cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000105
title: De novo assembly of a haplotype-resolved human genome

description: The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next generation sequencing (NGS) and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15 Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and novel coding sequences and revealed their impact on genes function. This haplotype-resolved genome represents the most complete de novo genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.
DOI: 10.26036/cnphis0000106
title: De novo assembly of a haplotype-resolved human genome.

description: Here we provide the first de novo haplotype-resolved diploid genome sequence of an Asian individual using a unique de novo assembly pipeline. Our pipeline uses fosmid pooling and whole genome shotgun strategies, based on next generation sequencing (NGS) technology. The assembled genome contains 5.15 Gb, with a haplotype N50 of 484 kb. This haplotype-resolved genome represents the most complete genome assembly so far. Our analysis further identified previously undetected indels and novel coding sequences, and thus provides the most complete representation of an individual’s genetic variation. We generated ~614,850 fosmid clones ranging from 20 kb-80 kb with a mean of 36kb, approximately 30 fosmid clones were pooled and each pool had one or two DNA libraries sequenced using Hiseq 2000. In total, 1,712 Gb of raw sequence data was generated for all the pooled fosmid libraries.
DOI: 10.26036/cnphis0000108
title: High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

description: We used C57BL/6JBomTac (BL6) and 129S6/SvEvTac (Sv129) mice, known as obesity prone and obesity resistant, respectively, to dissociate changes in the gut microbiota associated with HF feeding from those associated with obesity. Using HiSeq-based whole genome sequencing we identified taxonomic and functional differences in the gut microbiota of the two mouse strains fed regular low fat or HF diets. HF feeding rather than obesity development led to distinct changes in the microbiota.
DOI: 10.26036/cnphis0000845
title: Heliconius melpomene amaryllis Variation

description: Heliconius butterflies are studied because their striking wing patterns show mimicry between different species in different locations. This sequence will be compared to our Heliconius melpomene reference sequence to identify the genetic changes underlying the differences and similarities in these wing patterns.
DOI: 10.26036/cnphis0000846
title: Heliconius melpomene rosina Genome Sequencing

description: Heliconius butterflies are studied because their striking wing patterns show mimicry between different species in different locations. This sequence will be compared to our Heliconius melpomene reference sequence to identify the genetic changes underlying the differences and similarities in these wing patterns.
DOI: 10.26036/cnphis0000847
title: Rotylenchulus reniformis Genome sequencing

description: The Reniform Nematode Genome Sequencing Project
DOI: 10.26036/cnphis0000848
title: Jaculus jaculus Genome Sequencing

description: Jaculus jaculus (Lesser Egyptian Jerboa) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000849
title: Salmonella enterica subsp. enterica serovar Montevideo str. 315996572 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Montevideo str. 315996572</b>. This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000850
title: Salmonella enterica subsp. enterica serovar Montevideo str. 495297-1 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Montevideo str. 495297-1</b>. This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000851
title: Salmonella enterica subsp. enterica serovar Montevideo str. 515920-2 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Montevideo str. 515920-2</b>. This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000852
title: Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB110209-0054 genome sequencing project

description: <b><i>Salmonella enteric</i>a subsp. <i>enterica</i> serovar Montevideo str. NC_MB110209-0054</b>. This strain will be used for comparative genome analysis.
DOI: 10.26036/cnphis0000854
title: Salmonella enterica subsp. enterica serovar Montevideo str. CASC_09SCPH15965 genome sequencing project

