Similar Datasets
Project description:Replication timing analysis of Recql4 -/- Klhdc3 -/- vs control using TIGER on whole genome sequencing in triplicate
| PRJNA1137410 | ENA
Project description:MotivationGenomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges.ResultsWe present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale.Availability and implementationTIGER is available at https://github.com/TheKorenLab/TIGER.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8913259 | biostudies-literature
Project description:Aim: to identify the transcriptional responses to acquisition of conjugative megaplasmids by Pseudomonas fluorescens, and how these effects are impacted by known compensatory mutations. Full abstract TBC.
2021-04-17 | GSE151570 | GEO
Project description:Purpose: Sixteen GSM Samples from GSE34399 was used to identify four different types of replication timing domains. Methods: 1. Chromosome 1 of Bj_Rep1 was manually annotated. 2. We developed a new supervised method called DNN-HMM (Deep Neural Network-Hidden Markov Model), and used the manual annotation as the training set to learn a model. 3. The model learnt in Step 2 was used to divide the un-annotated Repli-seq datas into four different replication domains (early replication domain, down transition zone, late replication domain, up transition zone). Result: We used DNN-HMM to identify four different replication timing domains respectively in fifteen cell lines. The accuracy of identification was about 87%, and the overlapping percentage of two independent replicates of Bj cell line was about 83%. Data File Formats :(bed) chrom - The name of the chromosome chromStart - The starting position of the feature in the chromosome chromEnd - The ending position of the feature in the chromosome category - The domain identified (denoted by: ERD, short for early replication domain; DTZ, short for down transition zone; LRD, short for late replication domain; UTZ, short for up transition zone)
2015-05-25 | GSE53984 | GEO
Project description:Developing stickleback embryos were dissociated and sorted for S-phase and G0/G1-phase cell populations. DNA was extracted from each population and sequenced. In a mixed S-phase population, regions that replicate earlier are at higher copy number (up to 2x) than regions that replicate later. The read depth in S-phase, normalized to the read depth in G-phase, thus represents replication timing.
2018-10-20 | GSE121537 | GEO
Project description:Human RECQL4, a member of the RecQ helicase family, plays a role in maintaining genomic stability, but its precise function remains unclear. The N-terminus of RECQL4 has similarity to Sld2, a protein required for the firing of DNA replication origins in budding yeast. Consistent with this sequence similarity, the Xenopus laevis homolog of RECQL4 has been implicated in initiating DNA replication in egg extracts. To determine whether human RECQL4 is required for firing of DNA replication origins, we generated cells in which both RECQL4 alleles were targeted, resulting in either lack of protein expression (knock-out; KO) or expression of a full-length, mutant protein lacking helicase activity (helicase-dead; HD). Interestingly, both the RECQL4 KO and HD cells were viable and exhibited essentially identical origin firing profiles as the parental cells. Analysis of the rate of fork progression revealed increased rates in the RECQL4 KO cells, which might be indicative of decreased origin firing efficiency. Our results are consistent with human RECQL4 having a less critical role in firing of DNA replication origins, than its budding yeast homolog Sld2.
| S-EPMC10987555 | biostudies-literature
Project description:modENCODE_submission_668 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Genotype: se/e; Sex: Female NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line Kc167
2009-07-29 | E-GEOD-17279 | biostudies-arrayexpress
Project description:modENCODE_submission_669 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by synchronizing tissue culture cell and differentially labeling early and late replicating intermediates. The differentially labeled replication intermediates were then hybridized to Agilent genomic tiling arrays to identify early and late replicating domains. Keywords: CHIP-chip For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Sex: Male NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Cell Line S2-DRSC
2010-05-15 | E-GEOD-17280 | biostudies-arrayexpress
Project description:Stickleback genome-wide replication timing from whole embryo
| PRJNA497600 | ENA