organism: Homo sapiens
description: Protocols: MCF7 cells were grown in RPMI 1640 medium upplemented with 10% fetal bovine serum (FBS) and 2.0 g/L sodium bicarbonate at 37Â°C in humidified incubator (5% CO2). MCF7 cells at logarithmic growth phase were harvested and seeded into 5 cm plate at the density of 5 x 10^6/mL for 24 hours. Two experimental groups were set up: (1) 5Aza (final concentration of 20 uM) for 72 hours. 5Aza-containg medium containing was refreshed every 24 hours. (2) TSA (final concentration of 0.3 uM) for 48 hours. 'MCF7 cells were grown to 85% confluence in 6 cm tissue culture dish. Cells were washed twice with 1X PBS. Total RNA was extracted using TRI Reagent (Invitrogen) according to the manufacturer''s protocol. The RNA quality was assessed by 1.2% (w/v) agarose gel electrophoresis and quantified by a UV spectrophotometer.' 5 micro-g of total RNA with RIN (RNA integrity number) ranged from 8.0 to 10 was subjected to the removal of rRNA using Ribo-Zero Gold kit for human/mouse/rat (Epicentre). The sequencing library for rRNA-depleted RNA was then prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina) which produced directional RNA-seq libraries. Briefly, the rRNA-depleted RNA was fragmented and first-strand cDNA was synthesized using random hexamers with SuperScript III (Invitrogen). The second-strand cDNA was synthesized with dTTP replaced by dUTP to generate double-stranded cDNA following by end repair, addition of a single A base and adapter ligation. The adapter-ligated double-stranded cDNA library was enriched with 6 to 10 cycles of PCR using KAPA HiFi DNA polymerase (Kapa Biosystems). The RNA libraries were quantified by qPCR and quality tested using Agilent 2100 Bioanalyzer with High Sensitivity DNA chip.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2016-06-30T17:01:22Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-03-09T02:19:29Z
attributes.tag: External Id
attributes.value: SAMEA3495632
attributes.tag: INSDC center name
attributes.value: National Yang-Ming University
attributes.tag: INSDC first public
attributes.value: 2016-06-30T17:01:22Z
attributes.tag: INSDC last update
attributes.value: 2018-03-09T02:19:29Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-3794:MCF7-Control-1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: MCF-7
attributes.tag: common name
attributes.value: human
attributes.tag: sample name
attributes.value: E-MTAB-3794:MCF7-Control-1
attributes.tag: scientific_name
attributes.value: Homo sapiens