description: <b><i>Salmonella enterica</i> subsp. <i>enterica</i> serovar Montevideo str. CASC_09SCPH15965</b>. This strain will be used for comparative genome analysis.
DOI: 10.14457/cmu.the.2009.750
title: ผู้พลัดถิ่น
DOI: 10.14457/cmu.the.2009.751
title: ผลของสัดส่วนความยาวที่มีต่อลักษณะเฉพาะการถ่ายเทความร้อน ของท่อความร้อนแบบสั่นชนิดวงรอบที่มีเส้นผ่านศูนย์กลางไม่สม่ำเสมอ
DOI: 10.14457/cmu.the.2009.752
title: แบบจำลองเชิงตัวเลขของการถ่ายเทความร้อนภายในเซลล์เชื้อเพลิงชนิดเมมเบรนแลกเปลี่ยนโปรตอน
DOI: 10.14457/cmu.the.2009.754
title: วิจัยเชิงปฏิบัติการในชั้นเรียน เพื่อพัฒนาการจัดการเรียนการสอนที่มุ่งเน้นการพัฒนาทักษะด้านการประยุกต์ใช้คณิตศาสตร์ ในชีวิตประจำวันของนักเรียนชั้นมัธยมศึกษาปีที่ 1 โรงเรียนขุนยวมวิทยา จังหวัดแม่ฮ่องสอน
DOI: 10.14457/cmu.the.2009.755
title: ผลการใช้รูปแบบกระบวนการสอนคิดสร้างสรรค์ เพื่อสอนเขียนนิทานอนุรักษ์ภูมิปัญญาท้องถิ่น สำหรับนักศึกษามหาวิทยาลัยราชภัฏเชียงใหม่
DOI: 10.14457/cmu.the.2009.756
title: ผลของไคโตซานร่วมกับสารเคลือบผิวที่บริโภคได้ ต่อคุณภาพหลังการเก็บเกี่ยวของสัมพันธ์สายน้ำผึ้ง
DOI: 10.14457/cmu.the.2009.757
title: สภาวะที่เหมาะสมในการเจริญของเส้นใย และการผลิตหัวเชื้อเห็ดห้า [Phlebopus portentosus]
DOI: 10.14457/cmu.the.2009.758
title: ภาวะสุขภาพและพฤติกรรมความปลอดภัย ในการทำงานของเกษตรกรชาวนา
DOI: 10.26036/cnphis0000109
title: Dysbiosis of the fecal microbiota in the TNBS-induced Crohn’s disease mouse model

description: Crohn’s disease (CD) is characterized by chronic transmural inflammation. The symptom of the mice model induced by 2, 4, 6-Trinitrobenzenesulfonic acid (TNBS) is closed to human under CD condition, so this kind of animal is widely used in the related researches. Although the dysbiosis of the fecal microbiota have been proved to play an important role in the patients with CD, the composition of the gastrointestinal microbiota in the mouse model under disease condition is still unclear. In the current study, male seven-weeks BALB/c mice were anesthetized and intrarectal administrated by ethanol (ET group), TNBS in ethanol (TN group) and phosphate buffered saline (PBS) (CK group) as control. The symptoms of individuals under the CD condition were observed, and the changes of the bacterial taxonomic structure and functional composition were revealed by NGS 16S sequencing. The BALB/c mice in TN group demonstrated CD-like symptoms and the damages in the intestinal tract. The NGS 16S results exhibited that the diversity and microbial composition under CD condition are significantly different with those in ET group. The KO profile were generated from PICRUSt, and function modules such as methanogenesis (M00347) and microcin C transport system (M00349) were found enriched in the individuals in the TN group. This study proved that mouse model induced by TNBS could develop the similar symptom to CD patient, and we firstly showed the significant intestinal microbes changes both on taxonomic structure and functional composition in this mouse model.
DOI: 10.26036/cnphis0000110
title: Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Read Fragment technologies

description: The cell line BT-474 is a popular cell line for studying the biology of cancer and developing novel drugs. However, there is no published complete genome sequence for this highly utilized scientific resource. In this study we sought to provide a comprehensive and useful data set for the scientific community by generating a whole genome sequence for BT-474.
DOI: 10.26036/cnphis0000111
title: Giant panda genome sequencing project

description: The giant panda, Ailuropoda melanoleuca, is a critically endangered mammal confined to portions of six isolated mountain ranges in south-central China. There are fewer than 3,000 giant pandas currently alive in the wild and fewer than two hundred in captivity. The giant panda is unusual for feeding almost exclusively on bamboo plants though being evolutionarily related to meat-eating carnivores such as bears and dogs. The genome sequence of the giant panda will aid conservation efforts and the study of interactions between genetics and diet. The panda genome has 20 pairs of autosomes and two sex chromosomes. The first draft of this genome has approximately 73-fold coverage of the estimated 2.46 Gb genome. The sequence was derived from a female captive-bred panda, named Jingjing, who came from the Chengdu Research Base of Giant Panda Breeding.
DOI: 10.26036/cnphis0000112
title: Silkworm Genome Resequencing Project

