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    GRIPseq data for S. Purpuratus 24 hpf

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    README file instructions for creating each of the files in this database (3.059Kb)
    GRIPseq mapped reads, Pol(II) experimental no. 1, .bam file (1005.Mb)
    GRIPseq mapped reads, Pol(II) experimental no. 1, .bai (indexed) file (3.240Mb)
    GRIPseq mapped reads, Pol(II) experimental no. 1, .tdf file (avg read count 25bp window) (584.4Mb)
    GRIPseq mapped reads, Pol(II) experimental no. 2, .bam file (525.4Mb)
    GRIPseq mapped reads, Pol(II) experimental no. 2, .bai (indexed) file (3.095Mb)
    GRIPseq mapped reads, Pol(II) experimental no. 2, .tdf file (avg read count 25bp window) (525.6Mb)
    GRIPseq mapped reads, IgG alone control, .bam file (37.55Mb)
    GRIPseq mapped reads, IgG alone control, .bai (indexed) file (1.995Mb)
    GRIPseq mapped reads, IgG alone control, .tdf file (avg read count 25bp window) (116.3Mb)
    GRIPseq, Pol(II) experimental no. 1, raw reads, all R1 combined (219.3Kb)
    GRIPseq, Pol(II) experimental no. 1, raw reads, all R2 combined (218.8Kb)
    GRIPseq, Pol(II) experimental no. 2, raw reads, all RI combined (233.7Kb)
    GRIPseq, Pol(II) experimental no. 2, raw reads, all R2 combined (231.7Kb)
    GRIPseq, IgG alone control, raw reads, all R1 combined (209.6Kb)
    GRIPseq, IgG alone control, raw reads, all R2 combined (202.7Kb)
    Date
    2015-01-19
    Author
    Tulin, Sarah  Concept link
    Barsi, Julius C.  Concept link
    Bocconcelli, Carlo  Concept link
    Smith, Joel  Concept link
    Metadata
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    Citable URI
    https://hdl.handle.net/1912/7101
    Related Material/Data
    https://hdl.handle.net/1912/8259
    DOI
    10.1575/1912/7101
    Keyword
     gene regulation; transcription factor binding site; Pol II; ChIPseq; sea urchin 
    Abstract
    This dataset is the result of a new method for identifying putative cis-regulatory elements genome wide, termed GRIPseq for Genome-wide Regulatory element Immunoprecipitation. Our protocol combines elements of chromatin conformation capture (e.g., 3C, 4C, Hi-C), chromatin immunoprecipitation, and paired-end high-throughput sequencing with molecular tools that enrich for active cis-regulatory elements across the genome. Our pioneer dataset, available to the community, derives from the purple sea urchin, Stronglyocentrotus purpuratus, mesenchyme blastula embryos collected at 24 hpf. We benchmark our results against independent findings, i.e., rigorously tested cis-elements previously identified and find good congruence at the loci we have investigated, and in particular we find a strong signal-to-noise ratio for known distal elements, marking an improvement over existing methods. A corollary of this approach is the ability, in many cases, to link cis-regulatory elements to the genes they regulate.
    Description
    This database contains the sequencing reads and mapped reads for GRIPseq 24hpf for S. Purpurats. README.txt is a guide to using the files in the database.
    Collections
    • Bell Center Data Sets
    Suggested Citation
    Dataset: Tulin, Sarah, Barsi, Julius C., Bocconcelli, Carlo, Smith, Joel, "GRIPseq data for S. Purpuratus 24 hpf", 2015-01-19, DOI:10.1575/1912/7101, https://hdl.handle.net/1912/7101
     
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