cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnp0000706
title: 基于单细胞多组学测序技术开展蝾螈发育和器官再生研究

description: In situ regeneration is urgently required for clinical purposes, however, due to limited understanding of the biological mechanism, such powerful biotechnology is still unavailable for most tissues. Axolotl Ambystoma mexicanum is an ideal study model, since its anatomical similarity of its limbs to human limbs and to its superior capability of regenerate entire multi-tissue structures in situ, including limb, tail, cardiac muscle and retina. This unique capacity offers an important model system to study the molecular and cellular mechanism underlying complex tissue regeneration. Upon limb amputation, epidermal cells from adjacent sites immediately respond and migrate to cover the wound area within 24 hours1-3, underneath the newly formed epidermis, multiple types of cells start to migrate and proliferate to form limb bud tissue named blastema, a mass of cells capable of growth and regeneration into organs or body parts, which then keeps proliferating while the cells inside start to de-differentiate and re-differentiate, patterning into completely regenerated limb within 33 days.
DOI: 10.26036/cnp0000790
title: Natural selection and repeated patterns of molecular evolution following allopatric divergence

description: We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, &gt;90% of POGs are under purifying selection, and &lt;10% are under positive selection. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time.
DOI: 10.26036/cnp0000452
title: Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida

description: Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the BV clade (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only a partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is in this group is low, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
DOI: 10.26036/cnp0001205
title: 雪豹基因组

description: 雪豹基因组测序及组装
DOI: 10.26036/cnp0001589
title: Raw RNA sequence reads of 9 tissue of Heilongjiang brown frog

description: Raw RNA sequence reads of 9 tissue of Heilongjiang brown frog
DOI: 10.26036/cnp0000828
title: 杜洛克16S数据

description: 杜洛克粪便菌群16S rRNA基因测序数据
DOI: 10.26036/cnp0000707
title: 28 Cod Rad Research

description: 28 Cod Rad Research
DOI: 10.26036/cnp0000849
title: Ulva compressa transcriptome

description: Transcriptome sequencing of green alga Ulva compressa under different conditions
DOI: 10.26036/cnp0000496
title: genetic introgression between Castanopsis species

description: Castanopsis fabri and Castanopsis lamontii
DOI: 10.26036/cnp0000956
title: Transcriptome of Borneol chemotype of Cinnamomum camphora

description: Transcriptome of Borneol chemotype of Cinnamomum camphora
DOI: 10.26036/cnp0000948
title: Effects of a sudden drop in salinity on S. subcrenata metabolism

description: In this experiment, the effects of a sudden drop in salinity on the antioxidant defense system and related gene expression of the ark shell Scapharca subcrenata were examined. The sudden drop in seawater salinity after a rainstorm was simulated, and subsequently differentially expressed metabolic markers were identified by LC-MS non-targeted metabolomics. When the salinity dropped to 14‰ (S14), the total anti-oxidant content, activity of Na+/K+-ATPase, superoxide dismutase (SOD), and catalase (CAT), content of malondialdehyde, and expression levels of Mn-SOD, CAT, and C-type lectin of S. subcrenata were significantly higher than in groups with salinity of 22‰ (S22) or 30‰ (S30) (P &lt; 0.05). Using the metabolomics technique, 361, 271, and 264 metabolites with significant differences were identified from S22 vs. S14, S30 vs. S14, and S30 vs. S22, respectively. The drop in salinity was accompanied by up-regulation of phosphatidylcholine (PC) (20:4 (5Z, 8Z, 11Z, 14Z)/P-18: 1 (11Z)), PC (16:0/22: 6 (4Z, 7Z, 10Z, 13Z, 16Z, 19Z)), phosphatidylethanolamine (PE) (18:4 (6Z, 9Z, 12Z, 15Z)/24:1 (15Z)), phosphatidylinositol (PI) (20:1 (11Z)/0:0), phalluside-1, C16 sphinganine, and LacCer (d18:0/14:0) and by significant down-regulation of PI-Cer (d18:1/14:0) and PE (14:0/16:1(9Z). The results of this study illustrate how these nine metabolites can be used as metabolic markers for the response of S. subcrenata to a sudden drop in salinity. They also provide the theoretical groundwork for selection of bottom areas with salinity that is optimal for release and proliferation of S. subcrenata, which is needed to restore the declining populations of this species.
DOI: 10.26036/cnp0000910
title: Genome Comparison of Seven Fungal Species Isolated from Mangrove

