reference strain s pyogenes atcc 19615  (ATCC)

Journal: bioRxiv

Article Title: A reparative neutrophil subpopulation promotes spinal cord regeneration in zebrafish by controlling macrophage inflammation via Il-4

doi: 10.64898/2026.02.25.707887

Figure Lengend Snippet:

Article Snippet: 1 nL of gRNA mix (1 μL of Tracer (5nM, Merck KGaA, Darmstadt, Germany; Cat#TRACRRNA05N), 1 μL of each gRNA (20μM,Merck KGaA, Darmstadt, Germany), 1 μL of phenol red (Sigma-Aldrich, St. Louis, MO, USA; Cat#P0290) and 1 μL of Cas9 (20μM, New England Biolabs, Ipswich, MA, USA; Cat#M0386M) was injected into one-cell stage embryos. gRNA efficiency was tested by restriction fragment length polymorphism analysis (RFLP) in a proportion of larvae for each experiment as an internal experimental control ( Keatinge et al ., 2021 ).

Techniques: CRISPR

Journal: bioRxiv

Article Title: Defective BRCA1-mediated DNA end resection drives tandem duplication formation and FANCM synthetic lethality

doi: 10.64898/2026.02.20.706968

Figure Lengend Snippet:

Article Snippet: Cas9-sgRNA target sites in the mouse genome sequence were identified using the Heidelberg CCtop tool: https://cctop.cos.uni-heidelberg.de . sgRNA in vitro synthesis was performed using the Engen sgRNA Synthesis Kit (New England Biolabs, E3322S) and purified using the Clean and Concentrate Kit (Zymo Research, R1017). sgRNA was electrophoresed on a denaturing gel (Novex 10% TBE-Urea; ThermoFisher Scientific, EC6875BOX), to assess quality prior to transfection.

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform

doi: 10.1186/s12864-025-12268-4

Figure Lengend Snippet: A) The effect of performing DASH directly on unwashed Klenow reactions in 50 µL (unwashed 50 µL rxn) as opposed to performing DASH after a beads cleanup in 20 µL (washed 20 µL rxn), on the detection (left) and read length (right) of spiked PDV (Phocine distemper virus), of non-depleted transcripts PGK1 (phosphoglycerate kinase 1), ND1/ND2/ND6 (NADH dehydrogenase subunit 1/2/6), COI (cytochrome c oxidase subunit I), and CYB (cytochrome B), and of depleted ribosomal 18S and 28S RNA in metagenomic sequencing libraries of TURBO + DASH-depleted human serum samples. B) Increasing the Cas9 concentration lowers the loss of depletion observed when using direct DASH. C) Performing Klenow reactions in smaller volumes further reduces this loss of depletion

Article Snippet: This ribonucleoprotein complex was formed by a 10 min preincubation at 37 °C of 1 μL Cas9 buffer, 2300 ng sgRNAs, and 3.4 μL Cas9 enzyme (M0386S, NEB) added up to 10 μL with water.

Techniques: Virus, Sequencing, Concentration Assay

Journal: BMC Genomics

Article Title: Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform

doi: 10.1186/s12864-025-12268-4

Figure Lengend Snippet: The effect of omitting Cas9 inactivation by proteinase K (no protK) and subsequent heat inactivation at 95 °C (no 95 °C) on the detection of spiked PDV (Phocine distemper virus), non-depleted transcripts PGK1 (phosphoglycerate kinase 1), ND1/ND2/ND6 (NADH dehydrogenase subunit 1/2/6), COI (cytochrome c oxidase subunit I), CYB (cytochrome B), ACTB (actin beta), and B2M (β2 microglobulin), and on the depletion of ribosomal RNAs 18S, 28S, and 16S in TURBO + DASH-depleted human serum samples. DASH was performed in a 40 µL volume directly on the second strand Klenow reactions

Article Snippet: This ribonucleoprotein complex was formed by a 10 min preincubation at 37 °C of 1 μL Cas9 buffer, 2300 ng sgRNAs, and 3.4 μL Cas9 enzyme (M0386S, NEB) added up to 10 μL with water.

Techniques: Virus

Journal: BMC Genomics

Article Title: Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform

doi: 10.1186/s12864-025-12268-4

Figure Lengend Snippet: A) The effect of performing DASH directly on unwashed Klenow reactions in 50 µL (unwashed 50 µL rxn) as opposed to performing DASH after a beads cleanup in 20 µL (washed 20 µL rxn), on the detection (left) and read length (right) of spiked PDV (Phocine distemper virus), of non-depleted transcripts PGK1 (phosphoglycerate kinase 1), ND1/ND2/ND6 (NADH dehydrogenase subunit 1/2/6), COI (cytochrome c oxidase subunit I), and CYB (cytochrome B), and of depleted ribosomal 18S and 28S RNA in metagenomic sequencing libraries of TURBO + DASH-depleted human serum samples. B) Increasing the Cas9 concentration lowers the loss of depletion observed when using direct DASH. C) Performing Klenow reactions in smaller volumes further reduces this loss of depletion

Article Snippet: This ribonucleoprotein complex was formed by a 10 min preincubation at 37 °C of 1 μL Cas9 buffer, 2300 ng sgRNAs, and 3.4 μL Cas9 enzyme (M0386S, NEB) added up to 10 μL with water.

Techniques: Virus, Sequencing, Concentration Assay

Journal: BMC Genomics

Article Title: Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform

doi: 10.1186/s12864-025-12268-4

Figure Lengend Snippet: The effect of omitting Cas9 inactivation by proteinase K (no protK) and subsequent heat inactivation at 95 °C (no 95 °C) on the detection of spiked PDV (Phocine distemper virus), non-depleted transcripts PGK1 (phosphoglycerate kinase 1), ND1/ND2/ND6 (NADH dehydrogenase subunit 1/2/6), COI (cytochrome c oxidase subunit I), CYB (cytochrome B), ACTB (actin beta), and B2M (β2 microglobulin), and on the depletion of ribosomal RNAs 18S, 28S, and 16S in TURBO + DASH-depleted human serum samples. DASH was performed in a 40 µL volume directly on the second strand Klenow reactions

Article Snippet: This ribonucleoprotein complex was formed by a 10 min preincubation at 37 °C of 1 μL Cas9 buffer, 2300 ng sgRNAs, and 3.4 μL Cas9 enzyme (M0386S, NEB) added up to 10 μL with water.

Techniques: Virus