human htert immortalized fibroblast cells were grown in mem containing high glucose supplemented with glutamine and 15% fetal bovine serum ( fbs ) ( atlanta biologicals ) . transfections of 100  nm sirnas duplex against ddsr1 : sense 5cuaguguguugcaaauaaauu-3 , antisense 5p - uuuauuugcaacacacuaguu-3 and non - specific sirna ( on - target plus non - targeting pool # d-001,810 - 10 ; dharmacon ) were done using dharmafect 1 as per manufacturer 's instructions . total rna was isolated 72  h after transfection using the rneasy plus mini kit ( qiagen ) . cdna synthesis was carried out using the high capacity cdna reverse transcription kit ( applied biosystems ) . qpcr was performed in triplicates with the iq sybr green supermix ( bio - rad ) on a bio - rad cfx-96 real - time pcr system . the comparative ct method was employed to confirm ddsr1 knockdown using the primers forward 5-aagagtggaaaattcatcccca-3 and reverse 5-tgtcatgtttcagatattttcccca-3. normalization was performed to housekeeping gene tbp using the primers forward cgccagcttcggagagttc and reverse acaaccaagattcactgtggataca . rna labeling and hybridization were carried out by the laboratory of molecular technology , leidos biomedical research , inc . total rna was reverse - transcribed , labeled , and hybridized using genechip human gene 2.0 st array following the ambion wt expression kit protocol . probe cell intensity ( .cel ) files were imported into the r package and normalized using the robust multiarray averaging ( rma ) normalization method . 1 ) . distribution of probe intensity values assessed with normalized data did not show any significant outliers ( fig . 1c ) . to investigate the intensity bias and to reduce the signal - to - noise ratio ma plot was applied to raw and normalized data as shown in ( fig . the relation between the 2 groups ( sins and siddsr1 ) after rma normalization is presented in ( fig . data were analyzed using partek genomics suite 6.6 ( partek incorporated ) and differentially expressed genes ( deg ) were defined as genes having   1.5-fold change of expression in pairwise comparisons , with a p - value of <  0.05 in fig . 3 . a more detailed discussion of data is published in sharma et al . . human htert immortalized fibroblast cells were grown in mem containing high glucose supplemented with glutamine and 15% fetal bovine serum ( fbs ) ( atlanta biologicals ) . transfections of 100  nm sirnas duplex against ddsr1 : sense 5cuaguguguugcaaauaaauu-3 , antisense 5p - uuuauuugcaacacacuaguu-3 and non - specific sirna ( on - target plus non - targeting pool # d-001,810 - 10 ; dharmacon ) were done using dharmafect 1 as per manufacturer 's instructions . total rna was isolated 72  h after transfection using the rneasy plus mini kit ( qiagen ) . cdna synthesis was carried out using the high capacity cdna reverse transcription kit ( applied biosystems ) . qpcr was performed in triplicates with the iq sybr green supermix ( bio - rad ) on a bio - rad cfx-96 real - time pcr system . the comparative ct method was employed to confirm ddsr1 knockdown using the primers forward 5-aagagtggaaaattcatcccca-3 and reverse 5-tgtcatgtttcagatattttcccca-3. normalization was performed to housekeeping gene tbp using the primers forward cgccagcttcggagagttc and reverse acaaccaagattcactgtggataca . rna labeling and hybridization were carried out by the laboratory of molecular technology , leidos biomedical research , inc . total rna was reverse - transcribed , labeled , and hybridized using genechip human gene 2.0 st array following the ambion wt expression kit protocol . probe cell intensity ( .cel ) files were imported into the r package and normalized using the robust multiarray averaging ( rma ) normalization method . microarray quality control was performed on the raw and normalized data . 1 ) . distribution of probe intensity values assessed with normalized data did not show any significant outliers ( fig . 1c ) . to investigate the intensity bias and to reduce the signal - to - noise ratio ma plot was applied to raw and normalized data as shown in ( fig . the relation between the 2 groups ( sins and siddsr1 ) after rma normalization is presented in ( fig . data were analyzed using partek genomics suite 6.6 ( partek incorporated ) and differentially expressed genes ( deg ) were defined as genes having   1.5-fold change of expression in pairwise comparisons , with a p - value of <  0.05 in fig . 3 . a more detailed discussion of data is published in sharma et al . .
long non - coding rnas ( lncrnas ) play important roles in regulating diverse biological processes including dna damage and repair . 
 we have recently reported that the dna damage inducible lncrna dna damage - sensitive rna1 ( ddsr1 ) regulates dna repair by homologous recombination ( hr ) . since lncrnas also modulate gene expression , we identified gene expression changes upon ddsr1 knockdown in human fibroblast cells . 
 gene expression analysis after rnai treatment targeted against ddsr1 revealed 119 genes that show differential expression . 
 here we provide a detailed description of the microarray data ( ncbi geo accession number gse67048 ) and the data analysis procedure associated with the publication by sharma et al . , 2015 in embo reports 
 [ 1 ] .