You will be presented with the full text of a biomedical research paper. Please write an abstract for this paper. Your response should include the abstract and no additional text.

Paper text:
( 2014 )  in vivo genome - wide analysis of multiple tissues identifies gene regulatory networks , novel functions and downstream regulatory genes for bapx1 and its co - regulation with sox9 in the mammalian vertebral column .  .
the bapx1/nkx3.2 protein was tagged in vivo with the s - peptide epitope to give specificity to the isolation of the bapx1/nkx3.2 s - peptide fusion protein for immunoprecipitation . in a similar fashion ,
the bapx1/nkx3.2 cdna was engineered so as to have an in - frame fusion with the v5 epitope tag that has a well - established high degree of specificity for the corresponding anti - v5 antibody and is commonly used in in vitro cell culture systems following the overexpression of the v5-tagged protein . in this case
the vertebral columns of mid - gestation ( e12.5 ) mouse embryos carrying the bapx1/nkx3.2 s - peptide allele were carefully dissected away from surrounding embryonic tissues , disaggregated into micro pieces and chromatin immunoprecipitation was performed to identify the dna sequences bound by bapx1/nkx3.2 protein in the native in vivo murine vertebral column .
the  quick and easy  bac modification kit ( gene bridges ) was used to generate bapx1/nkx3.2 gene targeting constructs as we have previously described ,   using c57bl/6j strain murine bac clones containing the bapx1/nkx3.2 gene obtained from the bacpac resources centre at children s hospital oakland research institute ( chori ) .
fragments of each modified region flanked by short and long homology arms with a total average length of >  10  kb were subcloned into a minimal vector with the gene bridges bac subcloning kit .
normal karyotype es clones positive by dna blotting with probes external to the gene targeting constructs were used to generate germline transmitting chimeras as we have previously described .
the resulting highly chimeric mice were crossed to c57bl/6j mice and stable mouse lines were established expressing the s - peptide tagged bapx1/nkx3.2 protein .
the frt - flanked neomycin g418 antibiotic selection cassette in the targeted bapx1/nkx3.2 allele was deleted by crossing to flpe  deleter mice ( 129s4/svjaesor - gt(rosa)26sor tm1(flp1)dym / j ( stock # 3946 ) from jackson laboratories ) , .
rna in situ analysis was performed as previously described   on the resulting modified allele carrying embryos to verify that there were no detectable changes in expression of the gene - targeted locus .
for analysis of the vertebral column the e12.5 embryos were sectioned through the sagittal plane .
wildtype or baxp1/nkx3.2 gene - targeted mouse lines were mated and noon of the plug date was designated as e0.5 . at e12.5 embryos were isolated and the vertebral columns ( tagged with s - peptide for baxp1/nkx3.2 or wildtype mouse embryos for sox9 ) were carefully dissected away from other organs and pooled .
chromatin ( ~  2  mg ) was used for chromatin immunoprecipitation as previously described for bapx1/nkx3.2 and sox9 . with 15  ng of purified chip dna from each sample
, the sequencing library was generated according to the manufacturer s instructions ( illumina ) , .
antibodies used for bapx1/nkx3.2 and sox were anti s - peptide antibody ( bethyl laboratories , a190 - 134a ) and anti - sox9 antibody ( r&d systems , af3075 ) respectively .
the illumina genome analyzer pipeline was used to map reads that had passed signal filtering to the murine mm9 genome .
the peak calling algorithm macs was used to match unique reads with 2 or less mismatches , with default settings as previously described .
all data was deposited in gene expression omnibus ( geo ) under accession number gse36672 .
many binding sites , however , were located far from a tss ; some located at over 25  kb distally in the intergenic ( 1052 ) and less located over 25  kb in the intragenic regions ( 722 ) .
dna - binding motif analysis used the top several hundred peaks and the masked repeat genome sequence spanned on either side from the summit of these peaks by 50  bp .
we identified the bapx1/nkx3.2 binding motif   enriched in about 40% of the bapx1/nkx3.2 binding sites , .
gene enrichment test for regions bound by sox9 and bapx1 , we submitted the analyzed chip - seq data as bed format to genomic regions enrichment of annotations tool ( great )   version 1.8 with the following parameters , species assembly - mm9 and association rule - single nearest gene : 100,000  bp maximum extension , curated regulatory domains included .
