Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). The ChIP-Seq method was used to assay chromatin fragments bound by specific or general transcription factors as described below. DNA isolated by ChIP-Seq was size-selected (~225 bp) and sequenced. Short reads of 25-36 bp were mapped to the human reference genome, and enriched regions of high read density relative to a total input chromatin control reads were identified. The sequence reads with quality scores (fastq files) and alignment coordinates (BAM files) from these experiments are available for download. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol. Biological replicates from each experiment were completed. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Sequence data produced by the Illumina data pipeline software were quality filtered and then mapped to NCBI Build37 (hg19) using the integrated Eland software; 32 nt of the sequence reads were used for alignment; up to two mismatches were tolerated; reads that mapped to multiple sites in the genome were discarded. To identify likely binding sites, peak calling was applied to the aligned sequence data sets using Model-based Analysis of Chip-Seq MACS (Zhang Y, et al., 2008) (http://liulab.dfci.harvard.edu/MACS/00README.html). MACS models the shift size of ChIP-Seq tags empirically, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to capture local biases in the genome, allowing for more robust predictions (Zhang Y, et al., 2008). Protocol Notes: Several changes and improvements were made to the original ChIP-Seq protocol (Jonshon et al.,2008). The major differences between protocols are the number of cells and magnetic beads used for IP, the method of sonication used to fragment DNA, and the number of cycles of PCR used to amplify the sequencing library. The most current protocol used by the Myers lab can be found at http://hudsonalpha.org/myers-lab/protocols. The protocol field for each file denotes the version of the protocol used as being PCR1x, PCR2x or a version number (for examples, v041610.1). The sequencing libraries labeled as PCR2x were made with two rounds of amplification (25 and 15 cycles) and those labeled as PCR1x were made with one 15-cycle round of amplification. These experiments were completed prior to January 2010 and were originally aligned to NCBI Build36 (hg18). They have been re-aligned to NCBI Build37 (hg19) with the Bowtie software (Langmead, et al., 2009) for this data release (http://bowtie-bio.sourceforge.net/index.shtml). The libraries labeled with a protocol version number were competed after January 2010 and were only aligned to NCBI Build37 (hg19). Please refer to the Myers Lab website (http://hudsonalpha.org/myers-lab/protocols) for details on each protocol version. Verification: The MACS (http://liulab.dfci.harvard.edu/MACS/00README.html) peak caller was used to call significant peaks on the individual replicates of a ChIP-Seq experiment. Afterwards, the irreproducible discovery rate (IDR) method, developed by Li et al. (submitted), was used to quantify the consistency between pairs of ranked peaks lists from replicates. The IDR methods uses a model that assumes that the ranked lists of peaks in a pair of replicates consist of two groups - a reproducible group and an irreproducible group. In general, the signals in the reproducible group are more consistent (i.e. with a larger rank correlation coefficient) and are ranked higher than the irreproducible group. The proportion of peaks that belong to the irreproducible component and the correlation of the reproducible component are estimated adaptively from the data. The model also provides an IDR score for each peak, which reflects the posterior probability of the peak belonging to the irreproducible group. The aligned reads were pooled from all replicates and the MACS peak caller was used to call significant peaks on the pooled data. Only datasets containing at least 100 peaks passing the IDR threshold are considered valid and submitted for release.

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE Project. RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). Biological replicates of ENCODE cell lines were grown on separate culture plates, total RNA was purified and polyA selected two times. mRNA was then fragmented by magnesium-catalyzed hydrolysis, reverse transcribed to cDNA by random priming and amplified. The cDNA was sequenced on an Illumina Genome Analyzer (GAI or GAIIx). The DNA sequences were aligned to the NCBI Build37 (hg19) version of the human genome using the sequence alignment programs ELAND (Illumina) or Bowtie (Langmead et al., 2009). The first 10 residues of sequencing have a weak characteristic nucleotide bias of unknown origin. This RNA-seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. This is the first NCBI Build37 (hg19) release of this track (Jan 2012). This release includes the 3 datasets (Jurkat, A549/DEX100nm, and A549/EtOH2pct) previously released on NCBI Build36 (hg18) and adds data for several more cell types and growth conditions in replicate. Four types of download files are available for each replicate including the Raw Data (fastq), Transcripts GencodeV7 (gtf), Raw Signal (bigwig), and Alignments (bam). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Experimental Procedures Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell) except for H1-hESC for which frozen cell pellets were purchased from Cellular Dynamics. Cells were lysed in RLT buffer (Qiagen RNEasy kit) and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNase digestion step to remove residual genomic DNA. mRNA was isolated from at least 10 ug of total RNA with oligo(dT) two times (Dynabeads mRNA PurificationgKit, Invitrogen). Alternatively, cells were lysed and mRNA was purified directly two times with oligo(dT) (Dynabeads mRNA DIRECT Kit, Invitrogen). 100 ng of mRNA was fragmented by magnesium-catalyzed hydrolysis and reverse transcribed to cDNA by random priming according to the protocol in Mortazavi et al. (2008). cDNA was prepared for sequencing on the Genome Analyzer flowcell according to the protocol for the ChIPSeq DNA genomic DNA kit (Illumina). The sequencing libraries were size-selected around 225 bp and amplified with 15 rounds of PCR. Libraries were sequenced with an Illumina Genome Analyzer I or an Illumina Genome Analyzer IIx according to the manufacturer's recommendations. Single end reads of 36 nt in length were obtained. Data Processing and Analysis Fastq files were made from qseq files generated by the Illumina pipeline (Casava 1.7). The Raw Signal files (bigWig) were generated from bedgraph files and the score was calculated as the number of reads at that position divided by the total number of reads divided by one million. Casava export files were aligned to the NCBI Build37 (hg19) version of the human genome with ELAND (Illumina), generating SAM files. Fastq files of experiments that were previously aligned to NCBI Build36 (hg18) were aligned to NCBI Build37 (hg19) using Bowtie (Langmead et al., 2009; parameters: -S -n 2 -k 11 -m 10 --best), also generating SAM files. SAM files were converted to BAM with SAMtools (Li et al., 2009). Gene expression within Gencode.v7 (Harrow et al., 2006) gene models was estimated using Cufflinks v0.9.3 (Roberts et al., 2011). Estimates of transcript abundance were reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). FPKM is calculated by dividing the total number of fragments that align to the gene model by the size of the spliced transcript (exons) in kilobases. This number is then divided by the total number of reads in millions for the experiment. FPKM is reported in the last column of the gtf (TranscriptGencV7) files. Raw Data (fastq), Raw Signal (bigWig), Alignments (bam) and Transcript Gencode V7 (gtf) files are available from the Downloads (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeHaibRnaSeq) page.

