cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100005
title: Genomic data from the Emperor penguin (<em>Aptenodytes forsteri</em>).

description: The Emperor penguin (<em>Aptenodytes forsteri</em>) is a large penguin, standing over 1 meter tall, with distinctive black, yellow and white markings. Like most penguins, the emperor penguins are indigenous to Antarctica and exist between the 66th and 78th parallels.

Famous for its unique social and reproductive behavior, the emperor penguin also possesses a number of other notable evolutionary qualities: its stature, its feathers, its incubation process, and its swimming capabilities. The <em>Aptenodytes forsteri</em> genome offers new insights into this remarkable bird.
DOI: 10.5524/100006
title: Genomic data from Adelie penguin (<em>Pygoscelis adeliae</em>).

description: The Adelie penguin (<em>Pygoscelis adeliae</em>) is an iconic penguin of moderate stature and a tuxedo of black and white feathers. The penguins are only found in the Antarctic region and surrounding islands. Being very sensitive to climate change, and due to changes in their behavior based on minor shifts in climate, they are often used as a barometer of the Antarctic.
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With its status as one of the adorable and cuddly flightless birds of Antarctica, they serve as an example for conservation, and as a result they are now categorised at low risk for endangerment. The sequence of the penguin can be of use in understanding the genetic underpinnings of its evolutionary traits and adaptation to its extreme environment; its unique system of feathers; its prowess as a diver; and its sensitivity to climate change. We hope that this genome data will further our understanding of one of the most remarkable creatures to waddle the planet Earth.<br> We sequenced the genome of an adult male from Inexpressible Island, Ross Sea, Antartica (provided by David Lambert) to a depth of approximately 60X with short reads from a series of libraries with various insert sizes (200bp- 20kb). 
The assembled scaffolds of high quality sequences total 1.23 Gb, with the contig and scaffold N50 values of 19 kb and 5 mb respectively. We identified 15,270 protein-coding genes with a mean length of 21.3 kb.
DOI: 10.5524/100008
title: Genomic data from the polar bear (<em>Ursus maritimus</em>).

description: The polar bear (<em>Ursus maritimus</em>) is one of the largest land carnivores, second only to the Alaskan brown bear. In an effort to adapt to the extremely cold Arctic environment, it has evolved many unique characteristics. However, ecological pressures pose a grave threat to the survival of polar bears. The polar bear genome provides significant contributions to research concerning evolution, biodiversity and climate change.<br>In 2010, the BGI completed the first draft of the genome sequence of a 25 years old male polar bear. Using next-generation sequencing technology (Illumina GA) to obtain about 101-fold genome coverage, and SOAPdenovo, the self-developed short reads assembly method, a high quality draft genome sequence was assembled with an N50 scaffold size of 15.9 megabases (Mb), and function elements annotation was finished. A reference gene set that contained around 21,000 genes for the polar bear was predicted. The transposable elements comprised approximately 37% of the polar bear genome.<br> The data also includes genome and SNP annotations, with SNP information from 18 polar bear and 10 brown bear individuals sampled from Greenland and Alaska.
DOI: 10.5524/100010
title: Genomic sequence from an Aboriginal Australian.

description: Here we present Aboriginal Australian (<em>Homo sapiens</em>) genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century.

The nuclear genome was sequenced to an overall depth of 6.4-fold. It had a high degree of fragmentation, but no genotype level evidence of sample contamination by DNA from sample handlers of European descent was detected. Over 2 million SNPs were identified after genome mapping and genotyping, approximately 6 percent of which were not previously reported. The mitochondrial genome (mtDNA) was sequenced to an average depth of 338x and found to belong to a new subclade of haplogroup O.
DOI: 10.5524/100011
title: Genome data from the leaf-cutting ant (<em>Acromyrmex echinatior</em>).

description: Here is presented high-quality (&gt;100x depth) Illumina genome sequence of the leaf-cutting ant <em>Acromyrmex echinatior</em>, a model species for symbiosis and reproductive conflict studies. They make a particularly good model as after humans, leaf-cutting ants form the largest and most complex animal societies on Earth. Part of the subfamily Myrmicinae, this particular species is found in the wild from Mexico to Panama and subsists mostly on a particular fungus of the genus <em>Leucocoprinus</em>, which it cultivates on a medium of masticated leaf tissue. With an estimated total size of 313 Mb, the genome is 28% made up of repeat sequences and has a GC content of 34%.
DOI: 10.5524/100013
title: Transcriptome from a lymphoblastoid cell line taken from the YH Han Chinese individual.

description: The transcriptome available here was generated from the same sample of peripheral blood mononuclear cells (PBMCs) from a consented donor (<em>Homo sapiens</em>) whose genome was deciphered in the YH project. YH is an anonymous male Han Chinese individual who has no known genetic diseases, and whose genome also serves as an Asian reference genome. These data were used to detect RNA-editing events using a pipeline that filtered and compared RNA-seq transcriptome and whole genome sequencing data (doi:10.1038/nbt.2122).

RNA was extracted from viable lymphoblastoid cell line of the YH individual, treated with DNase I to remove residual DNA, and double-stranded cDNA was synthesized from these RNA samples using random hexamer-primer and reverse transcriptase. For some of the libraries, samples were treated with Duplex-Specific thermostable nuclease (DSN) enzyme prior to cluster generation.

Sequencing libraries for strand specific transcriptome analysis were synthesized from fragmented RNA with random hexamer primers. After purification to remove dNTPs, second-strand synthesis was performed. Upon ligation with the Illumina PE adapters, the products were gel-recovered and subsequently digested with N-Glycosylase to remove the second-strand cDNA. Samples were then amplified by 15 cycles of PCR with Phusion polymerase and PCR primers with barcode sequence.

The libraries were prepared based on the Illumina pair end library protocol and subsequently sequenced by the Illumina HiSeq 2000 platform. Eight lanes of the flow cell were applied to the poly(A)+ RNA library, which was sequenced for 75 or 100 bp; five lanes were used for the poly(A) RNA library, which was sequenced for 90 bp.
DOI: 10.5524/100017
title: Genomic data from the roundworm <em>Ascaris suum</em>.

description: Available here is the draft genome for <em>Ascaris suum</em>, a roundworm species that infects pigs. It is a valuable resource for therapy and diagnostic test development for both <em>Ascaris suum</em> infection of pigs, and also human infection by the closely related species <em>A. lumbricoides</em>.

The <em>A. suum</em> genome was sequenced at ~80-fold coverage to generate an approximately 273 million base genome sequence encoding 18,542 protein-coding genes. Compared to other metazoan genomes, it has low repeat content (4.4%). Compared with other parasitic free-living roundworms and <em>C. elegan</em>, <em>A. suum</em> shares the highest homology with <em>Brugia malayi</em>, another animal parasite. The <em>A. suum</em> secretome (consisting of around 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissue, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and a foundation for developing new and urgently needed therapeutic intervention drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.
DOI: 10.5524/100019
title: Genome data from Jerdon’s jumping ant (<em>Harpegnathos saltator</em>).

description: Presented here is the sequenced genome of Jerdons jumping ant (<em>Harpegnathos saltator</em>). The jumping ant has a distinct caste and social behavior system, and its genome offers interesting insights into epigenetics in aging and behavior.

The Illumina Genome Analyzer platform was used to sequence a genomic library, obtaining more than 100-fold coverage of the estimated 330 Mb genome. The draft genomic assembly reached a scaffold N50 size of ~600 kb and covers more than 90% of the ants genome.
DOI: 10.5524/100020
title: Genome data from foxtail millet (<em>Setaria italica</em>).

