Literature DB >> 30175199

Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L).

Zachary M Turpin1, Daniel L Vera2, Savannah D Savadel1, Pei-Yau Lung3, Emily E Wear4, Leigh Mickelson-Young4, William F Thompson4, Linda Hanley-Bowdoin4, Jonathan H Dennis1, Jinfeng Zhang3, Hank W Bass1.   

Abstract

Presented here are data from Next-Generation Sequencing of differential micrococcal nuclease digestions of formaldehyde-crosslinked chromatin in selected tissues of maize (Zea mays) inbred line B73. Supplemental materials include a wet-bench protocol for making DNS-seq libraries, the DNS-seq data processing pipeline for producing genome browser tracks. This report also includes the peak-calling pipeline using the iSeg algorithm to segment positive and negative peaks from the DNS-seq difference profiles. The data repository for the sequence data is the NCBI SRA, BioProject Accession PRJNA445708.

Entities:  

Year:  2018        PMID: 30175199      PMCID: PMC6117953          DOI: 10.1016/j.dib.2018.08.015

Source DB:  PubMed          Journal:  Data Brief        ISSN: 2352-3409


  5 in total

1.  Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize.

Authors:  Daniel L Vera; Thelma F Madzima; Jonathan D Labonne; Mohammad P Alam; Gregg G Hoffman; S B Girimurugan; Jinfeng Zhang; Karen M McGinnis; Jonathan H Dennis; Hank W Bass
Journal:  Plant Cell       Date:  2014-10-31       Impact factor: 11.277

2.  Open chromatin reveals the functional maize genome.

Authors:  Eli Rodgers-Melnick; Daniel L Vera; Hank W Bass; Edward S Buckler
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-16       Impact factor: 11.205

Review 3.  A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development.

Authors:  Hank W Bass; Emily E Wear; Tae-Jin Lee; Gregg G Hoffman; Hardeep K Gumber; George C Allen; William F Thompson; Linda Hanley-Bowdoin
Journal:  J Exp Bot       Date:  2014-01-21       Impact factor: 6.992

4.  Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales.

Authors:  Justin A Fincher; Daniel L Vera; Diana D Hughes; Karen M McGinnis; Jonathan H Dennis; Hank W Bass
Journal:  Plant Physiol       Date:  2013-04-09       Impact factor: 8.340

5.  iSeg: an efficient algorithm for segmentation of genomic and epigenomic data.

Authors:  Senthil B Girimurugan; Yuhang Liu; Pei-Yau Lung; Daniel L Vera; Jonathan H Dennis; Hank W Bass; Jinfeng Zhang
Journal:  BMC Bioinformatics       Date:  2018-04-11       Impact factor: 3.169

  5 in total
  1 in total

1.  The regulatory landscape of early maize inflorescence development.

Authors:  Rajiv K Parvathaneni; Edoardo Bertolini; Md Shamimuzzaman; Daniel L Vera; Pei-Yau Lung; Brian R Rice; Jinfeng Zhang; Patrick J Brown; Alexander E Lipka; Hank W Bass; Andrea L Eveland
Journal:  Genome Biol       Date:  2020-07-06       Impact factor: 13.583

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.