Journal: Cell reports

Article Title: TIGER: Single-step in vivo genome editing in a non-traditional rodent

doi: 10.1016/j.celrep.2023.112980

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: To assess transgene copy number in F1 transgenic mice, we performed digital droplet PCR (ddPCR) on genomic DNA from representative F1 mice, as well as their wild type littermates. ddPCR reactions were assembled using 60ng gDNA template in QX200 ddPCR EvaGreen Supermix (Bio-Rad) and droplet formation was performed using an AutoDG Automated Droplet Generator (Bio-Rad).

Techniques: Virus, Recombinant, PCR Cloning, Cloning, Mutagenesis, Software, CRISPR

Journal: Current protocols in human genetics

Article Title: Droplet Digital PCR with EvaGreen Assay: Confirmational Analysis of Structural Variants

doi: 10.1002/cphg.58

Figure Lengend Snippet: Overview of the ddPCR with EvaGreen assay. (A) Schematic of the region of interest (ROI, upper) for copy number variant analysis and the reference (REF, lower). (B) Schematic of the ddPCR with EvaGreen workflow.

Article Snippet: DNA Nuclease free water 2x ddPCR EvaGreen Supermix (includes hot start DNA polymerase, dNTPs including dUTP; Bio-Rad) 20x ROI target primer (see ) 20x REF target (RPP30) primer/Taqman probe mix (see Reagents and Solutions recipe) 2x buffer control for EvaGreen (Bio-Rad) Droplet Generation Oil for Evagreen (Bio-Rad) 96-well plates 96-well plate centrifuge DG8 droplet generator cartridges (single-use; Bio-Rad) DG8 droplet generator cartridge holder (Bio-Rad) DdPCR droplet generation (DG) oil (Bio-Rad) DG8 gaskets (single-use; Bio-Rad) QX200 droplet generator (Bio-Rad) Eppendorf twin.tec semi-skirted 96 well plate Heat sealer Heat sealing PCR foil Thermal cycler Bio-Rad QX200 droplet reader QuantaSoft software

Techniques: Variant Assay

Journal: Current protocols in human genetics

Article Title: Droplet Digital PCR with EvaGreen Assay: Confirmational Analysis of Structural Variants

doi: 10.1002/cphg.58

Figure Lengend Snippet: Sample results from ddPCR with EvaGreen assay. (A) 1D plots for FAM (upper) and VIC (lower) channels. (B) 2D plot showing combined three clusters of droplets: blue, EvaGreen-positive (ROI); orange, EvaGreen- and VIC-positive(i.e., REF gene RRP30); and black, negative.

Article Snippet: DNA Nuclease free water 2x ddPCR EvaGreen Supermix (includes hot start DNA polymerase, dNTPs including dUTP; Bio-Rad) 20x ROI target primer (see ) 20x REF target (RPP30) primer/Taqman probe mix (see Reagents and Solutions recipe) 2x buffer control for EvaGreen (Bio-Rad) Droplet Generation Oil for Evagreen (Bio-Rad) 96-well plates 96-well plate centrifuge DG8 droplet generator cartridges (single-use; Bio-Rad) DG8 droplet generator cartridge holder (Bio-Rad) DdPCR droplet generation (DG) oil (Bio-Rad) DG8 gaskets (single-use; Bio-Rad) QX200 droplet generator (Bio-Rad) Eppendorf twin.tec semi-skirted 96 well plate Heat sealer Heat sealing PCR foil Thermal cycler Bio-Rad QX200 droplet reader QuantaSoft software

Techniques:

Journal: Current protocols in human genetics

Article Title: Droplet Digital PCR with EvaGreen Assay: Confirmational Analysis of Structural Variants

doi: 10.1002/cphg.58

Figure Lengend Snippet: Sample CNV Results using ddPCR with EvaGreen Assa

Article Snippet: DNA Nuclease free water 2x ddPCR EvaGreen Supermix (includes hot start DNA polymerase, dNTPs including dUTP; Bio-Rad) 20x ROI target primer (see ) 20x REF target (RPP30) primer/Taqman probe mix (see Reagents and Solutions recipe) 2x buffer control for EvaGreen (Bio-Rad) Droplet Generation Oil for Evagreen (Bio-Rad) 96-well plates 96-well plate centrifuge DG8 droplet generator cartridges (single-use; Bio-Rad) DG8 droplet generator cartridge holder (Bio-Rad) DdPCR droplet generation (DG) oil (Bio-Rad) DG8 gaskets (single-use; Bio-Rad) QX200 droplet generator (Bio-Rad) Eppendorf twin.tec semi-skirted 96 well plate Heat sealer Heat sealing PCR foil Thermal cycler Bio-Rad QX200 droplet reader QuantaSoft software

Techniques:

Journal: Neuron

Article Title: Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding.

