Journal: Proceedings of the Royal Society B: Biological Sciences

Article Title: Auditory brainstem development of naked mole-rats ( Heterocephalus glaber )

doi: 10.1098/rspb.2022.0878

Figure Lengend Snippet: Primary antibodies are used in immunofluorescence/Western blotting.

Article Snippet: Polyclonal rabbit anti-Kv3.3 antibody (APC-102, Alomone Labs) was used at 1 : 400; monoclonal mouse anti-GAPDH antibody (sc-32233, Santa Cruz) was used at 1 : 1000.

Techniques: Immunofluorescence, Concentration Assay, Western Blot

Journal: Laboratory investigation; a journal of technical methods and pathology

Article Title: Characterization of immune cell subtypes in three commonly used mouse strains reveals gender and strain-specific variations

doi: 10.1038/s41374-018-0137-1

Figure Lengend Snippet: Antibody combinations used in immunophenotyping

Article Snippet: Fixation/Permeabilization Solution Kit with BD Golgi-PlugTM kit and Mouse Foxp3 Buffer Set was used for intracellular staining and purchased from BD Biosciences. table ft1 table-wrap mode="anchored" t5 caption a7 iMC CD11b Vio Blue Gr-1 APC-eFluor780 * Ly6b FITC Macrophages CD11b Vio Blue F4/80 APC CD68 PE mDC CD11b Vio Blue CD11c PE CD80 APC CD86 FITC pDC * CD11b Vio Blue CD11c PE B220 Vio770 Siglec H FITC CD4 T-cells CD3 APC-Cy7 CD4 eFluor450 CD4 T-regs CD3 APC-Cy7 CD4 eFluor450 CD25 PE FoxP3APC CD8 T-cells CD3 APC-Cy7 CD8 FITC B cells B220 Vio770 CD19 PE NK cells CD3 APC-Cy7 NKp46 FITC Neutrophils CD11b Vio Blue Gr-1 APC-eFluor780 Ly6b FITC * F4/80 APC Open in a separate window * negative tor this antibody Antibody combinations used in immunophenotyping table ft1 table-wrap mode="anchored" t5 caption a7 Antibody Fluorochrome Vendor Clone Catalogue # Antibody Concentration (in 100 pL FACS buffer) CD3e APC-Cy7 Fisher Scientific 145–2C11 BDB557596 1 pL CD4 eFluor450 eBioscience GK1.5 48–0041-82 1 pL CD8 FITC eBioscience 53–6.7 11–0081-82 0.6 pL CD11b Vio Blue Miltenyi M1/70.15.11.5 130–097-336 3.75 pL CD11c PE Miltenyi N418 130102545 3.75 pL CD19 PE Miltenyi 6D5 130–102-598 5 pL CD25 PE eBioscience PC61.5 12–0251-81 0.5 pL CD68 PE Miltenyi FA-11 130–102-614 3.75 pL CD80 APC Miltenyi 16–10A1 130–102-584 3.75 pL CD86 FITC Miltenyi PO3.3 130–102-506 5 pL B220 APC-Vio770 Miltenyi RA3–6B2 130–102-267 3.75 pL F4/80 APC Miltenyi REA126 130–102-379 3.75 pL FoxP3 APC eBioscience FJK-16s 17–5773-82 5 pL Gr1 APC-eFluor780 eBioscience RB6–8C5 47–5931-80 1.2 pL Ly6b FITC abcam 7/4 ab53453 0.65 pL NKp46 FITC Miltenyi 29A1.4.9 130–102-300 3.75 pL SiglecH FITC eBioscience eBio440c 11–0333-82 0.5 pL Open in a separate window Details of antibodies used in the study

Techniques:

