, chromatin-associated complexes, and histone variants and post-translational modifications.Here we provide an updated CUT&RUN protocol that incorporates two variants, one is optimized to further reduce background noise which especially helps when working with low cell numbers and abundant antigens.In CUT&RUN is performed in situ on immobilized, intact cells without crosslinking. DNA fragmentation is achieved using micrococcal nuclease that is fused to Protein A and/or Protein G (pA/G-MNase). The fusion protein is directed to the desired target through binding of the Protein A/G moiety to the Fc region of an antibody bound to the target. DNA under the target is subsequently cleaved and released and the pA/G-MNase-antibody- chromatin complex is free to diffuse out of the cell. DNA cleavage products are extracted and then processed by next generation sequencing (NGS).All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day.

Proper citation: Antibodies Online Gmbh 2020. Bench top CUT&RUN with antibodies-online™ CUT&RUN Sets. protocols.io https://dx.doi.org/10.17504/protocols.io.bbteinje Copy   

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

Proper citation: New England Biolabs 2015. Standard RNA Synthesis Mixture for E2050. protocols.io https://dx.doi.org/10.17504/protocols.io.cr3v8m Copy   

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Authors: Alan J. Cone
Group: Ju Lab
Summary: Method to create a long-term stable store of organisms. Especially useful if you want to store already transformed versions of organisms to aid in future experiments.

Proper citation: Alan J. Cone 2015. Glycerol Stock. protocols.io https://dx.doi.org/10.17504/protocols.io.dbe2jd Copy   

