the overall aim was to identify specific and common genomic binding sites for brd4 in experimentally transformed dermal fibroblasts derived from hgps patients and control individuals through the analysis of brd4 chip - sequencing data . transformed cell lines were obtained by retroviral introduction of tert ( t ) , v12-hras ( r ) and sv40 large and small t antigens ( s ) of primary dermal fibroblasts from hgps patients ( trs - hgps ) and age - matched control wild - type individuals ( trs - wt ) as previously described , , . cells were grown in mem containing 15% fetal bovine serum ( fbs ) , 2  mm l - glutamine , 100  u  ml penicillin and 100  gml streptomycin , at 37  c in 5% co2 . briefly , 10    10 cells were cross - linked for 10  min with formalin 1% at room temperature , followed by 5  minute quenching with 125  mm glycine . after three washes with chilled pbs , cell pellets were snap - frozen and stored at   80  c . cells were resuspended in lysis buffer containing 1  mm edta , 0.8% sds , 20  mm tris  hcl ph  8 and protease inhibitor cocktail ( calbiochem ) and sonicated in a diagenode bioruptor 300 for 1215 cycles ( 30  s on , 60  s off ) . chromatin was diluted in chip dilution buffer ( 1% triton x-100 , 1  mm edta , 20  mm tris  hcl ph  8 , 150  mm nacl and protease inhibitor cocktail ) and immunoprecipitated overnight with pre - coated anti - igg magnetic beads ( dynabeads , invitrogen ) previously incubated with anti - brd4 antibody ( 7  g , bethyl labs , lot a301 - 985 ) for 6  h at 4  c . beads were washed sequentially for 5  min each in low - salt ( 20  mm tris  hcl ph  8 , 150  mm nacl , 2  mm edta , 1% triton x-100 , 0.1% sds ) , high - salt ( 20  mm tris  hcl ph  8 , 500  mm nacl , 2  mm edta , 1% triton x-100 , 0.1% sds ) , licl ( 10  mm tris ph  8.0 , 1  mm edta , 250  mm licl , 1% np-40 , 1% na - deoxycholate ) and te ( 10  mm tris hcl ph  8 , 1  mm edta ) buffer at 4  c followed by a room temperature wash in te buffer . beads were eluted in 1% sds and 100  mm nahco3 buffer for 25  min at 65  c and cross - linking was reversed for 8  h after addition of nacl ( final concentration 200  mm ) . after rnase a ( 1  mg / ml , qiagen ) and proteinase k ( 2  mg / ml , new england biolabs ) incubations , dna was column - purified following the manufacturer 's instructions ( qiaquick pcr purification kit , qiagen ) . library construction ( illumina truseq 2.0 protocol ) and sequencing were performed at the nci - sequencing facility ( saic - frederick , md ) using illumina hiseq 2000 . 4 input samples and 4 brd4-chip samples ( from trs - wt and trs - hgps cells , two independent cell lines in each group ) were multiplexed in two lanes . raw reads files in fastq format were deposited to the sra database at ncbi ( table  1 ) . all samples showed all base quality   25 and a small number of truseq adapter sequences was detected in the wt1 brd4 reads . raw reads of each sample in fastq format were then aligned to reference human genome ( hg19 ) using novoalignmpi ( v3.0.2 , novocraft ) and the adapter sequence contamination in wt1 brd4 sample was removed during mapping using in addition , the program was instructed to only report the uniquely aligned reads by skipping the  -r  option . the mapping results in bam format were preprocessed using picard tools   ( v1.119 ) to reorder , sort reads and the duplicated reads were removed as well . the clean bam files were in turn converted to bed format using  bamtobed  script in bedtools   ( v2.19 ) in order to be analyzed using sicer   ( v1.1 ) . given the reported binding nature of brd4 , 200  bp window size and 400  bp gap size were chosen in the peak calling step using sicer . peak signals were visualized using integrative genomics viewer ( igv )   for basic quality check ; in addition , diffbind   was applied to the peak data to examine the correlation of wt and hgps samples using all default settings . in order to investigate potential differences in brd4 binding patterns in wt and hgps samples first , the union of the peaks in each biological group was calculated using the  find_union_islands.py  script in sicer , and then the intersection of peaks in each group was achieved using the  intersect  command in bedtools , and finally , the sample - specific peaks were derived by comparing the union peak sets with the intersected peak sets from different samples using , 3078 wt - specific and 5574 hgps - specific brd4 binding sites were detected and the annotation of the peaks was done using important genomic features e.g. , promoter , 5/3 utr , exon , intron , non - coding were used to annotate the peaks and differential enrichment in specific features were compared between wild type and hgps samples , as interpreted in . command in bedtools and annotated using homer . all annotated specific and common genomic binding sites between wt and hgps cell lines are provided in table  3 , table  4 , table  5 . the following are the supplementary data related to this article.table  3wt - specific sites.table  4hgps - specific sites.table  5wt and hgps common sites . transformed cell lines were obtained by retroviral introduction of tert ( t ) , v12-hras ( r ) and sv40 large and small t antigens ( s ) of primary dermal fibroblasts from hgps patients ( trs - hgps ) and age - matched control wild - type individuals ( trs - wt ) as