Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function.
Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function.
Project description:Sequencing shows that macroH2A1-emerin interaction occurs in lamina-associated domains on a genome-wide scale. We decided to verify that the biotinylated signal is indeed enriched in the chromatin domains positioned at the nuclear periphery. In this regard, we purified the biotinylated chromatin from HeLa S3 clonal cell line stably coexpressing BirA-emerin and BAP-macro-H2A1 using proximity utilizing biotinylation native chromatin immunoprecipitation (PUB-nChIP). Instead of analysing the protein fraction, we isolated DNA from the biotinylated chromatin pull down and performed high throughput sequencing in order to get insight into the genome wide distribution of the isolated DNA. Importantly, PUB-nChIP-seq of the DNA purified from HeLa S3 clonal cell line stably coexpressing BirA-emerin and BAP-macro-H2A1 showed high levels of enrichment at the lamina associated domains, which were identified previously in HeLa cells using anti-Lamin B1 and anti-Lamin A chIP-seq (Lund et al., 2015). The enrichment of BirA-emerin labelled BAP-macro-H2A at LADs is visibly clear at both the chromosome level and at individual LADs. To test if this enrichment was significant, the genome was divided into 100kb windows and monte carlo simulation using 10,000 iterations was performed to examine if probes overlapping LADs were significantly different to the genomic average. For both replicates, at both LMNA and LMNB1 LADs, the enrichment of biotinylated BAP-macroH2A1 observed was significant relative to the genome wide average.
Project description:The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor STAT1 in HeLa S3 cells. The STAT1 ChIP was performed using HeLa S3 cells that are stimulated using gamma-interferon. We have also generated a seqenced input DNA dataset for gamma-interferon stimulated HeLa S3 cells. Raw data for this study is available for download from the Short Read Archive database at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000703. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project description:The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf