Enrich and sequence densely 5-methylcytosine-rich genomic regions from U87-MG glioblastoma DNA using an anti-5mC antibody to identify hypermethylated CpG-island promoters associated with tumor-suppressor silencing, independent of any single-base bisulfite chemistry.
Use a cytosine base editor (BE4max) with CRISPR-STOP guides to introduce a premature stop codon (CAG/CAA/CGA -> TAG/TAA/TGA) into a stably integrated EGFP cassette, achieving DSB-free gene inactivation read out as loss of green fluorescence by flow cytometry.
Identify and quantify bivalent chromatin domains (co-occurrence of activating H3K4me3 and repressive H3K27me3) at developmental gene promoters in human iPSC-derived neural progenitor cells using native (non-crosslinked) MNase-based chromatin immunoprecipitation, to map poised regulatory loci that resolve upon neuronal differentiation.
Generate single-base-resolution genome-wide 5-methylcytosine maps from limited genomic DNA inputs (100 ng) of HCT116 colorectal cancer cells to quantify locus-specific CpG methylation and compare DNMT-wild-type versus DNMT1/3B double-knockout lines.
Identify genes essential for K562 leukemia cell proliferation by deconvoluting sgRNA abundance changes in a genome-wide Brunello pooled CRISPR knockout screen via Illumina sequencing and MAGeCK analysis of dropout from an early to a late timepoint.
Precisely quantify the editing efficiency and indel allele spectrum at a single CRISPR-Cas9 target site using targeted amplicon next-generation sequencing analyzed with CRISPResso2, enabling sub-percent detection and allele-resolution that Sanger-based tools cannot achieve.
Generate strand-specific, poly(A)-enriched mRNA sequencing libraries from HEK293T total RNA suitable for differential gene expression analysis on Illumina platforms, with RIN-gated input QC and accurate strand assignment for antisense transcript discrimination.
Map genome-wide open chromatin in cryopreserved human PBMCs using the Omni-ATAC protocol, minimizing mitochondrial read contamination and maximizing signal-to-noise to identify cell-state-specific accessible regulatory elements and transcription factor footprints.
Provide a fast, gel-based estimate of CRISPR-Cas9 editing efficiency at a target locus by detecting heteroduplex mismatches with T7 Endonuclease I, enabling same-day go/no-go decisions on guide RNA activity before committing to deep sequencing.
Capture single-cell 3' transcriptomes from dissociated mouse spleen using the 10x Chromium platform, targeting 8,000 recovered cells per sample with high viability and low ambient RNA to resolve splenic immune cell subsets.
Prepare dual-indexed 16S rRNA V3-V4 amplicon libraries from human stool genomic DNA for Illumina MiSeq sequencing, with rigorous mock-community and negative controls to enable accurate, contamination-aware taxonomic profiling of the gut microbiome.
Generate a clonal HPRT1 knockout HEK293T line using transient Cas9 ribonucleoprotein (RNP) nucleofection, exploiting 6-thioguanine selection to enrich functional knockouts and minimize off-target risk relative to plasmid delivery.
Map genome-wide H3K27me3 Polycomb-repressive domains in mouse embryonic stem cells (E14 mESCs) at low cell input using antibody-tethered MNase (CUT&RUN), and quantitatively compare H3K27me3 occupancy between naive (2i/LIF) and primed (EpiLC) states using calibrated spike-in normalization.
Define genome-wide nucleosome positions and occupancy in budding yeast using a micrococcal nuclease digestion titration, and quantify nucleosome eviction and repositioning at GAL-regulon promoters upon switching cells from glucose to galactose, to relate chromatin remodeling to transcriptional activation.
Generate quantitative, spike-in-normalized H3K27ac ChIP-seq libraries from crosslinked K562 cells to map active enhancers and promoters genome-wide, enabling reliable comparison of global acetylation changes between treatment conditions.