Project description:Phylogenetic relationships of mammals inferred using ultra conserved elements
| PRJNA390442 | ENA
Project description:Phylogenomic reappraisal of the suckermouth armored catfish family Loricariidae (Teleostei: Siluriformes) using thousands of ultraconserved elements
| PRJNA496344 | ENA
Project description:Target-enrichment of ultra-conserved elements and exons in Chrysogorgia (Octocorallia)
| PRJNA681648 | ENA
Project description:New perspectives on the evolutionary history of the catfish family Heptapteridae using genome-scale analyses ultraconserved elements (Teleostei, Siluriformes)
| PRJNA723556 | ENA
Project description:The complete mitochondrial genome of the soldier catfish Osteogeneiosus militaris from Vietnam (Teleostei; Siluriformes)
Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
Project description:Understanding the origin of morphological diversity across vertebrates is central to evolutionary developmental biology. cis-regulatory elements (CRE) such as enhancers and promoters interpret precise spatiotemporal cues to control and coordinate gene expression. To get insights into both conserved and species-specific variations during early limb patterning and outgrowth, we leverage genome-wide comprehensive assessment of chromatin accessibility and transcriptional changes during mouse forelimb and chicken wing bud development. Our analysis reveals temporal modulation of chromatin accessibility and expression as well as their temporal relationship during the progression of mouse forelimb and chicken wing bud development. Transcription factor binding site enrichment analysis and putative TF occupancy as inferred by integrating TF binding motifs and chromatin accessibility information reveal temporal TF-DNA interactions during forelimb/wing bud patterning. Finally, the integration of accessibility, expression, and TF binding site information allowed to identify candidate gene targets of HAND2 and GLI3 that include conserved as well as species-specific transcriptional regulator-gene interactions.