Project description:The northern white rhinoceros (Ceratotherium simum cottoni) genome and annotation were previously published, but the annotation contained few genes, with many annotation misalignments, and nomenclature not matching HGNC/VGNC naming conventions, making transcriptional studies very difficult. We used in vivo collected granulosa cells for RNA sequencing and de novo transcript assembly through StringTie to identify all nucleotide gene sequences in our samples. Through extensive manual curation we were able to generate a greatly improved genome annotation increasing gene numbers by 81%. This will greatly enable researchers in this field to utilize the genome and annotation to complete transcriptional studies with this species.
Project description:This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. These experiments included an Input control, and a H3K27Ac ChIP-seq experiment to annotate active enhancers and ensure hat the ChIP-seq experiment with antibodies performed as expected.
Project description:This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. To ensure antibody quality, as this was the first time CENPA ChIP-seq was performed in the NMR, we performed H3K27Ac and CENPA ChIP-seq experiments on a TeloHAOEC cell line.
Project description:This project encompasses a de novo genome assembly of the cochineal bug, Dactylopius opuntiae, incorporating RNA-seq and MS/MS mass spectrometry proteomics as evidence for gene calling and protein annotation.
