Journal: Cell Reports Medicine

Article Title: Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas

doi: 10.1016/j.xcrm.2023.101082

Figure Lengend Snippet:

Article Snippet: For near-complete knockdown of NFKBIA , G418-resistant primary human astrocytes transduced to stably express wildtype IDH1 or mutant IDH1- ( R132H ) were transfected with Accell human NFKBIA small interfering (si)RNA or non-targeting control siRNA (Dharmacon), at 20nM concentration using lipofectamine 2000 reagent (Invitrogen) at 1:1 ratio for 48 h. For complete clustered regularly interspaced short palindromic repeats (CRISPR) knockout of NFKBIA , astrocytes were transfected with IκBα Double Nickase Plasmid (h) (sc-400034-NIC, Santa Cruz)—consisting of a pair of plasmids each encoding a D10A mutated Cas9 nuclease and a target-specific 20-nucleotide (nt) guide RNA (gRNA)—using plasmid transfection medium (sc-108062) and Ultra-Cruz transfection reagent (sc-395739) at 1:1.5 ratio and were incubated for 72 h. After incubation, cells were screened for GFP-positivity to select for successfully transfected cells.

Techniques: Plasmid Preparation, Recombinant, Transfection, Activation Assay, Methylation, Marker, DNA Methylation Assay, Sequencing, Empire Assay, Software

Journal: Cell host & microbe

Article Title: Functional and genomic variation between human-derived isolates of Lachnospiraceae reveals inter- and intra-species diversity

doi: 10.1016/j.chom.2020.05.005

Figure Lengend Snippet: Key Resources table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Biological Samples and Strains Fecal samples from healthy donors or patients prior to allogeneic hematopoietic stem cell transplant This study N/A Lachnospiraceae isolates This study N/A Bacterial Culturing Gibco Bacto Brain Heart Infusion Fisher Scientific DF0037178 BD BBL Columbia Agar with 5% sheep blood Fisher Scientific B21263X Gibco Bacto Yeast Extract Fisher Scientific DF0127-17-9 L-Cysteine Sigma Aldrich #C-7352 Whole Genome Sequencing Reagents .1mm zirconia-silica beads Fisher Scientific NC0362415 Phenol, equal., pH 8.0 Fisher Scientific BP17501-40 Chloroform Fisher Scientific C298-500 Isoamyl Alcohol Fisher Scientific A393-500 Sodium Chloride, 1M Teknova S0254 TRIS, 1M, pH 8.0 Fisher Scientific E199-500ML EDTA, .5M, pH 8.0 Fisher Scientific E177-500ML 20% SDS Fisher Scientific BP1311-1 Sodium Acetate, 3M, pH 5.2 Teknova S0298 TRIS-EDTA, 1X, pH 8.0 Fisher Scientific BP2473-500 Rnase A Fisher Scientific 50-100-3354 Quit broad-range dsDNA kit (500) Invitrogen {"type":"entrez-protein","attrs":{"text":"Q32853","term_id":"75280860","term_text":"Q32853"}} Q32853 QIAamp DNA mini Kit (250) Qiagen 51306 QIAseq FX DNA Library Kit (96) Qiagen 180475 Agilent HS D1000 ScreenTape Agilent 5067-5584 Agilent HS D1000 Reagents Agilent 5067-5585 Quit 2.0 Fluorometer Life Technologies {"type":"entrez-protein","attrs":{"text":"Q32866","term_id":"75280873","term_text":"Q32866"}} Q32866 Deposited Data Lachnospiraceae genomes This study.

Techniques: Sequencing, Software

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: Cell Reports

Article Title: Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation

doi: 10.1016/j.celrep.2021.109101

Figure Lengend Snippet:

Article Snippet: For microarray analysis, RNA was extracted from THP1 or stimulated human CD4+ T cells using the RNeasy Mini kit (QIAGEN).