( 2014 )  in vivo genome - wide analysis of multiple tissues identifies gene regulatory networks , novel functions and downstream regulatory genes for bapx1 and its co - regulation with sox9 in the mammalian vertebral column .  .
the bapx1/nkx3.2 protein was tagged in vivo with the s - peptide epitope to give specificity to the isolation of the bapx1/nkx3.2 s - peptide fusion protein for immunoprecipitation . in a similar fashion ,
the bapx1/nkx3.2 cdna was engineered so as to have an in - frame fusion with the v5 epitope tag that has a well - established high degree of specificity for the corresponding anti - v5 antibody and is commonly used in in vitro cell culture systems following the overexpression of the v5-tagged protein . in this case
the vertebral columns of mid - gestation ( e12.5 ) mouse embryos carrying the bapx1/nkx3.2 s - peptide allele were carefully dissected away from surrounding embryonic tissues , disaggregated into micro pieces and chromatin immunoprecipitation was performed to identify the dna sequences bound by bapx1/nkx3.2 protein in the native in vivo murine vertebral column .
the  quick and easy  bac modification kit ( gene bridges ) was used to generate bapx1/nkx3.2 gene targeting constructs as we have previously described ,   using c57bl/6j strain murine bac clones containing the bapx1/nkx3.2 gene obtained from the bacpac resources centre at children s hospital oakland research institute ( chori ) .
fragments of each modified region flanked by short and long homology arms with a total average length of >  10  kb were subcloned into a minimal vector with the gene bridges bac subcloning kit .
normal karyotype es clones positive by dna blotting with probes external to the gene targeting constructs were used to generate germline transmitting chimeras as we have previously described .
the resulting highly chimeric mice were crossed to c57bl/6j mice and stable mouse lines were established expressing the s - peptide tagged bapx1/nkx3.2 protein .
the frt - flanked neomycin g418 antibiotic selection cassette in the targeted bapx1/nkx3.2 allele was deleted by crossing to flpe  deleter mice ( 129s4/svjaesor - gt(rosa)26sor tm1(flp1)dym / j ( stock # 3946 ) from jackson laboratories ) , .
rna in situ analysis was performed as previously described   on the resulting modified allele carrying embryos to verify that there were no detectable changes in expression of the gene - targeted locus . for analysis of the vertebral column the e12.5 embryos were sectioned through the sagittal plane .
wildtype or baxp1/nkx3.2 gene - targeted mouse lines were mated and noon of the plug date was designated as e0.5 . at e12.5 embryos were isolated and the vertebral columns ( tagged with s - peptide for baxp1/nkx3.2 or wildtype mouse embryos for sox9 ) were carefully dissected away from other organs and pooled .
1 . chromatin ( ~  2  mg ) was used for chromatin immunoprecipitation as previously described for bapx1/nkx3.2 and sox9 . with 15  ng of purified chip dna from each sample
, the sequencing library was generated according to the manufacturer s instructions ( illumina ) , .
antibodies used for bapx1/nkx3.2 and sox were anti s - peptide antibody ( bethyl laboratories , a190 - 134a ) and anti - sox9 antibody ( r&d systems , af3075 ) respectively .
the illumina genome analyzer pipeline was used to map reads that had passed signal filtering to the murine mm9 genome .
the peak calling algorithm macs was used to match unique reads with 2 or less mismatches , with default settings as previously described .
all data was deposited in gene expression omnibus ( geo ) under accession number gse36672 .
many binding sites , however , were located far from a tss ; some located at over 25  kb distally in the intergenic ( 1052 ) and less located over 25  kb in the intragenic regions ( 722 ) .
dna - binding motif analysis used the top several hundred peaks and the masked repeat genome sequence spanned on either side from the summit of these peaks by 50  bp .
we identified the bapx1/nkx3.2 binding motif   enriched in about 40% of the bapx1/nkx3.2 binding sites , .
gene enrichment test for regions bound by sox9 and bapx1 , we submitted the analyzed chip - seq data as bed format to genomic regions enrichment of annotations tool ( great )   version 1.8 with the following parameters , species assembly - mm9 and association rule - single nearest gene : 100,000  bp maximum extension , curated regulatory domains included .
this work pertains to geo submission gse36672 , in vivo and in vitro genome wide binding ( chip - seq ) of bapx1/nkx3.2 and sox9 proteins . 
 we have previously shown that data from a genome wide binding assay combined with transcriptional profiling is an insightful means to divulge the mechanisms directing cell type specification and the generation of tissues and subsequent organs [ 1 ] . 
 our earlier work identified the role of the dna - binding homeodomain containing protein bapx1/nkx3.2 in midgestation murine embryos . 
 microarray analysis of egfp - tagged cells ( both wildtype and null ) was integrated using chip - seq analysis of bapx1/nkx3.2 and sox9 dna - binding proteins in living tissue .