tomato microarray data sets and probe sequences Search Results


97
ATCC cell lines b16 f1 atcc atcc crl 6323 nap1 hem1 ko
Cell Lines B16 F1 Atcc Atcc Crl 6323 Nap1 Hem1 Ko, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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New England Biolabs cdna
Transcriptome analysis of 59 selected genes associated with oral chemosensation, displayed as a heatmap showing mean fold changes in gene expression of the SSB-fed diet groups in relation to the respective water-fed group (=1) in the form of a color code. The gene expression was analyzed using one customized <t>cDNA</t> microarray per group from <t>pooled</t> <t>RNA</t> samples of the CV from mice that received either a standard diet (chow, n = 10–11) or Western-type diet (WD, n = 7–8) with water (Water) or a sugar-sweetened beverage (SSB) as a drink for 24 weeks.
Cdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Thermo Fisher biotin labeled complementary dna
Transcriptome analysis of 59 selected genes associated with oral chemosensation, displayed as a heatmap showing mean fold changes in gene expression of the SSB-fed diet groups in relation to the respective water-fed group (=1) in the form of a color code. The gene expression was analyzed using one customized <t>cDNA</t> microarray per group from <t>pooled</t> <t>RNA</t> samples of the CV from mice that received either a standard diet (chow, n = 10–11) or Western-type diet (WD, n = 7–8) with water (Water) or a sugar-sweetened beverage (SSB) as a drink for 24 weeks.
Biotin Labeled Complementary Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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93
Addgene inc cdna ha pkc δ
(A) GNAQQ209L transfected alone or combined with <t>PKC</t> δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated <t>cDNA</t> plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.
Cdna Ha Pkc δ, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Danaher Inc rabbit polyclonal anti wnt7b antibody
(A) PTGS2 knockdown efficiency in NHEKs transfected with mock or PTGS2-specific siRNA. (B) qRT-PCR analysis of <t>WNT7B</t> mRNA expression in NHEKs (n=3) transfected with mock or PTGS2-specific siRNA, followed by treatment with or without poly(I:C), with the addition of prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), or 11β-prostaglandin F2α (11b-PGF2α). ‡Prostaglandin D2 induced significant cytotoxicity. (C) Representative western blot of Wnt7b protein expression in NHEKs treated as in Fig. 4B (n=3). (D) Western blot quantification for n=3 repeats performed as described in Fig. 4C. (E) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C), with or without celecoxib. (F) Quantification of hair follicles in CSLM images from Fig. 4D (n=15–17). (G) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C) and celecoxib, with or without dmPGE2. (H) Quantification of hair follicles in CSLM images from Fig. 4E (n=10–11). *denotes p<0.05.
Rabbit Polyclonal Anti Wnt7b Antibody, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Thermo Fisher microarray glass slide with dapi
(A) PTGS2 knockdown efficiency in NHEKs transfected with mock or PTGS2-specific siRNA. (B) qRT-PCR analysis of <t>WNT7B</t> mRNA expression in NHEKs (n=3) transfected with mock or PTGS2-specific siRNA, followed by treatment with or without poly(I:C), with the addition of prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), or 11β-prostaglandin F2α (11b-PGF2α). ‡Prostaglandin D2 induced significant cytotoxicity. (C) Representative western blot of Wnt7b protein expression in NHEKs treated as in Fig. 4B (n=3). (D) Western blot quantification for n=3 repeats performed as described in Fig. 4C. (E) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C), with or without celecoxib. (F) Quantification of hair follicles in CSLM images from Fig. 4D (n=15–17). (G) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C) and celecoxib, with or without dmPGE2. (H) Quantification of hair follicles in CSLM images from Fig. 4E (n=10–11). *denotes p<0.05.
Microarray Glass Slide With Dapi, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Bio-Rad iscript cdna synthesis kit
(A) PTGS2 knockdown efficiency in NHEKs transfected with mock or PTGS2-specific siRNA. (B) qRT-PCR analysis of <t>WNT7B</t> mRNA expression in NHEKs (n=3) transfected with mock or PTGS2-specific siRNA, followed by treatment with or without poly(I:C), with the addition of prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), or 11β-prostaglandin F2α (11b-PGF2α). ‡Prostaglandin D2 induced significant cytotoxicity. (C) Representative western blot of Wnt7b protein expression in NHEKs treated as in Fig. 4B (n=3). (D) Western blot quantification for n=3 repeats performed as described in Fig. 4C. (E) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C), with or without celecoxib. (F) Quantification of hair follicles in CSLM images from Fig. 4D (n=15–17). (G) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C) and celecoxib, with or without dmPGE2. (H) Quantification of hair follicles in CSLM images from Fig. 4E (n=10–11). *denotes p<0.05.
Iscript Cdna Synthesis Kit, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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90
Addgene inc cdna ha pkc α
(A) GNAQQ209L transfected alone or combined with <t>PKC</t> δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated <t>cDNA</t> plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.
Cdna Ha Pkc α, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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SuperArray Bioscience Corporation pathwayfinder cdna array
CD4 + CD28 null T cell clones express CD158b/j, but do not express KARAP/DAP12. CD4 + CD28 null T cells were sorted from patients with RA, and clones were established by limiting dilution. Clones were analyzed by flow cytometry for expression of CD28 and CD158b/j. Four representative clones (#1 through #4) are shown. All clones expressed CD4 (unpublished data; A). RT-PCR was used to amplify transcripts for KARAP/DAP12 and β-actin from PBMCs (lane 1), Jurkat T cells (lane 2), and CD4 + CD28 null T cell clones #1–#4 (lanes 3–6, respectively). <t>cDNA</t> was omitted for the negative control (lane 7) (B). Western blotting was used to detect KARAP/DAP12 and β-actin protein (bottom panels) in Jurkat T cells (lane 1), Jurkat T cells transfected with KARAP/DAP12 + vaccinia virus (lane 2), and CD4 + CD28 null T cell clones (lanes 3–7) (C).
Pathwayfinder Cdna Array, supplied by SuperArray Bioscience Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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TeleChem International microarray slide
CD4 + CD28 null T cell clones express CD158b/j, but do not express KARAP/DAP12. CD4 + CD28 null T cells were sorted from patients with RA, and clones were established by limiting dilution. Clones were analyzed by flow cytometry for expression of CD28 and CD158b/j. Four representative clones (#1 through #4) are shown. All clones expressed CD4 (unpublished data; A). RT-PCR was used to amplify transcripts for KARAP/DAP12 and β-actin from PBMCs (lane 1), Jurkat T cells (lane 2), and CD4 + CD28 null T cell clones #1–#4 (lanes 3–6, respectively). <t>cDNA</t> was omitted for the negative control (lane 7) (B). Western blotting was used to detect KARAP/DAP12 and β-actin protein (bottom panels) in Jurkat T cells (lane 1), Jurkat T cells transfected with KARAP/DAP12 + vaccinia virus (lane 2), and CD4 + CD28 null T cell clones (lanes 3–7) (C).
Microarray Slide, supplied by TeleChem International, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Santa Cruz Biotechnology klf6 rabbit polyclonal antibodies
Primers used for QPCR validation of microarray data
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Microarrays Inc oligonucleotide probe
Primers used for QPCR validation of microarray data
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Image Search Results


