ERX331257 E-MTAB-1961:MCF7_rep1 E-MTAB-1961:MCF7_rep1 ERP004151 E-MTAB-1961 RNA-seq of mRNA from MCF7 breast cancer cells and samples derived from normal breast tissues ERS362599 SAMEA2225914 E-MTAB-1961:MCF7 cells MCF7_rep1 RNA-Seq TRANSCRIPTOMIC cDNA MCF7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37C incubator with 5% CO2. MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Each 6 cm dish was rinsed twice with 1X PBS. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2% (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry. The normal breast tissue mRNA were purchased from Origene (Catalog No.: CR559104 and CR561898). The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit (Illumina Inc., USA) as per manufacturers instruction. Briefly, total RNA with RIN (RNA integrity number) greater than 7.5 was subjected for poly-A mRNA isolation using poly-T oligo-attached magnetic beads. The poly-A mRNA was fragmented and first-strand cDNA was synthesized using random hexamers following by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated cDNA library was sized-selected by agarose gel and amplified by PCR. 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: disease breast adenocarcinoma ERX331258 E-MTAB-1961:NB_CR559104 E-MTAB-1961:NB_CR559104 ERP004151 E-MTAB-1961 RNA-seq of mRNA from MCF7 breast cancer cells and samples derived from normal breast tissues ERS362600 SAMEA2225915 E-MTAB-1961:CR559104-FR0001BA18 NB_CR559104 RNA-Seq TRANSCRIPTOMIC cDNA MCF7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37C incubator with 5% CO2. MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Each 6 cm dish was rinsed twice with 1X PBS. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2% (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry. The normal breast tissue mRNA were purchased from Origene (Catalog No.: CR559104 and CR561898). The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit (Illumina Inc., USA) as per manufacturers instruction. Briefly, total RNA with RIN (RNA integrity number) greater than 7.5 was subjected for poly-A mRNA isolation using poly-T oligo-attached magnetic beads. The poly-A mRNA was fragmented and first-strand cDNA was synthesized using random hexamers following by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated cDNA library was sized-selected by agarose gel and amplified by PCR. 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: disease normal ERX331259 E-MTAB-1961:MCF7_rep2 E-MTAB-1961:MCF7_rep2 ERP004151 E-MTAB-1961 RNA-seq of mRNA from MCF7 breast cancer cells and samples derived from normal breast tissues ERS362599 SAMEA2225914 E-MTAB-1961:MCF7 cells MCF7_rep2 RNA-Seq TRANSCRIPTOMIC cDNA MCF7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37C incubator with 5% CO2. MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Each 6 cm dish was rinsed twice with 1X PBS. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2% (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry. The normal breast tissue mRNA were purchased from Origene (Catalog No.: CR559104 and CR561898). The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit (Illumina Inc., USA) as per manufacturers instruction. Briefly, total RNA with RIN (RNA integrity number) greater than 7.5 was subjected for poly-A mRNA isolation using poly-T oligo-attached magnetic beads. The poly-A mRNA was fragmented and first-strand cDNA was synthesized using random hexamers following by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated cDNA library was sized-selected by agarose gel and amplified by PCR. 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: disease breast adenocarcinoma ERX331260 E-MTAB-1961:NB_CR561898 E-MTAB-1961:NB_CR561898 ERP004151 E-MTAB-1961 RNA-seq of mRNA from MCF7 breast cancer cells and samples derived from normal breast tissues ERS362601 SAMEA2225916 E-MTAB-1961:CR561898-FR0042A6F NB_CR561898 RNA-Seq TRANSCRIPTOMIC cDNA MCF7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37C incubator with 5% CO2. MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Each 6 cm dish was rinsed twice with 1X PBS. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2% (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry. The normal breast tissue mRNA were purchased from Origene (Catalog No.: CR559104 and CR561898). The sequencing library for mRNA-seq was prepared using TruSeq RNA Sample Preparation Kit (Illumina Inc., USA) as per manufacturers instruction. Briefly, total RNA with RIN (RNA integrity number) greater than 7.5 was subjected for poly-A mRNA isolation using poly-T oligo-attached magnetic beads. The poly-A mRNA was fragmented and first-strand cDNA was synthesized using random hexamers following by second-strand cDNA synthesis, end repair, addition of a single A base and adapter ligation. The adapter-ligated cDNA library was sized-selected by agarose gel and amplified by PCR. 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: disease normal