cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002332
title: Holacanthus ciliaris Genome sequencing

description: Samples of Holacanthus ciliaris (voucher no. 279) were purchased from local aquarium and originally imported from Miami. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002333
title: Centropyge woodheadi Genome sequencing

description: Samples of Centropyge woodheadi (voucher no. 333) were purchased from local aquarium and originally imported from Vanuatu. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002334
title: Genicanthus semifasciatus Genome sequencing

description: Samples of Genicanthus semifasciatus (voucher no. 340) were purchased from local aquarium and originally imported from Cebu, Philippines. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002335
title: Genicanthus bellus Genome sequencing

description: Samples of Genicanthus bellus (voucher no. 341) were purchased from local aquarium and originally imported from Cebu, Philippines. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002336
title: Paracentropyge multifasciata Genome sequencing

description: Samples of Paracentropyge multifasciata (voucher no. 343) were purchased from local aquarium and originally imported from Indonesia. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0001650
title: Nothobranchius furzeri strain:GRZ Genome sequencing

description: Nothobranchius furzeri draft genome assembly. GRZ male whole genome shotgun sequencing
DOI: 10.26036/cnphis0001651
title: Synthetic metagenome samples: M-Y, M-3D Metagenome

description: The goal of this project was to demonstrate the use of Hi-C for sequencing metagenome samples. The M-Y and M-3D samples are synthetic mixtures of microbial species created as test cases for our method.
DOI: 10.26036/cnphis0001652
title: Single-neuron whole-genome analysis of spatial patterns of somatic mutation in the human brain

description: Single-neuron whole-genome sequencing analysis of spatial patterns of somatic mutation in the human brain.
DOI: 10.26036/cnphis0001653
title: GSE57097: Analysis of the Epigenomic and Transcriptional Landscapes during mammalian spermatogenesis [sperm; Bisulfite-Seq]

description: Summary: Adult germline stem cells (AGSCs) are multifunctional - they must self renew, maintain genome pluripotency, and prepare for gametogenesis – which involves meiotic and chromatin repackaging phases. To better understand AGSCs and gametogenesis, we derived high-resolution profiles of transcription, DNA methylation, 5hmC, and multiple histone modifications at key stages. First, AGSCs display chromatin ‘poising’ of enhancers and promoters of genes utilized in embryo development. Second, the pluripotency network in AGSCs is remarkably distinct from ESCs - lacking Nanog, Sox2, or Prdm14 expression. Third, spermatogenesis involves stage-specific transcription and distinctive chromatin dynamics, but virtually no changes in DNAme. Surprisingly, we observe co-incidence of RNA polymerase II, high H3K4me3, and DNA methylation at 20-35% of genes transcribed during gametogenesis - including piRNA clusters - but often observe attendant promoter 5hmC. Our work reveals key differences between AGSCs and other germ/stem cells, and reveals both logical and unexpected chromatin-transcription relationships accompanying germline developmental transitions. Overall Design: Methylation profiles of human sperm were generated by bisulfite sequencing using Illumina HiSeq 2000.
DOI: 10.26036/cnphis0001654
title: GOAT Genome sequencing

description: None
DOI: 10.26036/cnphis0001655
title: Aegypius monachus Transcriptome or Gene expression

description: PGI, National Museum of Korea, and collaborators are working on the Cinereous Vulture whole transcriptome sequencing and analysis.
DOI: 10.26036/cnphis0001656
title: Panagrolaimus davidi Genome sequencing

description: Genomic sequencing from the Antarctic nematode, Panagrolaimus davidi
DOI: 10.26036/cnphis0001657
title: Sequencing the highly duplicated and recent polyploid genome of oilseed rape (Brassica napus) crop

description: Whole Genome sequencing of three cultivars (Bristol, Aviso, Aburamasari) for the SEQ-POLYNAP Project granted by ANR
DOI: 10.26036/cnphis0001658
title: Single Molecule Sequencing and Genome Assembly of a Clinical Specimen of Loa loa, the Causative Agent of Loiasis

description: None
DOI: 10.26036/cnphis0001659
title: Mytilus galloprovincialis Genome sequencing

description: The principal aim of the study was to enrich a part of Mytilus galloprovincialis genome designing RNA-probes from a EST collection.
DOI: 10.26036/cnphis0002337
title: Centropyge aurantia Genome sequencing

description: Samples of Centropyge aurantius (voucher no. 352) were purchased from local aquarium. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002340
title: Centropyge heraldi Genome sequencing

description: Samples of Centropyge heraldi (voucher no. 365) were purchased from local aquarium and originally imported from Philippines. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002341
title: Centropyge interrupta Genome sequencing

description: Samples of Centropyge interrupta (voucher no. 367) were purchased from local aquarium and originally imported from Izu, Japan. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002342
title: Centropyge joculator Genome sequencing

description: Samples of Centropyge joculator (voucher no. 369) were purchased from local aquarium and originally imported from Cocos-Keeling Island. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002343
title: Centropyge flavicauda Genome sequencing

description: Samples of Centropyge flavicauda (voucher no. 388) were purchased from local aquarium and originally imported from Cebu. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002344
title: Centropyge eibli Genome sequencing

description: Samples of Centropyge eibli (voucher no. 389) were purchased from local aquarium and originally imported from Bali, Indonesia. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002345
title: Genicanthus melanospilos Genome sequencing

description: Samples of Genicanthus melanospilos (voucher no. 390) were purchased from local aquarium and originally imported from Cebu, Philippines. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0001660
title: Transcriptome profiling of muscle by RNA-Seq reveals significant digital gene expression profiling differences between Angus and Luxi Cattle

description: The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDR=0.001 AND |log2Ratio|=1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds. Overall design: Three Luxi and three Angus cattle that were eighteen months of age were generated by RNA-Seq
DOI: 10.26036/cnphis0001661
title: Homo sapiens Genome sequencing

description: Study for genetic alterations and tumor evolution in colorectal cancer liver metastasis
DOI: 10.26036/cnphis0001662
title: Transcriptome Proflings of 347 Single cells from 10 Distinct Populations

description: Analyze the transcriptomes of 347 cells from 10 distinct populations in both of low-coverage (~0.27 million reads per cell) and high-coverage (~5 million reads per cell) to identify cell-type-specific biomarkers, and to compare gene expression across samples specifically for cells of a given type as well as to reconstruct developmental lineages of related cell types.
DOI: 10.26036/cnphis0001663
title: Sepia esculenta Genome sequencing

description: for further exploration in Sepia research and provide new perspectives in understanding the molecular mechanisms underlying early embryonic development of cuttlefish.
DOI: 10.26036/cnphis0001664
title: Hippocampus Transcriptome or Gene expression

description: We utilized Illumina paired-end sequencing technology to characterize the transcriptomes of H. kelloggi and H. mohnikei, and developed the SSR markers to study their population genetics.
DOI: 10.26036/cnphis0001665
title: Marwari horse Genome sequencing

description: PGI, NMK, Xcelris Genomics, and collaborators are working on the Marwari horse whole genome sequencing and analysis
DOI: 10.26036/cnphis0001666
title: RNA-seq analysis of alternative splicing events in duplicated genes of Arabidopsis thaliana indicates considerable qualitative and quantitative divergence

description: Divergence of alternative splicing in duplicated genes is investigated Overall design: Three replicates of RNA-seq for Arabidopsis first true leaf tissue
DOI: 10.26036/cnphis0001667
title: Callithrix jacchus 186/17066 (reference individual) Genome Sequencing

description: The purpose of this project is to provide additional genomic DNA sequences for the marmoset reference animal used for the draft genome assembly (animal 186/17066) using the Ion Torrent platform.
DOI: 10.26036/cnphis0001668
title: Mus musculus strain:Black 6 Genome sequencing

description: Genome assembly of Mus Musculus
DOI: 10.26036/cnphis0002346
title: Genicanthus lamarck Genome sequencing

description: Samples of Genicanthus lamarck (voucher no. 405) were purchased from local aquarium and originally imported from Indonesia. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002347
title: Centropyge acanthops Genome sequencing

description: Samples of Centropyge acanthops (voucher no. 424) were purchased from local aquarium and originally imported from Kenya. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002348
title: Homo sapiens Raw sequence reads

description: Cell-free DNA was extracted from the plasma of lung transplant recipients, and the libraries were prepared under two techniques. We show that the library preparation method using ligation of single-stranded DNA to magnetic beads provides information about short (&lt;100 bp) cell-free DNA ( e.g. mitochondrial, microbial, and non-nucleosomal) that is not adequately captured by standard library preparation protocols, which utilize the binding of double-stranded adapters to DNA. Furthermore, we extracted genomic DNA from the pre-transplantation whole blood samples of donor-recipient pairs, and sequenced the amplified mitochondrial genomes to build consensus sequences. We compared the post-transplantation cfDNA of the recipient to the respective donor and recipient pair and were able to show the presence of mitochondrial DNA from the donor in the recipient plasma, which has potential as a biomarker for graft rejection.
DOI: 10.26036/cnphis0002350
title: Transcriptome Profiling of the Rumen Epithelial Tissues of Beef Cattle Differing in Residual Feed Intake

description: We functionally analyzed the rumen epithelial transcriptomes from low- and high- feed efficient beef steers to identify differences that might contribute to variation in feed efficiency. Overall design: RNA-seq was performed on the rumen epithelial tissues of 9 low RFI and 9 high RFI animals to obtain transcriptomes for functional analysis using bioinformatics.
DOI: 10.26036/cnphis0002351
title: Long non-coding RNA expression profiles in cold-induced injury of mouse livers

description: Hepatic injury provoked by cold storage is a major problem affecting liver transplantation, as exposure to cold induces apoptosis in hepatic tissues. Long noncoding RNAs (lncRNAs) are increasingly understood to regulate apoptosis, but the contribution of lncRNAs to cold-induced liver injury remains unknown. Using RNA-seq, we determined the differential lncRNA expression profile in mouse livers after cold storage and found that expression of the lncRNA TUG1 was significantly down-regulated. Over-expression of TUG1 attenuated cold-induced apoptosis in mouse hepatocytes and liver sinusoidal endothelial cells LSECs, in part by blocking mitochondrial apoptosis and ER stress pathways. Moreover, TUG1 attenuated apoptosis, inflammation and oxidative stress in vivo in livers subjected to cold storage. Over-expression of TUG1 also improved hepatocyte function and prolonged hepatic graft survival rates in mice. These results suggest that the lncRNA TUG1 exerts a protective effect against cold-induced liver damage by inhibiting apoptosis in mice, and suggests a potential role for TUG1 as a target for the prevention of cold-induced liver damage in liver transplantation. Overall design: Cold-storaged liver lncRNA profiles of male inbred C57BL/6 mice 8-12 week of age and weighing 25 to 30 g were generated by high-throughput, high-sensitivity HiSeq 2500 sequencing platform .
DOI: 10.26036/cnphis0002352
title: Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

description: Upon fertilization, parental chromatin undergoes extensive reprogramming to generate the highly dynamic chromatin of the inner cell mass (ICM) cells from which an organism is derived. How the chromatin regulatory landscape is established during this process has remained a mystery due to the technical difficulties in chromatin analysis using limited cell numbers. Using a low-input DNase I sequencing (liDNase-seq) method, we generated DNase I-hypersensitive site (DHS) maps of mouse preimplantation embryos. We found that the DHSs are progressively established during development, with Oct4 contributing to a drastic gain of DHSs at the 8-cell stage. In addition, single nucleotide polymorphism analysis revealed that imprinted gene promoters harbor allele-specific DHSs before the onset of allelic gene expression. Furthermore, Nfya is required for 2-cell promoter DHS formation and zygotic genome activation. Thus, our study not only reveals chromatin regulatory landscapes, but also identifies key transcription factors important for DHS establishment in mammalian embryos. Overall design: In this study, we modified scDNase-seq method to achieve de novo genome-wide DHS mapping using as few as 30 cells. Using this low-input DNase-seq (liDNase-seq) method, we have generated DHS maps of mouse preimplantation embryos from 1-cell to the morula stage, revealing the dynamics of chromatin accessibility during the natural developmental process. We constructed a total of 32 liDNase-seq datasets, including: two 1-cell embryo libraries, two 2-cell embryo libraries, two 4-cell embryo libraries, two 8-cell embryo libraries, two morula embryo libraries, two mouse ESC libraries, two 14 day growing oocyte library, two sperm library, two maternal PN3 pronuclei library, two paternal PN3 pronuclei library, two maternal PN5 pronuclei library, two paternal PN5 pronuclei library, two siRNA control 2-cell embryo libraries, two Nfya KD (siNfya#1 and siNfya#2) 2-cell embryo libraries, two siRNA control 8-cell embryo libraries and two Oct4 KD 8-cell (siOct4#1 and siOct4#2) embryo libraries. Five RNA-seq datasets were generated including two siRNA control 2-cell embryo libraries, two Nfya KD (siNfya#1 and siNfya#2) 2-cell embryo libraries and one 1-cell embryo library.
DOI: 10.26036/cnphis0002353
title: Comparative genomics of Phoebis species