previously described , , . cells were grown in mem containing 15% fetal bovine serum ( fbs ) , 2  mm l - glutamine , 100  u  ml penicillin and 100  gml streptomycin , at 37  c in 5% co2 . briefly , 10    10 cells were cross - linked for 10  min with formalin 1% at room temperature , followed by 5  minute quenching with 125  mm glycine . after three washes with chilled pbs , cell pellets were snap - frozen and stored at   80  c . cells were resuspended in lysis buffer containing 1  mm edta , 0.8% sds , 20  mm tris  hcl ph  8 and protease inhibitor cocktail ( calbiochem ) and sonicated in a diagenode bioruptor 300 for 1215 cycles ( 30  s on , 60  s off ) . chromatin was diluted in chip dilution buffer ( 1% triton x-100 , 1  mm edta , 20  mm tris  hcl ph  8 , 150  mm nacl and protease inhibitor cocktail ) and immunoprecipitated overnight with pre - coated anti - igg magnetic beads ( dynabeads , invitrogen ) previously incubated with anti - brd4 antibody ( 7  g , bethyl labs , lot a301 - 985 ) for 6  h at 4  c . beads were washed sequentially for 5  min each in low - salt ( 20  mm tris  hcl ph  8 , 150  mm nacl , 2  mm edta , 1% triton x-100 , 0.1% sds ) , high - salt ( 20  mm tris  hcl ph  8 , 500  mm nacl , 2  mm edta , 1% triton x-100 , 0.1% sds ) , licl ( 10  mm tris ph  8.0 , 1  mm edta , 250  mm licl , 1% np-40 , 1% na - deoxycholate ) and te ( 10  mm tris  hcl ph  8 , 1  mm edta ) buffer at 4  c followed by a room temperature wash in te buffer . beads were eluted in 1% sds and 100  mm nahco3 buffer for 25  min at 65  c and cross - linking was reversed for 8  h after addition of nacl ( final concentration 200  mm ) . after rnase a ( 1  mg / ml , qiagen ) and proteinase k ( 2  mg / ml , new england biolabs ) incubations , dna was column - purified following the manufacturer 's instructions ( qiaquick pcr purification kit , qiagen ) . library construction ( illumina truseq 2.0 protocol ) and sequencing were performed at the nci - sequencing facility ( saic - frederick , md ) using illumina hiseq 2000 . 4 input samples and 4 brd4-chip samples ( from trs - wt and trs - hgps cells , two independent cell lines in each group ) were multiplexed in two lanes . raw reads files in fastq format were deposited to the sra database at ncbi ( table  1 ) . all samples showed all base quality   25 and a small number of truseq adapter sequences was detected in the wt1 brd4 reads . raw reads of each sample in fastq format were then aligned to reference human genome ( hg19 ) using novoalignmpi ( v3.0.2 , novocraft ) and the adapter sequence contamination in wt1 brd4 sample was removed during mapping using in addition , the program was instructed to only report the uniquely aligned reads by skipping the  -r  option . the mapping results in bam format were preprocessed using picard tools   ( v1.119 ) to reorder , sort reads and the duplicated reads were removed as well . the clean bam files were in turn converted to bed format using  bamtobed  script in bedtools   ( v2.19 ) in order to be analyzed using sicer   ( v1.1 ) . given the reported binding nature of brd4 , 200  bp window size and 400  bp gap size were chosen in the peak calling step using sicer . peak signals were visualized using integrative genomics viewer ( igv )   for basic quality check ; in addition , diffbind   was applied to the peak data to examine the correlation of wt and hgps samples using all default settings . in order to investigate potential differences in brd4 binding patterns in wt and hgps samples first , the union of the peaks in each biological group was calculated using the  find_union_islands.py  script in sicer , and then the intersection of peaks in each group was achieved using the  intersect  command in bedtools , and finally , the sample - specific peaks were derived by comparing the union peak sets with the intersected peak sets from different samples using  -v 3078 wt - specific and 5574 hgps - specific brd4 binding sites were detected and the annotation of the peaks was done using important genomic features e.g. , promoter , 5/3 utr , exon , intron , non - coding were used to annotate the peaks and differential enrichment in specific features were compared between wild type and hgps samples , as interpreted in . all annotated specific and common genomic binding sites between wt and hgps cell lines are provided in table  3 , table  4 , table  5 . the following are the supplementary data related to this article.table  3wt - specific sites.table  4hgps - specific sites.table  5wt and hgps common sites .
hutchinson  gilford progeria syndrome ( hgps ) patients do not develop cancer despite a significant accumulation of dna damage in their cells . 
 we have recently reported that hgps cells are refractory to experimental oncogenic transformation and we identified the bromodomain - containing 4 protein ( brd4 ) as a mediator of the transformation resistance . 
 chip - sequencing experiments revealed distinct genome - wide binding patterns for brd4 in hgps cells when compared to control wild type cells . 
 here we provide a detailed description of the chip - seq dataset ( ncbi geo accession number gse61325 ) , the specific and common brd4 binding sites between hgps and control cells , and the data analysis procedure associated with the publication by fernandez et al . , 
 2014 in cell reports 9 , 248 - 260 [ 1 ] .