Techniques: Recombinant, Multiplex sample analysis, Cell Isolation, Activation Assay, Staining, Flow Cytometry, Expressing, Reverse Transcription, Transfection, TA Cloning, Plasmid Preparation, Methylation, Immunoprecipitation, Purification, DNA Library Preparation, Library Quantification, Control, Sequencing, Methylation Sequencing, Amplification, Software

Journal: Genome research

Article Title: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation.

doi: 10.1101/gr.275962.121

Figure Lengend Snippet: Figure 3. Characteristics of circdmrt1 and AMSDT in tongue sole testis. (A) The genomic locus of circdmrt1 in the dmrt1 gene. Circdmrt1 is produced at the dmrt1 gene locus containing exon 4. The back-splice junction of circdmrt1 was identified by Sanger sequencing. Arrows represent divergent primers bind- ing to the genome region of circdmrt1. (B) RT-PCR products with divergent and convergent primers showing circularization of circdmrt1 in 6-mpf tongue sole testis. (cDNA) Complementary DNA, (gDNA) genomic DNA. The black and white arrows represent the divergent and convergent primers, respectively. (C) qRT-PCR results revealing the abundance of circdmrt1 and dmrt1 mRNA in 6-mpf tongue sole testis treated with RNase R. The amounts of circdmrt1 and dmrt1 mRNA were normalized to the values measured in the mock group. The blue and red bars represent the mock-treated or RNase R-treated group, respectively. (D) Relative quantification for circdmrt1 in 10 tissues of tongue sole. (E) RNA fluorescence in situ hybridization for circdmrt1 in tongue sole testis. Circdmrt1 probe was labeled with fluorescein amidites (FAM) and detected by TSA-FAM (green signals). Nuclei were stained with 4,6-diamidino-2-phenyl- indole (DAPI). The cell membrane was stained with the wheat-germ agglutinin (WGA)/Alexa Fluor 555 conjugate dye. The bottom row shows enlargement of the regions outlined in the top row. Scale bars in top rows are 20 μm, and bars in bottom rows are 5 μm. (F) Expression levels of dmrt1 and circdmrt1 in tongue sole testis treated with dmrt1 siRNA. The transcription levels were normalized to Actb1 levels. (G) RT-PCR analysis for AMSDT in cDNA of 6-mpf tongue sole testis. The red line in the upper panel shows the location of AMSDT in Chr 5. The lower panel represents the Sanger sequencing of RT-PCR prod- ucts of AMSDT including the binding sites with cse-miR-196. (H) Relative quantification for AMSDT in 10 tissues of tongue sole. (I) RNA fluorescence in situ hybridization for AMSDT in tongue sole testis. The AMSDT probe was labeled with fluorescein amidites and detected by TSA-FAM (green signals). Nuclei were stained with DAPI. The cell membrane was stained with wheat-germ agglutinin/Alexa Fluor 555 conjugate dye. The bottom row shows enlargement of the regions outlined in the top row. Scale bars in top rows are 20 μm, and bars in bottom rows are 5 μm. Data in C, D, F, and H are the means ± SD of three experiments. (∗∗) P < 0.01, two-tailed t-test. Abbreviations: (LC) Leydig cell, (SC) Sertoli cell, (GC) germ cell.

Article Snippet: Two sets of primers for circdmrt1 were designed using circPrimer1.2 software: an outward-facing set to amplify the circRNA across the back-spliced junction (divergent primers, Supplemental Table S7), and an opposite-directed set to amplify the linear mRNA forms (convergent primers, Supplemental Table S7) in reverse-transcribed RNA (cDNA) and genomic DNA (gDNA) from the 6-mpf testis tissues of tongue sole. gDNA was extracted using a Genomic DNA Isolation kit according to the manufacturer’s instructions (Tiangen).

Techniques: Produced, Sequencing, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Quantitative Proteomics, Fluorescence, In Situ Hybridization, Labeling, Staining, Membrane, Expressing, Binding Assay, Two Tailed Test

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