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, P1-P11) are shown. The names of expression patterns are indicated on top of each column

, Numbers of loci as observed and expected are given within color-coded rectangles: Red and 1020 blue indicate over-and underrepresentation, respectively, according to the scale bar. Numbers 1021 in bold indicate significantly overrepresented terms. P1 is enriched for biological processes 1022 such as carbohydrate metabolic process

, P2 is associated with gene ontology (GO) terms related to androgen synthesis (cholesterol 1024 transport, steroid biosynthetic process). P3 is significantly associated with tube morphogenesis, p.1025

. Kaiser, P5 is associated with terms related to 1028 RNA processing, splicing, and transport. P6 was enriched for piRNA metabolic process, 1029 chromatin organization, and DNA methylation involved in gamete generation. P6-7 is 1030 associated with meiotic nuclear division and DNA repair. P7-P9 are over-represented in GO 1031 terms related to flagellum formation such as cilium assembly and cilium movement, angiogenesis, and muscle structure development, 2005.

, Supplementary Figure S9 Testicular gene expression and sex chromosomal localization. An 1035 ideogram of the X (panel A) and Y (panel B) chromosomes as well as the localization of 1036 transcripts from the 11 expression patterns P1-P11 are shown. For each expression pattern, p.46

, chromosomal positions of transcripts are displayed as vertical lines that are color-coded 1038 according to their corresponding biotype (blue = protein-coding

, Numbers of loci as observed and expected are given within color-coded 1040 rectangles: Red and blue indicate over-and underrepresentation, respectively, according to the 1041 scale bar. Numbers in bold indicate significant over-/underrepresentation (P value ? 0.05). P1 1042 is enriched whereas P5 and P7-P8 are depleted for X-linked genes. A substantial transcriptional 1043 reactivation of the sex chromosomes is, pp.9-10

, Supplementary Figure S10 Quantitative PCR validation of eight NUTs

, Histograms represent expression profiles of candidate genes (+/-SEM) relative to GAPDH 1046 mRNA levels. These experiments confirm the expression profiles of selected transcripts and, 1047 more importantly, validate the existence of these newly identified genes

, Supplementary Figure S11 A subgroup of meiotic lncRNAs have longer exons

, All 21,264 DE 1051 transcripts underwent multicomponent analysis followed by model-based clustering according 1052 to typical genomic features of lncRNAs: expression level (Max. abundance), expression 1053 specificity (Shannon entropy), sequence conservation, percentage of GC content, number (N°) 1054 of exons, cumulative (Cum.) exon length, average (Av.) exon size, and protein-encoding 1055 potential (PEP). Gray dots indicate mRNAs and colored dots lncRNAs and NUTs. This resulted 1056 in the classification of lncRNAs and NUTs into eight subgroups (clusters 1-8), A. Classification of lncRNAs and NUTs according to their genomic features

B. , Violin plot representation of selected genomic features for all differentially expressed 1059 mRNAs and lncRNAs as well as for a subgroup (cluster 6) of lncRNAs and NUTs: sequence 1060 conservation (phastCons score), number of exons, transcript length (in nucleotides, nt) and 1061 47 exon length (nt), 2275.

, These 1063 transcripts have a number of exons similar to that of other lncRNAs, while their exon length is 1064 more than five times that of known mRNAs (P < 7.10 -89 ) and of other lncRNAs, vol.302

P. , Evolutionary sequence conservation is also lower in noncoding transcripts than in 1066 mRNAs (P < 9, vol.6, pp.10-48, 1065.

C. , hypergeometric test) is shown and the number of lncRNAs and 1069 NUTs from cluster 6 reported in brackets for each expression pattern (P1-P11)