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: eLife

Article Title: Induction of osteogenesis by bone-targeted Notch activation

doi: 10.7554/eLife.60183

Figure Lengend Snippet:

Article Snippet: Commercial assay or kit , iScript cDNA Synthesis Kit , BIO-RAD , Cat# 170–8891 , .

Techniques: Recombinant, Variant Assay, Plasmid Preparation, Sequencing, Control, Gene Expression, Bicinchoninic Acid Protein Assay, cDNA Synthesis, Amplification, Magnetic Beads, Protease Inhibitor, Western Blot, Software, Staining

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