description: seven genome of 7 fungi species，isolating from mangrove Kandelia obovate and Acanthus ilicifolius were assembled and compared
DOI: 10.26036/cnp0000859
title: leopard coral grouper genome

description: Leopard coral grouper genome assembly raw data and assembly results
DOI: 10.26036/cnp0000850
title: Ulva linza transcriptome

description: Transcriptome sequencing of green alga Ulva linza
DOI: 10.26036/cnp0000011
title: blueberry degradome

description: Degradome cDNA libraries were constructed and sequenced for flowers, young fruits, and ripe fruits.
DOI: 10.26036/cnp0000023
title: 3 Cucumber NILs for F and M Locus

description: 3 Cucumber NILs for F and M Locus, G12:FFMM. H34: FFmm, M12: ffMM, with 3 bio-reps.
DOI: 10.26036/cnp0000032
title: Transcriptome of Kluyveromyces marxianus during ethanol fermentation

description: Kluyveromyces marxianus is a thermotolerant yeast and can grow at elevated temperatures (&gt; 40 °C), however, the growth of K. marxianus is strongly inhibited by accumulated inhibitors at elevated temperatures. The objective of this project is to reveal the transcriptomic responses of K. marxianus to heat and accumulated inhibitors during ethanol fermentation.
DOI: 10.26036/cnp0000015
title: De novo genome assembly of rattan (Calamus simplicifolius)

description: De novo genome assembly of rattan (Calamus simplicifolius) based on Illumina and PacBio platforms .
DOI: 10.26036/cnp0000020
title: Whole Genome sequencing of Physeter catodon

description: Sperm whale (Physeter macrocephalus/Physeter catodon) is the largest toothed whale and the only living member of the genus Physeter, we sequenced and assembled the genome for a stranded female sperm whale.
DOI: 10.26036/cnp0000030
title: Transcriptome of Saccharomyces cerevisiae during solid-state fermentation of crushed sweet sorghum stalks

description: Bioethanol production based on solid-state fermentation (SSF) of sweet sorghum stalks has been demonstrated to have great potential due to the its low pollution and low cost. A novel S. cerevisiae diploid strain TSH3 exhibited better SSF performance compared with the commonly used laboratory strain BY4743 during SSF of sweet sorghum stalks. The objective of this project is to investigate TSH3’s advantages compared with BY4743 and the dynamics of TSH3’s transcriptome during SSF of crushed sweet sorghum stalks.
DOI: 10.26036/cnp0000033
title: Transcriptome of Kluyveromyces marxianus expressing a SPT15 mutant

description: The Kluyveromyces marxianuswas TATA-binding protein Spt15 was engineered to improve ethanol tolerance and production. The Spt5-M2 mutant confers higher ethanol tolerance and productivity. The objective of this project is to investigate the changes in gene expression induced by Spt15-M2 mutant.
DOI: 10.26036/cnp0000019
title: Transcriptome of Xenocatantops brachycerus

description: Using the Illumina HiSeqTM 4000 platform, three transcriptomes of the adult male, adult female and larval of X. brachycerus were sequenced.
DOI: 10.26036/cnp0000029
title: Cranial irradiation in juvenile female rats induces late-onset obesity and metabolic disturbances

description: Female Wistar rats were subjected to a single dose of 6 Gy whole brain irradiation on postnatal day 11. The animals were sacrificed at 6 hours or 20 weeks after irradiation.
DOI: 10.26036/cnp0000034
title: RNA-seq and ChIP-seq of maize gif1 mutant

description: RNA-seq and ChIP-seq of maize gif1 mutant
DOI: 10.26036/cnp0000071
title: Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

