Journal: Scientific Reports

Article Title: Brain connectivity dynamics in cisgender and transmen people with gender incongruence before gender affirmative hormone treatment

doi: 10.1038/s41598-021-00508-y

Figure Lengend Snippet: Temporal properties of the FC states analyses. ( A ) Bar plot represents the fractional time windows from the 2-states solution, quantitative temporal metrics from the sliding windows k-means clustering approach are represented as box plots, namely dwell time of States 1 and 2 and number of transitions. TM and CM had significant differences in the time they dwelled in State 2. The meta-state dynamic metrics are charted as violin plots. CM differed from CW and TM in the change of meta-states and the total distance between clusters. ( B ) FC differences in State 2 from the 2-states solution between CM < TM using the threshold-free network-based statistics. L SMA, left supplementary motor area; R Supram, right supramarginal. Surf Ice software was used ( https://www.nitrc.org/projects/surfice/ ). ( C ) Bar plot represents the fractional time windows from the 4-states solution, quantitative temporal metrics from the sliding windows k-means clustering approach are represented as box plots, namely dwell time of States 1, 2, 3 and 4 and number of transitions. Finally, violin plots represent the 4-states cluster solution of the meta-state dynamics method. Plots were obtained with the ggpubr library ( https://cran.r-project.org/web/packages/ggpubr/index.html ) using the RStudio v1.4.1106 (PBC, Boston, MA, http://www.rstudio.com/ ). *Multiple comparison post-hoc test P < 0.05.

Article Snippet: Plots were obtained with the ggpubr library ( https://cran.r-project.org/web/packages/ggpubr/index.html ) using the RStudio v1.4.1106 (PBC, Boston, MA, http://www.rstudio.com/ ).

Techniques: Software, Comparison

Journal: Scientific Reports

Article Title: Brain connectivity dynamics in cisgender and transmen people with gender incongruence before gender affirmative hormone treatment

doi: 10.1038/s41598-021-00508-y

Figure Lengend Snippet: Correlations of the attention regulation Multidimensional Assessment Interoceptive Awareness (MAIA) dimension with metrics of the 4-states cluster solution. Within the transmen group, the number of transitions and the dwell time in State 3 as metrics of the sliding windows k-means clustering approach, were positively associated with the attention regulation dimension; there was also a positive correlation between this MAIA dimension and the meta-state span. Correlations are rho Spearman, and shadowed areas represent the 95% confidence interval. Plots were obtained with the ggpubr library ( https://cran.r-project.org/web/packages/ggpubr/index.html ) using the RStudio v1.4.1106 (PBC, Boston, MA, http://www.rstudio.com/ ).

Article Snippet: Plots were obtained with the ggpubr library ( https://cran.r-project.org/web/packages/ggpubr/index.html ) using the RStudio v1.4.1106 (PBC, Boston, MA, http://www.rstudio.com/ ).

Techniques:

Journal: Integrative and Comparative Biology

Article Title: CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona

doi: 10.1093/icb/icae108

Figure Lengend Snippet: Validation of sgRNAs for CRISPR/Cas9 in Ciona . Panel ( A ) shows schematic diagram of the protocol for validation of sgRNA mutagenesis (indel) efficacies in Ciona F0 embryos. See text and supplemental methods for detailed protocols. Panel ( B ) shows diagram of rationale for mutagenesis efficacy estimates by Illumina-based NGS. Indels represented as red blocks in target DNAs and amplicons. Different forward and reverse PCR primers (half-arrows) used to amplify targeted regions indicated in different colors. Note that, in theory, untargeted amplicons can serve as negative controls even if they are amplified from CRISPR'd embryos (see text for details).

Article Snippet: Bottom: Indel plots (deletions blue, insertions green) automatically generated by the Illumina sequencing “Amplicon-EZ” service from Azenta (Genewiz).

Techniques: Biomarker Discovery, CRISPR, Mutagenesis, Amplification

Journal: Integrative and Comparative Biology

Article Title: CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona

doi: 10.1093/icb/icae108

Figure Lengend Snippet: Example of sgRNA validation by a commercial NGS service. Top: Diagram of Rab11-related.b gene from C. robusta ( intestinalis Type A), indicating the target locations of three candidate sgRNAs (“2.45”, “2.187”, and “3.30”, thin diagonal lines). Thicker rectangles indicate exons, thinner lines indicate introns. ATG: Translation start codon. Bottom: Indel plots (deletions blue, insertions green) automatically generated by the Illumina sequencing “Amplicon-EZ” service from Azenta (Genewiz). Control sequences were amplified from larvae electroporated with unrelated sgRNAs instead. Note different y-axis scale for each plot. Asterisks indicate natural deletions identified, due to use of genetically diverse wild Ciona populations. Total mutagenesis efficacies (automatically calculated by the service) indicated in red parentheses. For sgRNA 3.30, the efficacy rate that was automatically calculated was not reliable due to the high prevalence of a naturally occurring deletion in this particular batch of animals.

Article Snippet: Bottom: Indel plots (deletions blue, insertions green) automatically generated by the Illumina sequencing “Amplicon-EZ” service from Azenta (Genewiz).

Techniques: Biomarker Discovery, Generated, Illumina Sequencing, Amplification, Control, Mutagenesis

Journal: Integrative and Comparative Biology

Article Title: CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona

doi: 10.1093/icb/icae108

Figure Lengend Snippet: Analysis of off-target effects (or lack thereof) in Ciona . Panel ( A ) left shows indel plot for the Dkk3.2.100 sgRNA, at its intended target (exon 2 of the Dkk3 gene, KH ID number KH.C8.904). Right: Indel profile plot zoomed in at the target site, showing a peak centered around a few basepairs 5′ to the PAM. Panel ( B ) shows one example of a candidate off-target of the Dkk3.2.100 sgRNA (KH.C9.571 intron). Top left panel shows indel plot from sequencing the KH.C9.571 intron off-target amplicon PCR-amplified from the same sample that gave the on-target plot in panel A. Top right panel shows off-target sequence and coordinates (KH genome assembly) as predicted by CRISPOR. Mismatches with the intended sgRNA (“guide”) target sequence are indicated by asterisks and bold font. The all-important sgRNA “seed” region is underlined, with the PAM in italics. Bottom panel shows zoomed-in indel profile plot for the KH.C9.571 intronic off-target site, showing that the negligible (<1%) frequency of scattered indels are not enriched at the predicted off-target PAM/seed region. Panel ( C ) shows analysis of sgRNA efficacy at a target with an alternative, non-canonical PAM for S. pyogenes Cas9 (AAG). An sgRNA (1) targeting the Irx.a gene at a sequence (bold letters) with an AAG alternative PAM (red italics) resulted in a 7% indel rate. There was no detectable indels by sgRNAs 2 and 3 targeting sequences with adjacent motifs not previously reported to function as alternative PAMs (TAC and ACC, gray italics).

Article Snippet: Bottom: Indel plots (deletions blue, insertions green) automatically generated by the Illumina sequencing “Amplicon-EZ” service from Azenta (Genewiz).

Techniques: Sequencing, Amplification