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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with <t>CD34+</t> HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 <t>CD34+</t> samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.
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Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by <t>ELISA</t> kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.
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Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by <t>ELISA</t> kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.
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Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by <t>ELISA</t> kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.
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Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by <t>ELISA</t> kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.
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The percentage of cell populations with expressions of cell surface markers CD34, CD24, CD133, CD117, and <t> CD44 </t> in A2780-M and A2780 cells.
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Image Search Results


Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with CD34+ HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 CD34+ samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.

Journal: Cell stem cell

Article Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.

doi: 10.1016/j.stem.2022.02.010

Figure Lengend Snippet: Figure 1. Lamin B1 loss promotes self-renewal and myeloid-biased differentiation in vitro (A) LMNB1 mRNA expression (log2 RPKM) in the BeatAML cohort of AML patient samples compared with CD34+ HSPCs or bone marrow mononuclear cells (MNCs) from matching healthy controls; n = 442 AML samples, 13 CD34+ samples, and 19 MNC samples; ****p < 0.0001, one-way ANOVA, mean ± SD. (B) Schematic of experimental workflow for LMNB1 knockdown in CB or PB CD34+ cells and LMNB1 ORF expression in del5q CD34+ AML cells. (C) Lamin B1 protein expression in PB HSPCs transduced with shRNAs targeting LMNB1 (LB1MID or LB1LO) relative to HSP90 control. Mean ± SD of two ex- periments. (D) Colony-forming potential of control, LB1MID, or LB1LO CB HSPCs per 1,000 CD34+ cells. BFU/CFU-E = erythroid, G = granulocyte, M = macrophage, GEMM = mixed lineage, nh = erythroid not hemoglobinized. Mean ± SD of n = 6 and n = 2 experiments for LB1LO and LB1MID, respectively; groups are not statistically different, two-way ANOVA.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD33-PE; clone WM53 BD cat#: 555450; RRID:AB_395843 CD19-BV605; clone SJ25C1 BD cat#: 562654; RRID:AB_2909453 CD11b-APC; clone ICRF44 BD cat#: 561015; RRID:AB_10561676 CD56-APCR700; clone NCAM16.2 BD cat#: 565140; RRID:AB_2744429 CD66b-PE; clone G10F5 BD cat#: 561650; RRID:AB_10894591 CD66b-BV421; clone G10F5 BD cat#: 562940; RRID:AB_2737906 CD45-APC; clone HI30 BD cat#: 555485; RRID:AB_398600 CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564; RRID:AB_2800449 CD3-BV786; clone SK7 BD cat#: 563800; RRID:AB_2744384 CD34-PE; clone 581 BD cat#: 555822; RRID:AB_396151 CD45RA-APC; clone HI100 BD cat#: 550855; RRID:AB_398468 CD38-PECy7; clone HB7 BD cat#: 335790; RRID:AB_399969 CD10-BV786; clone HI10a BD cat#: 564960; RRID:AB_2739025 CD90-Biotin; clone 5E10 BD cat#: 555594; RRID:AB_395968 Anti-LMNB1 Abcam cat#: ab16048; RRID:AB_443298 Anti-LBR Abcam cat#: ab32535; RRID:AB_775968 Anti-yH2AX ThermoFisher cat#: PA5-28778; RRID:AB_2546254 Anti-53BP1 Cell Signaling cat#: 2675; RRID:AB_490917 Bacterial and virus strains Stbl3 competent cells ThermoFisher cat#: C737303 Biological samples Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/ Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/ divisions/clinical-research-division/research/ co-operative-center-for-excellence-inhematology/hematopoietic-cell-procurementand-resource-development.html Chemicals, peptides, and recombinant proteins Ficoll-Paque Plus GE cat#:17-1440-02/6 Retronectin Takara cat#: T100A Recombinant human cytokines Peprotech https://www.peprotech.com/gb/ Recombinant human BMP-4 R&D Systems cat#: 314-BP-050 Recombinant human IL-7 R&D Systems cat#: 207-IL-010 Doxycycline Sigma cat#: D9891-10G SytoxGreen live-dead stain ThermoFisher cat#: S34860 poly-D-lysine Sigma cat#: A-003-E Vectashield Antifade Vector labs cat#: H-1200 EdU ThermoFisher cat#: C10640 DMSO Santa Cruz cat#: 487929-M Monastrol Sigma cat#: M8515 Nocodazole Sigma cat#: 487929-M Trizol ThermoFisher cat#: 15596026 Critical commercial assays CD34 Microbead kit Miltenyi cat#: 130-046-702 MethoCult Stem Cell Technologies cat#: H3434 (Continued on next page) Cell Stem Cell 29, 577–592.e1–e8, April 7, 2022 e1

Techniques: In Vitro, Expressing, Knockdown, Transduction, Control

Figure 2. Lamin B1 loss promotes myeloid- biased hematopoiesis in vivo (A) Engraftment of control or LB1LO CB HSPCs transplanted into NSG mice. Mice were trans- planted for 14 weeks, and human cell engraftment was determined as % human CD45+ transduced cells of total bone marrow cells. Mean ± SEM of two independent experiments, n = 14 mice for control, n = 12 mice for LB1LO; *p = 0.023, Welch’s t test. (B and C) Frequency of CD33+ myeloid cells and CD19+ B cells as % of human CD45+ cell engraft- ment. Quantitation (B) and representative flow plots (C) showing mean ± SD of n = 2 independent experiments, n = 14 mice for control, n = 12 mice for LB1LO; *p < 0.025 for both groups, Welch’s t test. (D and E) Frequency of human HSPC populations as % of human CD34+ cells 14 weeks post-trans- plant. Mean ± SD of two independent experiments, each condition consists of cells pooled from five mice of equivalent engraftment. Quantitation (D) and flow cytometric gating strategy (E) is as described in Doulatov et al. (2010).

Journal: Cell stem cell

Article Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.

doi: 10.1016/j.stem.2022.02.010

Figure Lengend Snippet: Figure 2. Lamin B1 loss promotes myeloid- biased hematopoiesis in vivo (A) Engraftment of control or LB1LO CB HSPCs transplanted into NSG mice. Mice were trans- planted for 14 weeks, and human cell engraftment was determined as % human CD45+ transduced cells of total bone marrow cells. Mean ± SEM of two independent experiments, n = 14 mice for control, n = 12 mice for LB1LO; *p = 0.023, Welch’s t test. (B and C) Frequency of CD33+ myeloid cells and CD19+ B cells as % of human CD45+ cell engraft- ment. Quantitation (B) and representative flow plots (C) showing mean ± SD of n = 2 independent experiments, n = 14 mice for control, n = 12 mice for LB1LO; *p < 0.025 for both groups, Welch’s t test. (D and E) Frequency of human HSPC populations as % of human CD34+ cells 14 weeks post-trans- plant. Mean ± SD of two independent experiments, each condition consists of cells pooled from five mice of equivalent engraftment. Quantitation (D) and flow cytometric gating strategy (E) is as described in Doulatov et al. (2010).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD33-PE; clone WM53 BD cat#: 555450; RRID:AB_395843 CD19-BV605; clone SJ25C1 BD cat#: 562654; RRID:AB_2909453 CD11b-APC; clone ICRF44 BD cat#: 561015; RRID:AB_10561676 CD56-APCR700; clone NCAM16.2 BD cat#: 565140; RRID:AB_2744429 CD66b-PE; clone G10F5 BD cat#: 561650; RRID:AB_10894591 CD66b-BV421; clone G10F5 BD cat#: 562940; RRID:AB_2737906 CD45-APC; clone HI30 BD cat#: 555485; RRID:AB_398600 CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564; RRID:AB_2800449 CD3-BV786; clone SK7 BD cat#: 563800; RRID:AB_2744384 CD34-PE; clone 581 BD cat#: 555822; RRID:AB_396151 CD45RA-APC; clone HI100 BD cat#: 550855; RRID:AB_398468 CD38-PECy7; clone HB7 BD cat#: 335790; RRID:AB_399969 CD10-BV786; clone HI10a BD cat#: 564960; RRID:AB_2739025 CD90-Biotin; clone 5E10 BD cat#: 555594; RRID:AB_395968 Anti-LMNB1 Abcam cat#: ab16048; RRID:AB_443298 Anti-LBR Abcam cat#: ab32535; RRID:AB_775968 Anti-yH2AX ThermoFisher cat#: PA5-28778; RRID:AB_2546254 Anti-53BP1 Cell Signaling cat#: 2675; RRID:AB_490917 Bacterial and virus strains Stbl3 competent cells ThermoFisher cat#: C737303 Biological samples Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/ Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/ divisions/clinical-research-division/research/ co-operative-center-for-excellence-inhematology/hematopoietic-cell-procurementand-resource-development.html Chemicals, peptides, and recombinant proteins Ficoll-Paque Plus GE cat#:17-1440-02/6 Retronectin Takara cat#: T100A Recombinant human cytokines Peprotech https://www.peprotech.com/gb/ Recombinant human BMP-4 R&D Systems cat#: 314-BP-050 Recombinant human IL-7 R&D Systems cat#: 207-IL-010 Doxycycline Sigma cat#: D9891-10G SytoxGreen live-dead stain ThermoFisher cat#: S34860 poly-D-lysine Sigma cat#: A-003-E Vectashield Antifade Vector labs cat#: H-1200 EdU ThermoFisher cat#: C10640 DMSO Santa Cruz cat#: 487929-M Monastrol Sigma cat#: M8515 Nocodazole Sigma cat#: 487929-M Trizol ThermoFisher cat#: 15596026 Critical commercial assays CD34 Microbead kit Miltenyi cat#: 130-046-702 MethoCult Stem Cell Technologies cat#: H3434 (Continued on next page) Cell Stem Cell 29, 577–592.e1–e8, April 7, 2022 e1

Techniques: In Vivo, Control, Quantitation Assay

Figure 3. Single-cell analysis of human HSC differentiation in vivo (A) Combined uniform manifold approximation and projection (UMAP) of human control and LB1LO CD34+ HSPCs engrafted in NSG mice after filtering and clustering (resolution = 6 3 104) using the Monocle 3 R package. Cells are colored by dataset of origin (control, dark gray; LB1LO, light blue), and clusters (outlined) were manually annotated based on expression of known lineage markers. (B) Relative expression (log10) of key hematopoietic lineage markers on the combined UMAP; yellow = highest level of expression (2.5), violet = lowest level (0), and gray = no detected transcripts. (C) UMAP of assigned predicted cell type identity based on transcriptional comparison of the combined dataset to the Atlas of Human Blood Cells dataset using the SingleR package. Inferred pseudotime trajectory determined by Monocle 3 is overlaid on the plot. (D) Relative frequencies (log2 fold change) of HSCs and progenitors in LB1LO versus control HSPCs based on unbiased SingleR analysis. (E) Violin plots of expression of myeloid and lymphoid lineage determination factors in single control or LB1LO LMPPs predicted by SingleR. Median expression is shown as white dots. See also Figure S3.

Journal: Cell stem cell

Article Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.

doi: 10.1016/j.stem.2022.02.010

Figure Lengend Snippet: Figure 3. Single-cell analysis of human HSC differentiation in vivo (A) Combined uniform manifold approximation and projection (UMAP) of human control and LB1LO CD34+ HSPCs engrafted in NSG mice after filtering and clustering (resolution = 6 3 104) using the Monocle 3 R package. Cells are colored by dataset of origin (control, dark gray; LB1LO, light blue), and clusters (outlined) were manually annotated based on expression of known lineage markers. (B) Relative expression (log10) of key hematopoietic lineage markers on the combined UMAP; yellow = highest level of expression (2.5), violet = lowest level (0), and gray = no detected transcripts. (C) UMAP of assigned predicted cell type identity based on transcriptional comparison of the combined dataset to the Atlas of Human Blood Cells dataset using the SingleR package. Inferred pseudotime trajectory determined by Monocle 3 is overlaid on the plot. (D) Relative frequencies (log2 fold change) of HSCs and progenitors in LB1LO versus control HSPCs based on unbiased SingleR analysis. (E) Violin plots of expression of myeloid and lymphoid lineage determination factors in single control or LB1LO LMPPs predicted by SingleR. Median expression is shown as white dots. See also Figure S3.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD33-PE; clone WM53 BD cat#: 555450; RRID:AB_395843 CD19-BV605; clone SJ25C1 BD cat#: 562654; RRID:AB_2909453 CD11b-APC; clone ICRF44 BD cat#: 561015; RRID:AB_10561676 CD56-APCR700; clone NCAM16.2 BD cat#: 565140; RRID:AB_2744429 CD66b-PE; clone G10F5 BD cat#: 561650; RRID:AB_10894591 CD66b-BV421; clone G10F5 BD cat#: 562940; RRID:AB_2737906 CD45-APC; clone HI30 BD cat#: 555485; RRID:AB_398600 CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564; RRID:AB_2800449 CD3-BV786; clone SK7 BD cat#: 563800; RRID:AB_2744384 CD34-PE; clone 581 BD cat#: 555822; RRID:AB_396151 CD45RA-APC; clone HI100 BD