Genome-wide mapping of RNA Polymerase II binding sites
Ontology highlight
ABSTRACT: Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of K562 & NB4 cells
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 RNA Polymerase III in K562 cells. We have also generated a sequenced input DNA datasets for K562 cells. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase III in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.
Project description:Proto-oncogene c-jun is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Jun dimerizes with another transcription factor Fos to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of transcription factor Jun in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.
Project description:Proto-oncogene c-myc encodes a bHLH leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Myc can dimerize with other factors like Max, Mad, Mnt and Miz and can influence transcription of genes. The c-myc oncogene contributes to the genesis of a wide variety of human tumors. A higher than normal level of c-myc gene expression has been observed in 50-80% of colon and breast cancers and a large proportion of human mortality from cancer is caused by abnormal expression of c-myc. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of transcription factor Myc in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.
Project description:Proto-oncogene c-Fos is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Fos dimerizes with another transcription factor Jun to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of transcription factor Fos in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.
Project description:We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase II in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of GM12878 cells. The GM12878 input data has been deposited in GEO as GSM487430.
Project description:We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human RNA Polymerase III in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase III in the genome of GM12878 cells.
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 PolII in HeLa S3 cells. The PolII ChIP was performed according to the same protocol as used for the STAT1 samples except that the cells were not stimulated using gamma-interferon prior to formaldehyde fixation. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of the PolII transcription factor in Human HeLa S3.
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 Examination of the STAT1 transcription factor in Human HeLa S3.
Project description:Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription by Pol II in embryonic stem (ES) cells, and thus an additional step where regulation of gene expression may occur. We report here that c-Myc, which occupies a third of actively transcribed genes in ES cells and is a key regulator of cellular proliferation, binds P-TEFb and contributes to release of promoter-proximal paused Pol II at these genes. ChIP-seq data for Pol II and additional factors controlling pause release in mouse ES cells.
Project description:Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf