Agents providing controls and standards for immunoprecipitation assays

1. A method of validating a chromatin immunoprecipitation (ChIP) assay result, the method comprising:

(a) obtaining an input sample of the genomic material of interest and of one or more polypeptide-oligonucleotide conjugate of the formula:

A-L-N,

wherein A is a polypeptide comprising 5 amino acids, L is a linker and N is an oligonucleotide comprising 10 nucleotides, wherein the sequence of the 10 nucleotides of N uniquely identifies an amino acid sequence and/or amino acid modification of A wherein A comprises an amino acid sequence derived from a histone protein selected from the group consisting of histone HI, H2A, H2AX, H2B, H3 and H4,

(b) performing a ChIP assay, thereby processing, in parallel to the genomic material of interest of (a), the one or more polypeptide-oligonucleotide conjugates of (a),

(c) obtaining a processed sample of the polypeptide-oligonucleotide conjugate and the genomic material of interest processed in (b), and

(d) analyzing the samples obtained in (c), thereby obtaining a value and/or signal for each of the analyzed processed samples, and

(e) validating the ChIP assay result based on the value and/or signal obtained in (d).

2. The method of claim 1 , wherein validating comprises one or more comparisons of the value and/or signal of the input sample and the value and/or signal of the processed sample of C1 with the value and/or signal of the input sample and the value and/or signal of the processed sample of C2, wherein

(a) C1 is the genomic material of interest and C2 is a polypeptide-oligonucleotide conjugate, wherein C2 is a polypeptide-oligonucleotide conjugate immunoprecipitated with an antibody that is specific for the polypeptide-oligonucleotide conjugate (C2S), or C2 is a polypeptide-oligonucleotide conjugate immunoprecipitated with an antibody that is non-specific for the polypeptide-oligonucleotide conjugate (C2N), and/or

(b) C1 is a polypeptide-oligonucleotide conjugate immunoprecipitated with an antibody that is specific for the polypeptide-oligonucleotide conjugate and C2 is a polypeptide-oligonucleotide conjugate immunoprecipitated with an antibody that is non-specific for the polypeptide-oligonucleotide conjugate.

3. The method of claim 2 , wherein when

(i) the value and/or signal of the processed sample in (a) of C1 and C2S is significantly higher than the value and/or signal of the input sample, then the genomic sample comprises an epitope specific for the antibody that is specific for C2S,

(ii) the value and/or signal of the processed sample in (a) of C1 and C2N is significantly higher than the value and/or signal of the input sample, then the genomic sample is non-specifically amplified and the value or signal obtained is discarded,

(iii) the value and/or signal of the processed sample in (a) of C1 is not significantly higher than the value and/or signal of the input sample and the value and/or signal of the processed sample of C2S is significantly higher than the value and/or signal of the input sample, then the genomic sample does not comprise an epitope specific for the antibody that is specific for C2S,

(iv) the value and/or signal of the processed sample in (a) of C1 is significantly higher than the value and/or signal of the input sample and the value and/or signal of the processed sample of C2S is not significantly higher than the value and/or signal of the input sample, then the genomic sample is non-specifically amplified and the value or signal obtained is discarded,

(v) the value and/or signal of the processed sample in (b) of C1 is significantly higher than the value and/or signal of the input sample and the value and/or signal of the processed sample of C2 is not significantly higher than the value and/or signal of the input sample, then the data obtained is analyzed,

(vi) the value and/or signal of the processed sample in (b) of C1 and C2 is significantly higher than the value and/or signal of the input sample, then the data obtained is not analyzed and is discarded.

4. The method of claim 2 , wherein the value and/or signal for the input sample and the processed sample are calculated as ratios.

