Biology subjects

Eling, N.

Publications and source records attributed to Eling, N..

3 recordsLinked to original sources

bioRxiv2018

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

Understanding male fertility requires an in-depth characterisation of spermatogenesis, the developmental process by which male gametes are generated. Spermatogenesis occurs continuously throughout a males reproductive window and involves a complex sequence of developmental steps, both of which make this process difficult to decipher at the molecular level. To overcome this, we transcriptionally profiled single cells from multiple distinct stages during the first wave of spermatogenesis, where the most mature germ cell type is known. This naturally enriches for spermatogonia and somatic cell types present at very low frequencies in adult testes. Our atlas, available as a shiny app (https://marionilab.cruk.cam.ac.uk/SpermatoShiny), allowed us to reconstruct the three main processes of spermatogenesis: spermatogonial differentiation, meiosis, and spermiogenesis. Additionally, we profiled the chromatin changes associated with meiotic silencing of the X chromosome, revealing a set of genes specifically and strongly repressed by H3K9me3 in the spermatocyte stage, but which escape post-meiotic silencing in spermatids.

developmental biology↗

bioRxiv2017

Robust expression variability testing reveals heterogeneous T cell responses

Cell-to-cell transcriptional variability in otherwise homogeneous cell populations plays a crucial role in tissue function and development. Single-cell RNA sequencing can characterise this variability in a transcriptome-wide manner. However, technical variation and the confounding between variability and mean expression estimates hinders meaningful comparison of expression variability between cell populations. To address this problem, we introduce a novel analysis approach that extends the BASiCS statistical framework to derive a residual measure of variability that is not confounded by mean expression. Moreover, we introduce a new and robust procedure for quantifying technical noise in experiments where technical spike-in molecules are not available. We illustrate how our method provides biological insight into the dynamics of cell-to-cell expression variability, highlighting a synchronisation of the translational machinery in immune cells upon activation. Additionally, our approach identifies new patterns of variability across CD4+ T cell differentiation.

bioinformatics↗

bioRxiv2017

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues

Animal bodies comprise a diverse array of tissues and cells. To characterise cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii1-4. We identify five transcriptionally distinct groups of differentiated cells that are spatially coherent, as revealed by spatial mapping5. Besides somatic musculature, ciliary bands and midgut, we find a group of cells located at the apical tip of the animal, comprising sensory-peptidergic neurons, and another group composed of non-apical neural and epidermal cells covering the rest of the body. These data establish a basic subdivision of the larval body surface into molecularly defined apical versus non-apical tissues, and support the evolutionary conservation of the apical nervous system as a distinct part of the bilaterian brain6.

evolutionary biology↗