Автоматизация планово-аналитической деятельности

Издание направлено на формирование и развитие у студентов нового типа экономического мышления, интереса и способностей к творческому решению задач, стоящих перед различными отраслями экономики на современном этапе с использованием новейших информационных технологий. Практикум предназначен для студентов специальности 1-25 01 07 "Экономика и управление на предприятии" специализаций 1-25 01 07 11 "Экономика и управление на предприятии промышленности", 1-25 01 07 20 "Экономика и управление на предприятии услуг"

Capture efficiency in a sample representing the median coverage among all sequenced samples shown by the percent of total targeted bases covered at particular coverage depths in a chromosome 11 target.

<p>(A) Percent of targeted bases covered using various thresholds of repeat masking (A) by size, or (B) (SW) scores. (C) Percent of targeted bases covered based on masking of percent GC content extremes. Upper panels show coverage by CATCH-Seq within a sample that showed median coverage among all other samples used in the capture. (D–F) Lower panels show coverage within the corresponding captured region for the same number of merged reads analyzed for CATCH-Seq under the same repeat masking or percent GC content thresholds from 15 individuals sequenced for the 1000 genomes project (merged WGS).</p

High density methylation data derived from bisulfite sequencing of a CATCH-Seq target.

<p>Scale of the captured region is indicated in the topmost track in kilobases (kb), followed by repeat structure in gray and black (RepMask), genes shown in blue (RefSeq), and CpG islands in green. Four CATCH-Seq tracks from the same cell type show DNA methylation levels across ∼2,700 target CpGs with hypomethylation depicted in green and hypermethylation in red. Six reduced representation bisulfite sequencing (RRBS) tracks for different cell and tissue types correspond with the same captured region, and demonstrate CpGs not covered by RRBS method compared to CATCH-Seq. The four CATCH-Seq tracks are from the same cell type as the topmost RRBS track. RRBS tracks are derived from previously reported data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111756#pone.0111756-Meissner1" target="_blank">[23]</a>. CpGs shown within CpG islands were all typically hypomethylated across all cell and tissue types depicted.</p

Read depth plot of a chromosome 11 target for a sample showing median coverage among all samples used for capture and bisulfite sequencing.

<p>Vertical bars indicate read depth with scale depicted on the left side of the panel. Red lines show percent GC content across non-overlapping 400 bp intervals spanning the target region with scale shown on the right side of the panel. Horizontal dotted line indicates 50% GC content. A repeat structure track (RepMask) is shown below the plot in gray derived from the UCSC genome browser for all repeats containing a Smith-Waterman score of at least 600, and larger than 200 bp in size. Genes are shown below the repeat track in dark blue and arrows depict gene orientation.</p

The effect of repeat blocking with increased concentrations of Cot-1 DNA within the CATCH-Seq hybridization step of a chromosome 11 target.

<p>Total numbers of on target and off target read yields in millions within non-repetitive sequences (A) or repetitive sequences (B). (C–H) On and off target read yields within repeat structures based on different thresholds of size (C,E,G) or divergence (D,F,H). Green and gray lines show on target and off target reads, respectively.</p

Repeat structure description within a chromosome 11 target used for Cot-1 tests.

a<p>total captured target size is 247.6 kb; target region shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111756#pone-0111756-g004" target="_blank">Figure 4</a>.</p>b<p>out of 50 million sampled reads at 20× Cot-1 concentration.</p>c<p>all repeat hg19 coordinates, sizes, and Smith-Waterman (SW) scores obtained from RepeatMasker within the UCSC Genome Browser. For descriptions of RepeatMasker, <a href="http://www.repeatmasker.org/" target="_blank">http://www.repeatmasker.org/</a>.</p><p>Repeat structure description within a chromosome 11 target used for Cot-1 tests.</p

Read depth plot of a chromosome 11 target for a sample showing median coverage among all samples used for capture.

<p>Vertical bars indicate read depth with scale depicted on the left side of the panel. Red lines show percent GC content across non-overlapping 400 bp intervals spanning the target region with scale shown on the right side of the panel. Horizontal dotted line indicates 50% GC content. A repeat structure track (RepMask) is shown below the plot in gray derived from the UCSC genome browser for all repeats containing a Smith-Waterman score of at least 600, and larger than 200 bp in size. Genes are shown below the repeat track in dark blue and arrows depict gene orientation.</p

Overview of the clone adapted template capture hybridization sequencing procedure.

<p>BAC clone templates are selected to span genomic coordinates of interest, and pooled by percent mass of the composite target. BACs are sheared, ligated with T7 adapters to transcribe biotinylated RNA probes, and then solution hybridized with prepared libraries. Following capture, libraries are amplified by PCR, or bisulfite converted prior to amplification for analysis of DNA methylation. Target enriched libraries are pooled and sequenced.</p

Additional file 1: Table S1. of Stress amplifies sex differences in primate prefrontal profiles of gene expression

Human brain regions of interest. Specific regions of human frontal cortex and anterior cingulate cortex in Allen Brain Atlas array data ( http://human.brain-map.org ) that we compared with squirrel monkeys. (XLSX 11 kb

Additional file 4: Table S4. of Stress amplifies sex differences in primate prefrontal profiles of gene expression

Correlations between qPCR and array. Determinations by qPCR correlated with array results regardless of whether prefrontal cortical regions were analyzed separately (18 females +10 males = 28 pairwise comparisons per region) or combined (3 regions x [18 females +10 males] = 84 pairwise comparisons). Abbreviations: dlPFC dorosolateral prefrontal cortex, vlPFC ventrolateral prefrontal cortex, vmPFC ventromedial prefrontal cortex. (XLSX 10 kb