cat#: 550855; RRID:AB_398468 CD38-PECy7; clone HB7 BD cat#: 335790; RRID:AB_399969 CD10-BV786; clone HI10a BD cat#: 564960; RRID:AB_2739025 CD90-Biotin; clone 5E10 BD cat#: 555594; RRID:AB_395968 Anti-LMNB1 Abcam cat#: ab16048; RRID:AB_443298 Anti-LBR Abcam cat#: ab32535; RRID:AB_775968 Anti-yH2AX ThermoFisher cat#: PA5-28778; RRID:AB_2546254 Anti-53BP1 Cell Signaling cat#: 2675; RRID:AB_490917 Bacterial and virus strains Stbl3 competent cells ThermoFisher cat#: C737303 Biological samples Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/ Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/ divisions/clinical-research-division/research/ co-operative-center-for-excellence-inhematology/hematopoietic-cell-procurementand-resource-development.html Chemicals, peptides, and recombinant proteins Ficoll-Paque Plus GE cat#:17-1440-02/6 Retronectin Takara cat#: T100A Recombinant human cytokines Peprotech https://www.peprotech.com/gb/ Recombinant human BMP-4 R&D Systems cat#: 314-BP-050 Recombinant human IL-7 R&D Systems cat#: 207-IL-010 Doxycycline Sigma cat#: D9891-10G SytoxGreen live-dead stain ThermoFisher cat#: S34860 poly-D-lysine Sigma cat#: A-003-E Vectashield Antifade Vector labs cat#: H-1200 EdU ThermoFisher cat#: C10640 DMSO Santa Cruz cat#: 487929-M Monastrol Sigma cat#: M8515 Nocodazole Sigma cat#: 487929-M Trizol ThermoFisher cat#: 15596026 Critical commercial assays CD34 Microbead kit Miltenyi cat#: 130-046-702 MethoCult Stem Cell Technologies cat#: H3434 (Continued on next page) Cell Stem Cell 29, 577–592.e1–e8, April 7, 2022 e1

Techniques: Single-cell Analysis, In Vivo, Control, Expressing, Comparison

Figure 4. Lamin B1 loss impairs DNA damage repair in MDS-derived cells (A) Schematic of iPSC reprogramming of CD34+ HSPCs of patients with MDS and derivation of TP53+/R209fs (TP53) and TP53+/R209fs;del5q (TP53;del5q) iPSC- MDS HPCs. (B) LMNB1 mRNA expression in MDS HPCs, mean ± SD of two replicates TP53+/R209fs (TP53), and four replicates TP53;del5q, *p < 0.04, t test. (C) Lamin B1 protein expression in TP53+/R209fs (TP53) and TP53;del5q MDS HPCs, transduced with control (+ctrl) or LMNB1 ORF (+LMNB1) lentiviruses; mean ± SD of two replicates, **p = 0.0034. (D) Enrichment score of DNA damage-related gene sets in GSEA analysis of TP53+/R209fs (TP53) versus TP53;del5q MDS HPCs and control versus LB1LO CB HSPCs, FDR q < 0.05 for all comparisons. (E) Frequency of micronuclei in TP53+/R209fs (TP53) and TP53;del5q HPCs after monastrol or nocodazole treatment. Mean ± SD of 2–3 experiments, >230 cells per condition, nocodazole **p < 0.001, Welch’s t test; ns, not statistically significant. (F and G) The number of g-H2AX and 53BP1 foci before (no IR) and 30 min post-irradiation in TP53;del5q MDS HPCs expressing control or LMNB1 ORF (+LMNB1). Quantitation of g-H2AX foci (F) and representative images (G). Boxplot showing median and quartiles of n = 2 combined experiments, >300 cells per condition, p < 0.0001, Mann-Whitney test. Scale bar, 10 mm. (H and I) The number of g-H2AX foci 30 min and 5 h post-irradiation in control or LB1LO CB HSPCs. Quantitation (H) and representative staining of g-H2AX and nuclear lamin B1 levels (I). Boxplot showing median and quartiles of n = 3 combined experiments, >300 cells per condition, ****p < 0.0001, Mann-Whitney test. Scale bar, 10 mm. See also Figure S4.