description: Accurate next generation sequencing (NGS) is critical for understanding genetic predisposition to human disease and thus aiding clinical diagnosis and personalized precision medicine. Recent breakthroughs in massively parallel sequencing, especially when coupled with sample multiplexing, have driven sequencing cost down and made clinical genetic tests broadly affordable. However, intractable index mis-assignment (commonly exceeds 1%) has been reported on some widely used sequencing platforms. Burdensome unique dual indexing is now used to reduce this problem. Here, we investigated this quality issue on BGI sequencers using three major library preparation methods: whole genome sequencing (WGS) with PCR, PCR-free WGS, and two-step targeted PCR. BGI sequencers utilize a unique DNA nanoball (DNB) technology that is based on rolling circle replication (RCR) for array preparation; this linear amplification is PCR free and can avoid error accumulation. We demonstrate here that single index mis-assignment from free indexed oligos on these sequencers occurs at a rate of only one in 36 million reads, suggesting virtually no index hopping during DNB creation and arraying, as expected for the RCR process. Furthermore, the DNB-based NGS applications have achieved an unprecedentedly low sample-to-sample mis-assignment rate of 0.0001% to 0.0004% using only single indexing. Therefore, single indexing with DNB sequencing technology provides a simple but effective method for sensitive research and clinical genetic assays that require the detection of low abundance sequences in a large number of samples.
DOI: 10.26036/cnp0000049
title: Impact-of-Vegetarian-Diet

description: Impact of short- and long-term vegetarian diet on the gut microbiota and immune repertoire
DOI: 10.26036/cnp0000059
title: MGISEQ-2000 demo data

description: demo data of WES/WES from MGISEQ-2000
DOI: 10.26036/cnp0000055
title: Transcriptomic analysis of a salt-tolerant yeast-Meyerozyma guilliermondii

description: Salt-tolerant yeast-Meyerozyma guilliermondii isolated from activated sludge used for wastewater treatment.
DOI: 10.26036/cnp0000062
title: Cucsa GuoBa

description: CSSL of Cucumber Guoba with 3 reps.
DOI: 10.26036/cnp0000078
title: A Cost-effective Method of Mate-pair Library Construction with Controlled Polymerization

description: we described a method of mate-pair library construction by controlling DNA polymerization with nick translation and primer extension. Compared with reported approaches, our approach can increase circularization efficiency by 8-fold and extremely eliminate read-pairs not crossing the circularization junction (39.3-fold change), resulting in an approximately 50% of increment of physical coverage when with the same number of read-pairs. In addition, the reagent cost for this approach has 88.6% reduction, whereas the minimum requirement of DNA input is only 1 μg. Furthermore, the feasibility of sequencing platform neutral has been demonstrated with data from four sequencing platforms. Overall, our approach advances the application of low-pass whole-genome sequencing in a clinical setting.
DOI: 10.26036/cnp0000084
title: 濒危鸟类（朱鹮）基因组

description: 古代朱鹮群体个体测序数据
DOI: 10.26036/cnp0000083
title: 病原学快速鉴定与病人个性化治疗研究

description: 深圳毗邻香港，是全国最大的口岸城市。由于人流、物流频繁，各种输入性传染病、新发传染病多先进入深圳，进而扩散至全国。在加强出入境的检查监控基础之上，尽可能撇除其他诸如疟疾、霍乱、脑膜炎、其他病毒出血热等可造成类似病征的疾病。因此，深圳对于新发突发传染病的防控具有重要意义。对于新发传染病人，根据不同的症状选取不同类型的样本。对于完成测序的样本，产出海量的数据后使用比对软件和病原数据库进行比对，进行病原鉴定。确定阳性鉴定标准和相对定量方法，使得能够比较不同样本间病原丰度的差异，为病情变化和差异提供参考。同时确定病原体是否有突变、耐药，指导临床用药。另外新方法的建立，能够在全市乃至全省范围内应用。为病毒的防控起到指导作用。同时对于感染流感或寨卡病毒引起疾病的病人，明确个体差异的不同，实现差异化治疗。找到同样病毒感染后表现出的特异性和共性的基因表达特点以及代谢通路。实现个性化治疗以及精准医疗。
DOI: 10.26036/cnp0000079
title: Grouper Genome

description: Groupers are bottom-associated fishes in the tropical and subtropical waters of all oceans. Among the 163 grouper species, 20 species are on the risk of extinction and an additional 22 species are considered to be threatened by the International Union for Conservation of Nature. Moreover, several grouper species are important cultured fish of great economic value. Most grouper species are functional protogynous hermaphrodites, but the genetic basis and the molecular mechanisms underlying regulation of this unique reproductive strategy remain enigmatic. In this study, we reported the fine genome of the orange-spotted grouper (Epinephelus coioides) and annotate its coding genes. Also, we designed several experiments and try to explain its functional protogynous hermaphrodites.
DOI: 10.26036/cnp0000060
title: Assembled contigs of 760 MetaHIT metagenomes

description: Assembled contigs of 760 MetaHIT metagenomes.
DOI: 10.26036/cnp0000072
title: Polypedates megacephalus RNA sequencing

description: We sequenced the transcripts of skin from ten Polypedates megacephalus(pooled male and female).
DOI: 10.26036/cnp0000081
title: Citrus grandis lncRNA Raw sequence reads

description: Aluminum stress responsive genes revealed by RNA-seq in Citrus grandis roots under aluminum stress, salicylic acid, hydrogen peroxide
DOI: 10.26036/cnp0000094
title: 枫杨转录组测序

description: 枫杨幼叶转录组测序
DOI: 10.26036/cnp0000096
title: The draft genome of five unimproved tropical plants

description: A rapid growth in the world population and global economy are expected to double the worldwide demand for food by 2050. Moreover, 88% of countries are currently facing a serious burden of malnutrition, especially those from Africa and Southern & South-Eastern Asia. Surprisingly, 30 species alone contribute 95% of the present food energy needs of humans with wheat, maize and rice providing the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition in these countries, a greater utilization of neglected or underused crops (orphan crops) could be a partial solution.Here we present draft genome information of five agriculturally, biologically, medicinally and economically important African orphan crops, namely; Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. The assembled genomes range in size from 217 to 654 Mb. In addition, we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes in V. subterranea, L. purpureus, F. albida, S. birrea and M. oleifera respectively. We have further analyzed the expansion and contraction of selected gene families, and characterized root-nodule-symbiosis genes, transcription factors and starch biosynthesis related genes in these genomes.
DOI: 10.26036/cnp0000101
title: Chiloscyllium plagiosum Genome sequencing and assembly

description: to perform the whole genome sequencing of bamboo shark
DOI: 10.26036/cnp0000103
title: 小鼠免疫组库评价

description: 角蛋白-18（CK18）是常用的肿瘤血清学检测标记物，灵敏度和特异性较高。为了开发CK18相关的特异性抗体，以及评价CK18免疫动物后机体免疫组库的变化，本研究利用二代高通量测序技术对三只小鼠的抗体重链IgH免疫组库文库进行了深度测序，通过生物软件Imonitor对下机数据进行了分析评价，通过对比已报道的具有空白背景的小鼠免疫组库数据，从多个角度评价了CK18免疫引起的变化。
DOI: 10.26036/cnp0000111
title: Tachypleus tridentatus genome project

description: Horseshoe crabs are a marine arthropod fossil species and exhibit a strong and unique innate immune defense. However, to date the molecular mechanisms underlying this immune function are still unclear.
DOI: 10.26036/cnp0000116
title: Vaccine evaluation with India Rhesus model

description: This project includes 15 India Rhesus monkey, and total 75 samples (Each individual includes five timepoints). Full-length Heavy chain of B cells were amplified and sequenced by Miseq.
DOI: 10.26036/cnp0000121
title: Recovery of gut microbiota of healthy adults following antibiotics exposure

description: To minimize the impact of antibiotics the gut microbes harbor and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing based metagenomics, we analyzed partial eradication and subsequent regrowth of gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin.Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and depletion of Bifidobacterium spp. and butyrate producers. Still, subjects’ gut microbiota recovered to near-baseline composition by 1.5 months, although nine common species which were present in all subjects prior to the treatment, remained undetectable in most of the subjects after 180 days. Species harboring beta-lactam resistance genes were positively selected for during and after the intervention. Harboring glycopeptide or aminoglycoside resistance genes increased odds of de novo colonization, while the former also decreased odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention, and their antibiotics resistance gene carriage modulates their recovery processes.
DOI: 10.26036/cnp0000122
title: Chromosome-level genome of Ginkgo biloba

description: Using Hi-C data, we ordered and oriented the scaffolds of the previous ginkgo draft genome assembly, resulting in 12 chromosomes spanning 9.03 Gb (~94% of the whole genome) sequences.
DOI: 10.26036/cnp0000126
title: culturable genome reference (CGR)

description: A reference catalog comprising 1,520 non-redundant high-quality genomes of human gut bacteria, generated from a culture-based isolation of over six thousand bacterial isolates from fecal samples of healthy individuals, termed the culturable genome reference (CGR).
DOI: 10.26036/cnp0000129
title: Transcriptome analysis of anti-cancer adaptions in cancer-resistant species

