cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001045
title: Small RNA transcriptome in the Squalius alburnoides complex

description: The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change. Overall design: 4 samples were analyzed corresponding to 4 genomic constitutions: PAA, PA, AA and PP. For each sample, a library based on 3 individuals of the same genomic constitution was prepared. From each individual, 3 types of tissues were collected for RNA extraction (brain, liver and muscle).
DOI: 10.26036/cnphis0001046
title: Transcriptome sequencing of the rock pigeon, Columba livia

description: Deep sequencing of mRNA from the rock pigeon Overall design: Analysis of ploy(A)+ RNA of different specimens: heart and liver from the rock pigeon (Danish Tumbler, Oriental Frill and Racing)
DOI: 10.26036/cnphis0001047
title: Iberian lynx fecal Metagenome

description: Metagenomic analysis of fecal samples from the endangered Iberian lynx (Lyns pardinus). The animal has a normal health status, calm, the sample was taken 8 hours before the last meal, the corporal status was good and healthy. The Iberian lynx (Lynx pardinus) is native to the Iberian Peninsula and is considered the most endangered felid species in the world. In this study we analysed the co-existence of gene sets to utilize primary and secondary energy supplies in endangered Iberian lynx distal gut.
DOI: 10.26036/cnphis0001048
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001049
title: Bubalus bubalis genome sequencing

description: Blood Samples
DOI: 10.26036/cnphis0000325
title: Mola mola isolate:MOLMO Genome sequencing and assembly

description: Sequencing for Mola mola (ocean sunfish), the largest bony fish in the world
DOI: 10.26036/cnphis0000326
title: Penicillium oxalicum Raw sequence reads

description: A cellulase hyper-producing mutant, EU2106, of P. oxalicum strain HP7-1 was identified after three rounds of ?-irradiation and two rounds of ethyl methanesulfonate/ultraviolet light mutagenesis
DOI: 10.26036/cnphis0000327
title: Penicillium oxalicum Transcriptome or Gene Expression

description: the goal of the project is to identify the differentially expressed genes between HP7-1 and EU2106.
DOI: 10.26036/cnphis0000328
title: Narenga porphyrocoma Transcriptome or Gene expression

description: drought resistance of Narenga porphyrocoma
DOI: 10.26036/cnphis0000329
title: Scleropages formosus (golden arowana) genome sequencing and assembly

description: golden arowana genome assembly
DOI: 10.26036/cnphis0000330
title: Borreliella afzelii strain:FP1 Genome sequencing and assembly

description: Genomic characteristics of Chinese Borrelia burgdorferi isolates
DOI: 10.26036/cnphis0000331
title: Borreliella burgdorferi strain:CS4 Genome sequencing and assembly

description: Genomic characteristics of Chinese Borrelia burgdorferi isolates
DOI: 10.26036/cnphis0000332
title: Borreliella afzelii strain:R9 Genome sequencing and assembly

description: Genomic characteristics of Chinese Borrelia burgdorferi isolates
DOI: 10.26036/cnphis0000333
title: Borrelia yangtzensis strain:QX-S13 Genome sequencing and assembly

description: Genomic characteristics of Chinese Borrelia burgdorferi isolates
DOI: 10.26036/cnphis0000334
title: Borreliella garinii strain:PD91 Genome sequencing and assembly

description: Genomic characteristics of Chinese Borrelia burgdorferi isolates
DOI: 10.26036/cnphis0001050
title: Phylloscopus trochilus Transcriptome or Gene expression

description: The goal of the study was to identify sequence variation in coding genes of the willow warbler Phylloscopus trochilus and explore how this variation is distributed between two subspecies (P.t.trochilus and P.t.acredula). RNA was isolated from whole brain originating from eight individuals of each subspecies and pooled together into subspecies-specific cDNA libraries. These libraries were normalized and sequenced using the 454 FLX Titanium technology. Two runs of sequencing generated 1.8 million reads after filtering steps, of which 84 % were mapped to the zebra finch genome. The alignments were overlapping with more than 12,000 predicted genes in the zebra finch genome and contained more than 162,000 single nucleotide polymorphism (SNPs).
DOI: 10.26036/cnphis0001051
title: Belgica antarctica isolate:Palmer_Station_2011 Genome sequencing

