cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002609
title: Swarm intelligence-enhanced detection of non-small cell lung cancer using tumor-educated platelets

description: We report RNA-sequencing data of 779 blood platelet samples, including 402 tumor-educated platelet (TEP) samples collected from patients with non-small cell lung cancer (NSCLC). In addition, we report RNA-sequencing data of blood platelets isolated from 377 individuals without reported cancer, but not excluding individuals with inflammatory conditions. This dataset highlights the ability of TEP RNA-based ''liquid biopsy'' diagnostics in patients with NSCLC. Overall design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.
DOI: 10.26036/cnphis0002601
title: Salmonella sp. Raw sequence reads

description: National Microbiology Laboratory at Guelph (formerly LFZ)
DOI: 10.26036/cnphis0002606
title: The genetic basis of mouth asymmetry in Perissodus microlepis

description: How polymorphisms consisting in left-right asymmetries are produced and maintained in natural populations is a tantalizing question, that remains largely unanswered. The scale-eating cichlid fish Perissodus microlepis is a remarkable example of extreme ecological specialization achieved by morphological and behavioral laterality. Its asymmetric mouth is accompanied by a pronounced lateralized foraging behavior, where a left-bending morph preferentially feeds on the scales of the right side of its prey, while the opposite is true for the right morph. This striking asymmetry made this fish a textbook example of the astounding degree of ecological specialization and negative frequency-dependent selection. Yet, the genetic basis underlying this spectacular laterality remains unknown. We addressed this question through analyses of wild-caught fish using high-throughput DNA sequencing data. A novel array of SNP markers was developed by ddRAD sequencing (ddRADseq) and the use of pooled DNA samples (PoolSeq). We obtained more than 155,000 SNPs using ddRADseq, and 3,900,000 SNPs with PoolSeq. Among these, we identified one (ddRAD) SNP, and 38 or 378 (PoolSeq) windows that are differentiated between the left and right morphs accounting for spurious associations due to geographic structuring. This allowed us to uncover candidate genomic regions that potentially contain genes for this trait. Then, this interesting trait has a genetic basis that is likely to be influenced by multiple loci. This result contributes to a greater understanding of the genetic bases of left-right asymmetry and, ultimately, the evolutionary processes governing the maintenance of this striking case of laterality
DOI: 10.26036/cnphis0002607
title: Selective modulation of inflammatory Natural Killer (NK) cell phenotypes following histone H3K27 demethylase inhibition [ATAC-Seq and ChIP-Seq]

description: Natural Killer cells are innate lymphocytes, participate in immune surveillance and elimination of stressed or transformed cells and critically shape the inflammatory cytokine environment to interact with cells of the innate and adaptive immune system, including macrophages, dendritic and Tcells. By performing a focused compound library screening, further validated by knockdown approaches, we here identify Jumonji-type histone 3 lysine 27 (H3K27) demethylases as key regulators of cytokine production in various human NK cell subsets. The prototypic H3K27 demethylase inhibitor GSK-J4 increases global levels of the repressive H3K27me3 mark around transcription start sites including NK cell effector cytokines, and thereby reduces IFN-?, TNF?, GM-CSF and IL-10 levels in IL-15 stimulated NK cells whilst sparing the cytotoxic killing capacity against cancer cells. The anti-inflammatory effect of GSK-J4 in highly inflammatory NK cell subsets, isolated from peripheral blood or tissue from rheumatoid arthritis patients, coupled with an inhibitory effect on formation of bone-resorbing osteoclasts, suggests a wider role and utility of histone demethylase inhibition in immunity and inflammation. Overall design: ATAC-seq and ChIP-Seq of histone modifications H3K4me3 and H3K27me3 in human NK cells treated with GSK-J4 with/without reference SP1 spike-in.
DOI: 10.26036/cnphis0002608
title: GenomeTrakr project: FDA-CFSAN, IFSH

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/cnphis0002610
title: Felis catus trio and duo raw sequencing reads

description: This project proposes to sequence 99 cats to support health care for the normal household cat and our fancy cat breeds too. Many cats suffer from obesity, diabetes, asthma, urinary tract infections, cancers, heart disease and infectious diseases, just like humans. Deciphering the genetic causes for these conditions requires a database that describes all the NORMAL DNA variation in cats as well as the bad mutations! This subproject includes cat trios and duos.
DOI: 10.26036/cnphis0002613
title: Felis catus Maine Coon Cross and Siamese

description: This set includes distantly-related, closely-related, and unrelated Maine Coon Cross and Siamese cats. They were provided as part of the 99 Lives Cat Genome Sequencing Initiative.
DOI: 10.26036/cnphis0002603
title: Epilachna varivestis isolate:Regurgitant Raw sequence reads

description: The interactions between host plants and their phytophagous insects are intrinsically complex and subject to remarkable co-evolution, where both have adapted strategies to avoid each other's defense systems. In this study, used Illumina MiSeq RNA sequencing to search for effectors that may ''modulate'' beetle feeding on host plants.
DOI: 10.26036/cnphis0002612
title: Felis catus multi-region domestic shorthair

description: These domestic shorthair cats from different regions over the world were sequenced as part of the 99 Lives Cat Genome Sequencing Initiative
DOI: 10.26036/cnphis0002614
title: Felis catus multi-breed raw sequence reads

description: These cats of multiple breeds were provided as part of the 99 Lives Cat Genome Sequencing Initiative.
DOI: 10.26036/cnphis0002615
title: Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens

description: Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations Overall design: scRNA-seq with pooled CRISPR-KO perturbations in 200,000 cells across six screens unstimulated BMDC, BMDC stimulated at 3hr, TFs in K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbations, *Note: that the raw SRA data consists of BAM files not FASTQ files
DOI: 10.26036/cnphis0002604
title: RNAseq analysis of NR0B1 LOF

description: We report analysis of transcriptional chanages following RNAi depletion of NR0B1 or NRF2 depletion in NSCLC cell lines as determined by RNAseq. Additionally we also determine the genomic location of NR0B1 in NSCLC lines by Chip-Seq. Overall design: Evaulation of RNAseq following NR0B1 depeltion in one cell line and NRF2 depletion in two cell lines.
DOI: 10.26036/cnphis0002611
title: Felis catus British Shorthair Duo

description: These two cats are provided for sequencing as part of the 99 Lives Cat Genome Sequencing Initiative for studying disease-related variation
DOI: 10.26036/cnphis0002621
title: RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment

description: To elucidate whether F. nucleatum plays a role in colorectal cancer tumorigenesis, RNA-seq analysis was performed to compare the gene expression profiles of F. nucleatum treated HT-29 cell line or not. Overall design: RNA-seq was performed in HT-29 colorectal cancer cells after F. nucleatum treatment
DOI: 10.26036/cnphis0002622
title: A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response

description: Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured. We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. A genome-scale CRISPR interference (CRISPRi) screen identified genes whose depletion perturbs ER homeostasis. Subjecting ~100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses revealed epistasis among the three UPR branches, bifurcated UPR branch activation between cells subject to the same perturbation, and differential activation of the branches across hits, including a feedback loop between the translocon and the IRE1a branch. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses. Overall design: 3 different pooled CRISPR screening experiments were conducted via Perturb-seq
DOI: 10.26036/cnphis0002619
title: Oryctolagus cuniculus breed:Netherlands dwarf rabbit Transcriptome or Gene expression

description: The dwarf phenotype characterizes the smallest of rabbit breeds and is governed by the effects of a single dwarfing allele. Dwarfs typically weight under 1 kg and have altered craniofacial morphology. The dwarf allele is a recessive lethal and homozygous individuals for this allele die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal rabbits (although smaller when compared to other breeds). Here, we show that the dwarf phenotype is caused by a ~12.1 kb deletion overlapping the promoter region and the first three exons of the HMGA2 gene, leading to gene inactivation. HMGA2 has been frequently associated with body size and homozygosity for null alleles are viable in mice but not in rabbits. To gain insights on how HMGA2 inactivation affects growth, viability and transcriptional regulation of interacting genes, we carried out RNA-seq analysis of rabbit embryos.
DOI: 10.26036/cnphis0002625
title: human gut metagenome Metagenome

description: This study presented the bacterial diversity of human stool sample from the Vogt-Koyanagi-Harada disease patients in Chinese population
DOI: 10.26036/cnphis0002616
title: Phylogeny of fungus-farming ant Sericomyrmex

description: We use phylogenomic markers, ultraconserved elements (UCEs), to reconstruct evolutionary history, perform dating analyses, and infer species boundaries in the fungus-farming ant genus Sericomyrmex. This is first such attempt for the genus Sericomyrmex, which is known for its difficult taxonomy. Our study is the first to utilize UCEs to recover the relationships of closely related, recently diverged ant species, and we find that UCEs contain enough variation to capture recent species- and population-level divergences. Our analyses indicate that the number of species in Sericomyrmex (11) is less than previously described (19), even though we recognize 3 new species.
DOI: 10.26036/cnphis0002618
title: Felis catus Raw sequence reads

description: This project proposes to sequence 99 cats to support health care for the normal household cat and our fancy cat breeds too. Many cats suffer from obesity, diabetes, asthma, urinary tract infections, cancers, heart disease and infectious diseases, just like humans. Deciphering the genetic causes for these conditions requires a database that describes all the NORMAL DNA variation in cats as well as the bad mutations!
DOI: 10.26036/cnphis0002623
title: Phthiraptera/Psocodea Genome sequencing

description: Raw sequencing reads from Illumina 1.5 or 1.9 from parasitic lice (Phthiraptera) and one close relative (Psocodea)
DOI: 10.26036/cnphis0002624
title: Monodelphis domestica Epigenomics

description: Hypermethylation at CpG islands associated with gene promoters is a late, stabilizing step that maintains transcriptional silence on the inactive X chromosome of eutherian mammals. In contrast to eutherians, there are limited genome wide data on DNA methylation from other vertebrates. Previous studies of single genes in various marsupial models revealed no differential DNA methylation of promoters between the sexes, leading to the conclusion that it plays no role in marsupial X-inactivation. Using reduced representation bisulfite sequencing, we analysed CpG methylation to generate male and female methylation profiles in four representative vertebrates (mouse, gray short-tailed opossum, platypus and chicken). Platypus and chicken displayed no large-scale differential DNA methylation between the sexes on the autosomes or the sex chromosomes. As expected, in female mice, we observed hypermethylation at transcription start sites of genes subject to X-inactivation. In opossum there was no differential DNA methylation detected between the sexes at transcription start sites of genes subject to X-inactivation. However, regions flanking transcription start sites (especially 1.25-3.75 kb upstream) of these genes were hypomethylated. For genes subject to X-inactivation, our data demonstrate that the difference between DNA methylation level at transcription start sites and their flaking regions is consistent between eutherian and marsupial mammals, which we propose has a silencing effect in both groups. Our study is the first genome wide analysis of DNA methylation from matched tissue in male and female chicken, platypus and opossum. It provides the first evidence for a regulatory role of DNA methylation in marsupial X-inactivation.
DOI: 10.26036/cnphis0002633
title: Popillia japonica Genome sequencing and assembly

description: Popillia japonica
DOI: 10.26036/cnphis0002617
title: RNA-sequencing analysis of ZjSGR transgenic Arabidopsis Transcriptome

description: None
DOI: 10.26036/cnphis0002628
title: Characterization of microsatellite sequences from Colossoma macropomum

description: None
DOI: 10.26036/cnphis0002629
title: S-Nitrocysteine (CysNO) responsive genes transcriptome profiling modulates diverse regulatory pathways in Oryzea sativa

description: To understand the nitric oxide induced signaling mechanism in crop plants. Overall design: 5mM CysNO treatment to seedling plant, Transcriptome profiling
DOI: 10.26036/cnphis0002631
title: Gut microbial interactions with the inflammatory cytokine production capacity

description: As part of the 500 Functional Genomics (500FG) project, stool samples from 471 healthy adults were subjected to metagenomic shotgun sequencing (one time point per individual). Concurrently, blood samples were collected from each individual and the cytokine production was measured in response to bacterial and fungal stimulations. Significant inter-individual variation was observed in the gut microbial profiles as well as the immunological profiles. Subsequent association testing showed that microbiome-host interactions modulate the inflammatory cytokine production capacity in healthy individuals.
DOI: 10.26036/cnphis0002634
title: Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (piPSC) vs. embryonic stages

description: Systematic in vitro and in vivo characterization of Leukemia-inhibiting factor (LIF)- and Fibroblast growth factor (FGF) -derived porcine induced pluripotent stem cells (Cell reprogramming -basic developmental studies in the pig) vs Porcine embryonic stages (Plurisys) Global gene expression analyses and comparisons of LIF piPSC, FGF piPSC, Parental fibroblast line day 7-8 porcine embryo, day 10-11 porcine embryo, day 12-13 porcine embryo. Gene network analyses of piPSC lines, pNF and ICM from day 7-8 porcine embryos. Overall design: RNA-Seq profiles of three embryonic stages with a minimum of 2 replicates. RNA-Seq profiles of piPSC and pNFs performed with 3 biological replicates for each line.
DOI: 10.26036/cnphis0002635
title: Planorbarius corneus, Radix swinhoei Genome sequencing