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Authors: Tibor Török
Summary: Ancient DNA work was performed in the specialized ancient DNA (aDNA) facilities of the Department of Genetics, University of Szeged, Hungary with strict clean-room conditions. In order to authenticate the results, we considered the latest recommendations of (Llamas et al. 2017) throughout of the experiments.DNA extraction:Note: This protocol is based on (Rohland and Hofreiter 2007), supplemented with partial predigestion (Damgaard et al. 2015) and using a GuHCl Binding Buffer modified after (Gamba et al. 2016).- 100 mg bone powder from tooth root, petrous bone or other dense bone was predigested in 1 ml 0,5 M EDTA 100 µg/ml Proteinase K for 30 minutes at 48 oC, to increase the proportion of endogenous DNA (Damgaard et al. 2015),- Then DNA solubilisation was done overnight at 48 oC in 1 ml extraction buffer containing 0.45 M EDTA, 250 µg/ml Proteinase K, 1% Triton X-100, and 50 mM DTT.- DNA was bound to silica (Rohland and Hofreiter 2007) adding 6 ml Binding Buffer (5,83 M GuHCl, 105 mM NaOAc, 46,8% isopropanol, 0,06% Tween-20) and 150 µl silica suspension to the 1 ml extract, and the pH was adjusted between 4-6 with HCl.- After 3 hours binding at room temperature silica was pelleted, and washed twice with 80% ethanol, then DNA was eluted in 100 µl TE buffer.NGS library constructionNote: We used the double stranded library protocol of (Meyer and Kircher 2010) with double indexing (Kircher, Sawyer, and Meyer 2012), except that all purifications were done with MinElute columns . We also applied partial UDG treatment of (Rohland et al. 2015), but decreased the recommended USER and UGI concentrations to half (0.03 U/μL) and at the same time increased the incubation time from 30 to 40 minutes. This modification removed uracils with comparable efficiency to the original method.DNA free negative control libraries were also made to detect possible contamination during handling or present in materials.Partial UDG treatment: AB1reagent volume (μL) per sample 2Buffer Tango (10X)     6 3dNTPs (25 mM each)     0,24 4 ATP (100 mM)     0,6 5USER (1 U/μL NEB)     1,8 6DNA extract   51,36 7  Total:   60 μL The reaction was incubated at 37oC for 40 minutes in PCR machine, with 40 oC lid temerature.Then 1,8 μL UGI (Uracil Glycosylase Inhibitor, 2U/μL NEB) was added to the reaction, which was further incubated at 37oC for 40 minutes.Blunt-End Repair:- To each reaction we added 3 μL  T4 polynucleotide kinase (10 U/μL) and 1,2 μL T4 DNA polymerase-t (5 U/μL), then incubated in PCR machine at 25°C for 15 minutes, followed by incubation at 12°C for 5 minutes and cooling to 4°C.- 350 ul MinElute PB buffer (QIAGEN) was added to the reaction, then it was purified on MinElute columns. DNA was eluted in 20 ul EB prewarmed to 55 oC.Adapter ligation: AB1reagent volume (μL) per sample 2  T4 DNA ligase buffer (10X)     4 3  PEG-4000 (50%)     4 4  adapter mix (50 μM each)     0,5   5  T4 DNA ligase (5 U /μL)     1 6   H2O   10,5  7   DNA   20 ul 8   Total:   40ul - We incubated the reaction at 22°C for 30 minutes in PCR machine.- Then 200 μL PB Buffer was added followed by MinElute purification. DNA was eluted in 20 ul EB.Adapter Fill-In:Note: We assembled the reaction below without library DNA, and the elution step from above was centrifuged directly on the fill-in reaction mix. AB1reagent volume (μL) per sample 2  H2O   14.1 3 ThermoPol reaction buffer (10X)     4 4 dNTPs (25 mM each)     0.4 5 Bst polymerase, large fragment (8 U/μL)     1.5 6  Library DNA (from adapter ligation)   20 7 Total:   40ul - The reaction was incubated at 37°C for 20 minutes, then 200 ul PB was added followed by MinElute purification. Library was eluted in 20 ul EB.Library preamplification:Libraries were preamplified in 2 x 50 µl reactions containing 800 nM each of IS7 and IS8 primers, 200 µM dNTP mix, 2 mM MgCl2, 0,02 U/µl GoTaq G2 Hot Start Polymerase (Promega) and 1X GoTaq buffer, followed by MinElute purification. PCR conditions were  96 oC 6 min, 11 cycles of  94 oC 30 sec, 58 oC 30 sec, 72 oC 30 sec, followed by a final extension of 64 oC 10 min. Libraries were eluted from the column in 50 µl 55 oC EB buffer (Qiagen), and concentration was measured with Qubit (Termo Fisher Scientific). Libraries below 5 ng/µl concentration were reamplified in the same reaction for additional 5-12 cycles, depending on concentration, in order to obtain 50 µl preamplified library with a concentration between 10-50 ng/µl. Double indexing:50 ng preamplified libraries were double indexed according to (Kircher, Sawyer, and Meyer 2012) in a 50 µl PCR reaction containing 1 x KAPA HiFi HotStart ReadyMix (Kapa Biosystems) and 1000 nM each of P5 and P7 indexing primers. PCR conditions were 98 oC 3 min, 6 cycles of 98 oC 20 sec, 66 oC 10 sec, 72 oC 15 sec followed by a final extension of 72 oC 30sec. Indexed libraries were MinElute purified and their concentration was measured with Qubit, and size distribution was checked on Agilent 2200 TapeStation Genomic DNA ScreenTape.Note: Lately we use 30 ng preamplified libraries and just 5 PCR cycles to avoid overamplification.Mitochondrial DNA capture and sequencing:Biotinilated mtDNA baits were prepared from three overlapping long-range PCR products as described in (Maricic, Whitten, and Pääbo 2010), but using the following primer pairs, L14759-H06378, L10870-H14799, L06363-H10888, described in (Haak et al. 2010).Capture was done according to (Maricic, Whitten, and Pääbo 2010) with the following modifications: Just four blocking oligos, given below were used in 3 µM (each) final concentration: BO1.P5.part1F: AATGATACGGCGACCACCGAGATCTACAC-Phosphate,BO2.P5.part2F ACACTCTTTCCCTACACGACGCTCTTCCGATCT-Phosphate,BO4.P7.part1 R GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-Phosphate,BO6.P7.part2 R CAAGCAGAAGACGGCATACGAGAT-Phosphate.- For one capture 300 ng biotinilated bait was used with 30 µl Dynabeads MyOne Streptavidin C1 magnetic beads (Thermo Fisher Scientific).- Double indexed libraries of 20 samples  (300 ng each) were mixed and concentrated on MinElute columns, then captured together in a 64 µl hybridization reaction. When fewer samples were enriched, we used proportionally smaller amounts of baits.