cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001720
title: Black-footed Ferret Genome Analysis

description: The black-footed ferret (Mustela nigripes) experienced an extreme bottleneck during the 20th century, reducing the species to a single population by the 1980''s. This lingering population continued to decline, leading to the 1985 initiation of a captive breeding program. The species was saved from extinction, however conservation efforts are ongoing with new challenges - potentially loss of fitness through inbreeding. All living individuals are descended from 7 ferrets that successfully bred in captivity. Tissue from these 7 ferrets as well as congeners that failed to breed have been preserved, and offer the chance to analyze the population genomics of the last black-footed ferret population and the individuals that formed the first generation of the captive program. These preserved tissues are also a resource for integrating historic genetics into the living population through genetic rescue via artificial insemination and cloning. To assess the value of archived tissues for genetic rescue we propose sequencing genomes of historic and living ferrets to measure changes in SNP variation across generations of captive breeding. Reductions in genetic diversity through drift, inbreeding and selection will be evaluated. We have generated sequences of short read DNA libraries for full genomes to a depth of ~20X from two cryopreserved cell lines derived from individuals captured in 1985, a living ferret born by artificial insemination from cryoprserved spermatozoa, and a natural born living ferret. From these samples we can produce preliminary assessments of differences in SNP variation between 20+ generations from the original wild population to the current breeding generation.
DOI: 10.26036/cnphis0001721
title: Identification of Mutation in a Rat Model for Human Parkinson’s Disease

description: Parkinson''s disease is a progressive disorder of the nervous system that affects walking, movement and coordination. This disease is diagnosed in more than 50,000 Americans each year. Recently, we have identified a rat model which shows early onset of a motor neuron defect phenotype similar to that in Parkinson’s patients. The goal of the project is to identify, through next generation sequencing , the underlying mutation of this rat model for human Parkinson’s disease. Whole genome sequencing will be performed for a set of distantly related rats with conditions mimicking human Parkinson’s disease. Litter mates of the mutant rats without phenotype will also be sequenced as controls. Based on the recessive inheritance model, candidate homozygous variants shared by the mutant rat while either absent or heterozygous in the control rat will be further tested in additional rats to confirm its segregation with the phenotype. Due to the lack of good Parkinson’s animal models, establishing and further characterizing this new rat model will shed important insights on this important human disease.
DOI: 10.26036/cnphis0001722
title: Rhincodon typus Whole Genome Sequencing

description: Whole genome sequencing of the whale shark (Rhincodon typus) using Illumina and 454 sequencing platforms.
DOI: 10.26036/cnphis0001723
title: Transcriptome of Schisandra sphenanthera Rehd. et Wils

description: None
DOI: 10.26036/cnphis0001724
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002405
title: Effective Detection of Variation in Single Cell Transcriptome using MATQ-seq

description: We report here a new single-cell RNA-seq assay, Multiple Annealing and dC-Tailing based Quantitative single-cell RNA-seq (MATQ-seq), which provides the accuracy and sensitivity that enable the detection of transcriptional variations existing in single cells of the same type. We performed a systematic characterization of the technical noise using pool-and-split averaged single-cell samples and showed that the biological variations in single cells were observed with statistical significance. Overall design: 10 HEK293T single cells and 10 HEK293T pool-and-split averaged single cell samples were sequenced with MATQ-seq. We also sequenced 6 MCF10A single cells and 6MCF10A pool-and-split averaged single cell samples. To characterize the capture efficiency, we also sequenced 6 averaged one-fifth MCF10A single-cell samples with ERCC spike-in. Additional 38 HEK293T single cells (HEK293T_clone1_SC*) and 10 HEK293T pool-and-split averaged single cell samples (HEK293T_clone1_SC_average*) were sequenced with MATQ-seq.
DOI: 10.26036/cnphis0002408
title: Phylloscopus trochiloides trochiloides isolate:LN10 Genome sequencing and assembly

description: Whole-genome pair-end sequencing of one Phylloscopus trochiloides trochiloides individual in one lane of the Illumina HiSeq 2000 instrument.
DOI: 10.26036/cnphis0002409
title: African cattle genome sequencing

description: None
DOI: 10.26036/cnphis0002410
title: GenomeTrakr Project: New Mexico State University, Food Safety Laboratory

description: Whole genome sequencing of cultured Salmonella enterica as part of the US Food and Drug Administration surveillance project for the rapid detection of foodborne contamination events.
DOI: 10.26036/cnphis0002411
title: Anas platyrhynchos Raw sequence reads

description: evolution
DOI: 10.26036/cnphis0002412
title: Phylloscopus plumbeitarsus isolate:BK2 Genome sequencing and assembly

description: Whole-genome pair-end sequencing of one Phylloscopus trochiloides plumbeitarsus individual in one lane of the Illumina HiSeq 2000 instrument.
DOI: 10.26036/cnphis0001725
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001726
title: Loligo pealei RNA and DNA sequencing

description: We performed RNA and DNA sequencing to identify RNA editing sites in the squid Loligo pealei
DOI: 10.26036/cnphis0001727
title: Speciaphid WGS of pea aphid biotypes

description: 33 Whole genome re-sequencing of pea aphid biotypes
DOI: 10.26036/cnphis0001728
title: Rice Root Associated Microbiomes

description: This study was designed to uncover factors driving differences in microbial diversity for root associated microbial communities in rice.
DOI: 10.26036/cnphis0001729
title: Homo sapiens Genome sequencing

description: CPT-seq (Contiguity-Preserving Transposition Seq)
DOI: 10.26036/cnphis0002413
title: Willet be one species or two?: A genomic view of the evolutionary history of Tringa semipalmata

description: The Willet (Tringa semipalmata; Scolopacidae) is composed of two morphologically and vocally distinct subspecies with broadly disjunct breeding distributions in North America. Nominate T. s. semipalmata breeds in coastal salt and brackish marshes along the Atlantic and Gulf coasts of eastern North America and the West Indies, and T. s. inornata breeds in wet grasslands and prairies in the northwestern interior of North America. To assess divergence and test for hybridization between the two subspecies, we sampled breeding and wintering populations and collected morphological data, mitochondrial DNA sequences from the ND2 locus, and nuclear DNA sequences from genomic libraries enriched for ultraconserved elements (UCEs). Mitochondrial haplotypes were reciprocally monophyletic between the two subspecies and divergence dating indicated a divergence time of roughly 730,000 years ago. The UCE dataset included 4,635 UCE loci containing 19,322 (single nucleotide polymorphisms; SNPs); based on these data individuals clustered by subspecies with no evidence of admixture, and no sub-structure within subspecies. Despite the apparent recent divergence based on mitochondrial data, we identified 42 nuclear loci that contained SNPs fixed for alternate alleles between the two subspecies, many more than expected by chance. Seventeen of the 42 loci with fixed differences were on the Z chromosome, which is a sex chromosome in birds. This suggests a role for sexual selection in the divergence of the two subspecies. Genetic, morphological, ecological, and behavioral differences suggest the two Willet subspecies merit treatment as separate species. Our study demonstrates that a genome-wide perspective is important for assessing taxon rank when the impacts of processes responsible for divergence vary across the genome.
DOI: 10.26036/cnphis0002414
title: Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [Tumor RRBS]

description: Adjacent CpG sites in mammalian genomes tend to be co-methylated due to the processivity of enzymes responsible for adding or removing the methyl group. Yet discordant methylation patterns have also be observed, and found to be related to stochastic or uncoordinated molecular processes. Here we focused on a systematic search and investigation of regions in the human genome that exhibit highly coordinated methylation. By examining the co-methylation patterns of multiple adjacent CpG sites, termed methylation haplotypes, in single bisulfite sequencing reads, we applied a greedy-searching strategy to defined blocks of tightly coupled CpG sites, called Methylation Haplotype Blocks (MHBs), based on 53 sets of whole genome bisulfite sequencing (WGBS) data, including 43 published sets from human adult tissues, ESC and in vitro differentiated cell lines, as well as 10 sets from human adult tissues generated in this study. The MHBs were then further validated with 101 sets of RRBS ENCODE data, and 637 sets of Illumina 450k methylation array data from TCGA tumor and normal samples. Globally, MHBs are enriched in but only partially overlap with several well-known genomic features, including CpG islands, promoters, enhancers and VMRs. To perform quantitative analysis of the MHBs, we defined a metric called Methylation Haplotype Load (MHL), which is covered both average methylation level and methylation complexity and therefore more informative than average methylation level or Shannon entropy. Using a feature selection strategy, we identified a set of tissue-specific MHBs that cluster by developmental germ-layers. Interestingly, examination of these MHBs revealed two distinct mechanisms for fate commitment during development: epigenetic silencing of pluripotent genes, such as NANOG, for mesoderm induction; and epigenetic induction (or de-suppression) of lineage-specific factors for ectoderm commitment. Overall design: Examination of co-methylation in primary tumor tissues
DOI: 10.26036/cnphis0002415
title: Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [WGBS]

description: Adjacent CpG sites in mammalian genomes tend to be co-methylated due to the processivity of enzymes responsible for adding or removing the methyl group. Yet discordant methylation patterns have also be observed, and found to be related to stochastic or uncoordinated molecular processes. Here we focused on a systematic search and investigation of regions in the human genome that exhibit highly coordinated methylation. By examining the co-methylation patterns of multiple adjacent CpG sites, termed methylation haplotypes, in single bisulfite sequencing reads, we applied a greedy-searching strategy to defined blocks of tightly coupled CpG sites, called Methylation Haplotype Blocks (MHBs), based on 53 sets of whole genome bisulfite sequencing (WGBS) data, including 43 published sets from human adult tissues, ESC and in vitro differentiated cell lines, as well as 10 sets from human adult tissues generated in this study. The MHBs were then further validated with 101 sets of RRBS ENCODE data, and 637 sets of Illumina 450k methylation array data from TCGA tumor and normal samples. Globally, MHBs are enriched in but only partially overlap with several well-known genomic features, including CpG islands, promoters, enhancers and VMRs. To perform quantitative analysis of the MHBs, we defined a metric called Methylation Haplotype Load (MHL), which is covered both average methylation level and methylation complexity and therefore more informative than average methylation level or Shannon entropy. Using a feature selection strategy, we identified a set of tissue-specific MHBs that cluster by developmental germ-layers. Interestingly, examination of these MHBs revealed two distinct mechanisms for fate commitment during development: epigenetic silencing of pluripotent genes, such as NANOG, for mesoderm induction; and epigenetic induction (or de-suppression) of lineage-specific factors for ectoderm commitment. Overall design: Examination of co-methylation in primary human tissues
DOI: 10.26036/cnphis0002416
title: Salmonella enterica subsp. enterica serovar Enteritidis strain:SEJ Genome sequencing

description: Salmonella enteridis SEJ Genome Assembly
DOI: 10.26036/cnphis0002417
title: Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [Plasma RRBS]

description: Adjacent CpG sites in mammalian genomes tend to be co-methylated due to the processivity of enzymes responsible for adding or removing the methyl group. Yet discordant methylation patterns have also be observed, and found to be related to stochastic or uncoordinated molecular processes. Here we focused on a systematic search and investigation of regions in the human genome that exhibit highly coordinated methylation. By examining the co-methylation patterns of multiple adjacent CpG sites, termed methylation haplotypes, in single bisulfite sequencing reads, we applied a greedy-searching strategy to defined blocks of tightly coupled CpG sites, called Methylation Haplotype Blocks (MHBs), based on 53 sets of whole genome bisulfite sequencing (WGBS) data, including 43 published sets from human adult tissues, ESC and in vitro differentiated cell lines, as well as 10 sets from human adult tissues generated in this study. The MHBs were then further validated with 101 sets of RRBS ENCODE data, and 637 sets of Illumina 450k methylation array data from TCGA tumor and normal samples. Globally, MHBs are enriched in but only partially overlap with several well-known genomic features, including CpG islands, promoters, enhancers and VMRs. To perform quantitative analysis of the MHBs, we defined a metric called Methylation Haplotype Load (MHL), which is covered both average methylation level and methylation complexity and therefore more informative than average methylation level or Shannon entropy. Using a feature selection strategy, we identified a set of tissue-specific MHBs that cluster by developmental germ-layers. Interestingly, examination of these MHBs revealed two distinct mechanisms for fate commitment during development: epigenetic silencing of pluripotent genes, such as NANOG, for mesoderm induction; and epigenetic induction (or de-suppression) of lineage-specific factors for ectoderm commitment. Overall design: Examination of co-methylation in human cfDNA
DOI: 10.26036/cnphis0002423
title: Ultraconserved elements from multiple snake families

description: Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3,776 nuclear loci from ultraconserved elements (1.34 million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ~100 times larger than used in previous studies.
DOI: 10.26036/cnphis0001730
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001731
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001732
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001733
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001734
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001735
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001736
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001737
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001738
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001740
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0002418
title: Vanessa cardui Transcriptome or Gene expression

description: Expanded color vision in butterflies: molecular logic behind three way stochastic choices. This project was aimed at understanding stochastic photoreceptor choice in insect eyes.
DOI: 10.26036/cnphis0002419
title: Gut microbiome of two Pachysoma spp.

description: The bacterial and fungal gut microbiomes of two Pachysoma species feeding on different substrates were sequenced to better understand the effect of host diet and phylogeny on the insect microbiomes of this species of dung beetle
DOI: 10.26036/cnphis0002420
title: Lateolabrax maculatus Raw sequence reads

description: Lateolabrax maculatus
DOI: 10.26036/cnphis0002421
title: NGS data for four invertebrates: Amphinemura sulcicollis, Isoperla grammatica, Baetis rhodani and Oniscus asellus.

description: A low-coverage genome was generated for each of four environmental key-species of macroinvertebrate taxa for the purposes of microsatellite marker development. As widespread and functionally important organisms, which are often neglected in favour of studies on vertebrates, this data will be a useful resource for further research.
DOI: 10.26036/cnphis0002424
title: Genomic reads from 15 cricetid genomes

description: Attached are the reads generated from survey sequencing of 15 cricetid genomes. These reads were sequenced in order to provide data for assembling and annotating mitichondrial genomes of each. The list of taxa included are as follows: Neotoma alstoni, Peromyscus pectoralis, Peromyscus mexicanus, Osgoodomys banderanus, Podomys floridanus, Neotomodon mexicanus, Peromyscus aztecus, Habromys lepturus, Sigmodon hispidus, Peromyscus polionotus, Peromyscus crinitus, Reithrodontomys mexicanus, Peromyscus attwateri, Isthmomys pirrensis, and Peromyscus megalops.
DOI: 10.26036/cnphis0002425
title: Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens more than 100 years-old

description: Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a recently developed target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs) from 51 large carpenter bee specimens (genus Xylocopa), representing 25 species with ages ranging from 2–121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration) and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count) with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and our DNA yield and sequence capture variables. Additionally, we reconstructed a phylogeny in order to confirm the validity of our sequence data. We recovered 6–972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06–9.8 ng/µL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts than specimens older than 20 years. We found breakpoints in our data between 21–39 years for pre- and post-library DNA concentration and UCE contig length beyond the negative effect of decreased specimen age. Our phylogenetic results confirmed the integrity of our sequences as specimens of the same species grouped together, and give preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss our phylogenetic results with regard to the promise of this UCE approach for large scale projects in insect phylogenomics using museum specimens.
DOI: 10.26036/cnphis0002427
title: Melanaphis sacchari Genome sequencing and assembly

description: The goal of the study was to develop microsatellite markers for sugarcane aphid and endosymbiont detection. There is uncertainty if there are multiple biotypes in the U.S. or if all aphids are one biotype. Genotyping with 52 microsatellite markers indicated that the samples were all one biotype with the exception of a single sample collected from Sinton, TX which had the predominant biotype as well as another biotype. Genotyping of the aphid samples with 12 microsatellite markers from Buchera aphidicola, the obligate aphid symbiont, had nearly identical results. Thus the invasive sugarcane aphid is spreading in the U.S. as primarily one asexual clone.
DOI: 10.26036/cnphis0001741
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001742
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001744
title: Sooty reference genome and diversity panel

description: The BCM-HGSC is sequencing and assembling the genome of the sooty mangabey, Cercocebus atys. This project is a collaboration with Dr. Guido Silvestri (Emory University). BCM-HGSC has produced an initial high-quality draft assembly of the sooty mangabey genome using the Illumina sequencing platform. In addition, BCM-HGSC has generated approximately 7x whole genome coverage using the Pacific Biosciences RS platform, and these long reads have been used to fill gaps and improve the continuity of the initial assembly. Sooty mangabeys are an important animal model for research related to human immunodeficiency virus (HIV) and AIDS. Sooty mangabeys are the natural hosts for a simian immunodeficiency virus (SIV-smm), and HIV-2 is derived from that SIV, likely as a result of cross-species transfer of the SIV. The mangabeys do not exhibit clinical pathology or other adverse effects from infection with their native SIV, and thus study of the host-virus interaction in this animal model is important for understanding of the mechanisms by which the mangabeys are able to control infection and avoid AIDS-like disease. The BCM-HGSC is generating a high quality draft assembly for this genome using DNA from a sooty mangabey obtained from Dr. Silvestri and Dr. Zach Johnson of the Yerkes National Primate Research Center (Emory University). In addition, BCM-HGSC has produced whole genome sequence coverage for several other unrelated sooty mangabeys in order to identify genetic variation within the species. All sequence reads are deposited in the NCBI sequence read archive.
DOI: 10.26036/cnphis0001745
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001749
title: The Sequencing of Salmonella enterica strains.

description: None
DOI: 10.26036/cnphis0001750
title: The Sequencing of Salmonella enterica strains.

description: None