cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000061
title: The performance of BGISEQ-500 for RNA-Seq

description: By assessing the results of 3 replicate libraries which sequenced by BGISEQ-500 (2 x 100 bp), this study evaluates the accuracy of gene expression quantification, technical repeatability and junction detection.
DOI: 10.26036/cnphis0000062
title: BGISEQ-500 ChIP-Seq SE50 demo data

description: ChIP-Seq is a method used to analyze protein interactions with DNA.ChIP-seq is used primarily to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms.It can be used to map global binding sites precisely for any protein of interest.H3K4me3 ChIP-Seq sample on human Hela cell line is a ChIP DNA sample. So the sample can be used to estimate the accuracy of high-throughput sequencing platform for ChIP sequencing.
DOI: 10.26036/cnphis0000063
title: The microbiota at the female reproductive tract in successful IVF-ET and RIF

description: Repeated implantation failure (RIF) is a critical problem which imperils the success of in vitro fertilization and embryo transfer (IVF-ET), but its causes remain unclear. Microorganisms residing the upper genital tract have emerged as possible contributors to RIF. Here we characterized the microbiota at three sites of the reproductive tract in women with successful IVF-ET and those with RIF. 16S rRNA sequencing revealed pronounced difference in the composition of microbiota at the genital tract between these two groups. The cervico-uterine microbiota of RIF patients was featured by reduced diversity and depletion of numerous signature taxa across the reproductive tract. This compositional shift was coupled with alterations in a wide spectrum of microbial functions, especially in multiple pathways of nutrient metabolism. Altogether, our study provided evidence for the link between genital microbiome and outcome of IVF-ET.
DOI: 10.26036/cnphis0000810
title: Daubentonia madagascariensis Genome sequencing

description: Draft Assembly of Aye-Aye (Daubentonia madagascariensis) using next-generation sequencing data.
DOI: 10.26036/cnphis0000811
title: Teladorsagia circumcincta Genome Sequencing

description: The Genome Institute and collaborators are sequencing the brown stomach worm, Teladorsagia circumcinta (aka Ostertagia circumcincta). This is economically the most important parasite of sheep throughout temperate regions of the world and has developed multiple resistances to drugs. Globally, these parasites lead to millions of dollars in economic losses due to low production of meat, wool and milk and the high costs of treatment. These brownish, thread-like worms infect the gastric glands of the stomach in small ruminants (sheep and goats), causing weight loss, decreased wool production and death. Sequencing T. circumcincta will aid in vaccine development and the study of the immune response in this host-parasite system. A vaccine against T. cicumcincta would reduce economic losses associated with infection, particularly in regions where multiple-drug resistant strains exist.
DOI: 10.26036/cnphis0000812
title: Population genomics in lake and stream stickleback populations

description: None
DOI: 10.26036/cnphis0000813
title: Contributions of selection and mutation in explaining the recombination-genomic diversity association in Drosophila

description: Whole genome resequencing of Drosophila pseudoobscura and close relatives to obtain genome-wide diversity and divergence measures.
DOI: 10.26036/cnphis0000814
title: Natural history shapes genetic structure: Comparative range-wide population genetics of endemic aquatic turtles in the Chihuahuan desert

