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TranscriptomicsExpression profiling of 3 and 24 months mouse skeletal muscle (RNA-seq)
Aging in multicellular organisms is characterized by gradual decline of organ functionality. To study the aging process, we used mRNA sequencing (mRNA-seq) to identify gene expression changes during aging in healthy mice. Skeletal muscle tissues of wild-type mice at 3 months and 24 months of age wer...
ORGANISM(S): Mus musculus 
2018-11-03 | E-MTAB-5176 | biostudies-arrayexpress
GenomicsMNase and HpaII sensitivity assays in MCF7 breast cancer cells
DNA are packaged into nucleosomes and chromatin. We performed incomplete MNase digestion of chromatin to identify nucleosome-free regions that may indicate active promoters and regulatory regions. Additionally, HpaII digestion was performed which cleaves CCGG sites when the internal C remains unmodi...
ORGANISM(S): Homo sapiens 
2015-02-25 | E-MTAB-1958 | biostudies-arrayexpress
GenomicsChIP-Seq for RNA Polymerase II in MCF7 breast cancer cells
Enrichment PolII binding at TSS and gene body is an indication of active transcription. The genome-wide PolII occupancy was determined using ChIP-Seq in MCF7. ChIP was performed using an antibody against total RNA PolII (ab5408-100; Abcam). ChIP DNA and input DNA were sequenced with an Illumina HiSe...
ORGANISM(S): Homo sapiens 
2015-02-25 | E-MTAB-1952 | biostudies-arrayexpress
GenomicsGenome-wide methylome profiling of normal breast and breast tumors
To improve our understanding of the effect of differential methylation on gene expression between normal and tumor breast cells, we employed high-throughput sequencing technology to determine and compare CpG methylation of normal breast and four breast tumor genomes at single-base resolution. By com...
ORGANISM(S): Homo sapiens 
2015-02-25 | E-MTAB-2014 | biostudies-arrayexpress
TranscriptomicsRNA-seq of mRNA from MCF7 breast cancer cells and samples derived from normal breast tissues
To improve our understanding of the effect of differential methylation on gene expression between normal and tumor breast cells, we carried out RNA sequencing evaluate mRNA expression changes in normal breast tissue and MCF7 breast cancer cell line. We identified 6632 protein-coding genes to be sign...
ORGANISM(S): Homo sapiens 
2015-02-25 | E-MTAB-1961 | biostudies-arrayexpress
TranscriptomicsChIP-chip of H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, H3K9Me2, H3K27Me3, CTCF and HP1a in MCF7 breast cancer cells
We report the high-throughput profiling of histone modifications, CTCF and HP1a binding sites in MCF7 breast cancer cells. ChIP-chip experiments were performed using the Agilent Human Genome CGH Microarray 1x1M. Regulatory markers H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, CTCF are known to be positively cor...
ORGANISM(S): Homo sapiens 
2015-02-25 | E-MTAB-1935 | biostudies-arrayexpress
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