Zhong, C.-Q. | Search bioRxiv

bioRxiv2021

DreamDIA-XMBD: deep representation features improve the analysis of data-independent acquisition proteomics

We developed DreamDIA-XMBD, a software suite for data-independent acquisition (DIA) data analysis. DreamDIA-XMBD adopts a data-driven strategy to capture comprehensive information from elution patterns of target peptides in DIA data and achieves considerable improvements on both identification and quantification performance compared with other state-of-the-art methods such as OpenSWATH, Skyline and DIA-NN. More specifically, in contrast to existing methods which use only 6 to 10 selected transitions from spectral library, DreamDIA-XMBD extracts additional features from dozens of theoretical elution profiles originated from different ions of each precursor using a deep representation network. To achieve higher coverage of target peptides without sacrificing specificity, the extracted features are further processed by non-linear discriminative models under the framework of positive-unlabeled learning with decoy peptides as affirmative negative controls. DreamDIA-XMBD is written in Python, and is publicly available at https://github.com/xmuyulab/Dream-DIA-XMBD for high coverage and precision DIA data analysis.

bioinformatics↗

bioRxiv2021

Generation of human blastocyst-like structures from pluripotent stem cells

Human blastocysts are comprised of the first three cell lineages of the embryo: trophectoderm, epiblast, and primitive endoderm, all of which are essential for early development and organ formation1,2. However, due to ethical concerns and restricted access to human blastocysts, we lack a comprehensive understanding of early human embryogenesis. To bridge this knowledge gap, we need a reliable model system that recapitulates early stages of human embryogenesis. Here we report a [~]three-dimensional (3D), two-step induction protocol for generating blastocyst-like structures (EPS-blastoids) from human extended pluripotent stem (EPS) cells. Morphological and single-cell transcriptomic analyses revealed that EPS-blastoids contain key cell lineages and are transcriptionally similar to human blastocysts. Furthermore, EPS-blastoids also exhibited the developmental potential to undergo post-implantation morphogenesis in vitro to form structures with a cellular composition and transcriptome signature similar to human embryos that had been cultured in vitro for 8 or 10 days. In conclusion, human EPS-blastoids provide a new experimental platform for studying early developmental stages of the human embryo. HighlightsA method for generating human blastoids from EPS cells. Human blastoids resemble blastocysts in terms of morphology and cell lineage composition. Single-cell transcriptomic analyses reveal EPI, PE, and TE cell lineages in human blastoids. Human blastoids mimic in vitro the morphogenetic events of pre- and early post-implantation stages.

developmental biology↗