the mouse b lymphocyte cell lines wehi-231 expressing shrna construct control ( wehi - ct ) or a shrna construct directed against the transcription factor tfii - i ( wehi - tkii - i - kd ) were used to investigate the effect of tfii - i depletion on global gene expression and ctcf binding . to identify genes regulated by tfii - i , we extracted total rna from wehi - ct and wehi - tfii - i - kd from three independent samples .
the quantity and the quality of the rna samples were assessed by a nanodrop spectrophotometer and agilent bioanalyser .
data preprocessing was carried out with bioconductor package  lumi  , and we used log2 transformation followed by quantile normalization , .
reproducibility between biological replicates was evaluated by calculating the correlation coefficient r ( see example of the scatter plot fig . 
clustering of the microarray was performed to ensure correct segregation between control and tfii - i knockdown samples ( fig . 
identification of differentially expressed genes between wehi - ct and wehi - tfii - i - kd was made using bioconductor package 
we identified 117 genes differentially regulated with a fold chance   2 and p - value    0.05 listed in table  1 . as a confirmation of the knockdown efficiency , we found gtf2i , the gene coding for tfii - i , being the gene the most down regulated in our data . to identify the ctcf binding sites that were affected by tfii - i depletion , we carried two independent chip - seq assays ctcf in wehi - ct and wehi - tfii - i - kd cells with ctcf antibody .
briefly , cells were collected and crosslinked with 1% folmaldehyde in pbs for 10  min at room temperature .
crosslinking reaction was stooped with glycerine 125  mm and cells were washed with pbs and stored at   80  c until assay was carried out .
cells were lysed and dna sheered by sonication with cell lysis / chip buffer ( 0.25% np-40 , 0.25% trinton - x , 0.25% sodium deoxycholate , 0.1% sds , 50  mm tris ph  8.0 , 50  mm nacl , 5  mm edta ) for 15  s , 15 times .
lysed cells were centrifuged for 15  min at 14,000  rpm at 4  c and supernantant was collected .
1  mg of protein was precleared for 2  h with protein g agarose beads ( 50% slurry blocked with salmon sperm ) at 4  c .
immunoprecipitation was carried out by adding 2  g of antibody and 30  l of agarose g beads and nutated overnight at 4  c .
after immunoprecipitation , beads were pelleted by centrifugation and were washed 4 times to remove unspecific binding using buffers with varying concentrations of salt .
buffers 1 to 3 contained 0.1% sds , 1% triton - x , 2  mm edta , 20  mm tris ph  8.0 and 150  mm nacl , 300  mm nacl , 500  mm nacl respectively .
buffer 4 contained 0.25  m licl , 1% np-40 , 1% sodium deoxycholate , 1  mm edta and 10  mm tris ph8.0 .
two additional washes with te were done to remove any residual buffer from the beads .
complexes bound to the beads were eluted with 500  l of elution buffer ( 1% sds , 1  mm edta , 50  mm tris ph  8.0 ) at 65  c for 25  min with occasional vortexing .
crosslink reversal was achieved by adding 0.2  mm nacl at 65  c overnight .
next proteins ( including dna bound factors and antibodies ) were degraded by a treatment with proteinase k , carried at 45  c for 1  h and a second incubation of 15  min at 65  c . pcr purification kit ( qiagen ) was used to retrieve the dna following manufactured instruction and store at   20  c .
dna was sent to the iric ( institut de recherche en immunologie et cancrologie , montreal , canada ) sequencing facility where both the library construction and sequencing ( 100bases , paired - end , hiseq2000 , illumina ) were carried out ( table  2 ) .
quality of the sequencing was assessed using fastqc software , an example is presented in fig . 
dna sequences obtained were trimmed to 45 bases , filtered for high quality scores ( >  30 ) , and duplicates were removed before being aligned to the mouse genome ( u.s . national center for biotechnology information ( ncbi ) build 37 , july 2007 , mm9 ) using the bwa algorithm  .
quality of the alignment was assessed using samstat and only the sequences with mapq score   30 were kept for further analysis ( fig . 
the model based analysis of chip - seq peak - finding algorithm was used to identify peaks in wehi - ct and wehi - tfii - i - kd conditions using the default settings and an example of peak model obtain with macs is presented in fig . 
overlap for ctcf binding sites between biological replicates was assessed using the intersect function of bedtools , the results are shown with venn diagram ( fig . 
homer was used to annotate ctcf peaks , determine their genomic distribution and generated the bedgraph files to visualize the results in ucsc genome browser ( homer.salk.edu/ ) .
we used previously published ctcf chip - seq data available in the ucsc genome browser as controls for our dataset ( fig . 
the mouse b lymphocyte cell lines wehi-231 expressing shrna construct control ( wehi - ct ) or a shrna construct directed against the transcription factor tfii - i ( wehi - tkii - i - kd ) were used to investigate the effect of tfii - i depletion on global gene expression and ctcf binding .
to identify genes regulated by tfii - i , we extracted total rna from wehi - ct and wehi - tfii - i - kd from three independent samples .
the quantity and the quality of the rna samples were assessed by a nanodrop spectrophotometer and agilent bioanalyser .
data preprocessing was carried out with bioconductor package  lumi  , and we used log2 transformation followed by quantile normalization , .
reproducibility between biological replicates was evaluated by calculating the correlation coefficient r ( see example of the scatter plot fig . 
clustering of the microarray was performed to ensure correct segregation between control and tfii - i knockdown samples ( fig . 
