normal c57bl/6 mice and mice containing foxo1 knock - in ( foxo1tag ) , foxp3-ires - rfp and bira alleles or foxp3-ires - rfp and bira alleles were previously described .
treg cells in mice carrying the foxp3-ires - rfp allele were marked by red fluorescence protein ( rfp ) .
all mice were maintained under specific pathogen - free conditions , and animal experimentation was conducted in accordance with institutional guidelines .
cd62l nave cd4 t , cd8 t , and foxp3 treg cells were isolated by facs - sorting , and then fixed for 10  min at 25  c with 10% formaldehyde .
after incubation , glycine was added to a final concentration of 0.125  m to 
the lysates were pelleted , re - suspended and sonicated to reduce dna length to 300500 base pairs ( bp ) .
the chromatin prepared from t cells of c57bl/6 mice was incubated with protein - a - anti - foxo1 ( ab39670 , abcam ) or an isotype control antibody overnight .
the chromatin prepared from t cells of foxo1tag / tag bira foxp3-ires - rfp or control bira mice was incubated with streptavidin overnight .
the immune complexes were washed , and eluted in 500  l of elution buffer containing 50  mm tris , 10  mm edta and 1.0% sds . precipitated chip dna and input dna were incubated at 65  c to reverse the crosslinking .
after digestion with rnase and proteinase k , the chip and input dna were purified with phenol / chloroform extraction and ethanol precipitation .
the purified dna was repaired , ligated with an adaptor , and amplified by pcr for 1520 cycles .
initial quality control of the sequencing was performed using fastqc ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) . after verifying acceptable base calling quality , nucleotide distribution , and adapter contamination ,
reads were aligned to the mouse mm9 ( ncbi , build 37 , july 2007 ) reference genome obtained through the ucsc table browser ( http://genome.ucsc.edu/ ) using version 0.12.7 of the bowtie short read alignment software   ( http://bowtie-bio.sourceforge.net/index.shtml ) .
peak calling was then performed on the aligned reads . for the cd4 and treg cell - types , macs   ( version 1.4.1 , http://liulab.dfci.harvard.edu/macs/ )
macs makes use of the inherent tendency of clusters of sense and antisense reads flanking protein - dna interaction sites to model fragment length .
it then considers this estimate when defining windows used to scan the genome for enrichment according to a poisson distribution . for the analysis of the cd8 data
, we developed a novel peak - calling algorithm bcp   ( http://rulai.cshl.ed/bcp/ ) , which employs a bayesian hidden markov model , to perform segmentation of the genome and identify enrichment .
this method expands peak - calling capabilities to more diffuse , less punctate enrichment , as seen in many histone modification chip - seq and dnase i hypersensitivity sequencing assays .
because bcp does not have an integrated method for dealing with potential pcr duplicates , we preprocessed the read alignments to include only one instance of each unique chromosome start and end position . in both cases , we employed the empirical fdr ( efdr ) metric as described by yong , z. , et al .   to minimize false positives .
this entailed using the input alignments as the treatment data and the chip alignments as the control to infer the background peak - calling rate .
the p - value of peak calling used by macs or bcp was then adjusted to ensure that the fraction of background peaks divided by called peaks did not exceed the efdr threshold .
this was set to 0.01 for macs but 0.05 for bcp since , in our experience , it was less sensitive to low density peak false calls .
the bedtools suite of utilities   was used for post - processing tasks such as finding overlapping antibody and biotin immunoprecipitated peaks .
normal c57bl/6 mice and mice containing foxo1 knock - in ( foxo1tag ) , foxp3-ires - rfp and bira alleles or foxp3-ires - rfp and bira alleles were previously described .
treg cells in mice carrying the foxp3-ires - rfp allele were marked by red fluorescence protein ( rfp ) .
all mice were maintained under specific pathogen - free conditions , and animal experimentation was conducted in accordance with institutional guidelines .