description: Transcriptome and genome sequencing of Belgica antarctica, the only insect endemic to Antarctica.
DOI: 10.26036/cnphis0001052
title: Flying lemur, or colugo, of Southeast Asia

description: 55X assembled sequence coverage of a flying lemur genome. Total input sequence coverage of Illumina reads was 60X (45X 230-330 short inserts, 15X 3kbs, and 5X 8kbs) using a genome size estimate of 3.0Gb.
DOI: 10.26036/cnphis0001053
title: Genome sequencing of Chlorocebus aethiops cynosuros

description: This project will provide the genomic sequence of multiple Chlorocebus aethiops cynosuros individuals as part of the Vervet Subspecies Phylogeny project.
DOI: 10.26036/cnphis0001054
title: Pristionchus pacificus Genome sequencing

description: Whole genome sequencing of 104 Pristionchus pacificus strains.
DOI: 10.26036/cnphis0001055
title: RNASeq analysis of Salmonella B cell infection model

description: We report the transcriptome analysis of S. enterica 14028 during infection of murine B cells. Mice spleens were infected with Salmonella enterica 14028. Mouse spleens were harvested and cells FACS sorted into various immune cells containing bacteria. Short reads were mapped to the S. enterica 14028 genome. Overall design: Mice were infected with S. enterica strain 14028. Spleens were collected, homogenized and cells FACS sorted. Total RNA was extracted using the Ambion mirVana RNA isolation kit. Purified RNA was depleted of rRNA utilizing the epicentre ribozero metabacteria and eukaryotic kits.
DOI: 10.26036/cnphis0001056
title: Gene Expression Changes in a Tumor Xenograft by a Py-Im Polyamide

description: Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5’-WGGWWW-3’ with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. A FITC-labeled analogue of this polyamide can be detected in tumor-derived cells by confocal microscopy. RNA deep sequencing (RNA-seq) of tumor tissue allowed the identification of further affected genes, a representative panel of which were interrogated by qRT-PCR and correlated with cell culture expression levels. Overall design: Xenografts. Grafting with A549-luc-C8. Experiments were performed in female SCID-beige mice (Charles River) between 8 and 12 weeks of age. Cells were injected into the left flank area of the animals as suspensions of 25 x 106 mL-1 in RPMI, 200 µL per injection. Treatment and tumor proliferation monitoring. Mice were treated following the schedule delineated in treatment protocol. Tumor proliferation was monitored using the XENOGEN imaging device. The animals were anesthetized with 2 5 % isoflurane and subsequently transferred to the imaging chamber, whereupon the isoflurane levels were reduced to 1-2.5 %. The floor of the imager was heated to +37 ºC to avoid hypothermia. Breathing frequency was monitored and not allowed to drop below 1 s-1, adjusting the isoflurane levels accordingly at all times. Endpoint criteria and euthanasia. Animal endpoint criteria encompassed weight loss of over 15 %, restriction of motor function by the engrafted tumor, dehydration of over 10 % and moribund behavior. Where appropriate, the animals were euthanized by asphyxiation in a CO2 chamber. Tumor tissue harvest. Animals were resected and tumors excised using standard forceps, scissors and surgical blades. The tumors were combined into one sample per condition and mechanically sheared in TRIZOL, employing a specialized device (tissue tearer, model 985370). Total RNA workup was performed following the standard TRIZOL procedure, followed by a DNAse digest.
DOI: 10.26036/cnphis0001057
title: Dendroctonus ponderosae Genome sequencing

description: Bark beetles (Coleoptera: Scolytinae) are pests of many forests around the world. The mountain pine beetle, Dendroctonus ponderosae Hopkins, is a serious insect pest of Western North American pine forests. Increasingly, genome sequences of non-model organisms will require assembly from individual organisms lacking inbreeding to reduce heterozygosity, which presents a difficult challenge in genome assembly. We present a draft de novo genome of this major forest insect pest assembled from Illumina paired-end short-insert sequencing reads of genome DNA from an individual field-collected pupa and scaffolded with Illumina mate-pair sequencing reads of genomic DNA from pooled field-collected pupae, paired-end short-insert whole transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. The resources we have developed in the mountain pine beetle provide the second reference genome in Coleoptera, the first for a forest insect pest, and can inform research in areas such as gene discovery; functional and population genomics; and comparative analyses in this and other Dendroctonus species and more generally to Scolytinae and other Coleoptera.
DOI: 10.26036/cnphis0001058
title: Real time evolution of new genes by innovation, amplification and divergence

description: Experimental evolution of DA19306 (Salmonella typhimurium LT2 hisA::FRT trpF::FRT araB::FRT-tet-FRT / F''128 lacI::FRT zzf1831::T-his(hisA[D10G dup13-15]) dinB::FRT). Evolved for improved HisA and TrpF activity of the mutant hisA gene carried on the F'' episome by serial passage in liquid M9+0.2% glycerol. The Illumina reads contain the chromosome, the F'' plasmid and pSLT.
DOI: 10.26036/cnphis0000335
title: Litopenaeus vannamei Transcriptome or Gene expression

description: Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique.
DOI: 10.26036/cnphis0000337
title: Ictalurus punctatus strain:channel catfish Genome sequencing and assembly

description: The Ictalurus punctatus genome is one of the most important freshwater fish species around the world, occupies a prominent position in the aquaculture industry of the United States.
DOI: 10.26036/cnphis0000338
title: Oryza brachyantha Genome sequencing and assembly

description: Oryza brachyantha is a wild rice species that is found in central Africa. It is tufted, slender, distributed in central Africa, and usually lives on rocks or in shallow water. Oryza brachyantha is a phyletically basal species in the genus Oryza. The unique phylogenic position and compact genome make this species an excellent model for comparative genomic in this genus. We chose the commonly used accession IRGC101232 for genome sequencing.
DOI: 10.26036/cnphis0000339
title: Comparative analysis of two rat inbred lines

description: Here we re-sequenced two rat inbred genomes in Illumina platform, which the depth is as high as 35X. We used the BN genome as the reference to map all reads to it and the coverage is 90% or more. Based on alignment, we identified SNPs, InDels, SVs, CNVs for each strain. Then we also validate our SNPs and/or InDels by using Sanger sequencing, which the accurate rate reached up to 94.75%. According these data, we constructed two detailed genetic variation maps. Finally, we also assembly a draft genome for each line combining concensus of themselves based on these resequencing data. These results will support our following medical research dramatically.
DOI: 10.26036/cnphis0000340
title: Sorghum bicolor strain:Keller, E-Tian, Ji2731 Genome sequencing and assembly

description: Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fibre and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height and production of grain and biomass. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecies variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations. In addition, 17,111 CNVs were detected. This is a first report on the identification of genome-wide patterns of genetic variation in sorghum. Because some genes might exist in sorghum but are missed in the currently assembled BTx623 sorghum genome. We assembled unmapped reads with SOAPdenovo and obtained contigs with a total length of 7.2 Mb of sequences. Annotation of these contigs showed 73 putative absent genes with an average length of 409bp (only coding regions were considered). A BLAST search against Arabidopsis, rice and maize genome databases revealed that 33 of these genes showed homology with known proteins (E value &lt; 1e-617 ).
DOI: 10.26036/cnphis0000342
title: Homo sapiens Raw sequence reads.SRP075387

description: low-coverage whole-genome sequencing of plasma DNA
DOI: 10.26036/cnphis0000343
title: Camelus bactrianus Raw sequence reads

description: We leveraged the high-throughput data generated by Miseq sequencing of the variable domains of the antibody heavy chains from three Bactrian camels to conduct in-depth comparative analyses of the immunoglobulin repertoire. These include analyses of the complementary determining region 3 (CDR3) length and distribution, mutation rate, antibody characteristic amino acids, the distribution of the cysteine (Cys) codons and the non-classical VHHs.For the first time, a relatively complete picture of the Bactrian camel antibody immune repertoire including conventional antibody (Ab) and HCAbs has been depicted through PCR and in silico analysis based on high-throughput sequencing data.
DOI: 10.26036/cnphis0000344
title: Bos mutus strain:yakQH1 Genome sequencing and assembly