Transcriptome analysis of 59 selected genes associated with oral chemosensation, displayed as a heatmap showing mean fold changes in gene expression of the SSB-fed diet groups in relation to the respective water-fed group (=1) in the form of a color code. The gene expression was analyzed using one customized cDNA microarray per group from pooled RNA samples of the CV from mice that received either a standard diet (chow, n = 10–11) or Western-type diet (WD, n = 7–8) with water (Water) or a sugar-sweetened beverage (SSB) as a drink for 24 weeks.

Journal: Nutrients

Article Title: Long-Term Consumption of a Sugar-Sweetened Soft Drink in Combination with a Western-Type Diet Is Associated with Morphological and Molecular Changes of Taste Markers Independent of Body Weight Development in Mice

doi: 10.3390/nu14030594

Figure Lengend Snippet: Transcriptome analysis of 59 selected genes associated with oral chemosensation, displayed as a heatmap showing mean fold changes in gene expression of the SSB-fed diet groups in relation to the respective water-fed group (=1) in the form of a color code. The gene expression was analyzed using one customized cDNA microarray per group from pooled RNA samples of the CV from mice that received either a standard diet (chow, n = 10–11) or Western-type diet (WD, n = 7–8) with water (Water) or a sugar-sweetened beverage (SSB) as a drink for 24 weeks.

Article Snippet: The isolated RNA samples per mouse were reverse transcribed to cDNA using the LunaScript RT Supermix Kit (New England Biolabs GmbH, Frankfurt am Main, Germany).

Techniques: Expressing, Microarray, Western Blot

(A) GNAQQ209L transfected alone or combined with PKC δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated cDNA plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.

Journal: Cancer cell

Article Title: RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma

doi: 10.1016/j.ccell.2017.04.002

Figure Lengend Snippet: (A) GNAQQ209L transfected alone or combined with PKC δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated cDNA plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.

Article Snippet: cDNA: HA-PKC δ(kinase dead) , addgene , 16389.

Techniques: Transfection, Western Blot, Positive Control, Expressing

KEY RESOURCES TABLE

Journal: Cancer cell

Article Title: RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma

doi: 10.1016/j.ccell.2017.04.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: cDNA: HA-PKC δ(kinase dead) , addgene , 16389.

Techniques: Recombinant, Activation Assay, Microarray, Fractionation, Expressing, Cell Culture

(A) PTGS2 knockdown efficiency in NHEKs transfected with mock or PTGS2-specific siRNA. (B) qRT-PCR analysis of WNT7B mRNA expression in NHEKs (n=3) transfected with mock or PTGS2-specific siRNA, followed by treatment with or without poly(I:C), with the addition of prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), or 11β-prostaglandin F2α (11b-PGF2α). ‡Prostaglandin D2 induced significant cytotoxicity. (C) Representative western blot of Wnt7b protein expression in NHEKs treated as in Fig. 4B (n=3). (D) Western blot quantification for n=3 repeats performed as described in Fig. 4C. (E) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C), with or without celecoxib. (F) Quantification of hair follicles in CSLM images from Fig. 4D (n=15–17). (G) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C) and celecoxib, with or without dmPGE2. (H) Quantification of hair follicles in CSLM images from Fig. 4E (n=10–11). *denotes p<0.05.

Journal: The Journal of investigative dermatology

Article Title: After skin wounding, noncoding dsRNA coordinates prostaglandins and Wnts to promote regeneration

doi: 10.1016/j.jid.2017.03.023

Figure Lengend Snippet: (A) PTGS2 knockdown efficiency in NHEKs transfected with mock or PTGS2-specific siRNA. (B) qRT-PCR analysis of WNT7B mRNA expression in NHEKs (n=3) transfected with mock or PTGS2-specific siRNA, followed by treatment with or without poly(I:C), with the addition of prostaglandin E2 (PGE2), prostaglandin F2α (PGF2α), or 11β-prostaglandin F2α (11b-PGF2α). ‡Prostaglandin D2 induced significant cytotoxicity. (C) Representative western blot of Wnt7b protein expression in NHEKs treated as in Fig. 4B (n=3). (D) Western blot quantification for n=3 repeats performed as described in Fig. 4C. (E) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C), with or without celecoxib. (F) Quantification of hair follicles in CSLM images from Fig. 4D (n=15–17). (G) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in mouse wounds injected with poly(I:C) and celecoxib, with or without dmPGE2. (H) Quantification of hair follicles in CSLM images from Fig. 4E (n=10–11). *denotes p<0.05.

Article Snippet: Proteins were separated under denaturing conditions on a NuPage 4–12% Bis-Tris gel (ThermoFisher), transferred onto a PVDF membrane, and probed overnight with rabbit polyclonal anti-Wnt7b antibody (1:1000, ab94915, Abcam, Cambridge, MA) followed by an HRP-conjugated secondary antibody.

Techniques: Knockdown, Transfection, Quantitative RT-PCR, Expressing, Western Blot, Light Microscopy, Injection

(A) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in C57BL6/NJ mouse wounds injected with or without polyinosinic:polycytidylic acid (poly(I:C)). (B) Wnt ligands most strongly upregulated or downregulated in gene expression microarray comparing NHEKs treated with vehicle or poly(I:C), published under (GSE92646) (C) Representative immunofluorescent image of Wnt7b protein in C57BL6/NJ mouse wounds (scale bar = 100 μm). (D) qRT-PCR analysis of WNT7B mRNA expression in NHEKs (n=3) treated with various doses of poly(I:C). (E) Western blot analysis of Wnt7b protein expression in NHEKs treated with or without poly(I:C), with β-actin as a loading control.

Journal: The Journal of investigative dermatology

Article Title: After skin wounding, noncoding dsRNA coordinates prostaglandins and Wnts to promote regeneration

doi: 10.1016/j.jid.2017.03.023

Figure Lengend Snippet: (A) Representative confocal scanning light microscopy (CSLM) image of regenerated hair follicles in C57BL6/NJ mouse wounds injected with or without polyinosinic:polycytidylic acid (poly(I:C)). (B) Wnt ligands most strongly upregulated or downregulated in gene expression microarray comparing NHEKs treated with vehicle or poly(I:C), published under (GSE92646) (C) Representative immunofluorescent image of Wnt7b protein in C57BL6/NJ mouse wounds (scale bar = 100 μm). (D) qRT-PCR analysis of WNT7B mRNA expression in NHEKs (n=3) treated with various doses of poly(I:C). (E) Western blot analysis of Wnt7b protein expression in NHEKs treated with or without poly(I:C), with β-actin as a loading control.

Article Snippet: Proteins were separated under denaturing conditions on a NuPage 4–12% Bis-Tris gel (ThermoFisher), transferred onto a PVDF membrane, and probed overnight with rabbit polyclonal anti-Wnt7b antibody (1:1000, ab94915, Abcam, Cambridge, MA) followed by an HRP-conjugated secondary antibody.

Techniques: Light Microscopy, Injection, Gene Expression, Microarray, Quantitative RT-PCR, Expressing, Western Blot, Control

(A) qRT-PCR analysis of WNT7B mRNA expression in background (C57BL6/NJ) and TLR3 KO mouse wounds (n=8). (B) WNT7B mRNA expression in TLR3 KO mouse wounds injected with vehicle or recombinant IL-6 (n=8). (C) WNT7B mRNA expression in background or STAT3 KO mouse wounds (n=8). (D) WNT7B mRNA expression in NHEKs transfected with mock or TLR3-specific siRNA, followed by treatment with or without poly(I:C). *denotes p<0.05.

Journal: The Journal of investigative dermatology

Article Title: After skin wounding, noncoding dsRNA coordinates prostaglandins and Wnts to promote regeneration

doi: 10.1016/j.jid.2017.03.023

Figure Lengend Snippet: (A) qRT-PCR analysis of WNT7B mRNA expression in background (C57BL6/NJ) and TLR3 KO mouse wounds (n=8). (B) WNT7B mRNA expression in TLR3 KO mouse wounds injected with vehicle or recombinant IL-6 (n=8). (C) WNT7B mRNA expression in background or STAT3 KO mouse wounds (n=8). (D) WNT7B mRNA expression in NHEKs transfected with mock or TLR3-specific siRNA, followed by treatment with or without poly(I:C). *denotes p<0.05.

Article Snippet: Proteins were separated under denaturing conditions on a NuPage 4–12% Bis-Tris gel (ThermoFisher), transferred onto a PVDF membrane, and probed overnight with rabbit polyclonal anti-Wnt7b antibody (1:1000, ab94915, Abcam, Cambridge, MA) followed by an HRP-conjugated secondary antibody.

Techniques: Quantitative RT-PCR, Expressing, Injection, Recombinant, Transfection

(A) GNAQQ209L transfected alone or combined with PKC δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated cDNA plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.

Journal: Cancer cell

Article Title: RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma

doi: 10.1016/j.ccell.2017.04.002

Figure Lengend Snippet: (A) GNAQQ209L transfected alone or combined with PKC δ or ε into 293FT cells increased Ras-GTP levels. 293FT cells were transfected with indicated cDNA plasmids for 24 hr. Ras-GTP pull-down was performed and detected by western blot with a pan-Ras antibody. TPA stimulation was used a positive control. Expression levels of GNAQQ209L were monitored with Glu-Glu (EE) tag. PKC δ and ε were detected via HA tags.

Article Snippet: cDNA: HA-PKC α (catalytic domain) , addgene , 21234.

Techniques: Transfection, Western Blot, Positive Control, Expressing

KEY RESOURCES TABLE

Journal: Cancer cell

Article Title: RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma

doi: 10.1016/j.ccell.2017.04.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: cDNA: HA-PKC α (catalytic domain) , addgene , 21234.

Techniques: Recombinant, Activation Assay, Microarray, Fractionation, Expressing, Cell Culture

CD4 + CD28 null T cell clones express CD158b/j, but do not express KARAP/DAP12. CD4 + CD28 null T cells were sorted from patients with RA, and clones were established by limiting dilution. Clones were analyzed by flow cytometry for expression of CD28 and CD158b/j. Four representative clones (#1 through #4) are shown. All clones expressed CD4 (unpublished data; A). RT-PCR was used to amplify transcripts for KARAP/DAP12 and β-actin from PBMCs (lane 1), Jurkat T cells (lane 2), and CD4 + CD28 null T cell clones #1–#4 (lanes 3–6, respectively). cDNA was omitted for the negative control (lane 7) (B). Western blotting was used to detect KARAP/DAP12 and β-actin protein (bottom panels) in Jurkat T cells (lane 1), Jurkat T cells transfected with KARAP/DAP12 + vaccinia virus (lane 2), and CD4 + CD28 null T cell clones (lanes 3–7) (C).

Journal: The Journal of Experimental Medicine

Article Title: Selective Activation of the c-Jun NH 2 -terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4 + T Cells

doi: 10.1084/jem.20020383

Figure Lengend Snippet: CD4 + CD28 null T cell clones express CD158b/j, but do not express KARAP/DAP12. CD4 + CD28 null T cells were sorted from patients with RA, and clones were established by limiting dilution. Clones were analyzed by flow cytometry for expression of CD28 and CD158b/j. Four representative clones (#1 through #4) are shown. All clones expressed CD4 (unpublished data; A). RT-PCR was used to amplify transcripts for KARAP/DAP12 and β-actin from PBMCs (lane 1), Jurkat T cells (lane 2), and CD4 + CD28 null T cell clones #1–#4 (lanes 3–6, respectively). cDNA was omitted for the negative control (lane 7) (B). Western blotting was used to detect KARAP/DAP12 and β-actin protein (bottom panels) in Jurkat T cells (lane 1), Jurkat T cells transfected with KARAP/DAP12 + vaccinia virus (lane 2), and CD4 + CD28 null T cell clones (lanes 3–7) (C).

Article Snippet: After 4 h, total RNA was harvested. cDNA was synthesized and used to probe the PathwayFinder cDNA Array (SuperArray) according to the manufacturer's instructions.