cd44 cd62l nave cd4 t , cd8 t , and foxp3 treg cells were isolated by facs - sorting , and then fixed for 10  min at 25  c with 10% formaldehyde .
after incubation , glycine was added to a final concentration of 0.125  m to 
the lysates were pelleted , re - suspended and sonicated to reduce dna length to 300500 base pairs ( bp ) .
the chromatin prepared from t cells of c57bl/6 mice was incubated with protein - a - anti - foxo1 ( ab39670 , abcam ) or an isotype control antibody overnight .
the chromatin prepared from t cells of foxo1tag / tag bira foxp3-ires - rfp or control bira mice was incubated with streptavidin overnight .
the immune complexes were washed , and eluted in 500  l of elution buffer containing 50  mm tris , 10  mm edta and 1.0% sds . precipitated chip dna and input dna were incubated at 65  c to reverse the crosslinking .
after digestion with rnase and proteinase k , the chip and input dna were purified with phenol / chloroform extraction and ethanol precipitation .
the purified dna was repaired , ligated with an adaptor , and amplified by pcr for 1520 cycles .
initial quality control of the sequencing was performed using fastqc ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) . after verifying acceptable base calling quality , nucleotide distribution , and adapter contamination ,
reads were aligned to the mouse mm9 ( ncbi , build 37 , july 2007 ) reference genome obtained through the ucsc table browser ( http://genome.ucsc.edu/ ) using version 0.12.7 of the bowtie short read alignment software   ( http://bowtie-bio.sourceforge.net/index.shtml ) .
peak calling was then performed on the aligned reads . for the cd4 and treg cell - types , macs   ( version 1.4.1 , http://liulab.dfci.harvard.edu/macs/ )
macs makes use of the inherent tendency of clusters of sense and antisense reads flanking protein - dna interaction sites to model fragment length .
it then considers this estimate when defining windows used to scan the genome for enrichment according to a poisson distribution . for the analysis of the cd8 data
, we developed a novel peak - calling algorithm bcp   ( http://rulai.cshl.ed/bcp/ ) , which employs a bayesian hidden markov model , to perform segmentation of the genome and identify enrichment .
this method expands peak - calling capabilities to more diffuse , less punctate enrichment , as seen in many histone modification chip - seq and dnase i hypersensitivity sequencing assays .
because bcp does not have an integrated method for dealing with potential pcr duplicates , we preprocessed the read alignments to include only one instance of each unique chromosome start and end position . in both cases , we employed the empirical fdr ( efdr ) metric as described by yong , z. , et al .   to minimize false positives
this entailed using the input alignments as the treatment data and the chip alignments as the control to infer the background peak - calling rate .
the p - value of peak calling used by macs or bcp was then adjusted to ensure that the fraction of background peaks divided by called peaks did not exceed the efdr threshold .
this was set to 0.01 for macs but 0.05 for bcp since , in our experience , it was less sensitive to low density peak false calls .
the bedtools suite of utilities   was used for post - processing tasks such as finding overlapping antibody and biotin immunoprecipitated peaks .
 the forkhead box o ( foxo ) family of transcription factors has a critical role in controlling the development , differentiation , and function of t cells . 
 however , the direct target genes of foxo transcription factors in t cells have not been well characterized . in this study 
 , we focused on mapping the genome wide foxo1-binding sites in nave cd4 + t cells , cd8 + t cells , and foxp3 + regulatory t ( treg ) cells . by using chromatin immunoprecipitation coupled with deep sequencing ( chip - seq ) , we identified foxo1 binding sites that were shared among or specific to the three t cell populations . here 
 we describe the experiments , quality controls , as well as the deep sequencing data . 
 part of the data analysis has been published by ouyang w et al . in nature 2012 
 [ 1 ] and kim mv et al . in immunity 2013 
 [ 2 ] , and the associated data set were uploaded to ncbi gene expression omnibus . 