Journal: Laboratory investigation; a journal of technical methods and pathology

Article Title: Characterization of immune cell subtypes in three commonly used mouse strains reveals gender and strain-specific variations

doi: 10.1038/s41374-018-0137-1

Figure Lengend Snippet: Details of antibodies used in the study

Article Snippet: Fixation/Permeabilization Solution Kit with BD Golgi-PlugTM kit and Mouse Foxp3 Buffer Set was used for intracellular staining and purchased from BD Biosciences. table ft1 table-wrap mode="anchored" t5 caption a7 iMC CD11b Vio Blue Gr-1 APC-eFluor780 * Ly6b FITC Macrophages CD11b Vio Blue F4/80 APC CD68 PE mDC CD11b Vio Blue CD11c PE CD80 APC CD86 FITC pDC * CD11b Vio Blue CD11c PE B220 Vio770 Siglec H FITC CD4 T-cells CD3 APC-Cy7 CD4 eFluor450 CD4 T-regs CD3 APC-Cy7 CD4 eFluor450 CD25 PE FoxP3APC CD8 T-cells CD3 APC-Cy7 CD8 FITC B cells B220 Vio770 CD19 PE NK cells CD3 APC-Cy7 NKp46 FITC Neutrophils CD11b Vio Blue Gr-1 APC-eFluor780 Ly6b FITC * F4/80 APC Open in a separate window * negative tor this antibody Antibody combinations used in immunophenotyping table ft1 table-wrap mode="anchored" t5 caption a7 Antibody Fluorochrome Vendor Clone Catalogue # Antibody Concentration (in 100 pL FACS buffer) CD3e APC-Cy7 Fisher Scientific 145–2C11 BDB557596 1 pL CD4 eFluor450 eBioscience GK1.5 48–0041-82 1 pL CD8 FITC eBioscience 53–6.7 11–0081-82 0.6 pL CD11b Vio Blue Miltenyi M1/70.15.11.5 130–097-336 3.75 pL CD11c PE Miltenyi N418 130102545 3.75 pL CD19 PE Miltenyi 6D5 130–102-598 5 pL CD25 PE eBioscience PC61.5 12–0251-81 0.5 pL CD68 PE Miltenyi FA-11 130–102-614 3.75 pL CD80 APC Miltenyi 16–10A1 130–102-584 3.75 pL CD86 FITC Miltenyi PO3.3 130–102-506 5 pL B220 APC-Vio770 Miltenyi RA3–6B2 130–102-267 3.75 pL F4/80 APC Miltenyi REA126 130–102-379 3.75 pL FoxP3 APC eBioscience FJK-16s 17–5773-82 5 pL Gr1 APC-eFluor780 eBioscience RB6–8C5 47–5931-80 1.2 pL Ly6b FITC abcam 7/4 ab53453 0.65 pL NKp46 FITC Miltenyi 29A1.4.9 130–102-300 3.75 pL SiglecH FITC eBioscience eBio440c 11–0333-82 0.5 pL Open in a separate window Details of antibodies used in the study

Techniques: Concentration Assay

Journal: Laboratory investigation; a journal of technical methods and pathology

Article Title: Characterization of immune cell subtypes in three commonly used mouse strains reveals gender and strain-specific variations

doi: 10.1038/s41374-018-0137-1

Figure Lengend Snippet: Cell suspensions from BM and spleen were isolated from 8-week old mice. The cells were stained with B220 and CD19 antibodies for B cells, and CD3 and NKp46 antibodies for NK cells. The cells were then subjected to flow cytometry to determine cell-type percentages. (A) B cells in BM, (n≥10). (B) B cells in the spleen, (n ≥11). (C) NK cells in BM, (n≥9). (D) NK cells in the spleen, (n≥7). Results are shown as scatter plots depicting average cell percentages (percent of live cells). Error bars denote SEM. Each dot represents the value from a single mouse. (♂) and (♀) represent male and female mice respectively. **p ≤ 0.01, ***p ≤ 0.001, ****p≤0.0001.