Techniques: Clone Assay, Flow Cytometry, Expressing, Reverse Transcription Polymerase Chain Reaction, Negative Control, Western Blot, Transfection, Virus

Stimulation through CD158b/j results in an up-regulation of ATF-2 and HSP27 transcripts. The PathwayFinder cDNA Array is spotted in duplicate with 23 cDNAs. Represented on the membrane are the ERK (egr-1 and c-fos), JNK (ATF-2, hsf1, HSP27, and HSP90), NF-κB (iNos, NF-κB, and IκBα), NFAT (IL-2, Fas, and CD5), TGF-β (p16, p21, and p57 Kip2 ), Wnt (c-myc), p53 (p21, gadd45, pig7, pig8, mdm2, and bax), and CREB pathways (egr-1, CYP19, and c-fos). The membrane also included a negative control (pUC18) and two positive controls (β-actin and GAPDH) (A). A CD4 + CD28 null CD158b/j + T cell clone was stimulated with control mouse IgG or anti-CD158j mAb and cross-linked with rabbit anti–mouse IgG Ab. Total RNA was harvested and used to probe the PathwayFinder cDNA Array (B).

Journal: The Journal of Experimental Medicine

Article Title: Selective Activation of the c-Jun NH 2 -terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4 + T Cells

doi: 10.1084/jem.20020383

Figure Lengend Snippet: Stimulation through CD158b/j results in an up-regulation of ATF-2 and HSP27 transcripts. The PathwayFinder cDNA Array is spotted in duplicate with 23 cDNAs. Represented on the membrane are the ERK (egr-1 and c-fos), JNK (ATF-2, hsf1, HSP27, and HSP90), NF-κB (iNos, NF-κB, and IκBα), NFAT (IL-2, Fas, and CD5), TGF-β (p16, p21, and p57 Kip2 ), Wnt (c-myc), p53 (p21, gadd45, pig7, pig8, mdm2, and bax), and CREB pathways (egr-1, CYP19, and c-fos). The membrane also included a negative control (pUC18) and two positive controls (β-actin and GAPDH) (A). A CD4 + CD28 null CD158b/j + T cell clone was stimulated with control mouse IgG or anti-CD158j mAb and cross-linked with rabbit anti–mouse IgG Ab. Total RNA was harvested and used to probe the PathwayFinder cDNA Array (B).

Article Snippet: After 4 h, total RNA was harvested. cDNA was synthesized and used to probe the PathwayFinder cDNA Array (SuperArray) according to the manufacturer's instructions.

Techniques: Membrane, Negative Control, Control

Phosphorylation of JNK is initiated by stimulation specifically through CD158j. Two CD4 + CD28 null CD158j + T cell clones (top panels) and a CD4 + CD28 null CD158b1 + T cell clone (bottom panels) were stimulated with anti-CD3 and/or anti-CD158b/j mAbs and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against total JNK (right panels; A). Jurkat T cells were infected with either wild-type vaccinia virus (WR) or vaccinia virus containing CD158j cDNA and were analyzed for expression of CD158j by flow cytometry (B). Jurkat T cells infected with WR vaccinia virus or CD158j + vaccinia virus were stimulated with anti-CD3 and/or anti-CD158b/j mAbs and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (top left panels) and MKK4 (bottom left panel). The blots were stripped and reprobed with Abs against β-actin (top right panels) or MKK4 (bottom right panel) (C).

Journal: The Journal of Experimental Medicine

Article Title: Selective Activation of the c-Jun NH 2 -terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4 + T Cells

doi: 10.1084/jem.20020383

Figure Lengend Snippet: Phosphorylation of JNK is initiated by stimulation specifically through CD158j. Two CD4 + CD28 null CD158j + T cell clones (top panels) and a CD4 + CD28 null CD158b1 + T cell clone (bottom panels) were stimulated with anti-CD3 and/or anti-CD158b/j mAbs and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against total JNK (right panels; A). Jurkat T cells were infected with either wild-type vaccinia virus (WR) or vaccinia virus containing CD158j cDNA and were analyzed for expression of CD158j by flow cytometry (B). Jurkat T cells infected with WR vaccinia virus or CD158j + vaccinia virus were stimulated with anti-CD3 and/or anti-CD158b/j mAbs and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (top left panels) and MKK4 (bottom left panel). The blots were stripped and reprobed with Abs against β-actin (top right panels) or MKK4 (bottom right panel) (C).

Article Snippet: After 4 h, total RNA was harvested. cDNA was synthesized and used to probe the PathwayFinder cDNA Array (SuperArray) according to the manufacturer's instructions.

Techniques: Phospho-proteomics, Clone Assay, SDS Page, Membrane, Infection, Virus, Expressing, Flow Cytometry

Mutation of transmembrane lysine residue in CD158j abolishes ability to induce JNK phosphorylation. Jurkat T cells were transiently transfected with constructs containing the CD158j cDNA or the CD158j233I cDNA. Cell-surface expression was confirmed by flow cytometry (A). Jurkat T cells transfected with either CD158j or CD158jK233I were stimulated with anti-CD3 or anti-CD158b/j mAb and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against total JNK (right panels) (B).

