Ontology highlight
ABSTRACT:
PROVIDER: PRJNA708355 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).
2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress
Project description:The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development. ChIP-seq data from naive and primed human embroynic stem cells.
2015-11-22 | E-GEOD-69646 | biostudies-arrayexpress
Project description:Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice. The ability to reveal the regulatory architecture of the genes at the whole genome level by constructing the regulatory network is critical for understanding the biological processes and developmental programs of the organism. Here we conducted an eQTL guided function-related co-expression analysis for identifying the putative regulators and constructing gene regulatory network. The Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcript levels. one replicates were sampled from each RIL, three for parents, and three replicates for each parent resulting in a dataset of 216 microarrays.
2014-02-05 | E-GEOD-49020 | biostudies-arrayexpress
Project description:Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes. Histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), chromatin modifiers (p300), transcription factors (NR2F1, TFAP2A), chromatin accessibility (ATACseq) and gene expression (RNAseq) were assayed in CNCCs derived from iPSCs/ESCs from 2 chimpanzee and 3 human individuals.
2015-09-11 | E-GEOD-70751 | biostudies-arrayexpress
Project description:The regulatory landscapes of human ovarian ageing
| PRJNA836755 | ENA
Project description:Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
2016-12-06 | GSE84793 | GEO
Project description:Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
| PRJNA267839 | ENA
Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting. Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.
2013-07-01 | E-GEOD-48431 | biostudies-arrayexpress
Project description:RNA was isolated from 23 old barley plants (shoots and roots), line Rolap. PARE libraries were constructed for both barley organs, followed by sequencing of NGS libraries.
2021-02-17 | GSE145423 | GEO
Project description:The aim of the study was the elucidation of drought-induced molecular events related to plant hormones occurring in crown tissue of barley, the key organ for cereal survival. Experiments involving large-scale measurements of gene expression at transcript and protein level, hormone abundance, and phenotypic variability in a set of selected barley mutants were carried out to uncover how disturbance of GAs, BRs and SLs homeostasis may affect the barley multivariate response to drought. The characterization included early stages of plant development and continued to the later stages, with observation of effects on the whole-plant architecture and yield formation. The integration of all data allowed to enrich the knowledge of regulatory networks in barley exposed to drought.
2023-10-10 | E-MTAB-13358 | biostudies-arrayexpress