Additional file 1: of Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair

The following additional data are available with the online version of this paper. Figure S1. In vitro assessment of sgRNA efficacy. Table S1. The sequences of the oligonucleotides used in this study. Table S2. The sequences and locations of the predicted off-target sites for the two sgRNAs used in design 1. Table S3. Oligonucleotide sequences for Sanger sequencing of sgRNA_U1 and sgRNA_D1 predicted off-target sites (three or fewer mismatches). (DOCX 922 kb

Mentha viridis L.

原著和名: ミドリハクカ科名: シソ科 = Labiatae採集地: 千葉県 千葉市 千葉大学 (下総 千葉市 千葉大学)採集日: 1967/8/13採集者: 萩庭丈壽整理番号: JH042898国立科学博物館整理番号: TNS-VS-99289

Additional file 3: Figure S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Overlap of off-target detection for the EMX1 and VEGFA guides tested by different assays. Off-targets are only shown if they were detected by at least a single study and with a frequency of 0.1 %. See Additional file 1: Tables S1 and Additional file 4: Table S2 for the modification frequencies and additional details on the off-targets for the guides EMX1 and VEGFA, respectively. Additional file 4: Table S2 also includes the data by Hsu et al. [7], who quantified cleavage at putative off-target loci predicted by the CRISPR Design website ( http://crispr.mit.edu/ ) with targeted deep sequencing, Tsai et al. [3], who isolated double-strand breaks with modified oligonucleotides followed by sequencing, Frock et al. [28], who detected translocations, and Kim et al. [33] and Kim et al. [27], who performed whole-genome sequencing to find CRISPR-induced modifications. For details on the different studies, see Additional file 1: Table S1. (PDF 17 kb

Acanthopanax trichodon Franch. et Savat.

原著和名: ミヤマウコギ科名: ウコギ科 = Araliaceae採集地: 千葉県 清澄山 (上総〜安房 清澄山)採集日: 1961/6/18採集者: 萩庭丈壽整理番号: JH042319国立科学博物館整理番号: TNS-VS-99231

Ilex serrata Thunb.

原著和名: ウメモドキ科名: モチノキ科 = Aquifoliaceae採集地: 愛知県 豊橋市 岩崎町 (三河 豊橋市 岩崎)採集日: 1968/10/20採集者: 萩庭丈壽整理番号: JH042317国立科学博物館整理番号: TNS-VS-99231

Additional file 2: Figure S2. of Aneuploidy screening of embryonic stem cell clones by metaphase karyotyping and droplet digital polymerase chain reaction

Quality of karyotype of JM8-derived clones is equivalent among distributing repositories. The figure shows the percentages of euploid clones sourced from the two main distributors of JM8-derived cells and GLT rate obtained with them. The numbers of clones in each instance is shown. These numbers illustrate that materials obtained from different distributors are of similar quality in terms of karyotype and GLT ability. Data was analysed using the Fisher Exact test that and showed no evidence of difference of quality between the two distributors. (PDF 77 kb

Additional file 6: Figure S5. of Aneuploidy screening of embryonic stem cell clones by metaphase karyotyping and droplet digital polymerase chain reaction

Outcome of chromosome counting by ddPCR with genomic DNA extracted from ear biopsies. The figure shows copy numbers obtained using the karyotype screen assay panel on DNA extracted from euploid ES cells (C), trisomic ES cells (Ts), X0 ES cells (Ns Y) and female mouse ear clip (E), using the same lysis method. Vertical bars are Standard Errors. The data illustrate that the assays are able detect the expected copy numbers on gDNA extracted from tisssues (2 Chr 1, 8 and 11) and that the number of these chromosomes is lower in genomes extracted from tissue cultures. (PDF 63 kb

Body weight, body composition, and food intake in male global germline <i>Fto</i> Knockout mice.

<p>A, Male body weight WT <i>Fto</i>^+/+, (n = 10), <i>Fto</i>^−/− (n = 10), B, Body length WT <i>Fto</i>^+/+, (n = 14), <i>Fto</i>^−/− (n = 8), C, Fat mass in males at 20 weeks of age, WT <i>Fto</i>^+/+, (n = 17), <i>Fto</i>^−/− (n = 8), D, Lean mass in males at 20 weeks of age, WT <i>Fto</i>^+/+, (n = 17), <i>Fto</i>^−/− (n = 8), E, Intraperitoneal glucose tolerance test (IPGTT) area under the curve (AUC) in males at 16 weeks of age. WT <i>Fto</i>^+/+, (n = 9), <i>Fto</i>^−/− (n = 10), F, Food intake in male mice at 10 weeks of age during a 24-hour period in metabolic cages. WT <i>Fto</i>^+/+, (n = 12), <i>Fto</i>^−/− (n = 9). Data are expressed as mean ± SE and in B–F individual data points are shown. Time-course data were analysed using the repeated-measures ANOVA model (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003166#s4" target="_blank">Materials and Methods</a>) (A). The other comparison p-values (B–F) correspond to a Welch <i>t</i>-test of the null hypothesis of no difference between genotypic groups. *P<0.05, **P<0.01, ***P<0.001.</p

Body weight, body composition, and food intake of male global adult onset KO mice.

<p>A, Weekly body weight of adult onset KO (n = 15) and vehicle-treated control mice (n = 10), B, Nose-to-anus body length of control (n = 10) and adult onset KO mice (n = 12) at 20 weeks of age, C, Fat mass was increased in adult onset KO mice (n = 14) compared to controls (n = 10) in 9-week old mice (P = 0.05) and further increased in adult onset KO mice (n = 12) compared to controls (n = 10) at 20 weeks, D, Lean mass was reduced in adult onset KO mice (n = 14 and n = 12) compared to controls (n = 10 and n = 10) at both 9 weeks and 20 weeks of age, E, Food intake at 10 weeks of age during a 24-hour period in metabolic cages, control (n = 10) and adult onset KO mice (n = 14). Data are expressed as mean ± SE. In B–E, individual data points are shown. Time-course data were analysed using the repeated-measures ANOVA model, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003166#s4" target="_blank">Materials and Methods</a> (A). The other comparison p-values (B–E), correspond to a Welch <i>t</i>-test of the null hypothesis of no difference between genotypic groups. *P<0.05, **P<0.01, ***P<0.001.</p

Energy expenditure and metabolism in male global germline <i>Fto</i> KO mice.

<p>A, VO₂ consumed, B, VCO₂ produced, and C, energy expenditure (EE), adjusted for variation in lean mass using multiple linear regression (ANCOVA). D, respiratory exchange ratio (RER). Measurements were made in male mice during the light and dark phases at 18-weeks of age. <i>Fto</i>^+/+ (n = 20), <i>Fto</i>^−/− (n = 9). Data are expressed as mean ± SE and individual data points are shown. For details of the lean-mass adjustment made in panels A–C, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003166#s4" target="_blank">Materials and Methods</a>, *P<0.05, **P<0.01, ***P<0.001.</p