description: This study provides multiple new insights into anti-cancer mechanisms in cancer-resistant species
DOI: 10.26036/cnp0000130
title: platypus_genome

description: Third generation sequencing raw reads of platypus and assembly genome.
DOI: 10.26036/cnp0000131
title: 蚊子携带的虫媒病毒鉴定

description: 从蚊子中发现和鉴定病毒
DOI: 10.26036/cnp0000136
title: Ginkgo biloba Raw sequence reads

description: Re-sequencing of the 545 ginkgo samples by BGI-SEQ500 generated a total of 428 billion paired-end reads
DOI: 10.26036/cnp0000147
title: Long Term Microgravity Effect on Macaca mulatta

description: Integrated transcriptomics, metabolomics and metagenomics data to study long term microgravity effect on Macaca mulatta.
DOI: 10.26036/cnp0000148
title: Study target genes of STAT3

description: This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification. Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. STAT3 associates with the vacuolar H+-ATPase on lysosomal membranes in a coiled coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing and increasing cytosolic and lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild type STAT3 as well as STAT3 mutants unable to activate target genes (Tyr-705-Phe and DNA binding mutant) or to regulate mitochondrial respiration (Ser-727-Ala). Upon cytosolic acidification, phospho-Tyr-705-STAT3 is rapidly dephosphorylated, transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium and to enhance cell survival. These data reveal STAT3 as a regulator of intracellular pH, and vice versa intracellular pH as a regulator of STAT3 localization and activity.
DOI: 10.26036/cnp0000150
title: BMSCs in different site of tumor-bearing mice

description: This project describes bone marrow stem cells in different sites of tumor-bearing mice.
DOI: 10.26036/cnp0000151
title: Characterization of mucosal and fluid microbiome across stages of gastric carcinogenesis

description: Characterization of mucosal and fluid microbiome across stages of gastric carcinogenesis
DOI: 10.26036/cnp0000162
title: 中国万种植物生命之树--生态保护与生物多样性进化研究&瑞丽植物园数字化

description: 中国万种植物生命之树--生态保护与生物多样性进化研究&瑞丽植物园数字化项目四个叶绿体基因组数据
DOI: 10.26036/cnp0000163
title: 外显子测序揭示牙齿脱落致病基因

description: 利用外显子测序技术发现一个巴基斯坦家系牙齿脱落的致病基因，并进行临床及功能学验证。
DOI: 10.26036/cnp0000165
title: Next generation sequencing platform comparision

description: This project focus on the application performance of different next generation sequencing platform.
DOI: 10.26036/cnp0000177
title: Coturnix japonica Genome sequencing and assembly

description: We did this work to characterize the mechanisms of early maturity and resolve the phylogeny of quail, detect domestication footprints in quail genome, and identify one widely used plumage color marker in the quail breeding.
DOI: 10.26036/cnp0000182
title: 草莓箭毒蛙基因组

description: 草莓箭毒蛙是在中美洲的一类箭毒蛙，物种间有很大的变异。不仅表现在颜色形态上，其栖息地、体型、发声及亲代照顾行为上均有所不同。因为其靓丽的颜色，成为很受欢迎的宠物。 随着第二代测序技术的不断成熟，以及测序成本的不断下降，我们可以通过高通量技术对草莓箭毒蛙进行测序、组装、注释；研究其基因组特点，同时从基因组水平对其毒性进行研究。
DOI: 10.26036/cnp0000193
title: An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

description: The human pre-implantation development involves extensive changes in chromatin structure and transcriptional activity. Here, by developing LiCAT-seq, a technique enabling simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells, we mapped the chromatin accessibility and transcriptome landscapes for human pre-implantation embryos. We observed global difference in chromatin accessibility between sperm and all stages of embryos, finding that the accessible regions in sperm tend to occur in gene-poor genomic regions. Integrative analyses between the two omics layers revealed strong association between the establishment of accessible chromatin and embryo genome activation (EGA), and uncovered transcription factors and endogenous retrovirus (ERVs) specific to EGA. In particular, a large proportion of the early activated genes and ERVs are bound by DUX4 and become accessible as early as the 2- to 4-cell stages. Our results thus offer new mechanistic insights into the molecular events inherent to human pre-implantation development.