description: Mitochondrial (mt) genome sequences are widely used for species identification and to study the phylogenetic relationships among Gastropoda. However, limited data on taxon sampling is available for Gastropoda, till date. In this study we sequenced the complete mt genomes of Radix swinhoei and Planorbarius corneus belonging to Gastropoda. Based on the sequences, we investigated the gene rearrangement of these two species with others Gastropoda and the phylogenetic relationships with respect to the ancestral gene order and their phylogenetic relationships.
DOI: 10.26036/cnphis0002637
title: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

description: 1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of “legacy” phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
DOI: 10.26036/cnphis0002620
title: Human gut microbiome with bacterial pathogen challenge

description: This project takes advantage of challenge studies with an important human pathogen, Vibrio cholera, the etiological agent of cholera, which causes severe diarrhea in developed countries. The goal of this study is to understand the dynamic interactions between the host, pathogen and microbiota and how these interactions play a role in determining the pathogen population in the host, the development of an immune response, and the diversity and ecology of the microbiota. The project uses a combination of genomic, transcriptomic and metagenomic technologies together with human challenge studies to generate new insights into the interaction of host, pathogen, and microbiota.
DOI: 10.26036/cnphis0002626
title: GenomeTrakr Project: Environmental Salmonella isolates, Emory University - FDA-CFSAN

description: Whole genome sequencing of environmental Salmonella isolates - Emory University - FDA-CFSAN
DOI: 10.26036/cnphis0002630
title: Phasianidae Genome sequencing

description: Raw sequence reads from ultraconserved element (UCE) target capture of Ithaginis and Rhizothera
DOI: 10.26036/cnphis0002632
title: Pooled CRISPR screening with single-cell transcriptome read-out

description: We combined CRISPR genome editing with single-cell RNA sequencing to assess complex phenotypes in pooled cellular screens. Our method for CRISPR droplet sequencing (CROP-seq) comprises four key components: a gRNA vector that makes individual gRNAs detectable in single-cell transcriptomes, a high-throughput assay for single-cell RNA-seq, a computational pipeline for assigning single-cell transcriptomes to gRNAs, and a bioinformatic method for analyzing and interpreting gRNA-induced transcriptional profiles. CROP-seq allowed us to link gRNA expression to the associated transcriptome responses in thousands of single cells using a straightforward and broadly applicable screening workflow. Additional information are available from the CROP-seq website http://crop-seq.computational-epigenetics.org Overall design: Drop-seq species mixing experiment was performed with human HEK293T and mouse 3T3 cells in a 1:1 proportion as described by Macosko et al. For CROP-seq, Jurkat cells were transduced with a gRNA library targeting high-level regulators of T cell receptor signaling and a set of transcription factors. After 10 days of antibiotic selection and expansion, cells were stimulated with anti-CD3 and anti-CD28 antibodies or left untreated. Both conditions were analyzed using CROP-seq, measuring TCR activation for each gene knockout. Our dataset comprises 5,905 high-quality single-cell transcriptomes with uniquely assigned gRNAs. All CROP-seq raw data files are multiplexed with single-cell reads. Each read 1 contains the cell barcode (12 bp) and a molecule barcode (8 bp) and read 2 contains the transcriptome read. The libraries are pooled by nature but also intrinsically labelled. The file CROP-seq_Jurkat_TCR.digital_expression.csv.gz contains gene level expression quantifications of each gene for each cell which corresponds to the cell barcode in read1. For the Drop-seq_HEK293T-3T3 sample (Drop-seq species mixing), reads aligning to two genomes were used to quantify for each cell barcode the amount of reads coming from each genome. In a similar way, in the CROP-seq_HEK293T sample (CROP-seq gRNA mixing), the number of gRNA molecules detected per cell barcode (which is possible due to the polyadenylation of these gRNA-containing transcripts when expressed from a Pol2 promoter as engineered) were counted.
DOI: 10.26036/cnphis0002638
title: Sequencing of plant species from the Lamiales

description: None