Journal: Cell stem cell

Article Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.

doi: 10.1016/j.stem.2022.02.010

Figure Lengend Snippet: Figure 4. Lamin B1 loss impairs DNA damage repair in MDS-derived cells (A) Schematic of iPSC reprogramming of CD34+ HSPCs of patients with MDS and derivation of TP53+/R209fs (TP53) and TP53+/R209fs;del5q (TP53;del5q) iPSC- MDS HPCs. (B) LMNB1 mRNA expression in MDS HPCs, mean ± SD of two replicates TP53+/R209fs (TP53), and four replicates TP53;del5q, *p < 0.04, t test. (C) Lamin B1 protein expression in TP53+/R209fs (TP53) and TP53;del5q MDS HPCs, transduced with control (+ctrl) or LMNB1 ORF (+LMNB1) lentiviruses; mean ± SD of two replicates, **p = 0.0034. (D) Enrichment score of DNA damage-related gene sets in GSEA analysis of TP53+/R209fs (TP53) versus TP53;del5q MDS HPCs and control versus LB1LO CB HSPCs, FDR q < 0.05 for all comparisons. (E) Frequency of micronuclei in TP53+/R209fs (TP53) and TP53;del5q HPCs after monastrol or nocodazole treatment. Mean ± SD of 2–3 experiments, >230 cells per condition, nocodazole **p < 0.001, Welch’s t test; ns, not statistically significant. (F and G) The number of g-H2AX and 53BP1 foci before (no IR) and 30 min post-irradiation in TP53;del5q MDS HPCs expressing control or LMNB1 ORF (+LMNB1). Quantitation of g-H2AX foci (F) and representative images (G). Boxplot showing median and quartiles of n = 2 combined experiments, >300 cells per condition, p < 0.0001, Mann-Whitney test. Scale bar, 10 mm. (H and I) The number of g-H2AX foci 30 min and 5 h post-irradiation in control or LB1LO CB HSPCs. Quantitation (H) and representative staining of g-H2AX and nuclear lamin B1 levels (I). Boxplot showing median and quartiles of n = 3 combined experiments, >300 cells per condition, ****p < 0.0001, Mann-Whitney test. Scale bar, 10 mm. See also Figure S4.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD33-PE; clone WM53 BD cat#: 555450; RRID:AB_395843 CD19-BV605; clone SJ25C1 BD cat#: 562654; RRID:AB_2909453 CD11b-APC; clone ICRF44 BD cat#: 561015; RRID:AB_10561676 CD56-APCR700; clone NCAM16.2 BD cat#: 565140; RRID:AB_2744429 CD66b-PE; clone G10F5 BD cat#: 561650; RRID:AB_10894591 CD66b-BV421; clone G10F5 BD cat#: 562940; RRID:AB_2737906 CD45-APC; clone HI30 BD cat#: 555485; RRID:AB_398600 CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564; RRID:AB_2800449 CD3-BV786; clone SK7 BD cat#: 563800; RRID:AB_2744384 CD34-PE; clone 581 BD cat#: 555822; RRID:AB_396151 CD45RA-APC; clone HI100 BD cat#: 550855; RRID:AB_398468 CD38-PECy7; clone HB7 BD cat#: 335790; RRID:AB_399969 CD10-BV786; clone HI10a BD cat#: 564960; RRID:AB_2739025 CD90-Biotin; clone 5E10 BD cat#: 555594; RRID:AB_395968 Anti-LMNB1 Abcam cat#: ab16048; RRID:AB_443298 Anti-LBR Abcam cat#: ab32535; RRID:AB_775968 Anti-yH2AX ThermoFisher cat#: PA5-28778; RRID:AB_2546254 Anti-53BP1 Cell Signaling cat#: 2675; RRID:AB_490917 Bacterial and virus strains Stbl3 competent cells ThermoFisher cat#: C737303 Biological samples Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/ Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/ divisions/clinical-research-division/research/ co-operative-center-for-excellence-inhematology/hematopoietic-cell-procurementand-resource-development.html Chemicals, peptides, and recombinant proteins Ficoll-Paque Plus GE cat#:17-1440-02/6 Retronectin Takara cat#: T100A Recombinant human cytokines Peprotech https://www.peprotech.com/gb/ Recombinant human BMP-4 R&D Systems cat#: 314-BP-050 Recombinant human IL-7 R&D Systems cat#: 207-IL-010 Doxycycline Sigma cat#: D9891-10G SytoxGreen live-dead stain ThermoFisher cat#: S34860 poly-D-lysine Sigma cat#: A-003-E Vectashield Antifade Vector labs cat#: H-1200 EdU ThermoFisher cat#: C10640 DMSO Santa Cruz cat#: 487929-M Monastrol Sigma cat#: M8515 Nocodazole Sigma cat#: 487929-M Trizol ThermoFisher cat#: 15596026 Critical commercial assays CD34 Microbead kit Miltenyi cat#: 130-046-702 MethoCult Stem Cell Technologies cat#: H3434 (Continued on next page) Cell Stem Cell 29, 577–592.e1–e8, April 7, 2022 e1

