Single-cell RNA sequencing of adult rat testes after Leydig cell elimination and restoration

Guan, Xiaoju; Ji, Minpeng; Wen, Xin; Huang, Fu; Zhao, Xingyi; Chen, Dan; Shao, Jingjing; Wang, Jiexia; Xie, Jiajia; Tian, Jing; Lin, Han Chieh; Duan, Peng; Zirkin, Barry R.; Su, Zhijian; Chen, Haolin

doi:10.1038/s41597-022-01225-5

Cited by 7 publications

(3 citation statements)

References 29 publications

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“…Next, we integrated published single cell RNA-seq ( scRNA-seq ) datasets of adult rat testicular cells (28) with our bulk RNA-seq datasets from PND 60 Taf7l Xm+/Y and Taf7l Xm-/Y testes to identify specific transcript-associations with each spermatogenic cell type. The dataset integration indicated that TAF7L deficiency led to an enrichment of spermatogonia genes, and a downregulation of genes associated to spermatocytes and spermatids ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Taf7l Regulates Early Stages of Male Germ Cell Development

Moreno-Irusta,

Dominguez,

Iqbal

et al. 2023

Preprint

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Male germ cell development is dependent on the orchestrated regulation of gene networks. TATA-box binding protein associated factors (TAFs) facilitate interactions of TATA-binding protein with the TATA element, which is known to coordinate gene transcription during organogenesis. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat.Taf7lwas prominently expressed in preleptotene to leptotene spermatocytes. To study the impact of TAF7L on the testis we generated a globalloss-of-functionrat model using CRISPR/Cas9genome editing. Exon 3 of theTaf7lgene was targeted. A founder was generated possessing a 110 bp deletion within theTaf7l locus, which resulted in a frameshift and the premature appearance of a stop codon. The mutation was effectively transmitted through the germline. Deficits in TAF7L did not adversely affect pregnancy or postnatal survival. However, theTaf7ldisruption resulted in male infertility due to compromised testis development and failed sperm production. Mutant germ cells suffer meiotic arrest at the zygotene stage, with defects in sex body formation and meiotic sex chromosome inactivation. This testis phenotype was more pronounced than previously described for the subfertileTaf7lnull mouse. We conclude that TAF7L is essential for male germ cell development in the rat.

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Section: Resultsmentioning

confidence: 99%

Taf7l Regulates Early Stages of Male Germ Cell Development

Moreno-Irusta,

Dominguez,

Iqbal

et al. 2023

Preprint

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show abstract

“…Next, we integrated published single‐cell RNA‐seq (scRNA‐seq) datasets of adult rat testicular cells 33 with our bulk RNA‐seq datasets from PND 60 Taf7l +/ Y and Taf7l −/ Y testes to identify specific transcript‐associations with each spermatogenic cell type. The dataset integration indicated that TAF7L deficiency led to an enrichment of spermatogonia genes and a downregulation of genes associated with spermatocytes and spermatids (Figure 4C,D).…”

Section: Resultsmentioning

confidence: 99%

TAF7L regulates early stages of male germ cell development in the rat

Moreno‐Irusta,

Dominguez,

Iqbal

et al. 2023

The FASEB Journal

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Male germ cell development is dependent on the orchestrated regulation of gene networks. TATA‐box binding protein associated factors (TAFs) facilitate interactions of TATA‐binding protein with the TATA element, which is known to coordinate gene transcription during organogenesis. TAF7 like (Taf7l) is situated on the X chromosome and has been implicated in testis development. We examined the biology of TAF7L in testis development using the rat. Taf7l was prominently expressed in preleptotene to leptotene spermatocytes. To study the impact of TAF7L on the testis we generated a global loss‐of‐function rat model using CRISPR/Cas9 genome editing. Exon 3 of the Taf7l gene was targeted. A founder was generated possessing a 110 bp deletion within the Taf7l locus, which resulted in a frameshift and the premature appearance of a stop codon. The mutation was effectively transmitted through the germline. Deficits in TAF7L did not adversely affect pregnancy or postnatal survival. However, the Taf7l disruption resulted in male infertility due to compromised testis development and failed sperm production. Mutant germ cells suffer meiotic arrest at late zygotene/early pachynema stages, with defects in sex body formation. This testis phenotype was more pronounced than previously described for the subfertile Taf7l null mouse. We conclude that TAF7L is essential for male germ cell development in the rat.

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“…At the same time, many traditional methods such as Principal Component Analysis (PCA), Non-Negative Matrix Factorization (NNMF), and Latent Dirichlet Distribution (LDA) come with limitations tied to their linearity. Nonlinear dimensionality reduction methods such as t-distributed stochastic neighbor embedding (t-SNE) have gained popularity in recent years for omics data analysis [ 39 – 42 ]. Nevertheless, these methods fall short in projecting new data into an already computed embedding.…”

Section: Introductionmentioning

confidence: 99%

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder

Uvarova,

Demenkov,

Kuzmicheva

et al. 2023

Journal of Integrative Bioinformatics

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Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.

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Single-cell RNA sequencing of adult rat testes after Leydig cell elimination and restoration

Cited by 7 publications

References 29 publications

Taf7l Regulates Early Stages of Male Germ Cell Development

Taf7l Regulates Early Stages of Male Germ Cell Development

TAF7L regulates early stages of male germ cell development in the rat

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder

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