Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162858 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lipomyces genome scale model based on the Lipomyces starkeyi NRRL-11557 genome.
Published in:
Genome-Scale Model Development and Genomic Sequencing of the Oleaginous Clade Lipomyces
Frontiers in Bioengineering and Biotechnology
Industrial Biotechnology
Volume 12 - 2024 | doi: 10.3389/fbioe.2024.1356551
2024-03-20 | MODEL2403190001 | BioModels
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Project description:A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.
2026-05-28 | E-MTAB-17094 | biostudies-arrayexpress
Project description:To confirm the loss of transcription factor (TF) occupancy at SNP-containing motifs, we performed ChIP-seq for three TFs in the Bl6xSpret hybrid mESC line. This dataset includes cross-link ChIP-seq data for CTCF, KLF4, and SOX2. Two biological replicates were generated for each TF. The protocol was adapted from Trovato et al. (2024), with minor modifications. Chromatin was sheared using a Bioruptor Pico (Diagenode) and incubated overnight at 4 °C with rotation with antibodies against KLF4 (AF3158, R&D Systems), CTCF (07-729, Merck Millipore), or SOX2 (AF2018, R&D Systems). Bead–immunocomplexes were reverse cross-linked after RNA and protein digestion, and DNA was purified using 1.4x SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on an AVITI platform, using Cloudbreak Low 2x150 bp runs (250 M clusters/run) for H3K27Ac and Cloudbreak High 2x75 bp runs (1000 M clusters/run). AVITI and Illumina adapters were trimmed using TrimGalore! v0.6.7 (Krueger et al., 2023). Trimmed reads were competitively aligned to the Bl6 and Spret genomes and filtered to discard reads with allelic mapping bias using a version of WASP extended to include indels (van de Geijn et al., 2015; Sigalova et al., 2025). Finally, duplicate reads were identified and removed using the Picard tool MarkDuplicates v2.15.0. (https://github.com/Krebslabrep/TF-chromatin.git).
2026-05-08 | E-MTAB-16466 | biostudies-arrayexpress