2018
DOI: 10.1101/289728
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Abstract: In contrast to mammalian erythroid cells that lost their nucleus at the end of the differentiation process, circulating chicken erythrocytes, like erythrocytes of most other non-mammalian vertebrates, are nucleated although their nucleus is believed to be transcriptionally silent. This major difference suggests that the erythroid differentiation process is likely to present both similarities and differences in mammals compared to other vertebrates. Since proteins are the major cellular effectors, analysis of t… Show more

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Cited by 5 publications
(6 citation statements)
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“…Since promoter 121 activity is not observable, we estimate the inflection time point of mean RNA level from 122 single-cell transcriptomic kinetic data [37], and retrieve the delay induced by RNA 123 degradation to deduce promoter wave time. Protein wave times correspond to the 124 inflection point of mean protein level, which can be directly observed with our 125 proteomic data [39]. A detailed description of promoter and protein wave time 126 estimation can be found in the Method section.…”
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confidence: 69%
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“…Since promoter 121 activity is not observable, we estimate the inflection time point of mean RNA level from 122 single-cell transcriptomic kinetic data [37], and retrieve the delay induced by RNA 123 degradation to deduce promoter wave time. Protein wave times correspond to the 124 inflection point of mean protein level, which can be directly observed with our 125 proteomic data [39]. A detailed description of promoter and protein wave time 126 estimation can be found in the Method section.…”
mentioning
confidence: 69%
“…First, individual gene parameters 520 defined in model (1) (all except θ and H) are estimated before network inference from a 521 number of experimental data types acquired during T2EC differentiation. They include 522 time stamped single-cell transcriptomic [37], bulk transcription inhibition kinetic [37] 523 and bulk proteomic data [39]. In a second step, genes are sorted regarding their wave 524 times (see "Results" section for a description of wave concept) estimated from the mean 525 of single cell transcriptomic data for promoter waves, and bulk proteomic data for 526 protein waves.…”
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confidence: 99%
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“…Proteomic data generation 157 Proteomic data were generated using a label-free quantification (LFQ) method ans mass 158 spectrometry by the Plateforme de Protéomique de l'Université Paris Descartes 159 (3P5) [19]. It has been shown in various species that P2A (2A peptide derived from porcine 163 teschovirus-1) presents a higher cleavage efficiency than T2A (2A peptide derived from 164 Thoseaasigna virus) [20], which was initially present in pSpCas9(BB)-2A-GFP (PX458) 165 vector.…”
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confidence: 99%