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE project. The track displays the methylation status of specific CpG dinucleotides in the given cell types as identified by the Illumina Infinium HumanMethylation27 BeadArray platform (http://www.illumina.com/pages.ilmn?ID=243). In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter. Detailed information for the CpG targets is in an XLS formatted spreadsheet on the Myers' lab protocols website (http://hudsonalpha.org/myers-lab/protocols). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). The Methyl27K platform uses bisulfite treated genomic DNA to assay the methylation status of 27,578 CpG sites within more than 14,000 genes. When genomic DNA is treated with sodium bisulfite, unmethylated cytosine of CpG dinucleotides are converted into uracils; methylated cytosines do not get converted. After bisulfite treatment, the methylation status of a site is assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state. A beta value is calculated by Illumina's Bead Studio software for each CpG target. This value represents the intensity value from the methylated bead type divided by the sum of the intensity values from the methylated and unmethylated bead types for any given CpG target. Bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA Methylation Kit (http://www.zymoresearch.com/epigenetics/dna-methylation/ez-96-dna-methylation-kit). One step of the protocol was modified. During the incubation, a 30 sec 95oC denaturing step every hour was included to increase reaction efficiency as recommended by the Illumina Infinium Human Methylation27 protocol. The bead arrays were run according to the protocol provided by Illumina (http://www.illumina.com/pagesnrn.ilmn?ID=275). The intensity data from the BeadArray was processed using Illumina's BeadStudio software with the Methylation Module v3.2. The data was then quality-filtered using p-values. Any beta value equal to or greater than 0.6 is considered fully methylated. Any beta value equal to or less than 0.2 is considered to be fully unmethylated. Beta values between 0.2 and 0.6 are considered to be partially methylated. Beta-values are quality filtered and spots that fall below the minimum intensity threshold are displayed as "NA". Score in the bed files is beta value x 1000

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE project. The track displays copy number variation (CNV) as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS). The Human 1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing between markers is 1.5 kb and the mean spacing is 2.4 kb. The B-allele frequency and genotyping single nucleotide polymorphism (SNP) data generated by the experiment are not displayed, but are available for download from the Downloads page. Where applicable, biological replicates of each cell line are reported separately. Possible uses of the data include correction of copy number in peak-calling for ChIP-seq, transcriptome, DNase hypersensitivity, and methylation determinations. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Isolation of genomic DNA and hybridization: Cells were grown according to the approved ENCODE cell culture protocols by the Myers lab and by other ENCODE production groups. The production group is reported in the metadata. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen). DNA concentration and quality were determined by fluorescence (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer), and 400 nanograms of each sample were hybridized to Illumina 1M-Duo DNA Analysis BeadChips. Processing and Analysis: The genotypes from the 1M-Duo Arrays were ascertained with BeadStudio by using default settings and formatting with the A/B genotype designation for each SNP. Primary QC for each sample was a cut-off at a call rate of 0.95. Copy Number Variation (CNV) analysis was performed with circular binary segmentation (DNAcopy) of the log R ratio values at each probe (Olshen et al., 2004). The parameters used were alpha=0.001, nperm=5000, sd.undo=1. The copy number segments are reported with the mean log R ratio for each chromosomal segment called by CBS. Log ratios of ~-0.2 to -1.5 can be considered heterozygous deletions, < -1.5 homozygous deletions, and > 0.2 amplifications. Primary QC for each sample was SD of < 0.6.

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Transcription Factor Binding Sites by ChIP-seq from ENCODE/HAIB

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