Article Snippet: Fixation/Permeabilization Solution Kit with BD Golgi-PlugTM kit and Mouse Foxp3 Buffer Set was used for intracellular staining and purchased from BD Biosciences. table ft1 table-wrap mode="anchored" t5 caption a7 iMC CD11b Vio Blue Gr-1 APC-eFluor780 * Ly6b FITC Macrophages CD11b Vio Blue F4/80 APC CD68 PE mDC CD11b Vio Blue CD11c PE CD80 APC CD86 FITC pDC * CD11b Vio Blue CD11c PE B220 Vio770 Siglec H FITC CD4 T-cells CD3 APC-Cy7 CD4 eFluor450 CD4 T-regs CD3 APC-Cy7 CD4 eFluor450 CD25 PE FoxP3APC CD8 T-cells CD3 APC-Cy7 CD8 FITC B cells B220 Vio770 CD19 PE NK cells CD3 APC-Cy7 NKp46 FITC Neutrophils CD11b Vio Blue Gr-1 APC-eFluor780 Ly6b FITC * F4/80 APC Open in a separate window * negative tor this antibody Antibody combinations used in immunophenotyping table ft1 table-wrap mode="anchored" t5 caption a7 Antibody Fluorochrome Vendor Clone Catalogue # Antibody Concentration (in 100 pL FACS buffer) CD3e APC-Cy7 Fisher Scientific 145–2C11 BDB557596 1 pL CD4 eFluor450 eBioscience GK1.5 48–0041-82 1 pL CD8 FITC eBioscience 53–6.7 11–0081-82 0.6 pL CD11b Vio Blue Miltenyi M1/70.15.11.5 130–097-336 3.75 pL CD11c PE Miltenyi N418 130102545 3.75 pL CD19 PE Miltenyi 6D5 130–102-598 5 pL CD25 PE eBioscience PC61.5 12–0251-81 0.5 pL CD68 PE Miltenyi FA-11 130–102-614 3.75 pL CD80 APC Miltenyi 16–10A1 130–102-584 3.75 pL CD86 FITC Miltenyi PO3.3 130–102-506 5 pL B220 APC-Vio770 Miltenyi RA3–6B2 130–102-267 3.75 pL F4/80 APC Miltenyi REA126 130–102-379 3.75 pL FoxP3 APC eBioscience FJK-16s 17–5773-82 5 pL Gr1 APC-eFluor780 eBioscience RB6–8C5 47–5931-80 1.2 pL Ly6b FITC abcam 7/4 ab53453 0.65 pL NKp46 FITC Miltenyi 29A1.4.9 130–102-300 3.75 pL SiglecH FITC eBioscience eBio440c 11–0333-82 0.5 pL Open in a separate window Details of antibodies used in the study

Techniques: Isolation, Staining, Flow Cytometry

Journal: Laboratory investigation; a journal of technical methods and pathology

Article Title: Characterization of immune cell subtypes in three commonly used mouse strains reveals gender and strain-specific variations

doi: 10.1038/s41374-018-0137-1

Figure Lengend Snippet: Cell suspensions from BM and spleen were isolated from 8-week old mice. The cells were stained with CD11c, B220 and Siglec H antibodies. CD11b antibody was included as a negative marker for pDCs. The cells were then subjected to flow cytometry to determine cell-type percentages. (A) pDCs in BM, (n≥11). (B) pDCs in the spleen, (n ≥9). Results are shown as scatter plots depicting average cell percentages (percent of live cells). Error bars denote SEM. Each dot represents the value from a single mouse. (♂) and (♀) represent male and female mice respectively.*p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p≤0.0001.

Article Snippet: Fixation/Permeabilization Solution Kit with BD Golgi-PlugTM kit and Mouse Foxp3 Buffer Set was used for intracellular staining and purchased from BD Biosciences. table ft1 table-wrap mode="anchored" t5 caption a7 iMC CD11b Vio Blue Gr-1 APC-eFluor780 * Ly6b FITC Macrophages CD11b Vio Blue F4/80 APC CD68 PE mDC CD11b Vio Blue CD11c PE CD80 APC CD86 FITC pDC * CD11b Vio Blue CD11c PE B220 Vio770 Siglec H FITC CD4 T-cells CD3 APC-Cy7 CD4 eFluor450 CD4 T-regs CD3 APC-Cy7 CD4 eFluor450 CD25 PE FoxP3APC CD8 T-cells CD3 APC-Cy7 CD8 FITC B cells B220 Vio770 CD19 PE NK cells CD3 APC-Cy7 NKp46 FITC Neutrophils CD11b Vio Blue Gr-1 APC-eFluor780 Ly6b FITC * F4/80 APC Open in a separate window * negative tor this antibody Antibody combinations used in immunophenotyping table ft1 table-wrap mode="anchored" t5 caption a7 Antibody Fluorochrome Vendor Clone Catalogue # Antibody Concentration (in 100 pL FACS buffer) CD3e APC-Cy7 Fisher Scientific 145–2C11 BDB557596 1 pL CD4 eFluor450 eBioscience GK1.5 48–0041-82 1 pL CD8 FITC eBioscience 53–6.7 11–0081-82 0.6 pL CD11b Vio Blue Miltenyi M1/70.15.11.5 130–097-336 3.75 pL CD11c PE Miltenyi N418 130102545 3.75 pL CD19 PE Miltenyi 6D5 130–102-598 5 pL CD25 PE eBioscience PC61.5 12–0251-81 0.5 pL CD68 PE Miltenyi FA-11 130–102-614 3.75 pL CD80 APC Miltenyi 16–10A1 130–102-584 3.75 pL CD86 FITC Miltenyi PO3.3 130–102-506 5 pL B220 APC-Vio770 Miltenyi RA3–6B2 130–102-267 3.75 pL F4/80 APC Miltenyi REA126 130–102-379 3.75 pL FoxP3 APC eBioscience FJK-16s 17–5773-82 5 pL Gr1 APC-eFluor780 eBioscience RB6–8C5 47–5931-80 1.2 pL Ly6b FITC abcam 7/4 ab53453 0.65 pL NKp46 FITC Miltenyi 29A1.4.9 130–102-300 3.75 pL SiglecH FITC eBioscience eBio440c 11–0333-82 0.5 pL Open in a separate window Details of antibodies used in the study