5. A method of normalizing chromatin immunoprecipitation (ChIP) assay data, the method comprising:

(a) obtaining an input sample of the genomic material of interest and of one or more of polypeptide-oligonucleotide conjugate of the formula:

A-L-N,

wherein A is a polypeptide comprising 5 amino acids, L is a linker, and N is an oligonucleotide comprising 10 nucleotides, wherein the sequence of the 10 nucleotides of N uniquely identifies an amino acid sequence and/or amino acid modification of A wherein A comprises an amino acid sequence derived from a histone protein selected from the group consisting of histone HI, H2A, H2AX, H2B, H3 and H4,

(b) performing a ChIP assay, thereby processing, in parallel to the genomic material of interest in (a), the one or more polypeptide-oligonucleotide conjugates of (a),

(c) obtaining a processed sample of the polypeptide-oligonucleotide conjugate and the genomic material of interest processed in (b),

(d) analyzing the samples obtained in (c), thereby obtaining a value and/or signal for each of the analyzed processed samples, and

(e) normalizing the values and/or signals obtained in (d) for each of the processed samples using the values obtained in (d) for each of the input samples.

6. The method of claim 5 , wherein parallel processing in (b) comprises contacting the genomic material with the one or more polypeptide-oligonucleotide conjugates.

7. The method of claim 6 , wherein the contacting of the genomic material with the one or more polypeptide-oligonucleotide conjugates is performed after fragmentation of the genomic material and before the resulting sample is contacted with an antibody.

8. The method of claim 5 , wherein performing a ChIP assay in (b) comprises one or more steps of:

(a) fragmenting genomic material of interest,

(b) contacting the fragmented genomic material and the one or more polypeptide-oligonucleotide conjugates with an antibody,

(c) immobilizing the antibody and specifically bound material,

(d) reducing the amount of non-specifically bound material,

(e) releasing the specifically bound material from the antibody,

(f) reversing a previous cross-linking reaction,

(g) fragmenting proteinaceous material, and/or

(h) purifying nucleic acid material.

9. The method of claim 5 , wherein analyzing the processed sample in (d) comprises performing a polymerase-chain reaction, a sequencing reaction, and/or a hybridization reaction.

10. The method of claim 5 , wherein normalizing in (e) comprises calculating ratios for input sample and processed sample for the genomic material and the one or more polypeptide-oligonucleotide conjugates.

11. The method of claim 1 , wherein A comprises 5 consecutive amino acids derived from any one sequence selected from the group consisting of

(SEQ ID NO: 1)

SGRGKQGCKARAK, 

(SEQ ID NO: 2)

VLLPKKTESHHKAKGK, 

(SEQ ID NO: 3)

PEPAKSAPAPKKGSKKAVTK,

(SEQ ID NO: 4)

AVSEGTKAVTKYTSSK,

(SEQ ID NO: 5)

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK,

(SEQ ID NO: 6)

QRLVREIAQDFKTDLRFQSSAVMALQEA, 

and

(SEQ ID NO: 7)

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLA.

12. The method of claim 1 , wherein A comprises an amino acid modification.

13. The method of claim 12 , wherein the amino acid modification is selected from the group consisting of acetylation, methylation (mono-, di-, tri-), phosphorylation, ubiquitination (mono-, di-, tri-, poly-), sumoylation, ADP-ribosylation, citrullination, biotinylation and cis-trans isomerization.

14. The method of claim 5 , wherein A comprises 5 consecutive amino acids derived from any one sequence selected from the group consisting of

(SEQ ID NO: 1)

SGRGKQGCKARAK, 

(SEQ ID NO: 2)

VLLPKKTESHHKAKGK, 

(SEQ ID NO: 3)

PEPAKSAPAPKKGSKKAVTK,

(SEQ ID NO: 4)

AVSEGTKAVTKYTSSK,

(SEQ ID NO: 5)

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK,

(SEQ ID NO: 6)

QRLVREIAQDFKTDLRFQSSAVMALQEA, 

and

(SEQ ID NO: 7)

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLA.

15. The method of claim 5 , wherein A comprises an amino acid modification.

16. The method of claim 15 , wherein the amino acid modification is selected from the group consisting of acetylation, methylation (mono-, di-, tri-), phosphorylation, ubiquitination (mono-, di-, tri-, poly-), sumoylation, ADP-ribosylation, citrullination, biotinylation and cis-trans isomerization.