identification of differentially expressed genes between wehi - ct and wehi - tfii - i - kd was made using bioconductor package 
we identified 117 genes differentially regulated with a fold chance   2 and p - value    0.05 listed in table  1 . as a confirmation of the knockdown efficiency
, we found gtf2i , the gene coding for tfii - i , being the gene the most down regulated in our data .
to identify the ctcf binding sites that were affected by tfii - i depletion , we carried two independent chip - seq assays ctcf in wehi - ct and wehi - tfii - i - kd cells with ctcf antibody .
briefly , cells were collected and crosslinked with 1% folmaldehyde in pbs for 10  min at room temperature .
crosslinking reaction was stooped with glycerine 125  mm and cells were washed with pbs and stored at   80  c until assay was carried out .
cells were lysed and dna sheered by sonication with cell lysis / chip buffer ( 0.25% np-40 , 0.25% trinton - x , 0.25% sodium deoxycholate , 0.1% sds , 50  mm tris ph  8.0 , 50  mm nacl , 5  mm edta ) for 15  s , 15 times .
lysed cells were centrifuged for 15  min at 14,000  rpm at 4  c and supernantant was collected .
1  mg of protein was precleared for 2  h with protein g agarose beads ( 50% slurry blocked with salmon sperm ) at 4  c .
immunoprecipitation was carried out by adding 2  g of antibody and 30  l of agarose g beads and nutated overnight at 4  c .
after immunoprecipitation , beads were pelleted by centrifugation and were washed 4 times to remove unspecific binding using buffers with varying concentrations of salt .
buffers 1 to 3 contained 0.1% sds , 1% triton - x , 2  mm edta , 20  mm tris ph  8.0 and 150  mm nacl , 300  mm nacl , 500  mm nacl respectively .
buffer 4 contained 0.25  m licl , 1% np-40 , 1% sodium deoxycholate , 1  mm edta and 10  mm tris ph8.0 .
two additional washes with te were done to remove any residual buffer from the beads .
complexes bound to the beads were eluted with 500  l of elution buffer ( 1% sds , 1  mm edta , 50  mm tris ph  8.0 ) at 65  c for 25  min with occasional vortexing .
crosslink reversal was achieved by adding 0.2  mm nacl at 65  c overnight .
next proteins ( including dna bound factors and antibodies ) were degraded by a treatment with proteinase k , carried at 45  c for 1  h and a second incubation of 15  min at 65  c . pcr purification kit ( qiagen ) was used to retrieve the dna following manufactured instruction and store at   20  c .
dna was sent to the iric ( institut de recherche en immunologie et cancrologie , montreal , canada ) sequencing facility where both the library construction and sequencing ( 100bases , paired - end , hiseq2000 , illumina ) were carried out ( table  2 ) .
quality of the sequencing was assessed using fastqc software , an example is presented in fig . 
2a ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) . using fastx tool kit ( http://hannonlab.cshl.edu/fastx_toolkit/ ) , dna sequences obtained were trimmed to 45 bases , filtered for high quality scores ( >  30 ) , and duplicates were removed before being aligned to the mouse genome ( u.s . national center for biotechnology information ( ncbi ) build 37 , july 2007 , mm9 ) using the bwa algorithm  .
quality of the alignment was assessed using samstat and only the sequences with mapq score   30 were kept for further analysis ( fig . 
the model based analysis of chip - seq peak - finding algorithm was used to identify peaks in wehi - ct and wehi - tfii - i - kd conditions using the default settings and an example of peak model obtain with macs is presented in fig . 
overlap for ctcf binding sites between biological replicates was assessed using the intersect function of bedtools , the results are shown with venn diagram ( fig . 
homer was used to annotate ctcf peaks , determine their genomic distribution and generated the bedgraph files to visualize the results in ucsc genome browser ( homer.salk.edu/ ) .
we used previously published ctcf chip - seq data available in the ucsc genome browser as controls for our dataset ( fig . 
here , we described a dataset containing gene expression profiling using illumina beadchips ( microarray ) and chip - seq analysis of ctcf binding in mouse b cell lymphocyte cell lines expressing a shrna construct against tfii - i , a general transcription factor .
these data were generated to analyze the influence of tfii - i on the genomic targeting of the epigenetic regulatory protein ctcf , and understand how these two factors co - regulate gene transcription . with this dataset , we were able to show that tfii - i is important for targeting ctcf to a cohort of promoter regions where they co - operate to activate transcription .
this finding sheds new light on how ctcf targeting at specific genomic regions can occur .
 ctcf is a key regulator of nuclear chromatin structure , chromatin organization and gene regulation . 
 the impact of ctcf on transcriptional output is quite varied , ranging from repression , to transcriptional pausing and transactivation . 
 the multifunctional nature of ctcf is mediated , in part , through differential association with protein partners having unique properties . 
 we identified the general transcription factor tfii - i as an interacting partner of ctcf . to gain an understanding of the function of tfii - i in regulating gene expression and ctcf binding genome wide , we conducted microarray experiments following tfii - i knockdown and chromatin immunoprecipitation of ctcf followed by next generation sequencing ( chip - seq ) from the same tfii - i depleted cells . here , we described the experimental design and the quality control and analysis that were performed on the dataset . 
 the data is publicly available through the geo database with accession number gse60918 . 
 the interpretation and description of these data are included in a manuscript in revision ( 1 ) . 
Direct link to deposited data
Experimental design, materials and methods
Cell line
Microarray and quality control
ChIP-seq
ChIP-seq quality control and analysis
Discussion
Conflict of interest