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This classification scheme, which we also applied to the mouse portion of the registry (Fig. 3), is intended to provide a useful high-level framework. However, the current cCRE classification scheme does not attempt to explicitly dissect complex multi-element modules. A notable subset (17%) of cCREs display complex or composite behaviours when examined across distinct biosamples, showing, for example, enhancer-like signatures in one cell type and a CTCF-only signature in another (Extended Data Fig. 1). These relationships can be readily extracted from the entire list of cCREs provided in Supplementary Tables 10, 11.

Placing cCREs into predicted functional groups on the basis of their epigenetic features ideally would be done with full knowledge of each feature in each biosample. However, as the breadth of biological systems expands, with a concomitant increase in the number of biosamples examined, it becomes very difficult to maintain full ascertainment of all features in all biosamples (Box 1 Fig. 2). The resulting gaps in knowledge complicate our assessment of function-associated signatures. To provide a guide for the completeness of the underlying data, we established the following tiers of cCRE function-related annotations. Specifically, cCREs are divided into tiers 1a, 1b, and 2 on the basis of their data support.

Overall, these initial functional assessments indicate that at least one-third of the cCRE-ELS compartment encodes transcriptional control elements that produce positive results in contemporary cell transfection assays, while a smaller number marked by stronger biochemical signatures are active in the more stringent transgenic mouse embryo system. However, it is important to acknowledge that each assay system has inherent limitations. None of the aforementioned methods interrogates cCREs in their native chromosomal context, nor do they test for combinatoric interactions among cCREs in cis. The assays also do not account for poised elements that exhibit DNase I hypersensitivity but are gated functionally by additional trans-acting signals or cell contexts. Furthermore, we acknowledge the possibility that not all open chromatin regions marked by high levels of H3K27ac function as enhancers; therefore, these regions will not test positive in the functional characterization experiments conducted here. These caveats are likely to be addressed in part by genome and epigenome editing approaches that enable in situ manipulation of regulatory DNA and associated chromatin.

Enhanced crosslinking and immunoprecipitation (eCLIP) identifies transcriptome wide RBP occupancy sites23. By modifying steps in CLIP-seq and iCLIP protocols, eCLIP requires fewer amplification cycles and results in fewer redundant reads. Additionally, with the eCLIP protocol, size-matched inputs are generated to serve as controls for peak calling and other downstream analyses. The experimental protocol is available at -5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf.

We require all eCLIP antibodies to undergo primary and secondary characterizations. Detailed RBP antibody standards are available at -8a2d-425b-b2a0-9c39fa296816/@@download/attachment/ENCODE_Approved_Nov_2016_RBP_Antibody_Characterization_Guidelines.pdf.

RNA Bind-n-Seq characterizes RBPs and their motifs in vitro61. Recombinant RBPs are purified and incubated with randomized RNAs. The RBPs are then captured, and bound RNAs are sequenced. The experimental protocol is available at -aaee-4358-a834-c6ee002938b8/@@download/attachment/RBNSExperimentalProtocol_Feb2016_96well.pdf.

We required all commercial histone antibodies to be validated by at least two independent methods, and antibody lots to be analysed independently. Detailed histone mark antibody standards are available at -387a-47c4-ab24-cebe64ead5ae/@@download/attachment/ENCODE_Approved_Oct_2016_Histone_and_Chromatin_associated_Proteins_Antibody_Characterization_Guidelines.pdf.

DNase-seq surveys open chromatin regions through genomic cleavage by endonuclease DNase I followed by sequencing. For ENCODE phase III, the DNase-seq protocol was updated, allowing for smaller quantities of input material. Experimental protocols are available at -d14c-4e77-bc52-5517b56daac0/@@download/attachment/Culturedcells_SOP_nuclei_DNase_crosslink_RNA_V1.pdf (cultured cells) and -9a7a-4277-b7be-4a3c1ce1cfc6/@@download/attachment/08112010_nuclei_isolation_human__tissue_V6_3.pdf (tissues). Additional details are available at -standards/dnase-seq/.

To map DNA methylation, WGBS uses bisulfite treatment to convert unmethylated cytosines into uracils, leaving methylated cytosines unchanged. Through sequencing and alignment to a transformed genome, CpG, CHG, and CHH methylation levels can be extracted. The experimental protocol is available at -5ebe-482b-9fa3-d93a968a7045/@@download/attachment/WGBS_V4_protocol.pdf (human) and -cf8f-4f26-b76b-d14a3b9721bd/@@download/attachment/Ecker_Methyl_Protocol_022315.pdf (mouse). Additional details are available at -standards/wgbs/.

