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Citations for Phase Genomics :
1 - 50 of 99 citations since 2019
Citations are collected from bioRxiv only, the total number of publications could be much larger.
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bioRxiv - Synthetic Biology 2024Quote: ... HiC reads QC analysis was performed by Phase Genomics. Each culture was sent in duplicate ...
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bioRxiv - Plant Biology 2024Quote: ... curassavica leaves using the Proximo Hi-C Plant Kit (Phase Genomics, Seattle, WA, USA) and was sequenced on an Illumina MiSeq instrument (paired-end 2×75bp ...
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bioRxiv - Plant Biology 2024Quote: ... digitatus leaves using the Proximo Hi-C (Plant) Kit and protocol v4.0 (Phase Genomics) with three extra wash steps and 12 PCR amplification cycles ...
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bioRxiv - Microbiology 2024Quote: ... as suggested by Phase Genomics’ protocols ...
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bioRxiv - Cancer Biology 2024Quote: ... Hi-C was performed using Phase Genomics Proximo Hi-C kits v4.0 (Phase genomics, Seattle, WA) according to the manufacturer’s instructions21 ...
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bioRxiv - Genetics 2024Quote: The raw fastq sequences were downloaded from Phase Genomics (Seattle, Washington, USA) and checked ...
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bioRxiv - Genomics 2024Quote: ... a chromatin interaction (Hi-C) library was generated using Proximo Hi-C Library Prep Kit (Phase Genomics) with in vivo cross-linking in the Genomic Sciences Laboratory of the North Carolina State University (USA) ...
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bioRxiv - Genomics 2024Quote: ... Then the high molecular weight DNA was purified and used for library preparation for generating 1.01 GB of assembly HiC data using Proximity Ligation technology workflow (Phase Genomics)
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bioRxiv - Genomics 2024Quote: ... PacBio Sequel II HiFi and Hi-C (Phase Genomics) data were assembled with Hifiasm v.0.16.1 (Cheng et al. ...
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bioRxiv - Microbiology 2024Quote: Meta-Hi-C sequencing was performed using the ProxiMeta kit provided by Phase Genomics exactly as directed in the standard protocol ...
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bioRxiv - Evolutionary Biology 2023Quote: ... We then used the resulting .bam file as the input file to the Phase Genomics Matlock suite of HiC functions (Kronenberg and Sullivan, 2018 https://github.com/phasegenomics/matlock) (Phase Genomics, Seattle, Washington, USA), which converted mapped reads into a HiC format that could be converted to a .hic and .assembly file using the 3d-dna script ‘run-assembly-visualizer.sh’ and visualized using the software Juicebox v1.11.08 (Durand et al ...
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bioRxiv - Genomics 2023Quote: ... Library constructions were performed by Phase Genomics, Inc ...
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bioRxiv - Genomics 2023Quote: We used intact leaf material and the Proximo TM Hi-C kit (Phase Genomics, USA) to generate libraries for Hi-C sequencing ...
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bioRxiv - Genomics 2023Quote: ... hyperodae were scaffolded by Phase Genomics using Hi-C data generated from pools of 10 individuals ...
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bioRxiv - Genomics 2023Quote: DNA was prepared using Proximo Hi-C kit (Animal) as recommended by the manufacturer (Phase Genomics, Seattle, WA, USA). Library preparation and sequencing were carried out at the UC Davis DNA Technologies Core and scaffolding with Proximo was performed by Phase Genomics (Supplementary Methods).
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bioRxiv - Genomics 2023Quote: ... The assembly was then scaffolded with Hi-C reads using the Proximo pipeline by Phase Genomics Ltd ...
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bioRxiv - Genomics 2023Quote: ... Library preparation and sequencing were carried out at the UC Davis DNA Technologies Core and scaffolding with Proximo was performed by Phase Genomics (Supplementary Methods).
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bioRxiv - Genomics 2023Quote: ... A pilot run on an Illumina iSeq 100 with 2 x 150 bp paired end sequencing run was performed for QC using hic_qc v1.0 (Phase Genomics, 2019) with i1 300 cycle chemistry ...
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bioRxiv - Genomics 2023Quote: ... Hi-C data were generated and used to scaffold the assembly by Phase Genomics (Seattle, WA, USA). Gaps between contigs in the scaffolded assembly were filled by TGS-GapCloser [61] using ONT DNA sequences ...
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bioRxiv - Genomics 2023Quote: ... Hi-C libraries using 1.5 M human cells as input were generated with Proximo Hi-C kits v4.0 (Phase Genomics, Seattle, WA) following the manufacturer’s protocol with the following modification ...
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bioRxiv - Genomics 2023Quote: ... and reverse-crosslinked using Proximo Hi-C Kit (Plant) v2.0 (Phase Genomics, Seattle, USA). The library was sequenced on a HiSeq4000 for ~300 M 150-bp paired-end sequencing.
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bioRxiv - Genomics 2023Quote: ... Library preparation was performed by Phase Genomics (https://phasegenomics.com/) using their standard protocol ...
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bioRxiv - Genomics 2023Quote: ... the values obtained for our samples far exceeded the quality thresholds set by Phase Genomics.
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bioRxiv - Genomics 2023Quote: ... The libraries were sequenced by Phase Genomics on an Illumina NovaSeq6000 ...
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bioRxiv - Genomics 2023Quote: ... Hi-C libraries were generated with 1.5 M human cells as input using Proximo Hi-C kits v4.0 (Phase Genomics, Seattle, WA) according to the manufacturer’s protocol with the following change ...