description: -
DOI: 10.26036/cnphis0000113
title: Homo sapiens YH1 genome sequencing and de novo assembly of an Asian individual

description: Genomic DNA was extracted from peripheral venous blood from a male Asian individual and sequenced to 71X depth of coverage using Illumina Genome Analyzer. A de novo assembly, named YH1, was subsequently generated from the short read data. A comparison of the Asian YH1 assembly, the African BGIAF assembly, and the reference genome assembly resulted in the identification of novel sequence data not represented in the reference assembly. The Homo sapiens whole genome shotgun (WGS) project has the project accession ADDF000000000. This version of the project (01) has the accession number ADDF010000000, and consists of sequences ADDF010000001-ADDF014862669.
DOI: 10.26036/cnphis0000114
title: Drosophila albomicans genome sequencing project

description: Drosophila albomicans has a pair of ''neo-sex'' chromosomes and vary numbers of B chromosomes. It is an important model organism for studying early sex chromsome evolution and fertility effects of B chromosomes on the host genome.
DOI: 10.26036/cnphis0000116
title: An excess of rare deleterious mutations revealed by deep resequencing of 200 human exomes

description: Targeted sequence capture coupled with massively parallel sequencing is a promising approach to identify genetic variants implicated in human diseases (1). Using these technologies, we sequenced the nearly complete set of coding exons in 200 Danes, with an average fold-coverage &gt;12x for each individual exome. In the targeted regions we detected 121,895 single-nucleotide polymorphisms (SNPs), including 53,707 novel SNPs. Using a statistical method for unbiased estimation of allele frequencies we found a strong excess of rare deleterious amino acid changing mutations in our sample. This excess is more pronounced for X-linked SNPs, suggesting that deleterious substitutions are mostly recessive. Our analyses support the hypothesis that common polygenic diseases are caused by many low-frequency variants rather than a few common variants.
DOI: 10.26036/cnphis0000117
title: Zea mays strain:Zheng58, Mo17, 5003, 478, 178, and Chang7-2 Genome sequencing

description: Whole genome re-sequencing analysis of Zheng58, Mo17, 5003, 478, 178, and Chang7-2,six elite maize lines. This effort will illustrate the genomic changes that have occurred in the large and complex genome coincident with its genetic improvement.
DOI: 10.26036/cnphis0000855
title: Salmonella enterica subsp. enterica serovar Montevideo str. 366867 genome sequencing project

description: This strain will be used for comparative analysis.
DOI: 10.26036/cnphis0000856
title: Salmonella enterica subsp. enterica serovar Montevideo str. 413180 genome sequencing project

description: This strain will be used for comparative analysis.
DOI: 10.26036/cnphis0000857
title: Ceratotherium simum simum Genome sequencing

description: Ceratotherium simum simum (Southern White Rhinoceros) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000858
title: Salmonella enterica subsp. enterica serovar Montevideo str. 556150-1 genome sequencing project

description: Salmonella is an important foodborne pathogen.
DOI: 10.26036/cnphis0000859
title: Salmonella enterica subsp. enterica serovar Montevideo str. 507440-20 Genome sequencing

description: Salmonella is an important foodborne pathogen.
DOI: 10.26036/cnphis0000860
title: Salmonella enterica subsp. enterica serovar Montevideo str. IA_2010008282 genome sequencing project

description: None
DOI: 10.26036/cnphis0000861
title: Salmonella enterica subsp. enterica serovar Montevideo str. IA_2010008283 genome sequencing project

description: None
DOI: 10.26036/cnphis0000862
title: Salmonella enterica subsp. enterica serovar Montevideo str. MB110209-0055 genome sequencing

description: Salmonella is an important foodborne pathogen.
DOI: 10.26036/cnphis0000863
title: Salmonella enterica subsp. enterica serovar Montevideo str. 315731156 genome sequencing