DNA replication timing provides insights into both gene regulation and spatiotemporal genome compartmentalization65. Production documents were generated for each experiment, and a representative experimental protocol for Repli-seq is available at: -9f55-41c1-b5ce-78dc7bd59a1e/@@download/attachment/Repliseq_Protocol.pdf.

We downloaded the SNPs tested by MPRA50 in human lymphoblastoid cells from Supplementary Table 1 of that study and reconstructed tested regions by generating a ±75-bp window around each SNP. We then intersected cCREs with these regions using bedtools intersect, requiring at least 25% of each cCRE to overlap. Of the cCREs that overlapped a tested region, we calculated the percentage that overlapped an MPRA+ region. We analysed all cCREs and GM12878-specific cCREs stratified by the cCRE group.

We downloaded SuRE peaks in human K562 cells from the Supplementary Data Set of an earlier study51. Using bedtools intersect, we compared the SuRE peaks with the hg38 cCREs lifted down to the hg19 genome version, counting the number of base pairs overlapping each cCRE or region of interest. We then calculated the total percentage of base pairs for each cCRE group that overlapped a SuRE peak.

to view the animation created in this example, click on the image below. simple flash animation - here - fla - simple flash animation you can download the fla file with that animation. save / open / export flash contentthe flash cs5 documents are saved (with file - save or 'ctrl+s') in the fla format, with '.fla' extension.rossell hope robbins (1912-1990), an acknowledged authority on witchcraft, was one of the half-dozen americans ever elected fellow of the royal society of literature. he authored over a dozen books and nearly 200 articles, including the definitive introduction to the catalogue of the witchcraft collection at cornell university library in 1979.this is the rare gift that every witch doctor, occult student, and paranormal investigator would find invaluable. every detailed fact, rumor, and rumor, are here. includes: the devil through the ages; the role of the devil in mythology; ancient witchcraft and demonology; a history of witchcraft, its magic and magick; the devil in european folklore; the devil in medieval literature; a history of the witchcraft persecutions; the rise of witchcraft in england; monsters and demons; witches; witchcraft and the law; black magic; hollows and haunted houses; witches and rappers; witchcraft trials in europe; the problem of witchcraft; the rise of the early modern witch-hunt; witchcraft in the united states; the devil in the new world; the role of witchcraft in the civil war.demonology is the study of demons, the study of evil, of supernatural or paranormal forces, and their connection with the christian faith. this book is a good introduction to the field, including topics such as humanoids and their nature, the hierarchy of demons, and the history and role of demons in the early christian world, along with a discussion of christian demonology. part i surveys the existence and nature of demons, including their physical appearance, their relationship to satan, and their origin and goals. part ii looks at the hierarchy of demons, with an introduction to the hierarchy, a survey of its role in satanology, and in-depth discussions of the related and lesser demons. 6a6f617c0c

Nature, in the broadest sense, is the physical world or universe. "Nature" can refer to the phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. Although humans are part of nature, human activity is often understood as a separate category from other natural phenomena.[1]

The word nature is borrowed from the Old French nature and is derived from the Latin word natura, or "essential qualities, innate disposition", and in ancient times, literally meant "birth".[2] In ancient philosophy, natura is mostly used as the Latin translation of the Greek word physis (φύσις), which originally related to the intrinsic characteristics of plants, animals, and other features of the world to develop of their own accord.[3][4]The concept of nature as a whole, the physical universe, is one of several expansions of the original notion;[1] it began with certain core applications of the word φύσις by pre-Socratic philosophers (though this word had a dynamic dimension then, especially for Heraclitus), and has steadily gained currency ever since.

During the advent of modern scientific method in the last several centuries, nature became the passive reality, organized and moved by divine laws.[5][6] With the Industrial revolution, nature increasingly became seen as the part of reality deprived from intentional intervention: it was hence considered as sacred by some traditions (Rousseau, American transcendentalism) or a mere decorum for divine providence or human history (Hegel, Marx). However, a vitalist vision of nature, closer to the pre-Socratic one, got reborn at the same time, especially after Charles Darwin.[1] 781b155fdc