Ell 100 ml of TBST buffer and removing the liquid by applying

Ell 100 ml of TBST buffer and removing the liquid by applying vacuum to the outside of the nylon mesh using micropipette tip. The phage bound to the antibodies was eluted by adding to the beads of 100 ml of 100 mM Tris-glycine buffer pH 2.2 followed by neutralization using 20 ml 1 M Tris buffer pH 9.1. The eluted phages were used for the amplification in bacteria. The amplified phages were incubated with 20 ml of serum overnight at room temperature followed by isolation of the antibodies-bound phages using 20 ml of protein G agarose beads. The phages were then eluted from antibodies/protein G complexes using low pH buffer as described above, and the DNA was isolated using phenolchloroform extraction and ethanol precipitation. The 21 nt long DNA fragments coding for CI 1011 custom synthesis random peptides were PCR-amplified using primers containing a sequence for annealing to the Illumina flow cell and the sequence complementary to the Illumina sequencing primer. The PCR-amplified DNA library was purified on agarose gel and DNA from all samples were multiplexed by adding 4-base bar code at the beginning of each DNA fragment.Nextgen Data ProcessingThe high-throughput sequencing was performed using Illumina Hiseq2000. A total of about 313 million raw reads were generated. The sequences were de-multiplexed to determine its source sample. The 21- base 16985061 nucleotides representing the 7-amino-acid peptide were extracted between base position 29 and 49. All identical 21-mer DNA sequences were collapsed into single sequence with its coverage (frequency) recorded in the result multi-FASTA file. These DNA sequences were translated to peptide sequences using the first frame. All barcode splitting, read trimming, and sequence collapsing were done using FASTXToolkit. Peptide translation, selection of subsets of sequences of shared DNA, abundant DNA passing minimum coverage threshold, were done through customized Perl script. Bl2seq wasGenerating Serum Antibody Repertoire ProfilesTwenty ml of mouse or human serum and 10 ml of the Ph.D.7 random peptide library (NEB) were diluted in 200 ml of the Tris Buffered Saline (TBST) buffer containing 0.1 Tween 20 and 1Serum Antibody Repertoire Profilingalso automated to handle batch processing of thousands of sequences in a very short time frame. The next generation sequencing data are deposited to the NIH Short Read Archive. The accession number for the sequences in the SRA database is K162 web SRP021104.Supporting InformationTable S1 The table shows 500 the most abundant peptides with corresponding copy numbers selected for the antibodies from each of the four anti-PAP sera. The selected peptides are not shared by the sera from unimmunized mice as well as from mice immunized with the PSA antigen. (DOC) Tables S2 S2A, S2B and S2C. The table shows the list of proteins selected by doing protein BLAST of peptide sequences against refseq_protein database for the Homo Sapiens (taxid:9606) with the maximal score 18.5 threshold parameter. In the column A, the proteins are sorted by the increase of the protein accession number. Highlighted in yellow are the proteins which have been retrieved multiple number of times by BLAST search against different peptides. The column B shows the 1676428 lengths of proteins inthe number of amino acids. The column C shows the number of the matches to peptides that retrieved proteins at the selected Evalue threshold. The column D shows the initial scores calculated as the number of matches in column C divided by protein length.Ell 100 ml of TBST buffer and removing the liquid by applying vacuum to the outside of the nylon mesh using micropipette tip. The phage bound to the antibodies was eluted by adding to the beads of 100 ml of 100 mM Tris-glycine buffer pH 2.2 followed by neutralization using 20 ml 1 M Tris buffer pH 9.1. The eluted phages were used for the amplification in bacteria. The amplified phages were incubated with 20 ml of serum overnight at room temperature followed by isolation of the antibodies-bound phages using 20 ml of protein G agarose beads. The phages were then eluted from antibodies/protein G complexes using low pH buffer as described above, and the DNA was isolated using phenolchloroform extraction and ethanol precipitation. The 21 nt long DNA fragments coding for random peptides were PCR-amplified using primers containing a sequence for annealing to the Illumina flow cell and the sequence complementary to the Illumina sequencing primer. The PCR-amplified DNA library was purified on agarose gel and DNA from all samples were multiplexed by adding 4-base bar code at the beginning of each DNA fragment.Nextgen Data ProcessingThe high-throughput sequencing was performed using Illumina Hiseq2000. A total of about 313 million raw reads were generated. The sequences were de-multiplexed to determine its source sample. The 21- base 16985061 nucleotides representing the 7-amino-acid peptide were extracted between base position 29 and 49. All identical 21-mer DNA sequences were collapsed into single sequence with its coverage (frequency) recorded in the result multi-FASTA file. These DNA sequences were translated to peptide sequences using the first frame. All barcode splitting, read trimming, and sequence collapsing were done using FASTXToolkit. Peptide translation, selection of subsets of sequences of shared DNA, abundant DNA passing minimum coverage threshold, were done through customized Perl script. Bl2seq wasGenerating Serum Antibody Repertoire ProfilesTwenty ml of mouse or human serum and 10 ml of the Ph.D.7 random peptide library (NEB) were diluted in 200 ml of the Tris Buffered Saline (TBST) buffer containing 0.1 Tween 20 and 1Serum Antibody Repertoire Profilingalso automated to handle batch processing of thousands of sequences in a very short time frame. The next generation sequencing data are deposited to the NIH Short Read Archive. The accession number for the sequences in the SRA database is SRP021104.Supporting InformationTable S1 The table shows 500 the most abundant peptides with corresponding copy numbers selected for the antibodies from each of the four anti-PAP sera. The selected peptides are not shared by the sera from unimmunized mice as well as from mice immunized with the PSA antigen. (DOC) Tables S2 S2A, S2B and S2C. The table shows the list of proteins selected by doing protein BLAST of peptide sequences against refseq_protein database for the Homo Sapiens (taxid:9606) with the maximal score 18.5 threshold parameter. In the column A, the proteins are sorted by the increase of the protein accession number. Highlighted in yellow are the proteins which have been retrieved multiple number of times by BLAST search against different peptides. The column B shows the 1676428 lengths of proteins inthe number of amino acids. The column C shows the number of the matches to peptides that retrieved proteins at the selected Evalue threshold. The column D shows the initial scores calculated as the number of matches in column C divided by protein length.

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