Techniques: Derivative Assay, Expressing, Transduction, Control, Irradiation, Quantitation Assay, MANN-WHITNEY, Staining

Figure 5. Lamin B1 loss alters 3D chromatin organization (A) A and B compartment scores in control or LB1LO CB HSPCs over a representative genomic region (chromosome 5: 80–130 Mb). Blue denotes positive signal in PC1 (A compartment); gray represents negative signal in PC2 (B compartment). Data are from two combined replicates. (B) Proportion of genomic regions switching between A and B compartments, or regions that did not switch compartments, in control compared with LB1LO CB HSPCs. Data are from two combined replicates. (C) Line of best fit of the mean whole genome Hi-C contact frequencies (normalized for depth) over genomic distance for control and LB1LO CB HSPCs; 100-kb resolution. (D–F) Contact matrices of control or LB1LO CB HSPCs at (D) EBF1, (E) HOXB, and (F) CEBPB loci. Control: control contacts in the top right triangle; observed: LB1LO contacts in the bottom left triangle. Significant loops called by HOMER are denoted with a blue square. mRNA expression is displayed on the right, mean ± SD of two replicates. Virtual 4C tracks generated from original Hi-C matrix signal denote the interaction signal at promoter and enhancer regions. CTCF ChIP-seq track from CD34+ cord blood HSPCs denotes regions of CTCF binding and loop anchors. See also Figure S5.

Journal: Cell stem cell

Article Title: Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.