description: Salmonella is an important foodborne pathogen.
DOI: 10.14457/cmu.the.2009.759
title: กระบวนการประสานการจัดทำแผนพัฒนาจังหวัด ขององค์กรปกครองส่วนท้องถิ่น ในจังหวัดน่าน
DOI: 10.14457/cmu.the.2009.760
title: การแนะแนวชีวิตผ่านนัยเปรียบ ของพระพุทธเจ้าในนิทานชาดก
DOI: 10.14457/cmu.the.2009.761
title: ผลของบราสิโนสเตียรอยด์ ต่อการเปลี่ยนแปลงเอทิลีนและสารชีวเคมี ในลำไยพันธุ์ดอ
DOI: 10.14457/cmu.the.2009.762
title: สู่โลกฝันกับนักเรียนพิเศษ
DOI: 10.26036/cnphis0000118
title: Ancient human genome sequence of an extinct Palaeo-Eskimo

description: We report the first ancient human genome. Obtained from ~4000 year old hair preserved in the Greenlandic permafrost, the genome represents a male individual from the first known culture to have settled the New World Arctic. Through the application of biochemical and statistical approaches, we ensured that the effect of DNA-damage and sequencing derived errors is negligible. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies.
DOI: 10.26036/cnphis0000119
title: Anas platyrhynchos genome sequencing

description: -
DOI: 10.26036/cnphis0000121
title: Harpegnathos saltator genome sequencing project

description: -
DOI: 10.26036/cnphis0000123
title: Glycine max Variation

description: Glycine max is a species of legume native to East Asia, widely grown for its edible bean which has numerous uses.
DOI: 10.26036/cnphis0000124
title: crab-eating macaque genome sequencing

description: a four-year old female cynomolgus/crab-eating macaque that was a captive-bred descendent of a crab-eating macaque from Vietnam
DOI: 10.26036/cnphis0000125
title: chinese rhesus macaque genome sequencing

description: a five-year old female Chinese rhesus macaque originating from the South-West of China
DOI: 10.26036/cnphis0000127
title: Complete Genome Sequencing of a Caucasian Male HapMap individual NA07022

description: The read data has been submitted to the Short Read Archive at NCBI (SRA008092) and can be downloaded from theFTP.
DOI: 10.26036/cnphis0000864
title: Chrysochloris asiatica Genome sequencing

description: Chrysochloris asiatica (Cape Golden Mole) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000865
title: Orycteropus afer afer Genome sequencing

description: Orycteropus afer (Aardvark) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000866
title: Elephantulus edwardii Genome sequencing

description: Elephantulus edwardii (Cape Elephant Shrew) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000867
title: Transcriptomics analysis of synovial fibroblasts by RNA-seq brings new insights into rheumatoid arthritis

description: Rheumatoid arthritis (RA) is a chronic autoimmune-disease of unknown origin that primarily affects the joints and ultimately leads to their destruction. Growing evidence suggests that synvovial fibroblasts play important roles in the initiation and the perpetuation of RA but underlying molecular mechanisms are not fully understood. In the present study, Illumina RNA-seq was used to profile two human normal control and two rheumatoid arthritis synvovial fibroblasts (RASFs) transcriptomes to gain insights into the roles of synvovial fibroblasts in RA. We found that besides known inflammatory and immune responses, other novel dysregulated networks and pathways such as Cell-To-Cell Signaling, Cellular Movement, Cellular Growth and Proliferation, and Cellular Development, may all contribute to the pathogenesis of RA. Our study provided a complete list of those dysregulated genes of both known and novel pathways in RASFs. 5,018 genes were upregulated and 917 genes were downregulated by at least two folds in RASFs vs. controls. Of note, 8,387 known isoforms and 6,826 novel isoforms were upregulated and 2,188 known isoforms and 5,919 novel isoforms were downregulated by at least two folds. The magnitude of difference and the number of differentially expressed known and novel gene isoforms were not detected by DNA microarray before. Since the activation and proliferation of RASFs has been implicated in the pathogenesis of rheumatoid arthritis, further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on molecular pathogenic mechanisms underlying synovial fibroblasts in arthritis and provide new leads of potential therapeutic targets.
DOI: 10.26036/cnphis0000868
title: Lophelia pertusa Genome Sequencing

description: This study provides a first inventory of the Lophelia genome and its associated microbiome.
DOI: 10.26036/cnphis0000869
title: Salmonella enterica subsp. enterica serovar Montevideo str. CT_02035318

description: None
DOI: 10.26036/cnphis0000870
title: Salmonella enterica subsp. enterica serovar Montevideo str. CT_02035320