description: Habitat fragmentation is important in shaping population genetic structure. Habitat requirements of different species, however, may translate to different effective levels of fragmentation, as dispersal may not be as limited for species as it is for others. In desert-spring ecosystem of Cuatro Ciénegas, the desert surrounding aquatic habitats may be a formidable barrier to dispersal for aquatic species, but relatively traversable for semi-aquatic species. Here I compare the population genetic structure across the entire species’ ranges for three endemic turtle species with differing aquatic requirements. A previous study characterized the semi-aquatic box turtle, Terrapene coahuila, as having little population genetic structure and high rates of dispersal among most habitats. Here I compare the genetic structure of the box turtle to two aquatic species. The aquatic pond turtle, Trachemys taylori, exhibited significant isolation by distance and high genetic differentiation among subpopulations, with a global FST of 0.076 (0.044, 0.108)— consistent with reduced dispersal among subpopulations. Even stronger genetic structure was identified across habitats for the softshell turtle, Apalone atra, a species that is highly sensitive to desiccation and leaves water for nesting only. For the softshell turtle, global FST was equal to 0.161 (0.006, 0.016), and nearly all of localities were significantly different from one another, indicating that dispersal is more limited for the softshell than for the other two turtle species. No correlation of genetic differentiation with geographic distance was exhibited. This evidence, combined with allelic patterns, support a scenario of softshell turtles from each pond being isolated from the others since the basin became substantially drier near the beginning of the Holocene. Taken together, these results suggest that the natural history of an organism is a substantial factor for current population genetic structure in this ecosystem. As a by-product of this work, 6.6% of Apalone atra genome was sequenced using next-generation sequences, and microsatellite markers were developed from these data. Code for developing microsatellite markers from 454 reads, and the marker resource for this species are made publically available.
DOI: 10.26036/cnphis0000815
title: Paradoxornis webbianus bulomachus Transcriptome or Gene expression

description: Characterization of transcriptome from a single individual of an ecologically important species, the vinous-throated parrotbill (Paradoxornis webbianus bulomachus) and its implications for adaptation genetics.
DOI: 10.26036/cnphis0000816
title: Ancylostoma caninum Genome Sequencing

description: The Genome Institute and collaborators are sequencing the dog hookworm, Ancylostoma caninum. Hookworm diseases are extremely common in the tropics and sub-tropics, with a disease burden comparable to measles and exceeding that of diabetes and lung cancer. A. caninum causes disease in dogs resulting often in severe anemia and death. This species, which belongs to the group of parasites most closely related to C. elegans, is a widely used model for hookworm infection.
DOI: 10.26036/cnphis0000818
title: Oesophagostomum dentatum Genome Sequencing

description: Oesophagostomum dentatum, the nodule worm, is a common parasite of domestic and feral pigs worldwide. Swine (Sus scrofa) is the only host and harbors the pre-adult and adult stages in the large intestines, especially the caecum. Eggs and early larval stages (L1 to L3) can be found in the environment.
DOI: 10.14457/su.res.2013.42
title: ผลของสารยับยั้งเอนโดไซโทซิสต่อประสิทธิภาพการถ่ายโอนยีนด้วยไคโตซาน/พอลิแอลอาร์จินีน/ดีเอ็นเอคอมเพล็กซ์ในเซลล์ HeLa
DOI: 10.14457/su.res.2017.26
title: การประเมินหลักสูตรศึกษาศาสตรมหาบัณฑิต สาขาวิชาการสอนภาษาไทย คณะศึกษาศาสตร์ มหาวิทยาลัยศิลปากร (หลักสูตรปรับปรุง 2557)
DOI: 10.14457/su.res.2017.27
title: การประเมินหลักสูตรศึกษาศาสตรบัณฑิต สาขาวิชาการศึกษาปฐมวัย คณะศึกษาศาสตร์มหาวิทยาลัยศิลปากร
DOI: 10.26036/cnphis0000064
title: The Microbiota Continuum along the Female Reproductive Tract and Its Relation to Uterine-related Diseases

description: Foetal development in humans is assumed to proceed in a sterile environment. Reports on bacteria detected in maternal fluids during pregnancy are typically associated with adverse consequences, and whether the female reproductive track harbour distinct microbial communities beyond the vagina has been a matter of debate. Here we performed systematic microbiota sampling within the female reproductive tract in 110 women of reproductive age, and examined the nature of colonization by bacterial sequencing and cultivation. The analysis uncovered distinct communities of microbes in the cervical canal, the uterus, the fallopian tubes, and the peritoneal fluid, differing from that of the vagina. Importantly, the results reflected an anatomical microbiota continuum along the female reproductive tract representative of a non-sterile environment. We also identified microbial taxa and potential functions that correlated with the menstrual cycle or were over-represented in subjects with adenomyosis or infertility due to endometriosis. The study presents detailed insight into the nature of the vagino-uterine microbiome, and suggests the microbiota in the upper reproductive tract as a target for improving female reproductive health. The study further holds new possibilities for detection of common diseases in the upper reproductive tract by surveying the vaginal or cervical microbiota.
DOI: 10.26036/cnphis0000066
title: Three Bauhinia species transcriptome sequence data