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bioRxiv - Genomics 2023Quote: ... maclovinus specimen by Phase Genomics Inc ...
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bioRxiv - Genomics 2023Quote: ... Chromosome-scale scaffolding was performed by Phase Genomics (Seattle, Washington, USA) with Proximo Hi-C (supplements 1.2) ...
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bioRxiv - Genomics 2023Quote: ... A Hi-C Plant Kit (Phase Genomics, Seattle, WA) was used to create a proximity ligation library that included four restriction enzymes (DpnII ...
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bioRxiv - Microbiology 2023Quote: ... processed by Phase Genomics in Seattle ...
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bioRxiv - Plant Biology 2023Quote: Hi-C was performed based on the Proximo Hi-C kit (Microbe) (Phase Genomics, Seattle, WA, USA) according to the manufacturer’s protocol as previously described (Seidl et al. ...
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bioRxiv - Genomics 2023Quote: ... dark-treated leaf tissue samples were harvested and cross-linked with formaldehyde for library preparation and Hi-C sequencing by Phase Genomics, yielding 543 million PE reads (150 bp) ...
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bioRxiv - Genomics 2023Quote: Fresh leaf tissue (see above) was used to generate a Hi-C library with the Proximo Hi-C Plant Kit from Phase Genomics (v4.0 protocol). Input material was ground in a mortar and pestle under liquid N2 ...
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bioRxiv - Genomics 2023Quote: Chromatin conformation capture (Hi-C) scaffolding was performed by Phase Genomics (Seattle, USA) using the Proximo Hi-C 2.0 Kit ...
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bioRxiv - Genomics 2023Quote: ... To perform scaffolding a sibling of the reference fish was used to generate and sequence a HiC library developed with the Proximo Hi-C kit (Phase Genomics: Seattle, WA) according to the manufacturers protocol ...
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bioRxiv - Genomics 2022Quote: ... library preparation and Hi-C sequencing was performed by Phase Genomics (WA, USA). Following the manufacturer’s instructions ...
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bioRxiv - Genomics 2022Quote: ... a Proximo Hi-C 2.0 Kit (Phase Genomics, WA, USA) was used to prepare the proximity ligation library and process it into an Illumina-compatible sequencing library ...
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bioRxiv - Genomics 2022Quote: ... library preparation for chromosome conformation capture (Hi-C) analyses used the Proximo Hi-C 2.0 Kit from Phase Genomics Inc ...
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bioRxiv - Microbiology 2022Quote: ... was assembled into MAGs using an updated algorithm of ProxiMeta™ on April 4th 2021 (Phase Genomics, Inc. 2021). This generated 374 MAGs analyzed in this study ...
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bioRxiv - Genomics 2022Quote: ... Hi-C binning was provided by Phase Genomics using its internal pipeline with MetaBAT results for hybrid assemblies as a starting point ...
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bioRxiv - Bioengineering 2022Quote: ... Samples were submitted to and sequenced by Phase Genomics (USA). Both the shotgun library and the Hi-C library were sequenced on the same platform ...
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bioRxiv - Genomics 2022Quote: A Hi-C library also was prepared using 100 μL of Rohu-1 blood with the Proximo Hi-C Animal Kit (Phase Genomics, Seattle, WA, USA). The final Hi-C DNA-Seq library was submitted to Novogene (www.en.novogene.com ...
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bioRxiv - Genomics 2022Quote: ... The chromosome-scale genome assembly was generated by Phase Genomics using the de novo assembly ...
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bioRxiv - Evolutionary Biology 2022Quote: ... employing the Phase Genomics HiC functions (Kronenberg and Sullivan, 2018, phasegenomics.github.io, https://github.com/phasegenomics/juicebox_scripts) (Phase Genomics, Seattle, Washington, USA) and Juicebox assembly tools (Dudchenko et al ...
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bioRxiv - Evolutionary Biology 2022Quote: ... 2015) and the edits were applied to the contig assembly using juicebox_assembly_converter.py by Phase Genomics.
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bioRxiv - Plant Biology 2022Quote: ... young Craterostigma leaf tissue with the Proximo™ HiC Plant kit (Phase Genomics) following the manufacture’s protocol ...
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bioRxiv - Plant Biology 2022Quote: Catharanthus roseus cv ‘SunstormTM Apricot’ leaf tissue collected at the same time as one replicate of the 10x scRNA-seq experiments was used with the Proximo Hi-C kit (Phase Genomics; CRO_AR) to generate Hi-C reads and sequenced on the Illumina NovaSeq 6000 generating paired-end 150 nt reads ...
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bioRxiv - Plant Biology 2022Quote: ... tabacum using the animal Proximo Hi-C kit (Phase Genomics, https://phasegenomics.com/) according to the manufacturer’s instructions ...
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bioRxiv - Microbiology 2022Quote: 10-15 mg of rind from duplicate wheels for each sample were fixed separately and then combined for further processing according to the ProxiMeta kit methodology from Phase Genomics (Seattle, WA). The multiplexed libraries were sequenced by Novogene (Sacramento ...
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bioRxiv - Plant Biology 2022Quote: ... The quality control script provided by Phase Genomics was used to assess the HiC data quality.
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bioRxiv - Genetics 2022Quote: ... library preparation and sequencing were performed by Phase Genomics (Seattle, WA).