Journal: The Journal of Experimental Medicine

Article Title: Selective Activation of the c-Jun NH 2 -terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4 + T Cells

doi: 10.1084/jem.20020383

Figure Lengend Snippet: Mutation of transmembrane lysine residue in CD158j abolishes ability to induce JNK phosphorylation. Jurkat T cells were transiently transfected with constructs containing the CD158j cDNA or the CD158j233I cDNA. Cell-surface expression was confirmed by flow cytometry (A). Jurkat T cells transfected with either CD158j or CD158jK233I were stimulated with anti-CD3 or anti-CD158b/j mAb and cross-linked with rabbit anti–mouse IgG Ab. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against total JNK (right panels) (B).

Article Snippet: After 4 h, total RNA was harvested. cDNA was synthesized and used to probe the PathwayFinder cDNA Array (SuperArray) according to the manufacturer's instructions.

Techniques: Mutagenesis, Residue, Phospho-proteomics, Transfection, Construct, Expressing, Flow Cytometry, SDS Page, Membrane

CD158j and DAP10 do not associate. RT-PCR was used to amplify transcripts for DAP10 from PBMCs (lane 1) and CD4 + CD28 null T cell clones (lanes 2–5). cDNA was omitted for the negative control (lane 6) (A). CD4 + CD28 null CD158b/j + T cell clones were stimulated with anti-CD3 or anti-CD158b/j in the presence or absence of 2.0 μM wortmannin. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against β-actin (right panels). Results from two T cell clones are shown (B). DAP10-expressing RBL cells (left panel) were stably transfected with CD158j alone (middle panel) or with CD158j and KARAP/DAP12 (right panel). Cell surface expression of CD158j was confirmed by flow cytometry (top panels). DAP10 or KARAP/DAP12 was immunoprecipitated from lysates of biotinylated transfected RBL cells. After SDS-PAGE and transfer to nitrocellulose membranes, coimmunoprecipitated cell-surface proteins were detected by streptavidin-HRP (middle panels). Immunoprecipitation of DAP10 and KARAP/DAP12 was confirmed by immunoblot with anti-DAP10 or anti-KARAP/DAP12 Ab (bottom panels) (C). DAP10 or KARAP/DAP12 was immunoprecipitated from Jurkat T cells (lanes 1–3) or RBL cells (lanes 4–6). After SDS-PAGE and transfer to a nitrocellulose membrane, samples (protein-G preclear, lanes 1 and 4; DAP10 immunoprecipitate, lanes 2 and 5; KARAP/DAP12 immunoprecipitate, lanes 3 and 6) were analyzed by Western blot using DAP10 Ab (D).

Journal: The Journal of Experimental Medicine

Article Title: Selective Activation of the c-Jun NH 2 -terminal Protein Kinase Signaling Pathway by Stimulatory KIR in the Absence of KARAP/DAP12 in CD4 + T Cells

doi: 10.1084/jem.20020383

Figure Lengend Snippet: CD158j and DAP10 do not associate. RT-PCR was used to amplify transcripts for DAP10 from PBMCs (lane 1) and CD4 + CD28 null T cell clones (lanes 2–5). cDNA was omitted for the negative control (lane 6) (A). CD4 + CD28 null CD158b/j + T cell clones were stimulated with anti-CD3 or anti-CD158b/j in the presence or absence of 2.0 μM wortmannin. After SDS-PAGE and transfer to a nitrocellulose membrane, the cell lysates were analyzed for phosphorylation of JNK (left panels). The blots were then stripped and reprobed with Abs against β-actin (right panels). Results from two T cell clones are shown (B). DAP10-expressing RBL cells (left panel) were stably transfected with CD158j alone (middle panel) or with CD158j and KARAP/DAP12 (right panel). Cell surface expression of CD158j was confirmed by flow cytometry (top panels). DAP10 or KARAP/DAP12 was immunoprecipitated from lysates of biotinylated transfected RBL cells. After SDS-PAGE and transfer to nitrocellulose membranes, coimmunoprecipitated cell-surface proteins were detected by streptavidin-HRP (middle panels). Immunoprecipitation of DAP10 and KARAP/DAP12 was confirmed by immunoblot with anti-DAP10 or anti-KARAP/DAP12 Ab (bottom panels) (C). DAP10 or KARAP/DAP12 was immunoprecipitated from Jurkat T cells (lanes 1–3) or RBL cells (lanes 4–6). After SDS-PAGE and transfer to a nitrocellulose membrane, samples (protein-G preclear, lanes 1 and 4; DAP10 immunoprecipitate, lanes 2 and 5; KARAP/DAP12 immunoprecipitate, lanes 3 and 6) were analyzed by Western blot using DAP10 Ab (D).

Article Snippet: After 4 h, total RNA was harvested. cDNA was synthesized and used to probe the PathwayFinder cDNA Array (SuperArray) according to the manufacturer's instructions.

