Journal: eLife

Article Title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

doi: 10.7554/eLife.108485

Figure Lengend Snippet: ( A ) Schematic illustrating annotation of cis -regulatory elements in RPCs and photoreceptor precursors by integration of scATAC-Seq and CUT&RUN 13LGS and mouse datasets. ( B ) Heatmaps show annotated accessible regulatory elements in both 13LGS and mouse. Promoters, activated enhancers (AEs), and poised enhancers (PEs), which are associated with histone markers associated with genes in clusters C2 and C3, which are selectively active in 13LGS RPCs and/or photoreceptor precursors. Shading indicates CUT&TAG signal for the corresponding histone modification within 2 kb of the scATAC-Seq peak center. Bar plots displaying the number of each category of regulatory element in each species that are conserved or species-specific. ( C ) Dot plots showing the enrichment of binding sites for Otx2 and Neurod1, TFs which are broadly expressed in both neurogenic RPC and photoreceptor precursors, which are enriched in both conserved cis -regulatory elements in both species. ( D ) Bar plots showing the number of conserved and species-specific enhancers per transcription start site (TSS) in four cone-promoting genes between 13LGS and mouse. ( E ) The gene regulatory networks (GRNs) regulating Thrb expression in 13LGS and mouse late N. RPCs. ( F ) An example of a Thrb-related regulon and its corresponding scATAC-Seq and CUT&RUN tracks. The arrow indicates the consistent regulatory relationships between GRN prediction and experimental validations. ( G ) The epigenetic model of cone specification in 13LGS and mouse.

Article Snippet: The total CUT&RUN DNA yield, up to 5 ng of total purified DNA, was used for library preparation, using reagents from CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-1001) or NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

Techniques: Modification, Binding Assay, Expressing

Journal: eLife

Article Title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

doi: 10.7554/eLife.108485

Figure Lengend Snippet: ( A ) Gene regulatory networks controlling Zic3 expression in 13LGS late-stage neurogenic RPCs, photoreceptor precursors, and cones. ( B ) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in 13LGS. ( C ) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in mouse.

Article Snippet: The total CUT&RUN DNA yield, up to 5 ng of total purified DNA, was used for library preparation, using reagents from CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-1001) or NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

Techniques: Expressing

Journal: Cell reports

Article Title: SMYD5 is a regulator of the mild hypothermia response

doi: 10.1016/j.celrep.2024.114554

Figure Lengend Snippet:

Article Snippet: The following antibodies were used for the CUT&RUN: H3K36me3 (Thermo Fisher Scientific, MA5–24687), H4K20me3 (EpiCypher, 13–0054), H3K4me3 (EpiCypher, 13–0041 or Abcam, ab8580), H3K27me3 (Thermo Fisher Scientific, MA5–11198), H3K9me3 (Abcam, ab176916), rabbit anti-SMYD5, and Rabbit IgG Antibody (Epicypher, 23613–0042).

Techniques: Mutagenesis, Inhibition, Reverse Transcription, BIA-KA, Sample Prep, CRISPR, Recombinant, Plasmid Preparation, Software

Journal: Scientific Data

Article Title: Chromatin conformation and histone modification profiling across human kidney anatomic regions

doi: 10.1038/s41597-024-03648-8

Figure Lengend Snippet: Index sequences of 18 CUT&RUN libraries presented in this study.

Article Snippet: For antibody binding, 0.5 µg H3K4me3 (Cat # 13-0041k, EpiCypher) and H3K27me3 (Cat # 13-0055, EpiCypher) antibodies were used and 0.5 µg rabbit IgG antibody (Cat # 13-0042k, EpiCypher) was used as a negative control.

Techniques: Modification

Journal: Scientific Data

Article Title: Chromatin conformation and histone modification profiling across human kidney anatomic regions

doi: 10.1038/s41597-024-03648-8

Figure Lengend Snippet: Sequencing depths of CUT&RUN libraries presented in this work.

Article Snippet: For antibody binding, 0.5 µg H3K4me3 (Cat # 13-0041k, EpiCypher) and H3K27me3 (Cat # 13-0055, EpiCypher) antibodies were used and 0.5 µg rabbit IgG antibody (Cat # 13-0042k, EpiCypher) was used as a negative control.

Techniques: Sequencing, Modification

Journal: Scientific Data

Article Title: Chromatin conformation and histone modification profiling across human kidney anatomic regions

doi: 10.1038/s41597-024-03648-8

Figure Lengend Snippet: Visualization of CUT&RUN peaks. ( a , b ) Circos plots for genome-wide H3K4me3 ( a ) and H3K27me3 ( b ) peak profiles across kidney cortex (outer layer), medulla (middle layer) and papilla (inner layer). Sizes of each chromosome are shown. A region of interest on chromosome 19 is highlighted with arrows and is shown with zoom-in ( c ). ( d , e ) Coverage plots of the called peaks over chromosome 3 ( d ) and chromosome 4 ( e ) for each CUT&RUN library (with duplicates merged).

Article Snippet: For antibody binding, 0.5 µg H3K4me3 (Cat # 13-0041k, EpiCypher) and H3K27me3 (Cat # 13-0055, EpiCypher) antibodies were used and 0.5 µg rabbit IgG antibody (Cat # 13-0042k, EpiCypher) was used as a negative control.

Techniques: Genome Wide