Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Schematic representation of mechanistic strategies of barcoding. (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Ligation, Reverse Transcription, Amplification, Sequencing, Multiplex Assay, Generated, Modification

Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Systematic comparison of barcoding strategies used in the category of molecular barcodes.

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Comparison, Software, Sequencing, Multiplex Assay, CRISPR, Plasmid Preparation, Microarray, Binding Assay, Amplification, Extraction, Ligation, DNA Sequencing, Multiplexing, Generated, Reverse Transcription, Staining, Flow Cytometry, High Throughput Screening Assay, Inhibition, Blocking Assay, Conjugation Assay, RNA Sequencing Assay, Transmission Assay, Incubation, Diagnostic Assay, Next-Generation Sequencing, Infection

Journal: Cell

Article Title: A trans -complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence

doi: 10.1016/j.cell.2021.02.044

Figure Lengend Snippet:

Article Snippet: BsaI restriction endonuclease , New England Biolabs , Cat#R3733S.

Techniques: Recombinant, SYBR Green Assay, Electroporation, Gel Extraction, Electron Microscopy, Synthesized, Sequencing, Software

Journal: Immunity

Article Title: DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity

doi: 10.1016/j.immuni.2021.10.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Zymo EZ-96 DNA Methylation Kit , Zymo , Cat# D5003.

Techniques: Selection, DNA Methylation Assay, Sequencing, Methylation, Software, DNA Extraction

Journal: Immunity

Article Title: DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity

doi: 10.1016/j.immuni.2021.10.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Zymo EZ-96 DNA Methylation Kit , Zymo , Cat# D5003.

Techniques: Selection, DNA Methylation Assay, Sequencing, Methylation, Software, DNA Extraction

Journal: Cell

Article Title: B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

doi: 10.1016/j.cell.2021.02.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Direct-zol DNA/RNA Miniprep Kit , Zymo Research , Cat# R2080.

Techniques: Virus, Recombinant, Sequencing, Mass Spectrometry, Software

Journal: Heliyon

Article Title: Halotolerant phosphate solubilizing bacteria isolated from arid area in Tunisia improve P status and photosynthetic activity of cultivated barley under P shortage

doi: 10.1016/j.heliyon.2024.e38653

Figure Lengend Snippet: Phylogenetic tree constructed using GENETYX software based on the sequences obtained from the 16S rDNA of the isolates. The method used is called Neighbors joining (NJ).

Article Snippet: Phylogenetic tree constructed using GENETYX software based on the sequences obtained from the 16S rDNA of the isolates.

Techniques: Construct, Software

Journal: Molecular cell

Article Title: Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity

doi: 10.1016/j.molcel.2022.02.002

Figure Lengend Snippet: Key Resources Table

Article Snippet: CasX protein mutants were constructed by PCR amplification of the CasX sequence in two pieces, with primers containing the deletion or insertion sequences. pBLO62.4 and pBLO62.5 were digested with AgeI and BamHI (NEB) and gel electrophoresis was utilized to separate the digested components.

Techniques: Recombinant, Modification, DNA Extraction, Purification, Clone Assay, Transfection, Cell Culture, Expressing, Plasmid Preparation, Software, Sequencing

Journal: Molecular cell

Article Title: Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity

doi: 10.1016/j.molcel.2022.02.002

Figure Lengend Snippet: Key Resources Table

Article Snippet: CasX protein mutants were constructed by PCR amplification of the CasX sequence in two pieces, with primers containing the deletion or insertion sequences. pBLO62.4 and pBLO62.5 were digested with AgeI and BamHI (NEB) and gel electrophoresis was utilized to separate the digested components.

Techniques: Recombinant, Modification, DNA Extraction, Purification, Clone Assay, Transfection, Cell Culture, Expressing, Plasmid Preparation, Software, Sequencing

Journal: Current biology : CB

Article Title: Prdm9 and meiotic cohesin proteins cooperatively promote DNA double-strand break formation in mammalian spermatocytes

doi: 10.1016/j.cub.2019.02.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: For library preparation, DNA was first end-repaired by incubation with 1 × T4 DNA Ligase Reaction Buffer with 0.25 mM dNTP, 3 units of T4 DNA polymerase (NEB, M0203S), 1 unit of Klenow Enzyme (NEB, M0210S) and 10 units of T4 PNK (NEB, B0202S) at 20°C for 30 min, followed by addition of 3’-A overhangs using Klenow Fragment 3’-5’ exo- (NEB, M0212S).

Techniques: Recombinant, Protease Inhibitor, Ligation, DNA HS Assay, Magnetic Beads, Purification, Software, Sequencing