Journal: Nucleic Acids Research

Article Title: Sequence and expression analysis of gaps in human chromosome 20

doi: 10.1093/nar/gks302

Figure Lengend Snippet: Chromatin distribution and DNA methylation profile across human chr 20-gap regions. ( A ) H3K27me3 is distributed across all three human chr-20 gap regions in EBV-PBLs. ( B ) MRE-Seq (hypomethylated) and MBD-Seq (hypermethylated) aligned peak reads within gaps 1 and 3. Methylation distribution is similar in PBL and human cerebellum for both gaps 1 and 3. ( C ) Methylation profile of gap 2 shows it to be enriched for both hypomethylated and hypermethylated CpGs, respectively. CpG island 4/1a (red rectangle) is enriched for both MBD-Seq and MRE-Seq reads suggesting it to be a differentially methylated locus. CpG islands 2–6 were annotated using the classification: 500-bp region of genomic DNA with ≥50% CG content and an observed CpG to expected CpG ratio of 0.6. CpG islands 1a–3a were classified based on a CpG island being a 500-bp region of genomic DNA with ≥55% CG content and an observed CpG to expected CpG ratio of 0.65. Images are drawn to scale. ( D ) Differentially methylated and paternally hypermethylated CpGs island 4/1a within gap 2 using bisulfite allelic sequencing and gDNA from mouse–human cell hybrid cell lines or diploid human cells.

Article Snippet: In situ hybridizations were performed using purchased control human cerebellum brain sections (70-year-old female donor, Cat # TCB-4089 Capital Biosciences) as previously published ( ) using Fluorescein -labeled oligos ( Supplementary Table S7 ).

Techniques: DNA Methylation Assay, Methylation, Sequencing

Journal: Nucleic Acids Research

Article Title: Sequence and expression analysis of gaps in human chromosome 20

doi: 10.1093/nar/gks302

Figure Lengend Snippet: De novo prediction and experimental verification of structured ncRNAs within human chr 20 gaps. ( A ) Expression confirmation of ncRNAs predicted by CMfinder using total universal reference RNA. ( B ) Expression of candidate ncRNAs in a human multi-tissue RNA panel. ( C ) Elevated expression of candidate ncRNAs: 5, 6, 9 and 12 in a human multi-region brain panel. ( D ) RNA structure of ncRNA numbers: 5, 6, 9 predicted using INFERNAL. The Vienna RNA conservation coloring scheme highlights the mutational pattern with respect to the structure and a circle around a variable base(s) marks consistent and compensatory mutations. The color coding is explained in a color scheme legend. There are six different canonical base pairs (G-C, C-G, A-U, U-A, G-U, U-G) described by the different colors ( x -axis), and if the base pair is not supported in a sequence of the alignment the color shading gets lighter ( y -axis, incompatible pairs). ( E ) Candidate ncRNA number 5 is specifically expressed in the nucleus of Purkinje cells in the human cerebellum. ( F ) Localized view of the DLGAP4 promoter (chr 20:34,355,500–34,385,499, hg18 + chr 20 gaps) showing candidate ncRNAs in gap 1. RNA-Seq tracks show forward and reverse aligned reads in blue and green, respectively.

Article Snippet: In situ hybridizations were performed using purchased control human cerebellum brain sections (70-year-old female donor, Cat # TCB-4089 Capital Biosciences) as previously published ( ) using Fluorescein -labeled oligos ( Supplementary Table S7 ).

Techniques: Expressing, Sequencing, RNA Sequencing

Journal: bioRxiv

Article Title: Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

doi: 10.1101/2024.11.07.622523

Figure Lengend Snippet: a Brightfield image of FFPE human cerebellum following barcoding in the DBiTplus workflow. Box represents the barcoded region. Brightfield image after cDNA retrieval shows the tissue morphology is preserved and is suitable for CODEX imaging. b The same tissue section from panel A is imaged with a 28-marker panel. Left: CODEX image showing AQP4 (Astrocytes), MAP2 (Synaptic neurons), NeuN (Neuronal nuclei and cell bodies) and Vimentin (Vasculature). Right top: Synaptic neurons marked by MAP2 in the molecular layer of the cerebellum. Right bottom: Large pear-shaped Purkinje cells, with their large cell bodies visualized in the Purkinje cell layer. c Brightfield image of FFPE of benign human lymph node. Box represents the barcoded region. Brightfield image after cDNA retrieval shows the tissue morphology is preserved and is suitable for CODEX imaging. d Size distribution from TapeStation traces of cDNA amplicon. e CODEX imaging on FFPE of human lymph node following the DBiTplus workflow. Three distinct regions are further analyzed for quality of CODEX staining. f Top: Region showing T cell subtypes: CD3ɛ (T cells), CD8 (Cytotoxic T cells), CD4 (Helper T cells) and SMA (Smooth muscles). Middle: CD3ɛ (T cells), SMA (Smooth muscles), CD20 (B cells) and CD21 (Follicular dendritic cells). Bottom: SMA (Smooth muscles), Ki67 (Proliferating germinal center B cells), Collagen IV (Blood vessels), CD31 (Vasculature).

Article Snippet: Human brain cerebellum paraffin sections ( HP-202 ), were purchased from Zyagen and made of freshly harvested tissues, fixed in 10% neutral buffered formalin, and processed for paraffin embedding.

Techniques: Imaging, Marker, Amplification, Staining, Muscles