description: The yak genome and high-altitude adaptation.
DOI: 10.26036/cnphis0001059
title: Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation

description: Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these ''relatively young'' genes was critical for the origin and radiation of eukaryotes. Overall design: Two Pacific oysters were used for methylome profiling in this study. One is an inbred oyster (05x7-T-G4-1.051#20) that was produced by four generations of sister-brother mating (coefficient of inbreeding, F = 0.59) and has been used for whole genome-sequencing. The other was a wild oyster collected from Weihai, Shandong Province, China. Both oysters were about two years of age. The inbred oyster was produced as single oysters and cultured intertidally at southern Puget Sound, Washington, USA, where the water temperature ranges from 7 to 16 °C. The wild oyster was an attached oyster from an oyster farm in its native range at Weihai, China, where the water temperature ranges from 4 to 27 °C. For DNA from each of the two individuals, we constructed two independent libraries. For each library, 5 µg genomic DNA mixed with 25 ng cl857 Sam7 Lambda DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 250 bp. End-repair, 3’-end dA addition and adapter ligation were subsequently performed. Methylated adapters were used according to the manufacturer’s instructions (Illumina). The bisulfite conversion of DNA was performed according to a modified NH4HSO3-based protocol and amplified with nine cycles of PCR. All libraries were subjected to 90-bp paired-end sequencing on an Illumina HiSeq 2000 platform.
DOI: 10.26036/cnphis0001060
title: Gallus gallus Oviduct Transcriptome

description: Using HiSeq2000 to sequence white leghorn different parts (ovary, magnum, isthmus and uterus) of oviduct at 40-weeks.
DOI: 10.26036/cnphis0001062
title: Amorphophallus bulbifer Transcriptome or Gene expression

description: Development of microsattlite markers by transcriptome sequencing.
DOI: 10.26036/cnphis0001063
title: Draft genome sequence by Washington University

description: A draft assembly of the <i>Tupaia belangeri</i> genome will be produced by Washington University.
DOI: 10.26036/cnphis0001064
title: Astyanax mexicanus Genome sequencing

description: <i>Astyanax mexicanus</i> provides a model for retinal degeneration diseases of old age.
DOI: 10.26036/cnphis0001065
title: Physeter macrocephalus Genome Sequencing

description: Metals are a well-known cause of respiratory disease. Chromium is best known as a human lung carcinogen, however it causes other lung disease such as respiratory distress, asthenia, emphysema, chronic irritation and fibrosis. Cr(VI) is considered a particularly important and dangerous environmental chemical because it induces lung disease, and exposure to it is widespread. It is listed as one of the "Top 20 Hazardous Substances" by the Environmental Protection Agency (EPA) and the Agency for Toxic Substances and Disease Registry. Accordingly, because the potential for exposure to this carcinogen is high, it is imperative that we discover ways to prevent its toxicity. Whales are known to accumulate levels of metals that are sufficient to seriously impair or even kill terrestrial mammals. For example, the concentrations of cadmium in the kidney cortex from a bowhead have been calculated to be two hundred parts-per-million, which would harm land-dwelling animals, but the bowheads seem unaffected, as 400 necropsies have been performed and no ill health observed. Hypoxia is a well-known cause of respiratory related diseases such as sleep apnea, chronic obstructive pulmonary disease and pulmonary emphysema. Marine mammals, however, can dive to great depths for prolonged periods of time and not experience these ill effects of hypoxia. The sperm whale is one of the deepest-diving mammals in the world. Several times a day the sperm whale dives to the deep ocean in search of food. A dive commonly averages 1,312 feet and lasts about 35 min. However, dives may last over two hours and reach over 3,280 feet, and possibly even over 9,842 feet. These dives are routinely performed, suggesting sperm whales have adapted key cellular and molecular mechanisms to deal with these hypoxic stresses. A genome assembly resource for sperm whale would allow scientists to test molecular pathways that adapted to such incredible hypoxic stress.
DOI: 10.26036/cnphis0001066
title: Chaenocephalus aceratus Genome sequencing