description: Foxtail millet (<em>Setaria italica</em>) (2n=18), is an annual grass grown both as cereal crop (grain production) and as forage food. It is primarily grown in temperate, subtropical and tropical areas. With approximately 6,000 varieties, millet is one member of the Panicoideae (grasses subfamily), which includes maize (<em>Zea mays</em>), sorghum (<em>Sorghum bicolor</em>), and sugar cane (<em>Saccharum officinarum</em>). It is a nutritious dietary staple, containing starch, proteins, and a number of vitamins and minerals, such as calcium, iron, and sodium. It feeds nearly one-third of the world population with main daily-calories intake, and is especially prevalent in dry climates or soil-poor regions that are not suited for the cultivation of many other crops. Millet is self-pollinating, has a short lifecycle, is small in stature, and has a small genome size; all of these useful attributes make it an invaluable functional genomics model system, and an excellent reference genome to aid in the sequencing of other larger grasses genomes.
DOI: 10.5524/100027
title: Genome data from the Tibetan antelope (<em>Pantholops hodgsonii</em>).

description: The Tibetan antelope (<em>Pantholops hodgsonii</em>) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. It is a medium sized antelope that displays both migratory and herd behavior. Of interest, it is the only member of the genus <em>Pantholops</em>. The Tibetan antelope are listed as an endangered species, which is due to commercial poaching for their fine underwool, competition with local domesticated herds, and commercial development of their range land.

The genome of the Tibetan antelope was sequenced using Illumina GA sequencing technology. Genome assembly and annotation was also completed. The data here can be used for understanding the unique adaptations this animal has for surviving in its extreme high-altitude and as a model for investigating specific genetic mechanisms and the biology of other ruminant species.
DOI: 10.5524/100028
title: Genomic data from the pigeonpea (<em>Cajanus cajan</em>).

description: Here we present the genome of the pigeonpea (<em>Cajanus cajan</em>), a widely farmed diploid legume species. It is an important reference genome for food crop development as many crop species, such as soybean (<em>Glycine max</em>), chickpea (<em>Cicer arietinum</em>), lentil (<em>Lens culinaris</em>), and alfalfa (<em>Medicago sativa</em>), are legumes. The genetic improvement of pigeonpea has ramifications for food protection as well, as it is cultivated primarily in small-scale holdings in semi-arid tropical regions of the developing world.

The 237.2 Gb of sequence were generated using the Illumina next-generation sequencing platform to generate. Scaffolds representing 72.7% (605.78 Mb) of the 833.07-Mb pigeonpea genome were assembled using the Illumina sequence and Sanger-based bacterial artificial chromosome end sequences and a genetic map. A few segmental duplication events, but no recent genome-wide duplication events, are observable.
DOI: 10.5524/100029
title: Genomic data from chronic hepatitis B infected humans and healthy controls.

description: Chronic hepatitis B (CHB) infection remains endemic in large parts of the world and, as such, is a major global health issue. However, a thorough understanding of the genetic variants involved in CHB infection susceptibility remains lacking.

This dataset comprises the raw exome sequencing data, SNP sets and InDel sets for 50 CHB patients and 40 healthy controls. The exome sequences were captured by NimbleGen2.1M array targeting 34 Mb of the human genome, containing 180,000 coding exons and 551 miRNA genes. The enriched library was then sequenced on Illumina HighSeq2000 and sequencing reads were aligned to human reference genome (NCBI build 36.3). The average sequencing depth per sample is 43X after the removal of read duplicates. These data provide a resource for identifying genetic variants predisposing humans to CHB infections.
DOI: 10.5524/100031
title: Genomic data from the Wuzhishan inbred pig (<em>Sus scrofa</em>).

description: The pig (<em>Sus scrofa</em>) is an economically important food source and also serves as an important model organism. Here we present the sequence of one male inbred Wuzhishan pig (WZSP) at generation F20. DNA was extracted from the ear of this species. We applied a whole genome shotgun strategy and next-generation sequencing technologies using Illumina HiSeq 2000 for sequencing, in total 340.53 Gb of raw data were generated and 210.79 Gb high quality data were used for assembly. The assembly result of WZSP was 2.6 Gbp, and the N50 size of contigs and scaffolds were 23.5 Kbp and 5.4 Mbp, respectively. 38% of the genome was identified as repeats and 20,326 genes were identified from homolog prediction.
DOI: 10.5524/100032
title: The genome of <em>Schistosoma haematobium</em>

description: <em>Schistosoma haematobium</em> is an important digenetic trematode, and is found in the Middle East, India, Portugal and Africa. It is a major agent of schistosomiasis. More specifically, it is associated with urinary schistosomiasis. Adults are found in the Venous plexuses around the urinary bladder and the released eggs traverse the wall of the bladder causing haematuria and fibrosis of the bladder. The bladder becomes calcified, and there is increased pressure on ureters and kidneys otherwise known as hydronephrosis. Inflammation of the genitals due to <em>S.haematobium</em> may contribute to the propagation of HIV. 

In this study, we sequenced the <em>S.haematobium</em> genome from 200 ng of genomic DNA template isolated from a single, mated pair of adult worms, and produced 33.5 Gb of usable sequence data, using Illumina-based technology at 74-fold coverage and comparedit to sequences from related parasites. We consistently showed low sequence heterozygosity and estimated the genome size to be 431-452 Mb, then assembled the data and used local assemblies to close most (96.1%) of the remaining gaps, achieving a final assembly of 385 Mb (365 contigs; N50 scaffold size 307 Kb). Also we included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.
DOI: 10.5524/100035
title: Resources for the MeDUSA (Methylated DNA Utility for Sequence Analysis) MeDIP-seq computational analysis pipeline for the identification of differentially methylated regions, and associated methylome data from 18 wild-type and mutant mouse ES, NP and MEF cells.

description: Here we present 18 genome-wide DNA methylation profiles of wild type and Thymine DNA glycosylase (<em>Tdg</em>) knockout cells, which serve as an excellent murine methylome resource. The 18 samples represent 6 biological cohorts: 6 samples were derived from mouse embryonic stem cells (3 <em>Tdg+/-</em>, 3 <em>Tdg-/-</em>), 6 samples were from mouse neural precursor cells (3 <em>Tdg+/-</em>, 3 <em>Tdg-/-</em>) and 6 samples were obtained from mouse embryonic fibroblasts (3 <em>Tdg+/+</em>, 3 <em>Tdg-/-</em>).

Next generation sequencing was performed on the libraries using an Illumina GAIIx for each sample. Paired end alignment against the mouse genome (Build NCBIM37) was performed using BWA (v0.5.8), and filtering to remove those reads failing to map was performed using SAMtools (v0.1.9) and a custom perl script. The Bioconductor (v2.7) package MeDIPs (v1.0.0) was used to normalize for size of the sequence library, done by calculating reads per million in tiled windows across the genome. Fragment length normalization was performed using a custom perl script. Wig tracks representing library size normalized alignment were generated using a combination of MEDIPS and custom R scripts. In addition to the total alignment wig track, strand specific wig tracks were also generated, enabling the user to infer whether the MeDIP signal is derived by methylation on the forward and/or reverse strand.

The MeDIP-seq data were processed using the analysis pipeline MeDUSA (Methylated DNA Utility for Sequence Analysis). MeDUSA brings together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control, and determination and annotation of differentially methylated regions.
DOI: 10.5524/100036
title: Type 2 Diabetes gut metagenome (microbiome) data from 368 Chinese samples and updated metagenome gene catalog

description: We provide data from the sequenced and analyzed gut metagenome of 368 Chinese individuals with Type 2 Diabetes (T2D) and healthy controls used in a newly developed two stage Metagenome-Wide Association Study (MWAS) aimed at identifying associations between gut microbiota and Type 2 Diabetes. The data here include the an updated metagenome gene catalog, metagenome assemblies, genetic and functional markers associated with T2D, and a novel form of marker- a Metagenomic Linkage Marker (MGL), that allows taxonomic species-level analyses without the need to identify, isolate, and culture novel bacterial species.