- After washing, bead-bound enriched libraries were resuspended in 20 µl water and released  from the beads in a 60 µl PCR reaction containing 1 X KAPA HiFi HotStart ReadyMix and 2000 nM each of IS5- IS6 library primers. PCR conditions were: 98 oC 1 min, 10 cycles of 98 oC 20 sec, 60 oC 30 sec, 72 oC 30 sec, followed by a final extension of 72 oC 30 sec. The captured and amplified library mix was purified on MinElute column and eluted in 15 µl EB.- Before sequencing, libraries were quantified with Qubit, and quality checked and Agilent 2200 TapeStation Genomic DNA ScreenTape. Sequencing was done at the SeqOmics Biotechnology Ltd., using MiSeq sequencer with MiSeq Reagent Kit v3 (Illumina, MS-102-3003) generating 2x150bp paired-end sequences.Note: Lately we perform low coverage shotgun sequencing prior to enrichment to estimate endogenous DNA content. Then 5-7 libraries with similar endogenous content are enriched together.Data analysisThe adapters of paired-end reads were trimmed with the cutadapt software (Martin 2011) in paired end mode. Read quality was assessed with FastQC (S. Andrews 2016). Sequences shorter than 25 nucleotide were removed from this dataset. The resulting analysis-ready reads were mapped to the GRCh37.75 human genome reference sequence using the Burrows Wheeler Aligner (BWA) v0.7.9 software (Li and Durbin 2009) with the BWA mem algorithm in paired mode and default parameters. Aligning to the GRCh37.75 human reference genome that also contains the mtDNA revised Cambridge Reference Sequence (rCRS, NC_012920.1) (R. M. Andrews et al. 1999) helped to avoid the forced false alignment of homologous nuclear mitochondrial sequences (NumtS) to rCRS, though the proportion of NumtS, derived from low copy nuclear genome, is expexted to be orders of magnitudes lower than mtDNA in aDNA libraries. Samtools v1.1 (Li et al. 2009) was used for sorting and indexing BAM files. PCR duplicates were removed with Picard Tools v 1.113 (Broad Institute 2016). Ancient DNA damage patterns were assessed using MapDamage 2.0 (Jónsson et al. 2013), and read quality scores were modified with the rescale option to account for post-mortem damage. Freebayes v1.02 (Garrison and Marth 2012) was used to identify variants and generate variant call format (VCF) files with the parameters -q 10 (exclude nucleotids with References: Andrews, R M et al. 1999. “Reanalysis and Revision of the Cambridge Reference Sequence for Human Mitochondrial DNA.” Nature genetics 23(2): 147. http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&>Andrews, S. 2016. “FastQC: A Quality Control Tool for High Throughput Sequence Data.” babraham bioinformatics. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.Broad Institute. 2016. “Picard Tools.” https://broadinstitute.github.io/picard/. http://broadinstitute.github.io/picard/.Damgaard, Peter B et al. 2015. “Improving Access to Endogenous DNA in Ancient Bones and Teeth.” Scientific Reports 5: 11184. http://dx.doi.org/10.1038/srep11184%5Cn10.1038/srep11184%5Cnhttp://www.nature.com/articles/srep11184#supplementary-information.Gamba, Cristina et al. 2016. “Comparing the Performance of Three Ancient DNA Extraction Methods for High-Throughput Sequencing.” Molecular Ecology Resources 16(2): 459–69.Garrison, Erik, and Gabor Marth. 2012. “Haplotype-Based Variant Detection from Short-Read Sequencing.” arXiv preprint arXiv:1207.3907: 9. http://arxiv.org/abs/1207.3907.Haak, Wolfgang et al. 2010. “Ancient DNA from European Early Neolithic Farmers Reveals Their near Eastern Affinities.” PLoS Biology 8(11).Jónsson, Hákon et al. 2013. “MapDamage2.0: Fast Approximate Bayesian Estimates of Ancient DNA Damage Parameters.” In Bioinformatics, , 1682–84.Kircher, Martin, Susanna Sawyer, and Matthias Meyer. 2012. “Double Indexing Overcomes Inaccuracies in Multiplex Sequencing on the Illumina Platform.” Nucleic Acids Research 40(1).Li, Heng et al. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics (Oxford, England) 25(16): 2078–79. http://bioinformatics.oxfordjournals.org/cgi/content/long/25/16/2078 (August 20, 2016).Li, Heng, and Richard Durbin. 2009. “Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform.” Bioinformatics (Oxford, England) 25(14): 1754–60. http://bioinformatics.oxfordjournals.org/cgi/content/long/25/14/1754 (August 22, 2016).Llamas, Bastien et al. 2017. “From the Field to the Laboratory: Controlling DNA Contamination in Human Ancient DNA Research in the High-Throughput Sequencing Era.” STAR: Science & Technology of Archaeological Research 3(1): 1–14. http://dx.doi.org/10.1080/20548923.2016.1258824.Maricic, T, M Whitten, and S Pääbo. 2010. “Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products.” PLoS ONE 5: e14004. http://dx.doi.org/10.1371/journal.pone.0014004.Martin, Marcel. 2011. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.journal 17(1): 10–12.McKenna, Aaron et al. 2010. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing next-Generation DNA Sequencing Data.” Genome Research 20(9): 1297–1303.Meyer, Matthias, and Martin Kircher. 2010. “Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing.” Cold Spring Harbor Protocols 5(6).Rohland, Nadin et al. 2015. “Partial Uracil-DNA-Glycosylase Treatment for Screening of Ancient DNA.” Philosophical transactions of the Royal Society of London. Series B, Biological sciences 370(1660): 20130624. http://www.ncbi.nlm.nih.gov/pubmed/25487342.Rohland, Nadin, and Michael Hofreiter. 2007. “Ancient DNA Extraction from Bones and Teeth.” Nature Protocols 2(7): 1756–62. http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.247.html%5Cnhttp://www.nature.com/nprot/journal/v2/n7/pdf/nprot.2007.247.pdf.

Proper citation: Tibor Török 2018. Ancient DNA protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.rmvd466 Copy   

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Authors: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
Group: Human Cell Atlas Method Development Community

Proper citation: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin 2020. 1: User-friendly protocol: Probe set design (SABER-FISH). protocols.io https:// Copy   

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