description: The Antarctic icefish (Chaenocephalus aceratus) provides several evolutionary models of human disease, including osteopenia, lipid storage diseases, and anemia. For osteopenia, a reduction in bone mineral density, identifying genetic factors in icefish that underlie the loss of bone mineral density in icefish over evolutionary time can lead to a better understanding of the mechanisms that lead to bone loss over developmental time in aging humans.Antarctic icefish have greatly reduced skeletal mineralization. Skeletal reduction in icefish occurs by at least two mechanisms. The first is by delaying activation of bone mineralization genes, such as co/7a7. This results in a skeleton that is largely cartilaginous. Regulatory genes that control the timing of bone mineralization in icefish are as yet unknown. The second mechanism of icefish skeletal reduction is a decrease in the extent of mineralization in the skeletal elements that do ossify. Little is yet known about factors that control this process. Molecular genetic comparison of icefish to closely related robustly skeletonized fish, such as the rockcod {Notothenia coriiceps), will help identify regulatory factors essential for the maintenance of bone mineral density. Antarctic icefish accumulate lipids in muscle, skeleton, and connective tissue. This phenotype resembles human disease states such as Chanarin-Dorfman syndrome and neutral lipid storage disease with myopathy. Icefish muscle cells are riddled with lipid vesicles but few studies have investigated the molecular genetic mechanisms that cause icefish to accumulate lipid deposits. In humans, such deposits are debilitating, but in icefish, they are favored by natural selection because they make the body less dense, thus facilitating prey capture off the ocean floor. Icefish have lost the ability to form red blood cells resulting in profound anemia. The cost of this disaptation is low due to the high capacity of cold water to dissolve oxygen and adaptive compensatory responses, including changes in the circulatory system that involve low blood viscosity, large bore capillaries, increased vascularity, cardiomegaly, and high blood flow with low pressure. In addition, icefish hemoglobin genes have become pseudo genes. This situation thus provides an opportunity to identify hematopoietic regulatory factors present in rockcod, the "wild-type control" but absent from icefish, the "evolutionary mutant". Such genes become candidates for genes involved in human anemias. A group in Korea is sequencing Notothenia coriiceps, a fish closely related to icefish that possesses a heavily mineralized skeleton, does not accumulate lipids in muscle and bone, and has a high hematocrit. Thus, a comparator genome sequence with the "healthy" phenotype will be available, making the sequencing of the icefish (C. aceratus), our disease model, even more valuable.
DOI: 10.26036/cnphis0001067
title: Drosophila mauritiana Pool-Seq

description: A pool of 107 D. mauritiana isofemale lines sequenced to approximately 110-fold coverage using Illumina paired-end reads (Pool-Seq).
DOI: 10.26036/cnphis0001068
title: Orcinus orca Genome sequencing

description: Whole genome assembly of Orcinus orca (killer whale) by the BCM-HGSC and collaborators in the Marine Mammals Genome Projects using multiple sequencing platforms.
DOI: 10.14455/nrct.img.2018.385
title: การขยายพันธุ์กล้วยน้ำว้ามะลิอ่องโดยระบบไบโอรีแอคเตอร์แบบจมชั่วคราว (TIB)
DOI: 10.14455/nrct.img.2018.386
title: การสร้างเสริมสุขภาพดีเอ็นเอโดยใช้อาลูเอสไออาร์เอ็นเติมหมู่เมททิล
DOI: 10.14457/kku.the.2008.490
title: การสร้างและผลการใช้แหล่งการเรียนรู้ในท้องถิ่น หน่วยการเรียนรู้ เรื่อง หนองหาน โดยการจัดกิจกรรมการเรียนการสอนที่เน้นผู้เรียนเป็นสำคัญ สำหรับนักเรียนชั้นประถมศึกษาปีที่ 6