ChIP results obtained with the monoclonal antibody directed against Pol II
ChIP assays were performed using human HeLa cells, the monoclonal antibody against Pol II (Cat. # 25309) and optimized PCR primer pairs for qPCR. ChIP was performed using sheared chromatin from 1 million cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers specific for the promoter and the coding region of the constitutively expressed GAPDH and ACTB genes, used as positive controls, and for exon 2 of the inactive myoglobin (MB) gene and the Sat2 satellite repeat, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).

ChIP-seq results obtained with the monoclonal antibody directed against Pol II
ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using 1 µg of the antibody against Pol II (Cat. # 25309) as described above. The immunoprecipitated DNA was subsequently analyzed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution along the complete sequence and a 400 kb region of the X-chromosome (figure 2A and B, respectively), and in a two genomic regions surrounding the GAPDH and ACTB positive control genes (figure 2C and D).

Cross reactivity of the monoclonal antibody directed against Pol II
To test the specificity an ELISA was performed using a serial dilution of the monoclonal antibody against Pol II (Cat. # 25309). The wells were coated with peptides containing the unmodified C-terminal repeat sequence as well as different phosphorylated peptides. Figure 3 shows that the antibody recognizes the unphosphorylated Pol II as well as most phosphorylated forms.

Western blot analysis using the monoclonal antibody directed against Pol II
Nuclear extracts (25 µg) from HeLa cells were analyzed by Western blot using the monoclonal antibody against Pol II (Cat. # 25309) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.

Immunofluorescence using the monoclonal antibody directed against Pol II
HeLa cells were stained with the antibody against Pol II (Cat. # 25309) and with DAPI. Cells were fixed with methanol and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the Pol II antibody (left) diluted 1:500 in blocking solution followed by an anti-mouse antibody conjugated to Alexa594. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.

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