doi: 10.1016/j.stem.2022.02.010

Figure Lengend Snippet: Figure 5. Lamin B1 loss alters 3D chromatin organization (A) A and B compartment scores in control or LB1LO CB HSPCs over a representative genomic region (chromosome 5: 80–130 Mb). Blue denotes positive signal in PC1 (A compartment); gray represents negative signal in PC2 (B compartment). Data are from two combined replicates. (B) Proportion of genomic regions switching between A and B compartments, or regions that did not switch compartments, in control compared with LB1LO CB HSPCs. Data are from two combined replicates. (C) Line of best fit of the mean whole genome Hi-C contact frequencies (normalized for depth) over genomic distance for control and LB1LO CB HSPCs; 100-kb resolution. (D–F) Contact matrices of control or LB1LO CB HSPCs at (D) EBF1, (E) HOXB, and (F) CEBPB loci. Control: control contacts in the top right triangle; observed: LB1LO contacts in the bottom left triangle. Significant loops called by HOMER are denoted with a blue square. mRNA expression is displayed on the right, mean ± SD of two replicates. Virtual 4C tracks generated from original Hi-C matrix signal denote the interaction signal at promoter and enhancer regions. CTCF ChIP-seq track from CD34+ cord blood HSPCs denotes regions of CTCF binding and loop anchors. See also Figure S5.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CD33-PE; clone WM53 BD cat#: 555450; RRID:AB_395843 CD19-BV605; clone SJ25C1 BD cat#: 562654; RRID:AB_2909453 CD11b-APC; clone ICRF44 BD cat#: 561015; RRID:AB_10561676 CD56-APCR700; clone NCAM16.2 BD cat#: 565140; RRID:AB_2744429 CD66b-PE; clone G10F5 BD cat#: 561650; RRID:AB_10894591 CD66b-BV421; clone G10F5 BD cat#: 562940; RRID:AB_2737906 CD45-APC; clone HI30 BD cat#: 555485; RRID:AB_398600 CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564; RRID:AB_2800449 CD3-BV786; clone SK7 BD cat#: 563800; RRID:AB_2744384 CD34-PE; clone 581 BD cat#: 555822; RRID:AB_396151 CD45RA-APC; clone HI100 BD cat#: 550855; RRID:AB_398468 CD38-PECy7; clone HB7 BD cat#: 335790; RRID:AB_399969 CD10-BV786; clone HI10a BD cat#: 564960; RRID:AB_2739025 CD90-Biotin; clone 5E10 BD cat#: 555594; RRID:AB_395968 Anti-LMNB1 Abcam cat#: ab16048; RRID:AB_443298 Anti-LBR Abcam cat#: ab32535; RRID:AB_775968 Anti-yH2AX ThermoFisher cat#: PA5-28778; RRID:AB_2546254 Anti-53BP1 Cell Signaling cat#: 2675; RRID:AB_490917 Bacterial and virus strains Stbl3 competent cells ThermoFisher cat#: C737303 Biological samples Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/ Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/ divisions/clinical-research-division/research/ co-operative-center-for-excellence-inhematology/hematopoietic-cell-procurementand-resource-development.html Chemicals, peptides, and recombinant proteins Ficoll-Paque Plus GE cat#:17-1440-02/6 Retronectin Takara cat#: T100A Recombinant human cytokines Peprotech https://www.peprotech.com/gb/ Recombinant human BMP-4 R&D Systems cat#: 314-BP-050 Recombinant human IL-7 R&D Systems cat#: 207-IL-010 Doxycycline Sigma cat#: D9891-10G SytoxGreen live-dead stain ThermoFisher cat#: S34860 poly-D-lysine Sigma cat#: A-003-E Vectashield Antifade Vector labs cat#: H-1200 EdU ThermoFisher cat#: C10640 DMSO Santa Cruz cat#: 487929-M Monastrol Sigma cat#: M8515 Nocodazole Sigma cat#: 487929-M Trizol ThermoFisher cat#: 15596026 Critical commercial assays CD34 Microbead kit Miltenyi cat#: 130-046-702 MethoCult Stem Cell Technologies cat#: H3434 (Continued on next page) Cell Stem Cell 29, 577–592.e1–e8, April 7, 2022 e1

Techniques: Control, Hi-C, Expressing, Generated, ChIP-sequencing, Binding Assay

Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by ELISA kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.

Journal: Nutrients

Article Title: Neuroprotective Effects of Sodium Butyrate and Monomethyl Fumarate Treatment through GPR109A Modulation and Intestinal Barrier Restoration on PD Mice

doi: 10.3390/nu14194163

Figure Lengend Snippet: Effects of NaB and MMF on the integrity and permeability of intestinal barrier. ( A ) The content of DAO in each group was detected by ELISA kits. (n = 5–6). ( B ) The content of D-LA in each group detected by ELISA kits. (n = 7). ( C ) Representative immunoblot for Occludin. ( E ) Representative immunoblot for Claudin-1. Alteration of the colon’s intestinal tight junction. Treatment with NaB and MMF increased the expression of the tight junction proteins ( D ) Occludin and ( F ) Claudin-1, which is measured by Western blotting. (n = 5–6). Data are presented as mean ± SEM. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 versus the MPTP + vehicle group.

Article Snippet: According to the manufacturer’s instructions, IL-6 ELISA Kit (EK0411, BOSTER, Wuhan, China) and TNF-ELISA Kit (EK0527, BOSTER, Wuhan, China) were used to determine the serum concentrations of the inflammatory factor interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α).

Techniques: Permeability, Enzyme-linked Immunosorbent Assay, Western Blot, Expressing

The percentage of cell populations with expressions of cell surface markers CD34, CD24, CD133, CD117, and  CD44  in A2780-M and A2780 cells.

Journal: BioMed Research International

Article Title: Establishment and Characterization of a Highly Metastatic Ovarian Cancer Cell Line

doi: 10.1155/2018/3972534

Figure Lengend Snippet: The percentage of cell populations with expressions of cell surface markers CD34, CD24, CD133, CD117, and CD44 in A2780-M and A2780 cells.

Article Snippet: Anti-CD117 (Cat: 11996-R007-PE) and anti-CD44 (Cat: 12211-MM02-FITC) antibodies were from Sino Biological Inc. (Beijing, China).

Techniques: