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US 2016/0097088 A1Published application
Methods of Genome Sequencing and Epigenetic Analysis
AssigneeCarnegie Institution of Washington
InventorsYixian ZHENG, Junling JIA, Xiaobin ZHENG
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Abstract
Novel methods of ChIP-seq are disclosed herein. These methods of ChIP-seq employ carrier DNA to prevent loss of DNA samples. The greater DNA yields achieved by this invention permit ChIP-seq of a small number of cells, permitting epigenetic analysis of primary cells of limited quantity.
Claims57
A method of sequencing genomic DNA from a sample of cells, the method comprising:
- a. Fragmenting chromatin in the sample of cells,
- b. Adding a carrier DNA to the fragmented chromatin of the sample of cells, wherein the carrier DNA is 5′ biotinylated DNA (“DNA1”),
- c. Precipitating the mixture of carrier DNA and fragmented chromatin,
- d. Annealing a blocking primer that is complementary to the DNA1,
- e. Amplifying the genomic DNA from the sample of cells, and
- f. Sequencing the amplified DNA;
- wherein the sample of cells comprise between 1 and 20,000 cells, and
- wherein the blocking primers prevent amplification of the DNA1.
5 more elements
A method of sequencing genomic DNA from a sample of cells, the method comprising:
- a. Fragmenting the chromatin of the sample of cells,
- b. Adding a carrier DNA to the fragmented chromatin of the sample of cells, wherein the carrier DNA is 5′ biotinylated with a 5′ overhang and a 3′ Spacer 3 modification (“DNA2”),
- c. Precipitating the mixture of carrier DNA and fragmented chromatin,
- d. Amplifying the genomic DNA from the sample of cells, and
- e. Sequencing the amplified DNA;
- wherein the sample of cells comprise between 1 and 20,000 cells.
3 more elements
A method of sequencing genomic DNA from a sample of cells, the method comprising:
- a. Combining a sample of cells of interest with a sample of bulking cells,
- b. Fragmenting the chromatin of the cells of interest and the bulking cells,
- c. Precipitating the fragmented chromatin of the cells of interest,
- d. Amplifying the genomic DNA from the sample of cells, and
- e. Sequencing the amplified DNA;
- wherein the sample of cells comprise between 1 and 20,000 cells, and
- wherein the bulking cells are yeast cells or E. coli cells.
4 more elements
Dependencies are inferred from the claim text.