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Citations for Phase Genomics :
51 - 100 of 109 citations for Ammonium Polyphosphate phase II 02 since 2020
Citations are collected from bioRxiv only, the total number of publications could be much larger.
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bioRxiv - Genomics 2021Quote: ... Further sample processing and sequencing was performed by Phase Genomics (Seattle, WA, USA) on an Illumina HiSeq 4000 ...
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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 - 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 - Genomics 2024Quote: ... Hi-C data were collected using Proximo Hi-C kits v4.0 (Phase Genomics) and sequenced on an Illumina NovaSeq 6000 ...
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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 - 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 - 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 2024Quote: ... The Hi-C library was quantified by qPCR and then sequenced by Phase Genomics on an Illumina NovaSeq6000 machine to generate 2×150bp paired-end reads.
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bioRxiv - Genomics 2024Quote: ... The Hi-C libraries were prepared and sequenced by Phase Genomics (Seattle, WA, USA).
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bioRxiv - Genomics 2021Quote: A Proximo Hi-C library was prepared as described (Phase Genomics Inc. Seattle, WA, USA) and sequenced on an Illumina HiSeq 2500 system with paired-end 150 bp reads ...
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bioRxiv - Genetics 2021Quote: ... An assembly file was prepared from the SALSA (21) output FINAL.fasta with juicebox_scripts (Phase Genomics). The assembly and .hic files were loaded into Juicebox (23 ...
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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 - 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 - Genomics 2023Quote: ... the values obtained for our samples far exceeded the quality thresholds set by Phase Genomics.
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bioRxiv - Plant Biology 2024Quote: ... A Hi-C library was prepared following the proximo Hi-C plant protocol (Phase Genomics) and sequenced on an Illumina NextSeq 500 platform with the paired-end mode and a read length of 150 bp.
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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breedingbioRxiv - Genomics 2020Quote: ... and a Hi-C library was prepared following the proximo Hi-C plant protocol (Phase Genomics). Both the Illumina paired-end and the Hi-C libraries were sequenced on an Illumina NextSeq 500 platform with the paired-end mode and read length of 150 bp.
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bioRxiv - Genomics 2021Quote: ... Chromosome-scale scaffolds were created by using the Proximo Hi-C genome scaffolding platform (Phase Genomics) in a method similar to that described by Bickhart et al ...
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bioRxiv - Genomics 2020Quote: ... a HiC library was constructed with Proximo Hi-C (Plant) Kit (Phase Genomics, Seattle, WA, USA) and sequenced on HiSeqX (Illumina) ...
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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 2024Quote: A single HiC library was prepared for Physcomitrellopsis africana using Proximo Hi-C kit (Phase Genomics) and sequenced as paired-end reads on an Illumina NovaSeq platform (Center for Genome Innovation ...
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bioRxiv - Genomics 2020Quote: ... scaffolding was accomplished using Proximity Guided Assembly (PGA) and Hi-C reads by Phase Genomics (Seattle, WA). Resulting scaffolds were polished and gap-filled using PBJelly ...
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bioRxiv - Genomics 2021Quote: ... the values obtained for our samples far exceeded the QC limits set by Phase Genomics (Seattle, WA) – e.g ...
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bioRxiv - Genomics 2021Quote: ... The .hic and .assembly files used by Juicebox were produced using the pipeline from Phase Genomics (65). The nomenclature for the chromosomes was based on the linkage group from the genetic maps and from the Northern pike orthologous chromosomes in an attempt to standardize nomenclature across salmonids (66).
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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 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 - 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 2024Quote: ... Manual curation was then performed in Juicebox (v2.15) and edits were applied to the scaffold assembly using ‘juicebox_assembly_converter.py’ from Phase Genomics (https://github.com/phasegenomics/juicebox_scripts).
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bioRxiv - Plant Biology 2020Quote: ... Hi-C libraries were constructed using the Proximo Hi-C plant kit following the manufacturer’s instructions (Phase Genomics) and sequenced on an Illumina HiSeq X Ten system with 2×150 bp mode at Nextomics Biosciences.
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bioRxiv - Genomics 2022Quote: ... The resulting .assembly file was exported and converted back into a .fasta file using juicebox_assembly_converter.py from Phase Genomics (https://github.com/phasegenomics/juicebox_scripts/blob/master/README.md.)
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bioRxiv - Plant Biology 2021Quote: ... The Hi-C library was prepared following the proximo Hi-C plant protocol (Phase Genomics, San Diego, CA, USA) and the libraries were sequenced to 116X depth on an Illumina platform with the paired-end mode and read length of 150 bp.
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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 2021Quote: ... Chromosome conformation was captured and a sequencing library prepared using a Microbe Proximo Hi-C Kit from Phase Genomics, according to the manufacturer’s ProxiMeta™ Hi-C Protocol (version 1.5 ...
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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 - Microbiology 2021Quote: The same fecal sample was used to generate a Hi-C library using the ProxiMeta Hi-C kit following the manufacturer’s protocol (Phase Genomics). The Hi-C method cross-links DNA molecules that are in close physical proximity within intact cells ...
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bioRxiv - Plant Biology 2020Quote: ... Hi-C libraries were constructed for the female parent following the Proximo™ Hi-C plant protocol (Phase Genomics, USA) and applied for sequencing on an Illumina HiSeq X platform (Illumina ...
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bioRxiv - Genomics 2021Quote: ... 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: ... 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 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 - Microbiology 2024Quote: ... library was prepared from an aliquot of the Fecal Reference standard using the ProxiMeta Hi-C v4.0 Kit from Phase Genomics according to the manufacturer provided protocol (Lieberman-Aiden et al ...
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bioRxiv - Genomics 2021Quote: ... Chromosomal level scaffolds were generated with the same DNA source using the ProximoTM Hi-C genome scaffolding software (Phase Genomics Inc) and finalized by alignment to the CanFam3.1 reference.
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bioRxiv - Genomics 2021Quote: ... A proximity ligation library was also prepared from the same sample using the ProxiMeta™ Hi-C kit from Phase Genomics, and the resulting 2×150 bp sequences were also downsampled to 100 million reads ...
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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: ... 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: ... 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 2024Quote: ... The Hi-C libraries were prepared from a frozen blood sample and sequenced by a commercial vendor (Phase Genomics, Seattle, WA) to produce 868 million Illumina paired-end reads (2x150 bp ...
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bioRxiv - Microbiology 2021Quote: We uploaded the metagenome assembly and the raw Hi-C sequencing data to the ProxiMeta cloud-based pipeline (Phase Genomics, December 2020), where it was processed ...
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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 - 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 - 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 ...