Techniques: Isolation, Staining, Marker, Flow Cytometry

Journal: Laboratory investigation; a journal of technical methods and pathology

Article Title: Characterization of immune cell subtypes in three commonly used mouse strains reveals gender and strain-specific variations

doi: 10.1038/s41374-018-0137-1

Figure Lengend Snippet: Details of antibodies used in the study

Article Snippet: CD80 , APC , Miltenyi , 16–10A1 , 130–102-584 , 3.75 pL.

Techniques: Concentration Assay

Journal: Nucleic Acids Research

Article Title: Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

doi: 10.1093/nar/gkx1222

Figure Lengend Snippet: Design, optimization and cross-comparison of HIT transcription activation systems. ( A–C ) Cartoons illuminating the mechanisms of optimized 4-OHT induced transcription activation using a direct fusion HIT construct (A), the HIT-SAM system (B), and the HIT-SunTag system (C). ( D–I ) Cross-comparison among three optimized HIT transcription activation systems. Transcription activation induced by HIT constructs was examined in the luciferase reporter assay (D), by quantification of relative mRNA level of endogenous expression for Klf4 (E) and Oct4 (F), and by flow-cytometry analyses of CD43 protein level on the cell surface (G–I). Representative plots (G) and quantitative analyses of median CD43 fluorescent intensities (H) and overall CD43 fluorescent intensities (I) of CD43+GFP+ positive population were shown. GFP fluorescence indicates successful transfection. Cells transfected with the same amount of reporter construct or sgRNA only while keeping the total amount of transfection constant were used as negative controls (NC) in the luciferase reporter assay. Cells transfected with an ER T2 tagged GFP construct while keeping the total amount of transfection constant were used as negative control (NC) in qRT-PCR assays. Cells transfected with an unrelated sgRNA (ctl sgRNA) and GFP were used as negative control (NC) in flow-cytometry analyses. Data showed mean ± SD. n = 3 biological replicates. ns: non-significant;* P < 0.05; ** P < 0.01; *** P < 0.001; two tailed t -tests. Three biological replicates means three independently transfected samples throughout this study. The readouts without drug induction were compared in t-tests against the negative controls (NCs) for background detection.

Article Snippet: As for the CD43 activation assay, 48 h after 4-OHT was added, live cells were collected and incubated with a CD43 antibody conjugated with APC (Miltenyi Biotec) according to the manufacturer's recommended protocol.

Techniques: Comparison, Activation Assay, Construct, Luciferase, Reporter Assay, Expressing, Flow Cytometry, Fluorescence, Transfection, Negative Control, Quantitative RT-PCR, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

doi: 10.1093/nar/gkx1222

Figure Lengend Snippet: HIT2: one CRISPR/Cas9 device for simultaneous genome editing and transcriptional activation in a drug inducible manner. ( A ) Cartoon illuminating the mechanism of the optimized drug inducible HIT2 system for simultaneous genome editing and transcriptional activation. ( B ) Simultaneous editing and activation by HIT2 and Cas9–NLS–GCN4 were examined using flow-cytometry. The percentage of GFP positive cells indicated HDR efficiency, while CD43 protein level on the cell surface represented transcription activation. Representative plots (upper panels) and quantitative analyses (lower panels) were shown. Data showed mean ± SD. n = 3 biological replicates. ns: non-significant;* P < 0.05; *** P < 0.001; **** P < 0.0001; two-tailed t -tests.