description: Comparative genomics study of Phoebis species, especially Phoebis sennae, to understand evolution and speciation of this group
DOI: 10.26036/cnphis0002354
title: Drosophila melanogaster Transcriptome or Gene expression

description: Transcriptome analysis of 10 hemiclonal genotypes of D. melanogaster, with 3 replicate male and female samples from each of 3 developmental stages (larvae, pupae and adults) within each genetic line.
DOI: 10.26036/cnphis0002355
title: Nibea albiflora Genome sequencing

description: Samples of Nibea albiflora (voucher no. 477) were collected from Zhoushan, China. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0001669
title: Drosophila melanogaster strain:Canton S Genome sequencing

description: Genome assembly of Drosophila Melanogaster
DOI: 10.26036/cnphis0001670
title: Sceloporus Genome sequencing

description: SWAG: Sceloporus not Wholly Annotated Genome
DOI: 10.26036/cnphis0001671
title: Systemic suppression of the rice shoot metabolism upon root rot nematode infection

description: Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth . Overall design: Differential expression analysis between controls rice shoots and shoots from root rot nematode (H. oryzae) infected rice at two time points.
DOI: 10.26036/cnphis0001672
title: Gene expression profiling in the endometrium of pregnant mammals

description: A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved or lost uterine expression during the origins of mammalian pregnancy, including the loss of genes responsible for the mineralization of the eggshell in the Mammalian and Therian stem-lineages, and the recruitment of genes into uterine expression that mediate maternal-fetal communication and maternal immunotolerance of the fetal allograft in the Therian and Eutherian stem-lineages. Our results indicate that one of the defining mammalian novelties evolved through a step-wise process that dramatically changed uterine gene expression, generating a suite of evolutionary innovations that support prolonged gestations. Overall design: We report genome-wide gene expression generated by mRNA-Seq from the pregnant endometrium of dog, armadillo, and the platypus.
DOI: 10.26036/cnphis0001673
title: Noninvasive in vivo monitoring of tissue-specific global gene expression in humans

description: Circulating cell-free RNA in the blood provides a potential window into the health, phenotype, and developmental programs of a variety of human organs. We used high-throughput methods of RNA analysis such as microarrays and next-generation sequencing to characterize the global landscape of circulating RNA in human subjects. By focusing on tissue-specific genes, we were able to identify the relative contributions of these tissues to circulating RNA and monitor changes during tissue development and neurodegenerative disease states.
DOI: 10.26036/cnphis0001674
title: Schmidtea mediterranea strain:CIW4 Genome sequencing and assembly

description: Schmidtea mediterranea C4 biotype.
DOI: 10.26036/cnphis0001676
title: Oryctolagus cuniculus domestication

description: Resequencing of 23 wild Oryctolagus cuniculus and 1 Lepus americanus outgroup species to survey for domestication signals.
DOI: 10.26036/cnphis0002356
title: Miichthys miiuy genome sequencing

description: Samples of Miichthys miiuy (voucher no. 491) were collected from Zhoushan, China. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).