chip-it ffpe chromatin preparation Search Results


chip it ffpe chromatin preparation kit  (Active Motif)
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Active Motif chip it ffpe chromatin preparation kit
A tissue-level cross-link reversal allows efficient extraction of high-quality chromatin from <t>FFPE</t> tissues. a Schematic diagram of chromatin extraction method from FFPE tissues (ChromEX-PE). A tissue-level, cross-link reversal was introduced by incubating deparaffinized tissue in the range of temperature from 25 to 75 °C before chromatin extraction. b Chrom-EX PE dramatically increases soluble chromatin from FFPE tissues. Chromatin was prepared by Chrom-EX PE with 65 °C overnight incubation or without incubation. A commercial kit from Active motif was used as control and for comparison. DNAs were purified from soluble fraction and insoluble pellet fraction and were quantified using Qubit dsDNA High Sensitivity assay. The percentage of soluble chromatin was calculated from mouse spleen, kidney, and liver FFPE tissues. The data were generated from two independent experiments. c Chrom-EX PE generates different sizes of chromatin in a controlled manner. Chromatin was prepared from mouse liver FFPE tissues by Chrom-EX PE in the range of temperatures from 25 °C to 75 °C. Deparaffinized tissue was incubated in the indicated temperature overnight in the chromatin stabilization buffer. In the range of 25–37 °C, a majority of soluble chromatin is larger than 1 kb. The temperature ranges (45–55 °C) produce nucleosomal DNA patterns. The majority of DNA was mononucleosomal DNA at 60 °C incubation and DNA size is closer or smaller than mononucleosomal DNA with temperature above 60 °C. d Chromatin yield by Chrom-EX PE from various mouse tissues. The tissue volume is measured in FFPE block and two 20-μm sections were processed by Chrom-EX PE at 65 °C condition with chromatin stabilization buffer. The DNA amount purified from soluble fraction was measured and the yield was calculated per tissue volume
Chip It Ffpe Chromatin Preparation Kit, supplied by Active Motif, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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A tissue-level cross-link reversal allows efficient extraction of high-quality chromatin from FFPE tissues. a Schematic diagram of chromatin extraction method from FFPE tissues (ChromEX-PE). A tissue-level, cross-link reversal was introduced by incubating deparaffinized tissue in the range of temperature from 25 to 75 °C before chromatin extraction. b Chrom-EX PE dramatically increases soluble chromatin from FFPE tissues. Chromatin was prepared by Chrom-EX PE with 65 °C overnight incubation or without incubation. A commercial kit from Active motif was used as control and for comparison. DNAs were purified from soluble fraction and insoluble pellet fraction and were quantified using Qubit dsDNA High Sensitivity assay. The percentage of soluble chromatin was calculated from mouse spleen, kidney, and liver FFPE tissues. The data were generated from two independent experiments. c Chrom-EX PE generates different sizes of chromatin in a controlled manner. Chromatin was prepared from mouse liver FFPE tissues by Chrom-EX PE in the range of temperatures from 25 °C to 75 °C. Deparaffinized tissue was incubated in the indicated temperature overnight in the chromatin stabilization buffer. In the range of 25–37 °C, a majority of soluble chromatin is larger than 1 kb. The temperature ranges (45–55 °C) produce nucleosomal DNA patterns. The majority of DNA was mononucleosomal DNA at 60 °C incubation and DNA size is closer or smaller than mononucleosomal DNA with temperature above 60 °C. d Chromatin yield by Chrom-EX PE from various mouse tissues. The tissue volume is measured in FFPE block and two 20-μm sections were processed by Chrom-EX PE at 65 °C condition with chromatin stabilization buffer. The DNA amount purified from soluble fraction was measured and the yield was calculated per tissue volume

Journal: BMC Genomics

Article Title: Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

doi: 10.1186/s12864-019-5639-8

Figure Lengend Snippet: A tissue-level cross-link reversal allows efficient extraction of high-quality chromatin from FFPE tissues. a Schematic diagram of chromatin extraction method from FFPE tissues (ChromEX-PE). A tissue-level, cross-link reversal was introduced by incubating deparaffinized tissue in the range of temperature from 25 to 75 °C before chromatin extraction. b Chrom-EX PE dramatically increases soluble chromatin from FFPE tissues. Chromatin was prepared by Chrom-EX PE with 65 °C overnight incubation or without incubation. A commercial kit from Active motif was used as control and for comparison. DNAs were purified from soluble fraction and insoluble pellet fraction and were quantified using Qubit dsDNA High Sensitivity assay. The percentage of soluble chromatin was calculated from mouse spleen, kidney, and liver FFPE tissues. The data were generated from two independent experiments. c Chrom-EX PE generates different sizes of chromatin in a controlled manner. Chromatin was prepared from mouse liver FFPE tissues by Chrom-EX PE in the range of temperatures from 25 °C to 75 °C. Deparaffinized tissue was incubated in the indicated temperature overnight in the chromatin stabilization buffer. In the range of 25–37 °C, a majority of soluble chromatin is larger than 1 kb. The temperature ranges (45–55 °C) produce nucleosomal DNA patterns. The majority of DNA was mononucleosomal DNA at 60 °C incubation and DNA size is closer or smaller than mononucleosomal DNA with temperature above 60 °C. d Chromatin yield by Chrom-EX PE from various mouse tissues. The tissue volume is measured in FFPE block and two 20-μm sections were processed by Chrom-EX PE at 65 °C condition with chromatin stabilization buffer. The DNA amount purified from soluble fraction was measured and the yield was calculated per tissue volume

Article Snippet: For the comparison of soluble chromatin yield, the ChIP-IT® FFPE Chromatin Preparation Kit (Active Motif, Cat # 53030) was utilized according to the manufacture’s instructions.

Techniques: Extraction, Incubation, Control, Comparison, Purification, Sensitive Assay, Generated, Blocking Assay

The chromatin generated by Chrom-EX PE is compatible with ChIP-qPCR and ChIP-seq. a The chromatin generated by Chrom-EX PE produced consistent and high enrichment in ChIP-qPCR approach. Two 20-μm sections from mouse liver FFPE tissues were processed by Chrom-EX PE at 65 °C condition. The resulting chromatin was immunoprecipitated as described in the Materials and Methods. ChIP DNAs were analyzed by qPCR and enrichment in the tested loci is shown as the percentage of input. Four individual mouse FFPE liver tissues were used in experiment. The genomic location of each primer pair along with peak profile of H3K4me3 and H3K27me3 marks are shown in the Additional file . b Chromatin generated by Chrom-EX PE produced comparable ChIP-seq peaks with the results from frozen tissues. ChIP-seq experiment was performed in the chromatin generated by Chrom-EX PE at 65 °C condition from two 20-μm sections of mouse liver FFPE tissues. As controls, ChIP-seq data was generated from frozen tissues as described in the Materials and Methods. Snapshot image are shown for 3 histone marks (H3K27ac, K27 ac; H3K4me3, K4me3; H3K27me3, K27me3) and RNA polymerase II (Pol II). ChIP-seq results were visualized in a 218 kb genomic region using the Integrative Genomics Viewer [ , ]. FFPE 1 and Frozen are the pair originated from the same mouse

Journal: BMC Genomics

Article Title: Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

doi: 10.1186/s12864-019-5639-8

Figure Lengend Snippet: The chromatin generated by Chrom-EX PE is compatible with ChIP-qPCR and ChIP-seq. a The chromatin generated by Chrom-EX PE produced consistent and high enrichment in ChIP-qPCR approach. Two 20-μm sections from mouse liver FFPE tissues were processed by Chrom-EX PE at 65 °C condition. The resulting chromatin was immunoprecipitated as described in the Materials and Methods. ChIP DNAs were analyzed by qPCR and enrichment in the tested loci is shown as the percentage of input. Four individual mouse FFPE liver tissues were used in experiment. The genomic location of each primer pair along with peak profile of H3K4me3 and H3K27me3 marks are shown in the Additional file . b Chromatin generated by Chrom-EX PE produced comparable ChIP-seq peaks with the results from frozen tissues. ChIP-seq experiment was performed in the chromatin generated by Chrom-EX PE at 65 °C condition from two 20-μm sections of mouse liver FFPE tissues. As controls, ChIP-seq data was generated from frozen tissues as described in the Materials and Methods. Snapshot image are shown for 3 histone marks (H3K27ac, K27 ac; H3K4me3, K4me3; H3K27me3, K27me3) and RNA polymerase II (Pol II). ChIP-seq results were visualized in a 218 kb genomic region using the Integrative Genomics Viewer [ , ]. FFPE 1 and Frozen are the pair originated from the same mouse

Article Snippet: For the comparison of soluble chromatin yield, the ChIP-IT® FFPE Chromatin Preparation Kit (Active Motif, Cat # 53030) was utilized according to the manufacture’s instructions.

Techniques: Generated, ChIP-qPCR, ChIP-sequencing, Produced, Immunoprecipitation

Highly correlated genome-wide ChIP-seq data are generated from mouse FFPE tissues by Chrom-EX PE. a Scatter plots showing the correlation between ChIP-seq datasets generated from the indicated repeats for FFPE liver tissue with H3K27Ac, H3K4me3 and H3K27me3 marks. The genome was divided into bins of 5 kb for H3K4me3 and H3K27Ac marks and 100 kb for H3K27me3 mark, and the number of mapped reads in the individual bins was calculated. r , Pearson correlation coefficient. b Scatter plots showing the correlation between ChIP-seq datasets generated from FFPE liver tissue by Chrom-EX PE and the corresponding frozen liver tissues by conventional ChIP-seq for H3K27Ac, H3K4me3 and H3K27me3 marks. c Scatter plots showing the correlation between ChIP-seq datasets generated from a pair of mouse spleen tissues. d Scatter plots showing the correlation between ChIP-seq datasets generated from FFPE liver tissue by Chrom-EX PE and the corresponding frozen liver tissues by conventional ChIP-seq for RNA polymerase II

Journal: BMC Genomics

Article Title: Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

doi: 10.1186/s12864-019-5639-8

Figure Lengend Snippet: Highly correlated genome-wide ChIP-seq data are generated from mouse FFPE tissues by Chrom-EX PE. a Scatter plots showing the correlation between ChIP-seq datasets generated from the indicated repeats for FFPE liver tissue with H3K27Ac, H3K4me3 and H3K27me3 marks. The genome was divided into bins of 5 kb for H3K4me3 and H3K27Ac marks and 100 kb for H3K27me3 mark, and the number of mapped reads in the individual bins was calculated. r , Pearson correlation coefficient. b Scatter plots showing the correlation between ChIP-seq datasets generated from FFPE liver tissue by Chrom-EX PE and the corresponding frozen liver tissues by conventional ChIP-seq for H3K27Ac, H3K4me3 and H3K27me3 marks. c Scatter plots showing the correlation between ChIP-seq datasets generated from a pair of mouse spleen tissues. d Scatter plots showing the correlation between ChIP-seq datasets generated from FFPE liver tissue by Chrom-EX PE and the corresponding frozen liver tissues by conventional ChIP-seq for RNA polymerase II

Article Snippet: For the comparison of soluble chromatin yield, the ChIP-IT® FFPE Chromatin Preparation Kit (Active Motif, Cat # 53030) was utilized according to the manufacture’s instructions.

Techniques: Genome Wide, ChIP-sequencing, Generated

Peak numbers and overlap rate of peaks from experimental repeats from FFPE samples

Journal: BMC Genomics

Article Title: Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

doi: 10.1186/s12864-019-5639-8

Figure Lengend Snippet: Peak numbers and overlap rate of peaks from experimental repeats from FFPE samples

Article Snippet: For the comparison of soluble chromatin yield, the ChIP-IT® FFPE Chromatin Preparation Kit (Active Motif, Cat # 53030) was utilized according to the manufacture’s instructions.

Techniques:

Peak numbers and overlap rate of peaks from FFPE and frozen tissue pairs

Journal: BMC Genomics

Article Title: Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

doi: 10.1186/s12864-019-5639-8

Figure Lengend Snippet: Peak numbers and overlap rate of peaks from FFPE and frozen tissue pairs

Article Snippet: For the comparison of soluble chromatin yield, the ChIP-IT® FFPE Chromatin Preparation Kit (Active Motif, Cat # 53030) was utilized according to the manufacture’s instructions.

Techniques: