neoplastic cell lines used in this study were te-1 , te-5 , and te-8 , which were established from well- , poorly- , and moderately - differentiated escc , respectively .
these cell lines were purchased from riken cell bank ( tsukuba , japan ) and cultured in rpmi-1640 medium supplemented with 10% fetal bovine serum .
het-1a , an sv40 large t antigen - harboring normal human esophageal squamous cell line , was purchased from american type culture collection ( manassas , va , usa ) and cultured using the begm kit ( lonza , basel , switzerland ) but without addition of the ga-1000 ( gentamycin - amphotericin b mix ) provided with the kit .
total rna was isolated from these cells using isogen reagent ( wako , osaka , japan ) according to the manufacturer 's protocol .
rna purity was evaluated by the rna integrity number ( rin ) , a representative index to assess rna quality determined using the agilent 2100 bioanalyzer ( agilent , santa clara , ca , usa ) .
the rin value of all rna samples used in this study was shown to be 10 .
the rna samples were then subjected to ribosomal and mitochondrial rna depletion using ribo - zero rrna removal kit ( illumina ) .
maltiplex rna - seq libraries were generated for samples using truseq stranded total library preparation kit ( illumina ) .
sequencing was carried out on hiseq2500 ( illumina ) according to the protocol of 2    125  bp run . as an output of this sequencing , 53 million to 66 million raw reads
trimming and filtering of the reads to remove adaptor sequences and low - quality nucleotides were performed using trimmomatic ( ver .
0.32 ) ( http://www.usadellab.org/cms/?page=trimmomatic).table 1overview of sequencing results and statistics.table 1sampleraw readscalled bases ( mbp)%q30aaverage qualityhet-1a53,656,462670793.5535.25te-153,331,576666693.2735.16te-558,934,174736793.2435.16te-865,921,940824093.2835.16aquality score 30 , an index to predict the probability of an error in base calling . overview of sequencing results and statistics .
quality score 30 , an index to predict the probability of an error in base calling .
for the individual cell lines , 90.392.3% of the filtered reads were mapped to the genome .
the statistics of sequencing and mapping results are summarized in table 1 and table 2 , respectively.table 2overview of mapping.table 2sampleraw reads ( m)cleaned reads ( mbp)reads mapped ( m)mapping rates ( % ) het-1a53.744.340.691.5te-153.342.938.890.5te-558.947.042.891.0te-865.954.650.392.1 assembly of transcriptomes from rna - seq data and quantification of their expression levels were performed using cufflinks ( ver .
fragments per kilobase of exon per million fragments mapped ( fpkm ) values are used as an index of expression level .
1 ) . using fpkm values of all annotated genes , the values of correlation coefficients between het-1a and te-1/5/8 are calculated to be 0.234 ( het-1a vs. te-1 ) , 0.323 ( het-1a vs. te-5 ) , and 0.401 ( het-1a vs. te-8 ) . correlation coefficients among the three escc - derived cell lines range from 0.419 to 0.697 .
these values possibly indicate that the individual escc - derived cell lines show a more similar gene expression pattern to each other than to het-1a . when analysis objects are filtered with the criteria of fpkm >  1 or >  10 for both of paired samples , the values of correlation coefficients increase to 0.8040.956.fig .
neoplastic cell lines used in this study were te-1 , te-5 , and te-8 , which were established from well- , poorly- , and moderately - differentiated escc , respectively .
these cell lines were purchased from riken cell bank ( tsukuba , japan ) and cultured in rpmi-1640 medium supplemented with 10% fetal bovine serum .
het-1a , an sv40 large t antigen - harboring normal human esophageal squamous cell line , was purchased from american type culture collection ( manassas , va , usa ) and cultured using the begm kit ( lonza , basel , switzerland ) but without addition of the ga-1000 ( gentamycin - amphotericin b mix ) provided with the kit .
total rna was isolated from these cells using isogen reagent ( wako , osaka , japan ) according to the manufacturer 's protocol .
rna purity was evaluated by the rna integrity number ( rin ) , a representative index to assess rna quality determined using the agilent 2100 bioanalyzer ( agilent , santa clara , ca , usa ) .
the rin value of all rna samples used in this study was shown to be 10 .
the rna samples were then subjected to ribosomal and mitochondrial rna depletion using ribo - zero rrna removal kit ( illumina ) .
maltiplex rna - seq libraries were generated for samples using truseq stranded total library preparation kit ( illumina ) .
sequencing was carried out on hiseq2500 ( illumina ) according to the protocol of 2    125  bp run . as an output of this sequencing , 53 million to 66 million raw reads
trimming and filtering of the reads to remove adaptor sequences and low - quality nucleotides were performed using trimmomatic ( ver .