Techniques: Reverse Transcription Polymerase Chain Reaction, Clone Assay, Negative Control, SDS Page, Membrane, Phospho-proteomics, Expressing, Stable Transfection, Transfection, Flow Cytometry, Immunoprecipitation, Western Blot

Primers used for QPCR validation of microarray data

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Primers used for QPCR validation of microarray data

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Biomarker Discovery, Microarray

Regulation of Klf isoform expression by ET-1 in cardiac myocytes (microarray analysis)

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Regulation of Klf isoform expression by ET-1 in cardiac myocytes (microarray analysis)

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Expressing, Microarray

Regulation of Klf expression by ET-1. Cardiac myocytes were exposed to 100 nM ET-1 for the times indicated. RNA was extracted and expression of mRNAs for different Klf family members (A, Klf2; B, Klf4; C, Klf6; D, Klf5; E, Klf9; F, Klf10; G, Klf3; H, Klf11; I, Klf15) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for at least 4 independent preparations of myocytes.

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Regulation of Klf expression by ET-1. Cardiac myocytes were exposed to 100 nM ET-1 for the times indicated. RNA was extracted and expression of mRNAs for different Klf family members (A, Klf2; B, Klf4; C, Klf6; D, Klf5; E, Klf9; F, Klf10; G, Klf3; H, Klf11; I, Klf15) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for at least 4 independent preparations of myocytes.

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Expressing

Klf2, Klf4 and Klf6, but not Klf5, are upregulated as immediate early genes by ET-1. Cardiac myocytes were unstimulated or exposed to 20 μM cycloheximide (CX, open bars), 100 nM ET-1 (black bars), or ET-1 in the presence of cycloheximide (grey bars) for 0.5 h (Klf2, Klf4, Klf6) or 1 h (Irs2, Klf5, Il1rl1). RNA was extracted and expression of mRNAs for Klf2, Klf4, Klf6 and Irs2 (A, immediate early genes) or Klf5 and Il1rl1 (B, second phase genes) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for 3 or 4 independent preparations of myocytes. ⁎ p < 0.01 relative to ET-1 alone (one-way ANOVA repeated measures with TUKEY post-test).

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Klf2, Klf4 and Klf6, but not Klf5, are upregulated as immediate early genes by ET-1. Cardiac myocytes were unstimulated or exposed to 20 μM cycloheximide (CX, open bars), 100 nM ET-1 (black bars), or ET-1 in the presence of cycloheximide (grey bars) for 0.5 h (Klf2, Klf4, Klf6) or 1 h (Irs2, Klf5, Il1rl1). RNA was extracted and expression of mRNAs for Klf2, Klf4, Klf6 and Irs2 (A, immediate early genes) or Klf5 and Il1rl1 (B, second phase genes) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for 3 or 4 independent preparations of myocytes. ⁎ p < 0.01 relative to ET-1 alone (one-way ANOVA repeated measures with TUKEY post-test).

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Expressing

Upregulation of Klf2, Klf4, Klf6 and Klf5 by ET-1 is mediated in part through the ERK1/2 cascade. Cardiac myocytes were unstimulated (Control), or exposed to inhibitors alone (10 μM U0126, 50 μM LY294002, 5 μM SB203580), to 100 nM ET-1 alone or to ET-1 in the presence of each inhibitor for 0.5 or 1 h. RNA was extracted and expression of mRNAs for Klf2, Klf4, Klf6 or Klf5 analysed by qPCR. A, Effects of U0126 on expression of Klf mRNAs at 0.5 (Klf2) or 1 h (Klf4, Klf5, Klf6). B, Effects of LY294002 or SB203580 on expression of Klf mRNAs at 1 h. Results are expressed relative to unstimulated controls and are means ± S.E.M. for 4 or 5 independent preparations of myocytes. ⁎ p < 0.05, # p < 0.001 relative to ET-1 alone (one-way ANOVA repeated measures with TUKEY post-test).

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Upregulation of Klf2, Klf4, Klf6 and Klf5 by ET-1 is mediated in part through the ERK1/2 cascade. Cardiac myocytes were unstimulated (Control), or exposed to inhibitors alone (10 μM U0126, 50 μM LY294002, 5 μM SB203580), to 100 nM ET-1 alone or to ET-1 in the presence of each inhibitor for 0.5 or 1 h. RNA was extracted and expression of mRNAs for Klf2, Klf4, Klf6 or Klf5 analysed by qPCR. A, Effects of U0126 on expression of Klf mRNAs at 0.5 (Klf2) or 1 h (Klf4, Klf5, Klf6). B, Effects of LY294002 or SB203580 on expression of Klf mRNAs at 1 h. Results are expressed relative to unstimulated controls and are means ± S.E.M. for 4 or 5 independent preparations of myocytes. ⁎ p < 0.05, # p < 0.001 relative to ET-1 alone (one-way ANOVA repeated measures with TUKEY post-test).

