Journal: Cell Reports

Article Title: The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability

doi: 10.1016/j.celrep.2021.110080

Figure Lengend Snippet:

Article Snippet: Rabbit anti-53BP1 , Santa Cruz Biotechnology , Cat#sc-22760; RRID: AB_2256326.

Techniques: Virus, Subcloning, Recombinant, Staining, Picogreen Assay, Proliferation Assay, Flow Cytometry, DNA Extraction, Sequencing, Luciferase, Software, Transfection, Modification, Magnetic Beads, Membrane

Journal: Diagnostic Pathology

Article Title: The ectopic expression of BRCA1 is associated with genesis, progression, and prognosis of breast cancer in young patients

doi: 10.1186/1746-1596-7-181

Figure Lengend Snippet: A (young group) BRCA1 protein immunohistochemical staining was positive. The positive products localized in the cytoplasm (× 400). B (young group) BRCA1 protein immunohistochemical staining was positive. The positive products localized in the nucleus (× 400). C (old group) BRCA1 protein immunohistochemical staining was positive. The positive products localized in the cytoplasm (× 400). D (young group) WWOX protein immunohistochemical staining was positive. The positive products localized in the cytoplasm (× 400). E (old group) WWOX protein immunohistochemical staining was positive. The positive products localized in the cytoplasm (× 400) . F (young group) ER protein immunohistochemical staining was positive. The positive product positioning in the nucleus (× 400). G (young group) positive immunohistochemical staining of PR proteins. The positive products localized in the nucleus (× 400) H (young group) C-erbB2 protein immunohistochemical staining was positive. The positive products localized in the membrane (× 400). I (young group) Ki67 protein immunohistochemical staining was positive. The positive products localized in the nucleus (× 400).

Article Snippet: The WWOX antibody was purchased from Beijing Boaosen Biotechnology Co., Ltd. BRCA1 antibody was purchased from Wuhan Boster Biological Engineering Co., Ltd. ER, PR, and Ki67 were expressed in the nucleus.

Techniques: Immunohistochemical staining, Staining, Membrane

Journal: Diagnostic Pathology

Article Title: The ectopic expression of BRCA1 is associated with genesis, progression, and prognosis of breast cancer in young patients

doi: 10.1186/1746-1596-7-181

Figure Lengend Snippet: Analysis of the correlation between the BRCA1 results and clinicopathological parameters in the young groups and old groups

Article Snippet: The WWOX antibody was purchased from Beijing Boaosen Biotechnology Co., Ltd. BRCA1 antibody was purchased from Wuhan Boster Biological Engineering Co., Ltd. ER, PR, and Ki67 were expressed in the nucleus.

Techniques:

Journal: Diagnostic Pathology

Article Title: The ectopic expression of BRCA1 is associated with genesis, progression, and prognosis of breast cancer in young patients

doi: 10.1186/1746-1596-7-181

Figure Lengend Snippet: A The PCR product of exon 2 of the BRCA1 gene (259 bp). B The PCR product of exon 20 of the BRCA1 gene (401 bp).

Article Snippet: The WWOX antibody was purchased from Beijing Boaosen Biotechnology Co., Ltd. BRCA1 antibody was purchased from Wuhan Boster Biological Engineering Co., Ltd. ER, PR, and Ki67 were expressed in the nucleus.

Techniques:

Journal: Diagnostic Pathology

Article Title: The ectopic expression of BRCA1 is associated with genesis, progression, and prognosis of breast cancer in young patients

doi: 10.1186/1746-1596-7-181

Figure Lengend Snippet: A The partial DNA sequencing results of exon 2 of BRCA1 gene of patient 6. B The partial DNA sequencing results of exon 20 of BRCA1 gene of patient 6.

Article Snippet: The WWOX antibody was purchased from Beijing Boaosen Biotechnology Co., Ltd. BRCA1 antibody was purchased from Wuhan Boster Biological Engineering Co., Ltd. ER, PR, and Ki67 were expressed in the nucleus.

Techniques: DNA Sequencing

Journal: Diagnostic Pathology

Article Title: The ectopic expression of BRCA1 is associated with genesis, progression, and prognosis of breast cancer in young patients

doi: 10.1186/1746-1596-7-181

Figure Lengend Snippet: Comparative analysis of the immunohistochemical results of young and old patient groups

Article Snippet: The WWOX antibody was purchased from Beijing Boaosen Biotechnology Co., Ltd. BRCA1 antibody was purchased from Wuhan Boster Biological Engineering Co., Ltd. ER, PR, and Ki67 were expressed in the nucleus.

Techniques: Immunohistochemical staining

Journal: Current environmental health reports

Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming

doi: 10.1007/s40572-018-0217-9

Figure Lengend Snippet: Candidate-gene studies of placental DNA methylation, gestational diabetes, maternal glucose levels and prepregnancy obesity

Article Snippet: Lower DNA methylation in GDM-exposed placentas compared to non-GDM (57.08 vs 52.73, P = 0.03) ↑ DNA methylation in maternal obesity placentas compared to normal BMI (53.64 vs 56.17, P =0.01) Ruchat et al 2013 Ref. 56 N=44 GDM N = 30 NGT N= 14 French-Canadian Saguenay (Quebec, Canada) E-21 birth cohort Maternal glucose following 2h post-OGTT (2nd trimester, wk 24–28) 450K Infinium Methylation BeadChip Array Pyrosequencing validation 16 CpG in placenta correlation with array (r ≥ 0.88; P < 0.001).

