Journal: Scientific Reports

Article Title: Dinaciclib potently suppresses MCL-1 and selectively induces the cell death in human iPS cells without affecting the viability of cardiac tissue

doi: 10.1038/srep45577

Figure Lengend Snippet: ( a – c ) The number of cells after dinaciclib treatment. Cell number in 49 fields (7 × 7) was calculated and shown in the graph (n = 4). ( a ) Total cell number. **p < 0.01 vs control. ( b ) Number of OCT4 positive cells. **p < 0.01 vs control. ( c ) Number of OCT4 negative cells. n.s., not significant. ( d ) The percentage of OCT4 positive cells. **p < 0.01 vs control. *p < 0.05 vs 6 nM. ( e ) Representative images of OCT4 positive cells (red). Nuclei were stained with Hoechst (blue). Scale bars = 200 μm.

Article Snippet: For immunocytochemistry: mouse monoclonal anti-cardiac troponin T antibody (cTnT; Thermo Scientific, Rockford, IL, USA), goat polyclonal anti-OCT4 antibody (R&D systems, Minneapolis, MN, USA), rabbit polyclonal anti-Ki67 antibody (Abcam, Cambridge, UK).

Techniques: Control, Staining

Journal: Cell Stem Cell

Article Title: Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

doi: 10.1016/j.stem.2019.03.012

Figure Lengend Snippet: Krüppel-like Factors Are Major Inducers of EGA and Naive-Specific TE Enhancers (A) KLF4 and KLF17 expression during early human embryonic development and stem cells, determined by re-analyzing single-cell RNA-seq data from Yan et al. (2013) . Single-cell data points are grouped according to developmental stage: oocytes (Oo); zygotes (Zy); 2-cell (2C); 4-cell (4C); 8-cell (8C); morula (Mo); with late blastocyst split into epiblast (Epi), primitive endoderm (PE), and trophectoderm (TE); p0 and p10 representing passage numbers of ESCs derived from blastocyst and naive (N) and primed (P) hESCs ( Theunissen et al., 2016 ). (B) Pairwise comparison of KLF4/17-induced acetylation loci. H3K27ac ChIP was performed 5 days after transducing primed hESCs with GFP-, KLF4-, or KLF17-expressing lentiviral vectors, thus identifying H3K27ac loci with increased signal (n = 4,446; adjusted p value < 0.05); pie charts represent its proportion (black part; in % of the 4,446 loci) overlapping with chromatin accessibility in hESCs (determined by ATAC-seq, with naive versus primed specific loci defined by ≥2-fold difference with adjusted p < 0.05), human embryo DNase-seq, H3K27ac (K27ac), and OCT4- or KLF4-enrichment (p < 10e−5) in indicated cells. Color scale corresponds to Spearman correlation of pairwise loci comparisons. (C) Genomic distribution of increased H3K27ac loci upon KLF4/17 overexpression in primed ESCs. (Left) Distribution between TSS (±500 bp) of coding genes and the non-TSS overlapping loci is shown: TEs (50% overlap from either TE or H3K27ac peak) or other regions; p values were computed with a permutation test (1,000 permutations); (right) distribution within indicated TE subfamilies with (blue) and without (gray) gain of H3K27ac enrichment is shown, further depicting loci with (light blue) or without (dark blue) increase expression in GFP versus both KLF4 and KLF17 (adjusted p value < 0.05). Numbers of integrants are indicated for each category. (D) KLF4 binding on LTR5Hs and HERVK (SINE-R) region of SVA. KLF4 ChIP-seq signal in naive hESCs was superimposed on multiple sequence alignment of corresponding TEs. The rectangle highlights the common enhancer piece bound by KLF4, the one which was cloned from a SVA into a GFP vector activatable by CRISPRa, but not by KLF4 or KLF17 when KLF-motif is mutated. Error bars were established using SEM and p value using t test ( ∗∗∗ ≤ 0.001). See for details. (E) KLF4-KLF17 overexpression in primed ESCs activates TE-close genes. Proportion of up- and downregulated genes upon KLF4-KLF17 overexpression is shown (y axes; p < 0.05), according to their distance to the closest TE (x axes). Upper and lower panels use TEs (SVA, LTR5Hs, and LTR7) with or without H3K27ac gains upon KLF4-KLF17 overexpression, respectively. See also Figure S2 and .

Article Snippet: anti-OCT4 - Rabbit polyclonal , Abcam , Abcam Cat# ab19857; RRID: AB_445175 ).

Techniques: Expressing, RNA Sequencing Assay, Derivative Assay, Over Expression, Binding Assay, ChIP-sequencing, Sequencing, Clone Assay, Plasmid Preparation

Journal: Cell Stem Cell

Article Title: Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

doi: 10.1016/j.stem.2019.03.012

Figure Lengend Snippet:

Article Snippet: anti-OCT4 - Rabbit polyclonal , Abcam , Abcam Cat# ab19857; RRID: AB_445175 ).

Techniques: Plasmid Preparation, Recombinant, ChIP-sequencing, RNA Sequencing Assay, Derivative Assay, Software, ChIA Pet Assay

Journal: Biology of reproduction

Article Title: Deletion of Mylk1 in oocytes causes delayed morula-to-blastocyst transition and reduced fertility without affecting folliculogenesis and oocyte maturation in mice.

doi: 10.1095/biolreprod.114.122127

Figure Lengend Snippet: FIG. 6. Delayed morula-to-blastocyst transition of mutant embryos. A) Left: microscopic images of 3.5 and 4 dpc embryos from Mylk1fl/fl and Mylk1fl/fl;GCre þ females. Eight-week-old Mylk1 mutant and control female siblings were mated with wild-type males. Plugged females were sacrificed at 3.5 dpc. Embryos were collected by uterine flushing and then cultured in vitro to 4 dpc. Right: blastocyst rates were scored based on 3.5 and 4 dpc embryos from Mylk1fl/fl and Mylk1fl/fl;GCreþ females, respectively. B) Left: confocal microscopic images of blastocysts from Mylk1fl/fl and Mylk1fl/fl;GCreþ females. The collected blastocysts were stained for Oct4 (green). DNA was counterstained with DAPI (blue), and morphology was determined by differential interference contrast (DIC) microscopy., Right: the average number of total cell in blastocysts from Mylk1fl/fl and Mylk1fl/

Article Snippet: Antibodies used in our experiments were available from the following companies: rabbit monoclonal anti-MLCK antibody (Abcam); rabbit polyclonal anti-phospho-myosin light chain 2 (pMLC2) (Ser19) antibody (CST); mouse monoclonal anti-b-actin antibody (Santa Cruz); goat polyclonal anti-Oct4 antibody (Santa Cruz); rabbit polyclonal anti-Bub3 antibody (Santa Cruz); rabbit monoclonal anti-a-tubulin antibody (CST); fluorescein isothiocyanate (FITC)-conjugated rabbit anti-goat immunoglobulin G (IgG) and FITCconjugated goat anti-rabbit IgG (Zhongshan Golden Bridge Biotechnology); and Cy5-conjugated goat anti-rabbit IgG (Jackson ImmunoResearch Laboratory).

Techniques: Mutagenesis, Control, Cell Culture, In Vitro, Staining, Microscopy