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Control, Expressing

Translation-state analysis of Klf mRNAs. Cardiac myocytes were unstimulated (Control) or exposed to 100 nM ET-1 (1 h). RNA was extracted for the total RNA pool. Polysomes were prepared from the same myocyte preparations using sucrose density centrifugation. A, A 254 profiles for sucrose density gradients. B, Agarose gel electrophoresis of RNA from each fraction with ethidium bromide staining to highlight 28 S, 18S and 5S ribosomal RNAs. Fractions 6–11 were pooled for polysomal RNA. Expression of mRNAs for Klf2 (C), Klf4 (D), Klf6 (E), Klf5 (F), Irs2 (H) or Il1rl1 (I) in total RNA and polysome RNA pools was analysed by qPCR. Results are expressed relative to levels in total RNA from unstimulated cells and are means ± S.E.M. for 3 or 4 independent preparations of myocytes. ⁎ p < 0.05, ⁎⁎ p < 0.001 relative to Control (total RNA); # p < 0.01 relative to ET-1 (total RNA) (one-way ANOVA with TUKEY post-test). G, Western blotting of Klf6 protein in cardiac myocytes exposed to ET-1 for the times indicated. A representative image is shown in the upper panel, with densitometric analysis in the lower panel (results are means ± S.E.M. for 3 independent myocyte preparations).

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: Translation-state analysis of Klf mRNAs. Cardiac myocytes were unstimulated (Control) or exposed to 100 nM ET-1 (1 h). RNA was extracted for the total RNA pool. Polysomes were prepared from the same myocyte preparations using sucrose density centrifugation. A, A 254 profiles for sucrose density gradients. B, Agarose gel electrophoresis of RNA from each fraction with ethidium bromide staining to highlight 28 S, 18S and 5S ribosomal RNAs. Fractions 6–11 were pooled for polysomal RNA. Expression of mRNAs for Klf2 (C), Klf4 (D), Klf6 (E), Klf5 (F), Irs2 (H) or Il1rl1 (I) in total RNA and polysome RNA pools was analysed by qPCR. Results are expressed relative to levels in total RNA from unstimulated cells and are means ± S.E.M. for 3 or 4 independent preparations of myocytes. ⁎ p < 0.05, ⁎⁎ p < 0.001 relative to Control (total RNA); # p < 0.01 relative to ET-1 (total RNA) (one-way ANOVA with TUKEY post-test). G, Western blotting of Klf6 protein in cardiac myocytes exposed to ET-1 for the times indicated. A representative image is shown in the upper panel, with densitometric analysis in the lower panel (results are means ± S.E.M. for 3 independent myocyte preparations).

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Control, Centrifugation, Agarose Gel Electrophoresis, Staining, RNA Expression, Western Blot

H 2 O 2 increases expression of Klf2, Klf4 and Klf6 mRNA in cardiac myocytes. A–C, Cardiac myocytes were exposed to 0.2 mM H 2 O 2 for the times indicated. RNA was extracted and expression of mRNAs for Klf2 (A), Klf4 (B), or Klf6 (C) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for at least 4 independent preparations of myocytes. D and E, Cardiac myocytes were unstimulated (Control) or exposed to 0.2 mM H 2 O 2 (1 h) in the absence or presence of 5 μM SB203580 or 10 μM U0126 (D), or 50 μM LY294002 (E). Expression of mRNAs for Klf2 (pale grey bars), Klf4 (black bars), or Klf6 (dark grey bars) was analysed by qPCR. Results are expressed relative to levels in unstimulated myocytes and are means ± S.E.M. for 5 (D) or 7 (E) independent preparations of myocytes. ⁎ p < 0.001, # p < 0.01 relative to H 2 O 2 alone (one-way ANOVA with TUKEY post-test).

Journal: Biochimica et Biophysica Acta

Article Title: Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: Effects of endothelin-1, oxidative stress and cytokines

doi: 10.1016/j.bbamcr.2008.03.007

Figure Lengend Snippet: H 2 O 2 increases expression of Klf2, Klf4 and Klf6 mRNA in cardiac myocytes. A–C, Cardiac myocytes were exposed to 0.2 mM H 2 O 2 for the times indicated. RNA was extracted and expression of mRNAs for Klf2 (A), Klf4 (B), or Klf6 (C) analysed by qPCR. Results are expressed relative to unstimulated controls and are means ± S.E.M. for at least 4 independent preparations of myocytes. D and E, Cardiac myocytes were unstimulated (Control) or exposed to 0.2 mM H 2 O 2 (1 h) in the absence or presence of 5 μM SB203580 or 10 μM U0126 (D), or 50 μM LY294002 (E). Expression of mRNAs for Klf2 (pale grey bars), Klf4 (black bars), or Klf6 (dark grey bars) was analysed by qPCR. Results are expressed relative to levels in unstimulated myocytes and are means ± S.E.M. for 5 (D) or 7 (E) independent preparations of myocytes. ⁎ p < 0.001, # p < 0.01 relative to H 2 O 2 alone (one-way ANOVA with TUKEY post-test).

Article Snippet: Nitrocellulose blots were probed with Klf6 rabbit polyclonal antibodies (Santa Cruz Biotechnology Inc.; Klf6(R-173), sc-7158, 1/500 dilution).

Techniques: Expressing, Control