description: Hong Kong’s emblem is the beautiful Bauhinia flower and appears on our flag. This is the flower of the orchid tree Bauhinia blakeana, which was first discovered in Hong Kong. What many people may not know is that it is a sterile hybrid, and how and why it ended up in Hong Kong is shrouded in mystery. One of the best ways to help uncover the secrets of any organism is by understanding its genetic makeup. Genomics, sequencing of the genetic code of organisms, provides a complete look into the genetic complement of any species. It is also one of the key technologies that will define the 21st century. While Hong Kong has made major advances in this field, the general public has a very poor awareness and understanding of what this field even is. By bringing together the emblematic and mysterious Bauhinia flower and the power and knowledge of genome technology, we can build a bridge between science and community— enlightening our understanding of this plant’s interesting biology and informing and educating the public about this exciting and rapidly advancing field. To build such a collaborative endeavor, we are launching the Hong Kong genome project through which we will sequence the genome of the Hong Kong emblem to better understand where it came from; train local students to assemble and analyse the data — crucial skills needed for this field to advance; and engage the public through local pride. This will be the first Hong Kong genome project: funded by the public; sequenced in Hong Kong; assembled and analysed by local students; and directly shared with the public. We also welcome contributions and interest from the rest of the world, hoping this serves as a model to inspire and inform other national genome projects, and aid the development of crucial genomic literacy and skills across the globe, inspiring and training a new generation of scientists to use these tools to tackle the biggest threats to mankind: climate change, disease, and food security.The data presented here are four transcriptome datasets: leaf and flower data from Bauhinia blakeana as well as leaf transcriptomes from the most likely parent species Bauhinia purpurea and Bauhinia variegata. Specimens were collected in Hong Kong, and sequenced at the laboratories of BGI Hong Kong using the Illumina HiSeq 4000 platform. RNA was extracted using protocols available at protocols.io (see: dx.doi.org/10.17504/protocols.io.gsnbwde). These data are made available here for analysis and the open-source teaching of transcriptomics analysis. For more on the project see: http://bauhiniagenome.hk/
DOI: 10.26036/cnphis0000067
title: A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning

description: The microbial diversity of environments like the human gut extends far beyond what is covered by reference genomes. Here we present a method for exhaustive and unsupervised co-abundance gene binning across a series of highly complex metagenomic samples. As the method does not rely on previously sequenced reference genomes it allows for discovery of new species, viruses and clonal heterogeneity. We demonstrate the method on human gut microbiome data and identify 7,381 co-abundance gene groups (CAGs) ranging in size from 3 to 6,319 genes. The CAGs represent a wide variety of biological entities including microbial genomes, phages and clonal differences. We name the 741 largest of these metagenomic species (MGS), because they correspond to microbial species. In addition, we establish microbial host affiliations by dependency-associations for many small CAGs. Longitudinal sampling in the same individuals indicates that some of these dependency-associations are important for the persistence of their microbial host
DOI: 10.26036/cnphis0000068
title: Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

