br Discussion Genome wide analyses

Discussion Genome-wide analyses of the mammalian transcriptome revealed that lncRNAs is pervasively transcribed in the genome and accumulating studies have demonstrated that lncRNAs as novel regulatory molecule plays critical roles in mammalian development [1,2], but little is known about the potential roles of lncRNAs in mammalian testis development. Here, we described a dataset composed of lncRNA and mRNA natural antibiotics profiling of neonatal (6-day-old) and adult (8-week-old) mouse testis. With this experiment, we were able to show 3025 of lncRNAs and 5964 of mRNA are differentially expressed between neonatal and adult mouse testes. Some known haploid male germ cell-specific lncRNAs was also found differentially expressed in this study, for example, Aldoart2, Speer5-ps1 and Speer9-ps1[5,6]. The dynamic change of lncRNA expression during mouse testis post-natal development indicated that lncRNAs might play crucial roles in mammalian testis development and spermatogenesis. Thus, this experiment provides a solid foundation for the identification and characterization of key lncRNAs involved in testis development or spermatogenesis.
Conflict of interest
Specifications table Value of the data Data, experimental design, materials and methods
Acknowledgments This work is financially supported by the Cyttron II project “Imaging Mass Spectrometry”, ISCIII (PI11/01401, PI13/01873, CP09/00229) and IDCSalud (Grant number 3371/002). MML is funded by Fundación Conchita Rabago and gratefully acknowledges the travel funding supplied by SePROT and the COST Action BM1104 for the Short Term Scientific Missions to LUMC. BB and RC are funded by the Marie Curie Actions of the European Union (BB no. 331866, SITH FP7-PEOPLE-2012-IEF, RC no. 303344, ENIGMAS FP7-PEOPLE-2011-IEF).
Experimental design Quantitative proteomic changes in response to Arabidopsis thaliana PNP (AtPNP-A; At2g18660) was performed as outlined in Fig. 1. Total soluble proteins were extracted from 10 to 30min Arabidopsis cell suspension culture samples either treated with water or with different concentrations (1nM and 10pM) of AtPNP-A. A total of three biological replicates of the mock-treated and three biological replicates of cells treated with each concentration of AtPNP-A were used per each time-point considered in this study. We performed a proteomic analysis using LTQ Orbitrap Velos after OFFGEL fractionation of the TMT-labeled tryptic peptides. The acquired mass data identification was performed using MASCOT and SEQUEST search engines and the interpretation was done using Scaffold Q+ software. The proteomics data presented here include the protein and spectrum identification results, gene ontology (GO) functional category and transcriptional profiling results. Here, 4641 proteins were identified in response to 1nM AtPNP-A and 3447 proteins in response to 10pM AtPNP-A, at FDR of 0.7% for protein and 1.6% for peptide. 11 unique proteins were differentially expressed in response to 1nM AtPNP-A while expression of 15 proteins was significantly regulated upon treatment with 10pM AtPNP-A. The functional categories of the proteins with significantly altered expression in response to AtPNP-A were annotated using TAIR GO search (http://www.arabidopsis.org/tools/bulk/go/index.jsp). The transcriptional profile of these proteins was also analyzed using Genevestigator (https://www.genevestigator.com/gv/plant.jsp) [2].
Materials and methods
Acknowledgments We thank Dr. Ludivine Thomas and the KAUST Bioscience core laboratory for helpful discussions and the PRIDE Team for assistance with data upload. Ilona Turek was supported by a King Abdullah University of Science and Technology doctoral scholarship.
Specifications Table Value of the data Data, experimental design, materials and methods
Acknowledgments BMcD is supported by the Wellcome Trust ISSF Fund and the University of Liverpool (097826/Z/11/Z).
Value of the data