Distribution pattern of GFP (green fluorescent protein) in a bivalve-inhabiting hydrozoan, Eutima japonica (Leptomedusae: Eirenidae)

Bright green auto-fluorescence was observed in the umbrellar margin, umbrellar marginal warts, tentacular bulbs, tentacles, and manubrium of laboratory-reared immature (1–14 days old) medusae of Eutima japonica from Japan and China. In vivo microscopic fluorescence spectra showed that the green fluorescence was similar to that of green fluorescent protein (GFP) found in Aequorea victoria, although the maximum emission wavelength (503 nm) was slightly bluer. No fluorescence was detected in the cirri, statocysts, radial canals, velum, or subumbrella of the medusae. The fluorescence distribution pattern in E. japonica more closely resembles that of Eugymnanthea inquilina from the Mediterranean Sea than that of Japanese Eugymnanthea japonica, which is the derived species of E. japonica. This suggests that the common fluorescence pattern is convergently evolved in the former two species, perhaps owing to the as yet unclarified physiological and/or ecological function of GFP and/or GFP-like proteins

Dataset for "Label-free enrichment of human pluripotent stem cell-derived early retinal progenitor cells for cell-based regenerative therapies"

<p>The raw dataset for "Label-free enrichment of human pluripotent stem cell-derived early retinal progenitor cells for cell-based regenerative therapies"</p> <p><span>DOI:</span><a href="https://doi.org/10.1016/j.stemcr.2023.12.001">https://doi.org/10.1016/j.stemcr.2023.12.001</a></p&gt

An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies

Abstract Background Single-cell technologies to analyze transcription and chromatin structure have been widely used in many research areas to reveal the functions and molecular properties of cells at single-cell resolution. Sample multiplexing techniques are valuable when performing single-cell analysis, reducing technical variation and permitting cost efficiencies. Several commercially available methods have been used in many scRNA-seq studies. On the other hand, while several methods have been published, multiplexing techniques for single nuclear assay for transposase-accessible chromatin (snATAC)-seq assays remain under development. We developed a simple nucleus hashing method using oligonucleotide-conjugated antibodies recognizing nuclear pore complex proteins, NuHash, to perform snATAC-seq library preparations by multiplexing. Results We performed multiplexing snATAC-seq analyses on a mixture of human and mouse cell samples (two samples, 2-plex, and four samples, 4-plex) using NuHash. The analyses on nuclei with at least 10,000 read counts showed that the demultiplexing accuracy of NuHash was high, and only ten out of 9144 nuclei (2-plex) and 150 of 12,208 nuclei (4-plex) had discordant classifications between NuHash demultiplexing and discrimination using reference genome alignments. The differential open chromatin region (OCR) analysis between female and male samples revealed that male-specific OCRs were enriched in chromosome Y (four out of nine). We also found that five female-specific OCRs (20 OCRs) were on chromosome X. A comparative analysis between snATAC-seq and deeply sequenced bulk ATAC-seq on the same samples revealed that the bulk ATAC-seq signal intensity was positively correlated with the number of cell clusters detected in snATAC-seq. Moreover, when we categorized snATAC-seq peaks based on the number of cell clusters in which the peak was present, we observed different distributions over different genomic features between the groups. This result suggests that the peak intensities of bulk ATAC-seq can be used to identify different types of functional loci. Conclusions Our multiplexing method using oligo-conjugated anti-nuclear pore complex proteins, NuHash, permits high-accuracy demultiplexing of samples. The NuHash protocol is straightforward, works on frozen samples, and requires no modifications for snATAC-seq library preparation

Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm

International audienceThe poles of the heart and branchiomeric muscles of the face and neck are formed from the cardiopharyngeal mesoderm within the pharyngeal apparatus. They are disrupted in patients with 22q11.2 deletion syndrome, due to haploinsufficiency of TBX1 , encoding a T-box transcription factor. Here, using single cell RNA-sequencing, we now identify a multilineage primed population within the cardiopharyngeal mesoderm, marked by Tbx1 , which has bipotent properties to form cardiac and branchiomeric muscle cells. The multilineage primed cells are localized within the nascent mesoderm of the caudal lateral pharyngeal apparatus and provide a continuous source of cardiopharyngeal mesoderm progenitors. Tbx1 regulates the maturation of multilineage primed progenitor cells to cardiopharyngeal mesoderm derivatives while restricting ectopic non-mesodermal gene expression. We further show that TBX1 confers this balance of gene expression by direct and indirect regulation of enriched genes in multilineage primed progenitors and downstream pathways, partly through altering chromatin accessibility, the perturbation of which can lead to congenital defects in individuals with 22q11.2 deletion syndrome