description: None
DOI: 10.26036/cnphis0000871
title: Salmonella enterica subsp. enterica serovar Montevideo str. CT_02035321 genome sequence project

description: None
DOI: 10.26036/cnphis0000872
title: Drosophila miranda strain:MSH22 Genome sequencing

description: This project aims to sequence and assemble Drosophila miranda''s neo-sex chromosomes in order to study its evolutionary pattern.
DOI: 10.26036/cnphis0000128
title: Drosophila suzukii Genome sequencing and assembly

description: Genome sequencing of Drosophila suzukii
DOI: 10.26036/cnphis0000129
title: Whole-exome capture sequencing of 100 lung SQCC patients and 98 target-capture sequencing of 98 lung SQCC Exome

description: Nature genetics
DOI: 10.26036/cnphis0000130
title: TARGET: Neuroblastoma (NBL)

description: There are ~214 fully characterized patient cases with neuroblastoma (all tumor/normal pairs, 10 with relapse sample as well) that will make up the TARGET NBL dataset, along with some cell lines and xenografts. The dataset includes 24 4S cases as well. Each fully characterized case has gene expression, tumor and paired normal copy number analyses, methylation and comprehensive next-generation sequencing to include whole genome and/or whole exome sequencing. A majority of these cases will also have mRNA-seq and methylation data available as well. There are additionally a large number of cases, both low and high risk, with partial molecular characterization to include some next generation and targeted Sanger sequencing making this a large and informative genomic dataset. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website listed above for additional information on this and other TARGET... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000131
title: TARGET: Acute Lymphoblastic Leukemia (ALL) Phase II

description: There are 175 fully characterized patient cases with relapsed precursor B-cell ALL (all tumor/normal pairs, 85 with relapse sample as well) that will make up Phase II of the TARGET ALL dataset, each with gene expression, tumor and paired normal copy number analyses, and comprehensive next-generation sequencing to include whole genome sequencing, mRNA-seq and miRNA-seq. Subsets of these cases will also have methylation and/or whole exome sequencing data available as well. There are additionally a large number of cases with partial molecular characterization making this a large and informative genomic dataset. All cases can be sorted according to data type via the Case Matrix on the TARGET Data Matrix. Please visit the TARGET website listed above for additional information on this and other TARGET genomics projects. Please see the TARGET Publication Guidelines at the OCG websitefor updated details on sharing of any TARGET substudy data.
DOI: 10.26036/cnphis0000132
title: TARGET: Acute Myeloid Leukemia (AML)

description: There are 200+ fully characterized patient cases with AML (all tumor/normal pairs, 100 with relapse sample as well) that make up the TARGET AML dataset, each with gene expression, tumor and paired normal copy number analyses, methylation and comprehensive next-generation sequencing to include whole genome sequencing, mRNA-seq and miRNA-seq. A subset of these cases will also have whole exome sequencing data available as well. There are additionally a large number of cases with partial molecular characterization making this a large and informative genomic dataset. Additionally, the TARGET AML cohort includes some highly aggressive subtypes including AML "induction failures." Upon diagnosis, AML patients without high-risk genetic markers undergo standard chemotherapy, called the primary induction phase. This phase lasts about 30 days and is designed to eliminate cancer cells. Success of treatment is measured by the percentage of myeloblasts, i.e. immature... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000133
title: TARGET: PPTP Cell Lines

description: As part of the TARGET initiative, some disease projects characterized tumor cell lines or xenografts, with or without matched normal comparators, as well as some normal non-involved tissues. These reagents will be available for in vitro validation experiments and their molecular characteristics will be available through the TARGET Data Matrix. MDLS includes acute leukemia cell lines and xenografts with matched primary and/or relapsed tumor information, neuroblastoma cell line and xenografts with matched controls, kidney tumor cell lines, normal brain tissues and embryonic stem cell lines. Additionally, in partnership with TARGET, 131 cell lines and xenografts from the NCI''s Pediatric Preclinical Testing Program Pediatric Preclinical Testing Programwill receive next generation sequencing of the whole exome, and will have associated expression and copy number data available through the TARGET Data Matrixonce generated. Please visit the TARGET website listed... (for more see dbGaP study page.)