description: BGISEQ-500 is a recently launched cPAS-based desktop sequencer, which has been used for RNA-seq and whole-genome sequencing. However, the performance of this high-throughput sequencing platform for metagenomic shotgun sequencing has not yet been evaluated.In this study, we generated a BGISEQ-500 metagenomic dataset from 20 healthy individuals including 8 sequencing replicates and 8 library replicates. By an in-house-developed overall-accuracy quality control method, BGISEQ-500 produced an average of 82.45 million high quality reads (96. 06% of raw reads) per sample with 90.56% of bases scoring Q30 and above. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Furthermore, we assessed the inter-platform variation using 20 pairwise cross-platform replicates on BGISEQ-500 and Illumina HiSeq 2000 and demonstrated a high consistency between platforms. Only 11,354 (3.25%) genes showed reproducible significant differences in relative abundance between platforms, with a bias towards genes with higher GC content being enriched on the HiSeq 2000 platform.Our results demonstrate excellent intra-platform stability and inter-platform consistency for metagenomic data using the BGISEQ-500 platform validating the applicability of this new sequencing platform for quantitative metagenomic studies. We hope that you find our data and manuscript of general interest and sufficient quality to be considered for publication in GigaScience.
DOI: 10.26036/cnphis0000069
title: 16S rDNA Sanger sequencing of LAB isolates

description: Genomic DNA of isolates were extracted and 16S rDNA genes were amplified with universal primers (27F: 5’ AGAG-TTTGATCCTGGCTCAG 3’; 1492R: 5’ AAGGAGGTGATCCAGCCGCA 3’).
DOI: 10.26036/cnphis0000072
title: A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

description: The rumen microbiome is responsible for the unique nature of ruminants. A thorough knowledge of the genetic potential of rumen symbiotic microbes is therefore crucial for the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed various diets whereas known rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of lignocellulosic material and production of methane. Genes coding for enzymes that deconstruct lignocellulosic substrates showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.
DOI: 10.26036/cnphis0000819
title: Dictyocaulus viviparus Genome Sequencing

description: Dictyocaulus viviparus, the bovine lungworm, is the cause of parasitic bronchitis in cattle (husk, verminous pneumonia, dictyocaulosis) with a world wide distribution in temperate areas. The predominant hosts are cattle, but it can also be found in small ruminants (sheep, goats) and deer. Infection occurs on pasture as infective larvae develop from L1 that are shed with the feces to free-living infective L3 that are ingested by cattle while grazing. Free-living larvae do not feed; survival on pasture is therefore limited to a few months depending on temperature and humidity. The parasite is able to interrupt development inside the host. Infective larvae that have been exposed to low temperatures on pasture before infection subsequently develop only to preadult larval stages that survive winter conditions as hypobiotic larvae in the lung and resume development in spring. These animals contaminate pastures the following spring and represent the major source of infection for other susceptible cattle.
DOI: 10.26036/cnphis0000820
title: Integrating Genomics, Transcriptomics, and T-Cell Biology: An RNA-seq Atlas of the Murine CD4+ Transcriptome

description: CD4+ cells are key regulators of the adaptive immune system and can be classified into two main groups: T helper cells (naive, Th1, Th2 and Th17 cells), and regulatory T cells, iTreg and nTreg cells). We performed mRNA-sequencing on these major CD4+ cell subtypes, and integrated multiple computational methods for analyzing gene/isoform expression, differential expression, and functional annotation. Our primary analysis not only provides evidence for the very high quality of the sequence data, but also reveals novel patterns of read distributions inside and adjacent to genes. We identify 168 novel transcripts, which are differentially expressed in the various CD4+ cell subtypes. Further, we identify a wealth of novel, uniquely differentially expressed ''signature'' transcripts for each cell type. nTreg cells have the largest number of these, with 477 signature genes in total, of which 58 are transcription factors. The data is compiled into an easily accessible online database publically available at http://www.thelpercell.com. Overall design: RNA-seq data of Murine CD4+ cells
DOI: 10.26036/cnphis0000821
title: Drosophila biarmipes genome sequencing project