Article Snippet: As for the CD43 activation assay, 48 h after 4-OHT was added, live cells were collected and incubated with a CD43 antibody conjugated with APC (Miltenyi Biotec) according to the manufacturer's recommended protocol.

Techniques: CRISPR, Activation Assay, Flow Cytometry, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

doi: 10.1093/nar/gkx1222

Figure Lengend Snippet: Comparisons of HIT systems with existing drug inducible designs. ( A–D ) Drug inducible efficiency and background activity of transcription activation was examined head-to-head between HIT systems and existing designs using the luciferase reporter assay (A), in which the expression of luciferase was controlled by a sgRNA target sequence (gLuc sgRNA), and the CD43 activation assay (B-D).Representative plots (B), quantitative analyses of the percentage of CD43 positive cells (C), and median CD43 fluorescent intensities (D) were shown. ( E ) Drug inducible efficiency and background activity of genome editing was examined using the FCR assay in comparison with existing designs. Representative plots (top) and quantifications (right bottom) were shown. NC, cells transfected with an unrelated sgRNA; PC, cells transfected with Cas9-NLS and BFP sgRNA. Data showed mean ± SD. n = 3 biological replicates. ns: non-significant;* P < 0.05; ** P < 0.01; **** P < 0.0001; two-tailed t -tests.

Article Snippet: As for the CD43 activation assay, 48 h after 4-OHT was added, live cells were collected and incubated with a CD43 antibody conjugated with APC (Miltenyi Biotec) according to the manufacturer's recommended protocol.

Techniques: Activity Assay, Activation Assay, Luciferase, Reporter Assay, Expressing, Sequencing, Comparison, Transfection, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

doi: 10.1093/nar/gkx1222

Figure Lengend Snippet: Selective and titratable drug induction of HIT systems. ( A and B ) Dose dependent transcription activation induced by HIT-SunTag (A) and HIT2 (B) with different concentration of β-estradiol or 4OHT was examined using the luciferase reporter assay. ( C and D ) Activation of endogenous gene CD43 was examined using flow cytometry. Quantitative analyses of the percentage of CD43 positive cells (C) and median CD43 fluorescent intensities (D) were shown. ( E ) Dose dependent genome editing activities of HIT2 were examined using the FCR assay upon treatment with different concentration of β-estradiol or 4-OHT. Data showed mean ± SD. n = 3 biological replicates. ns: non-significant; * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; two-tailed t -tests. Fold of activation by 4-OHT over the same concentration of β-estradiol was displayed.

Article Snippet: As for the CD43 activation assay, 48 h after 4-OHT was added, live cells were collected and incubated with a CD43 antibody conjugated with APC (Miltenyi Biotec) according to the manufacturer's recommended protocol.

Techniques: Activation Assay, Concentration Assay, Luciferase, Reporter Assay, Flow Cytometry, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Multimode drug inducible CRISPR/Cas9 devices for transcriptional activation and genome editing

doi: 10.1093/nar/gkx1222

Figure Lengend Snippet: Adaptation of HIT designs to SaCas9. ( A and B ) Drug inducible gene activation by NLS-dSaCas9–GCN4 in conjunction with scFv-2ER T2 -AD was examined in the luciferase reporter assay (A) and the endogenous CD43 activation assay (B). ( C ) Simultaneous genome editing and transcriptional activation by HIT2-SaCas9 were examined by the FCR activity and CD43 activation respectively. Cells transfected with the same amount of reporter construct while keeping the total amount of transfection constant were used as negative controls (NC). ISO represents cells stained with antibody isotype control. Data showed mean ± SD. n = 3 biological replicates. ns: non-significant;* P < 0.05; ** P < 0.01; *** P < 0.001; two-tailed t -tests.

Article Snippet: As for the CD43 activation assay, 48 h after 4-OHT was added, live cells were collected and incubated with a CD43 antibody conjugated with APC (Miltenyi Biotec) according to the manufacturer's recommended protocol.

Techniques: Activation Assay, Luciferase, Reporter Assay, Activity Assay, Transfection, Construct, Staining, Control, Two Tailed Test