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<t>.</t> <t>MG132</t> DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing <t>RNA-seq</t> expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.
Total Rna Isolation Kit Norgen Biotek, supplied by Norgen Biotek, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/total rna isolation kit norgen biotek/product/Norgen Biotek
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<t>.</t> <t>MG132</t> DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing <t>RNA-seq</t> expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.
Rna Isolation Kit Norgen, supplied by Norgen Biotek, 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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<t>.</t> <t>MG132</t> DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing <t>RNA-seq</t> expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.
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<t>.</t> <t>MG132</t> DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing <t>RNA-seq</t> expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.
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<t>.</t> <t>MG132</t> DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing <t>RNA-seq</t> expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.
Total Rna Isolation Kit Norgen Biotech, supplied by Norgen Biotek, 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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. MG132 DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing RNA-seq expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.

Journal: bioRxiv

Article Title: Proteasome inhibition reprograms chromatin landscape in breast cancer

doi: 10.1101/2023.10.13.562284

Figure Lengend Snippet: . MG132 DOCRs overlap SE biologically relevant in breast cancer tumors. A) Identification of super enhancers from control and MG132 treated MCF-7 cells. Enhancer regions are plotted in an increasing order based on normalized H3K27ac signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Examples of closest TSS to 3 top SEs in each class are shown B) Graph showing the level of H3K27ac signal observed at shared and unique super enhancers that overlap or do not overlap with DOCRs. C) Browser tracks showing examples of SEs 1) BCAS3 intron unique to control and overlaps with LOST DOCR; 2) Chr20 desert unique to MG24H, overlaps with GAIN; 3) SEMA4C/FAM178B unique to control and LINCO1754 unique to MG24H do not overlap with DOCRs. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, and SE region. SE chromosome start coordinates are shown on top. Tracks: Control (0), MG24H (24H). D) SE show individual tumor heterogeneity in DNA accessibility. Browser tracks of VMP1/MIR21 (Chr 17), SUMO1P1 (Chr 20) and PVT1 (Chr 8), SE regions are representative examples, cluster A, B and D. Tracks show read coverage of chromatin accessibility (NFR), differential NFR (DIFF), H3K27ac, SE, normalized ATAC signal for individual tumors showing High or Low proliferation, average normalized ATAC signal for non-basal (brown) and basal (green) breast tumors. Tracks: Control (0), MG24H (24H). E) Browser tracks of C1orf143 (LINC02869, Chr1), ZMYND8 (Chr 20), GSE1 (Chr 16), SE regions are representative examples, cluster C, E and F. F) Nongenic DOCR transcription is responsive to E2 treatment. Heatmaps showing GRO-seq signal at nongenic TSSs that overlap GAIN (left) and LOST DOCRs (right) in cells treated with vehicle (veh) and estradiol (E2). G) MG132 and E2 repress transcription of SUMO1P1 SE region. Graph showing RNA-seq expression (read counts) of the DOCR regions that overlap with the SUMO1P1 SE. Bottom : Graph showing RNA expression from the SE region, x-axis shows the primer sets used qPCR analysis. Graph showing RNA expression of selected regions within SE in cells treated with MG132 and E2. Primer genomic coordinates are indicated H) Tracks showing chromatin state and transcription features of TFF1 and ZNF217, representative genes induced and repressed by E2. Graphs show RNA expression TFF1 and ZNF217. RNA expression normalized to 5S rRNA.

Article Snippet: Total RNA was extracted from three biological replicates of vehicle and MG132 treated cells using total RNA isolation kit (Norgen Biotek, Thorold, ON, Canada).

Techniques: Control, RNA Sequencing, Expressing, RNA Expression