doi: 10.1016/j.neuron.2021.07.007

Figure Lengend Snippet: Figure 6. Double+ NPCs are essential to sustain regular neurogenesis and prevent cortical folding (A) Knockin strategy to generate split-Cre transgenics. (B–D) Lineage tracing in E12.5 and P0 split-Cre;Rosa-tdTomato cortices (B) and P7 split-Cre;Rosa-zsGreen cortices, showing co-staining of reporters with NeuN (C) and Pdgfra (D). Insets are 43 magnifications. Arrows mark double+ cells. (E–H) Tbr1/Satb2 immunolabeling of P0 control (N = 8) and split-Cre;Rosa-DTA (N = 5) cortices (E), E18.5 control (N = 4) and split-Cre;Rosa-DTR (N = 5) cortices after DT injection from E12.5 to E17.5 (F), and P0 control (N = 6) and split-Cre;RC::L-DTA (N = 4) cortices (G). Arrows mark cortical folds. Penetrance of folding phenotype indicated in upper right corner. Quantification of gyrification indices (H). (I) ddPCR analysis of genomic DNA from single Cre+ and split-Cre;RC::L-DTA P0 retinas. Insets are 33 magnifications of boxed regions. (J) Tbr1+ and Satb2+ neuron counts in E15.5 control (N = 4) and split-Cre;RC::L-DTA (N = 3) cortices. (K and L) Calculation of n-fraction (K) and p-fraction (L) in E15.5 control (N = 4) and split-Cre;RC::L-DTA (N = 3) cortices. (M–P) Expression and quantification of Pax6+ (M), Tbr2+ (N), and pHH3+ (O) cells inside and outside the VZ in E15.5 control (N = 4) and split-Cre;RC::L-DTA (N = 3) cortices. BLBP immunostaining of E18.5/P0 control and split-Cre;RC::L-DTA cortices (N = 4 total; 2 each stage, with n = 13 fibers traced per brain) (P). Representative aRG fiber tracings are shown. Quantification of curvature index of individual aRG fibers. (legend continued on next page)

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Viability Dye eFluor 780 eBioscience Cat# 65-0865-14 Hoechst 33342 Thermofisher Cat# 62249 B27 supplement minus vitamin A Thermofisher Cat# 12587010 Human FGF2 MACS Cat# 130-093-842 Animal-Free Recombinant Human EGF Peprotech Cat# AF-100-15 Cyclopamine Selleckchem Cat# S1146 Geltrex matrix Thermofisher Cat# 12760 StemProNeural Supplement Thermofisher Cat# A1050801 B27 supplement Thermofisher Cat# 17504 N-2 Supplement Thermofisher Cat# 17502 T3 (3,30,5-Triiodo-L-thyronine sodium salt) Sigma Cat# D6397 DNaseI Ambion Cat# AM2222 Critical commercial assays RNAscope Multiplex Fluorescent Detection Kit v2 ACD Cat# 323110 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Nucleofector Kits for Mouse Neural Stem Cells (mNSC) Lonza Cat# VPG-1004 Duolink In Situ Red Starter Kit Goat/Rabbit Sigma Aldrich Cat# DUO92105 MagMAX-96 Total RNA Isolation Kit Invitrogen Cat# AM1830 TruSeq Stranded mRNA Library Prep Kit Illumina Cat# 15028212 RNeasy Micro Kit QIAGEN Cat# 74004 RT2 First strand kit QIAGEN Cat# 330401 RT2 SYBR Green qPCR Mastermix QIAGEN Cat# 330500 QX200 droplet digital PCR (ddPCR) system, and ddPCR Supermix Bio-Rad Cat# 1864001, Cat#1863023 Click-iT Plus EdU Imaging Kit (Alexa Fluor 647 dye) Invitrogen Cat# C10640 Click-iT Plus TUNEL Assay kit (Alexa Fluor 647 dye) Invitrogen Cat# C10619 Deposited data RNA-seq data This study GEO: GSE151775 ATAC-seq data This study GEO: GSE84120 Ascl1 ChIP-seq data This study Array Express: E-MTAB-9751 (https://www. ebi.ac.uk/arrayexpress/experiments/) Neurog2 ChIP-seq data Sessa et al., 2017 GEO: GSE63621 scRNA-seq data of human COs Sivitilli et al., 2020 GEO: GSE137877 scRNA-seq data of human fetal cortex Zhong et al., 2018) GEO: GSE104276 Transcriptional interaction data MetaCore (GeneGo Inc.) https://portal.genego.com/ Uncropped western blot images This study Mendeley link: https://dx.doi.org/ 10.17632/wgpsd9yyk2.1 Experimental models: Cell lines P19 embryonic carcinoma cells ATCC CRL-1825; RRID: CVCL_2153 NIH 3T3 cells ATCC CRL-1658; RRID: CVCL_0594 Feeder-free H1 hESCs Wicell WA01; RRID: CVCL_9771 Experimental models: Organisms/strains Mus musculus: CD1 mouse (022) Charles River Strain Code: 022; RRID: IMSR_CRL:022 Mus musculus: Neurog2mCherryKI This study N/A Mus musculus: Ascl1GFPKI Leung et al., 2007 Jackson Laboratory Cat# 012881; RRID: IMSR_JAX:012881 Mus musculus: C57BL/6J Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mus musculus: Neurog2N-CreKI This study N/A (Continued on next page) Neuron 109, 1–17.e1–e11, September 15, 2021 e2

Techniques: Knock-In, Staining, Immunolabeling, Control, Injection, Expressing, Immunostaining