0.32 ) ( http://www.usadellab.org/cms/?page=trimmomatic).table 1overview of sequencing results and statistics.table 1sampleraw readscalled bases ( mbp)%q30aaverage qualityhet-1a53,656,462670793.5535.25te-153,331,576666693.2735.16te-558,934,174736793.2435.16te-865,921,940824093.2835.16aquality score 30 , an index to predict the probability of an error in base calling . overview of sequencing results and statistics .
quality score 30 , an index to predict the probability of an error in base calling .
the filtered reads were aligned to the ensembl human genome grch38 . p7 as a reference ( ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/ ) using bowtie ( ver .
the statistics of sequencing and mapping results are summarized in table 1 and table 2 , respectively.table 2overview of mapping.table 2sampleraw reads ( m)cleaned reads ( mbp)reads mapped ( m)mapping rates ( % ) het-1a53.744.340.691.5te-153.342.938.890.5te-558.947.042.891.0te-865.954.650.392.1
assembly of transcriptomes from rna - seq data and quantification of their expression levels were performed using cufflinks ( ver .
2.2.1 ) . fragments per kilobase of exon per million fragments mapped ( fpkm ) values are used as an index of expression level .
1 ) . using fpkm values of all annotated genes , the values of correlation coefficients between het-1a and te-1/5/8 are calculated to be 0.234 ( het-1a vs. te-1 ) , 0.323 ( het-1a vs. te-5 ) , and 0.401 ( het-1a vs. te-8 ) . correlation coefficients among the three escc - derived cell lines range from 0.419 to 0.697 .
these values possibly indicate that the individual escc - derived cell lines show a more similar gene expression pattern to each other than to het-1a . when analysis objects are filtered with the criteria of fpkm >  1 or >  10 for both of paired samples , the values of correlation coefficients increase to 0.8040.956.fig .
 esophageal cancer ( ec ) is the eighth most common cancer globally in 2012 and predominantly occurs in the man ( enzinger and mayer , 2003 ; conteduca et al . , 2012 ) . 
 ec is classified mainly into two types , esophageal squamous cell carcinoma ( escc ) and esophageal adenocarcinoma , accounting for 6070% and 2030% of all ec cases , respectively . in a previous statistical study 
 it was reported that the numbers of new ec cases and ec - related deaths worldwide in 2008 were estimated to be 482,300 and 406,800 , respectively ( jemal et al . , 2011 ) . 
 this high mortality rate is largely due to the characteristics of ec such as frequent distant / local metastasis and poor subjective symptoms leading to difficulty with early diagnosis . 
 patients affected with ec diagnosed at late stages mostly have unsatisfactory prognosis , even though various therapeutic options are available . 
 therefore , there is an urgent need to develop effective methods that enable the early detection of ec ( orringer , 1993 ) , prompting us to search for novel biomarkers for ec . here , we provide datasets from rna - seq analysis of het-1a , a normal human esophageal squamous cell line ( stoner et al . , 1991 ) , and te-1 , te-5 , and te-8 , which are well- , poorly- , and moderately - differentiated escc - derived cell lines , respectively ( nishihira et al . , 1993 ) . the raw data of these experiments have been deposited at dna data bank of japan ( ddbj ) under the accession ids drr084199 , drr084200 , drr084201 , and drr084202 . 
Direct link to deposited data
Experimental design, materials and methods
Experimental design, cell culture and RNA isolation
Sequencing, mapping and normalization
Expression analysis
Correlations of FPKM values per sample
Conflict of interest