Presentation is loading. Please wait.

Presentation is loading. Please wait.

Fig. 1. A graphical representation of the GGDNA workflow used to identify each single expressed TE transcript from ... Fig. 1. A graphical representation.

Published byShavonne Gregory Modified over 5 years ago

Similar presentations

Presentation on theme: "Fig. 1. A graphical representation of the GGDNA workflow used to identify each single expressed TE transcript from ... Fig. 1. A graphical representation."— Presentation transcript:

1 Fig. 1. A graphical representation of the GGDNA workflow used to identify each single expressed TE transcript from ... Fig. 1. A graphical representation of the GGDNA workflow used to identify each single expressed TE transcript from RNA-seq data of DLPFC in our sample. The reads generated by the RNA-seq procedures are first aligned to the annotated reference TE database from Repeatmasker, then reads at each single locus are assembled de novo. Transcripts with <95% sequence identity with the reference and/or align at <90% of their length are discarded during the step of quality control: reads that are discarded are identified with the symbol and reads that are carried on with the symbol . See also text for details of the procedures. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular Biology and Evolution, Volume 35, Issue 10, 20 July 2018, Pages 2435–2453, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Fig. 2. Validation of the actively transcribed HERV locus HERVKC4 on chromosome 19 in human DLPFC. A (top figure). ... Fig. 2. Validation of the actively transcribed HERV locus HERVKC4 on chromosome 19 in human DLPFC. A (top figure). The cartoon reports the sequence coordinates (not in scale) of the tested HERVKC4 (in red), the transcript assembled by GGDNA (in green) and the region captured by qPCR (in blue). B (middle figure). Visualization of the read alignment to the GGDNA transcript for each of the four RNA samples; highlighted in blue the region corresponding to the qPCR product. C (bottom figure). Result on agarose gel of the qPCR product for one RNA sample with the relative length size of 100 bp. Quantitative RT-PCR (qRT-PCR) validation experiments of four HERVKC4 transcripts were carried-out on four of the nineteen analyzed RNAs extracted from the human DLPFC samples (three controls and one Schizophrenia sample). The sequence identity of the purified PCR products has been confirmed by direct sequencing. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular Biology and Evolution, Volume 35, Issue 10, 20 July 2018, Pages 2435–2453, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Fig. 3. Evolutionary dynamics of highly conserved-in-primates and human-specific TE loci transcriptionally active in ... Fig. 3. Evolutionary dynamics of highly conserved-in-primates and human-specific TE loci transcriptionally active in DLPFC of human brain. DLPFC-expressed TEs having > 99% of individual loci represented by primate-specific sequences (table 2 and supplementary tables 1–4, Supplementary Material online) were identified and analyzed for expression of primate- and human-specific TEs. TE loci expressing the higher numbers of human-specific versus highly conserved-in-primate transcripts and vice versa were identified and analyzed in detail. Note that all TE loci that express the largest numbers of molecularly distinct human-specific TEs in human DLPFC display both common and distinct features of the evolutionary histories as represented by both highly conserved-in-primates and human-specific sequences. (A) The number of distinct TE loci expressing the largest numbers of human-specific TEs in human DLPFC are shown. All identified TE loci represented by markedly distinct numbers are human-specific and highly conserved-in-primate sequences. (B) TE loci that express the largest numbers of molecularly distinct human-specific TEs in human DLPFC display distinct evolutionary dynamics and show markedly distinct ratios of human-specific to highly conserved-in-primate sequences. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular Biology and Evolution, Volume 35, Issue 10, 20 July 2018, Pages 2435–2453, The content of this slide may be subject to copyright: please see the slide notes for details.

4 Fig. 4. TE transcriptome in the DLPFC of Schizophrenia patients
Fig. 4. TE transcriptome in the DLPFC of Schizophrenia patients. The heatmap presents the pattern of the 112 up- and ... Fig. 4. TE transcriptome in the DLPFC of Schizophrenia patients. The heatmap presents the pattern of the 112 up- and down-regulated TEs with Fold Change ± 4 comparing schizophrenic patients with controls. The vertical tree shows the distribution of schizophrenic patients (blue line) and controls (red line). The horizontal tree shows the distribution of the 112 expressed TEs and the colors in the body of the graph show which TEs are over- (yellow) or underexpressed (purple). The list of the up and down-regulated TEs used to build the graph are reported in supplementary table 5, Supplementary Material online. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular Biology and Evolution, Volume 35, Issue 10, 20 July 2018, Pages 2435–2453, The content of this slide may be subject to copyright: please see the slide notes for details.

Download ppt "Fig. 1. A graphical representation of the GGDNA workflow used to identify each single expressed TE transcript from ... Fig. 1. A graphical representation."