Techniques: DNA Methylation Assay, Control, Methylation, Expressing, Gene Expression, Biomarker Discovery, Software, Sampling, Clinical Proteomics

Journal: Current environmental health reports

Article Title: Adverse Maternal Metabolic Intrauterine Environment and Placental Epigenetics: Implications for Fetal Metabolic Programming

doi: 10.1007/s40572-018-0217-9

Figure Lengend Snippet: Global DNA methylation and epigenome-wide studies of gestational diabetes, maternal glucose and obesity

Article Snippet: Lower DNA methylation in GDM-exposed placentas compared to non-GDM (57.08 vs 52.73, P = 0.03) ↑ DNA methylation in maternal obesity placentas compared to normal BMI (53.64 vs 56.17, P =0.01) Ruchat et al 2013 Ref. 56 N=44 GDM N = 30 NGT N= 14 French-Canadian Saguenay (Quebec, Canada) E-21 birth cohort Maternal glucose following 2h post-OGTT (2nd trimester, wk 24–28) 450K Infinium Methylation BeadChip Array Pyrosequencing validation 16 CpG in placenta correlation with array (r ≥ 0.88; P < 0.001).

Techniques: DNA Methylation Assay, Biomarker Discovery, Methylation, Control, Microarray, Expressing, Mass Spectrometry

Journal: Cell

Article Title: Organism-level analysis of vaccination reveals networks of protection across tissues

doi: 10.1016/j.cell.2017.08.024

Figure Lengend Snippet: (A) Experimental workflow: mice were immunized with MVA at skin 21 days prior to intranasal WR challenge (or PBS as control) for 0.5 day, and single lung and liver memory CD8+ T cells (live CD3ε+CD44+CD62L− cells), including virus-specific cells were sorted by FACS prior to single-cell (sc) RNA-seq.

Article Snippet: InVivo MAb anti-mouse CD8β (Clone 53-5.8) , BioXCell , Cat#BE0223.

Techniques: Control, Virus, RNA Sequencing

Journal: Cell

Article Title: Organism-level analysis of vaccination reveals networks of protection across tissues

doi: 10.1016/j.cell.2017.08.024

Figure Lengend Snippet: (A) Heatmap of 1,476 single memory CD8+ T cells (columns) showing the top 40 differentially expressed genes (rows) between lung and liver of control (MVA vaccination only) and WR-challenged mice (FDR < 0.01, expression fold change > 3).

Article Snippet: InVivo MAb anti-mouse CD8β (Clone 53-5.8) , BioXCell , Cat#BE0223.

Techniques: Control, Expressing

Journal: Cell

Article Title: Organism-level analysis of vaccination reveals networks of protection across tissues

doi: 10.1016/j.cell.2017.08.024

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: InVivo MAb anti-mouse CD8β (Clone 53-5.8) , BioXCell , Cat#BE0223.

Techniques: Virus, Control, Purification, Western Blot, Expressing, Modification, Recombinant, Blocking Assay, SYBR Green Assay, Lysis, Reverse Transcription, Sensitive Assay, DNA Library Preparation, Software, Microscopy

Journal: bioRxiv

Article Title: A comprehensive genetic catalog of human double-strand break repair

doi: 10.1101/2024.08.03.606369

Figure Lengend Snippet: (A) Effect of GET3 on overall editing efficiency at TKOv3 Cut 2 in RPE1- Cas9 TKOv3-NT cells. Experiments carried out as in . Two GET3 -/- clones are tested. n = 12 for WT and 4 for GET3 -/- clones. Error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (B) Cas9 cutting efficiency at TKOv3 Cut site 2 estimated by qPCR. Primers annealing at both sides of the cut site are used to determine the percentage of cut molecules 6h after gRNA transfection in the indicated cell lines. Amplification levels were normalized to the endogenous gene GREB1. n = 6, error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (C) 53BP1 foci number per cell 12h after transfection with a multi-target gRNA (1.5 nM) in the indicated cell lines. Data shows foci count of two independent replicates merged. Statistical analysis was performed using One-way ANOVA. (D) Heatmap showing indel frequency variation (Log2 fold change) in the three cut sites of the screen for the reduced editing efficiency gene cluster . Two insertion events in the TKOv3 Cut site 2 that are consistently reduced or increased across most knockouts in this group are marked with a blue and a red triangle, respectively. (E) Frequency of +2 (left) and +1 (right) nucleotide insertions, relative to the overall editing efficiency, after transfection with the TKOv3 Cut site 2 gRNA in RPE1- Cas9 TKOv3 GET 3 -/- clones compared to wild type cells. Experiments carried out as in . n = 12 for WT and 4 for GET3 -/- clones. Error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (F) Variation in the frequency of +1 and +2 nucleotide insertions produced after transfection with decreasing concentrations (2-fold serial dilutions from our standard gRNA final concentration, 12 nM) of gRNA targeting TKOv3 Cut site 2 in RPE1- Cas9 TKOv3-NT Cells. n = 3, error bars show ±SD. (G) In-vitro Cas9 DNA cleavage assay showing differential gRNA mismatch tolerance. Schematic representation of the two constructs containing Cut site 1 and 2 sequence either unedited or including the most common +1 nucleotide insertion outcome observed in the screen data (left) (see Methods). Agarose gel showing digestion of the constructs with increasing concentrations of Cas9 ribonucleoparticle bearing gRNA targeting either Cut site 1 or 2 (right).

Article Snippet: Samples were permeabilized with PBS 0.5% Triton for 15 min, blocked in 5% BSA in PBS and stained with anti-53BP1 primary antibody (1:500, 5% BSA PBS, Novus NB100-304, Rabbit) for 1 hour at room temperature, and secondary antibody coupled to Alexa Fluor 488 (1:1000, 5% BSA PBS, Invitrogen A11008, goat).

Techniques: Clone Assay, Transfection, Amplification, Produced, Concentration Assay, In Vitro, DNA Cleavage Assay, Construct, Sequencing, Agarose Gel Electrophoresis