description: The <i>Drosophila biarmipes<i> genome is being sequenced by the Baylor College of Medicine as part of the modENCODE project to provide comparative sequencing data for the identification of functional DNA elements in the <i>D. melanogaster</i> genome.</i></i>
DOI: 10.14457/aru.res.2013.1
title: การมีส่วนร่วมในการพัฒนารูปแบบการจัดอุปกรณ์อำนวยความสะดวกและสภาพแวดล้อมที่ปลอดภัยสำหรับผู้สูงอายุ (ปีที่ 2)
DOI: 10.14457/aru.res.2013.3
title: การพัฒนาเนื้อหาระบบฝังตัวสำหรับการจัดการศึกษาเพื่ออาชีพ
DOI: 10.14457/su.res.2011.120
title: ความคิดเห็นของนักศึกษาที่มีต่อการจัดการศึกษาของคณะเภสัชศาสตร์ มหาวิทยาลัยศิลปากร
DOI: 10.14457/su.res.2014.53
title: ผลของสารสกัดจากขลู่ต่อการแสดงออกของโปรตีน COX-1 และ COX-2 ในเซลล์ HeLa
DOI: 10.14457/su.res.2014.54
title: การวิเคราะห์ข้อมูลตำรับยาแผนไทยโดยใช้เทคนิคทางปัญญาประดิษฐ์
DOI: 10.14457/su.res.2015.52
title: การประยุกต์ใช้เอนไซม์ดีฟีนิลกลัยซีนอะมิโนทรานสเฟอเรส สำหรับวิเคราะห์หาปริมาณกรดแอลฟาคีโตกลูตาริก
DOI: 10.26036/cnphis0000065
title: Here we performed a metagenome-wide association study (MWAS) on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls.

description: The gut microbiota has been linked to cardiovascular diseases, most notably through the production of trimethylamine and its hepatic conversion to the proatherogenic metabolite, trimethylamine-N-oxide. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here we perform a metagenome-wide association study on stools from 218 individuals with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular health. We further identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes), liver cirrhosis, and an autoimmune disease, rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.
DOI: 10.26036/cnphis0000070
title: The comparison of Macaca fascicularis gut microbiota to other mammalians and its changes under type 2 diabetes condition

description: The Macaca fascicularis model is widely used in scientific research and drug development as its genetics is very closed to human being. Comparing its similar feeding habits with human, the characteristics of Macaca fascicularis gut microbiota and its similarities to human and other mammalians remains unknown and knowledge of the functional interplay between the gut microbiota and host physiology in Macaca fascicularis is also limited. In our study, faecal samples from 20 Macaca fascicularis individuals were applied to metagenomic sequencing to construct the first gene catalogue of Macaca fascicularis gut bacteria. Totally 1.9 million non-redundant bacterial genes were identified.
DOI: 10.26036/cnphis0000071
title: A catalog of the Sprague-Dawley (SD) rat gut metagenome

description: As no gene set of the gut microbiome had been previously established for SD rat, here we describe the BGISEQ-500-based metagenomic sequencing, assembly and characterization of 5.3 million non-redundant microbial genes, derived from 651.2 Gb of single-end sequence and 611 Gb of paired-end sequence, from ninety-eight fecal samples were collected from 7 individual groups at 2 different time points (Day 0 and Day 30). Maybe it limits coverage of global microbiome diversity of Rat, but it is a first gene catalogue of Rat of strain Sprague-Dawley which is a good animal model for arthritis research
DOI: 10.26036/cnphis0000073
title: A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses

description: Background: The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing. Results: In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method, and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days.Conclusions: We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.
DOI: 10.26036/cnphis0000076
title: Exome sequencing of (ASW) African ancestry in South West US population

description: -
DOI: 10.26036/cnphis0000077
title: Exome sequencing of (PJL) Punjabi HapMap population

description: -
DOI: 10.26036/cnphis0000078
title: Exome sequencing of (GWD) Gambian in Western Division, The Gambia HapMap population

description: -
DOI: 10.26036/cnphis0000080
title: Exome sequencing of (MSL) Mende in Sierra Leone HapMap population

description: -