Similar presentations

Fig. 8 The two cases for the terminal edge e<sub>0</sub>

Fig. 8 The two cases for the terminal edge e<sub>0</sub>
J Exp Bot. 2017;68(17): doi: /jxb/erx352

J Exp Bot. 2017;68(17): doi: /jxb/erx352
Fig. 1. — The life cycle of S. papillosus. (A) The life cycle of S

Fig. 1. — The life cycle of S. papillosus. (A) The life cycle of S
Figure 3: MetaLIMS sample input.

Figure 3: MetaLIMS sample input.
FIG. 1.— Correlation of RPKM between (A) 1,509 TE families estimated from B73–104 and the in silico data with 5 outliers indicated in gray; (B) 1,514 TE.

FIG. 1.— Correlation of RPKM between (A) 1,509 TE families estimated from B73–104 and the in silico data with 5 outliers indicated in gray; (B) 1,514 TE.
Figure 1. An example of a thioviridamide-like molecule, thioalbamide, and inset, a proposed biochemical route to ... Figure 1. An example of a thioviridamide-like.

Figure 1. An example of a thioviridamide-like molecule, thioalbamide, and inset, a proposed biochemical route to ... Figure 1. An example of a thioviridamide-like.
Figure 1. Overview of the workflow of NetworkAnalyst 3.0.

Figure 1. Overview of the workflow of NetworkAnalyst 3.0.
Figure 1 The study area within Vienna Zoo is outlined in red

Figure 1 The study area within Vienna Zoo is outlined in red
Figure 4. (A) Venn diagram showing the overlap of peaks differentially changed in DHT as compared to NT with peaks ... Figure 4. (A) Venn diagram showing.

Figure 4. (A) Venn diagram showing the overlap of peaks differentially changed in DHT as compared to NT with peaks ... Figure 4. (A) Venn diagram showing.
Unless provided in the caption above, the following copyright applies to the content of this slide: Published by Oxford University Press on behalf of the.

Unless provided in the caption above, the following copyright applies to the content of this slide: Published by Oxford University Press on behalf of the.
Figure 1 Top: Annual modal paternity distance (PDc) estimated for each of 23 cohorts by MasterBayes ... Figure 1 Top: Annual modal paternity distance (PDc)

Figure 1 Top: Annual modal paternity distance (PDc) estimated for each of 23 cohorts by MasterBayes ... Figure 1 Top: Annual modal paternity distance (PDc)
Figure 1. BRCA1-associated R-Loop accumulation at a non-coding region upstream of ESR1 locus. (A) Alignment of DRIP-seq ... Figure 1. BRCA1-associated.

Figure 1. BRCA1-associated R-Loop accumulation at a non-coding region upstream of ESR1 locus. (A) Alignment of DRIP-seq ... Figure 1. BRCA1-associated.
Figure 1. Ratios of observed to expected numbers of exon boundaries aligning to boundaries of domain and disorder ... Figure 1. Ratios of observed to expected.

Figure 1. Ratios of observed to expected numbers of exon boundaries aligning to boundaries of domain and disorder ... Figure 1. Ratios of observed to expected.
Figure 1. autoMLST workflow depicting placement and de novo mode

Figure 1. autoMLST workflow depicting placement and de novo mode
Figure 1. The 12 species in this study and details of the improved G4-seq method. (A) Phylogenetic representation of ... Figure 1. The 12 species in this.

Figure 1. The 12 species in this study and details of the improved G4-seq method. (A) Phylogenetic representation of ... Figure 1. The 12 species in this.
Unless provided in the caption above, the following copyright applies to the content of this slide: Published by Oxford University Press on behalf of the.

Unless provided in the caption above, the following copyright applies to the content of this slide: Published by Oxford University Press on behalf of the.
Figure 1. Comparison of weighted estimates of diarrhoea prevalence in children under five by country between PMA2020 ... Figure 1. Comparison of weighted.

Figure 1. Comparison of weighted estimates of diarrhoea prevalence in children under five by country between PMA Figure 1. Comparison of weighted.
Figure 1. Nanopore methylation calls are consistent with expected results and established technologies. (A) Metaplot of ... Figure 1. Nanopore methylation.

Figure 1. Nanopore methylation calls are consistent with expected results and established technologies. (A) Metaplot of ... Figure 1. Nanopore methylation.
Fig. 1 Kaplan-Meier plot of cumulative incidence of cancer onset following dermatomyositis diagnosis stratified ... Anti-TIF1-Ab: anti-transcriptional.

Fig. 1 Kaplan-Meier plot of cumulative incidence of cancer onset following dermatomyositis diagnosis stratified ... Anti-TIF1-Ab: anti-transcriptional.
Figure 1. Chemical structures of DNA and tc-DNA

Figure 1. Chemical structures of DNA and tc-DNA

Similar presentations

Ads by Google