Bacterial DNA was extracted from faecal samples and subjected to unbiased, whole-genome shotgun (WGS) sequencing using the Illumina GAIIx and HiSeq2000. In summary, 145 samples were sequenced in stage I and 378.4 Gb of paired-end (PE) sequence data were generated; 200 samples were sequenced in stage II and 830.8 Gb of PE sequence data were generated, as well as 23 additional samples for a validation study on gut-microbiota-based T2D classification. By combining MetaHIT data and our sequence data in stage I we constructed an updated human gut microbial gene catalogue, which contained 4.3 million genes suitable for studies on Chinese individuals. In this updated gene catalogue, 21.3%, 47.1% and 60.9% of genes could be assigned to known genera, KEGG and eggNOG database respectively. Taking this gene catalogue as a reference, we identified gene, KO and OG markers, respectively, which seemed to be strongly associated with T2D in our two-stage case-control study, and 47 Metagenomic Linkage Groups (MLGs). These MLGs were further assembled into different contig sets, which could provide useful genetic, functional, and taxonomic information for the relevant bacterium.
DOI: 10.5524/100037
title: Single cell whole-exome sequences of bladder cancer from an individual.

description: This dataset contains single-cell and whole-tissue sequencing and annotation data from a muscle-invasive bladder transitional cell carcinoma from one individual. The data available includes: single-cell whole-exome sequences from 55 individual cells, including 44 from the tumor and 11 from normal adjacent tissue; whole-tissue DNA sequence data from this cancer and the matched normal. Additional data includes alignments, SNP calling, and high confidence somatic mutation calling and their allelic frequencies.
DOI: 10.5524/100040
title: The genome of Darwin’s Finch (<em>Geospiza fortis</em>).

description: The Medium Ground Finch <em>Geospiza fortis</em>, is one of species of finches first collected by Charles Darwin on the Galapagos islands, and is emblematic for its involvement in the development of evolutionary theory by Darwin and for confirming the action of natural selection. Also know as a Darwin finch, we have sequenced a female individual at 115X coverage of HiSeq data, and produced a high quality draft genome assembly. The genome size of <em>Geospiza fortis</em> is at about 1.07 Gb. The scaffold N50 size of this assembly is at about 5.2Mb and contig N50 size is about 30Kb. A total of 16,286 protein coding genes were annotated. As well as being a model for the study of evolutionary biology, the availability of this genome will also be helpful for the subsequent population studies of this species. As another songbird genome, this will allow researchers to validate the findings of vocal learning gene and behavior interaction that has been carried out in the previously studied zebra finch.
DOI: 10.5524/100042
title: Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer

description: DA and F344 are two inbred rat strains with numerous dichotomous phenotypes, including 
susceptibility to autoimmune disease models and inflammatory responses. While these strains 
have been extensively studied, little information is available about the DA and F344 genomes, as 
only the BN and SHR strains have been sequenced to date. Here we report the sequencing of the 
DA and F344 genomes using next-generation Illumina paired-end read technology, and the first 
de novo assembly of a rat genome. DA and F344 were sequenced with an average depth of 32-
fold, covered 98.9% of the BN reference genome, and included 97.97% of known rat ESTs. New 
sequences could be assigned to 59 million positions with previously unknown data in the BN 
reference genome. Differences between DA, F344 and BN included 19 million positions in novel 
scaffolds, 4.09 million SNPs (including 1.37 million new SNPs), 458,224 short insertions and 
deletions, and 58,174 structural variants. Genetic differences between DA, F344, and BN, 
including high-impact SNPs and short insertions and deletions affecting over 2,500 genes, are 
likely to account for most of the phenotypic variation between these strains. The new DA and 
F344 genome sequencing data should facilitate gene discovery efforts in rat models of human 
disease.
DOI: 10.5524/100001
title: Genomic data from <em>Escherichia coli</em> O104:H4 isolate TY-2482

description: The May 2011 outbreak of an <em>E. coli</em> infection in Europe resulted in serious concerns about the potential appearance of a new deadly strain of bacteria, <em>Escherichia coli</em> O104:H4 TY-2482. In response to this situation, and immediately after the reports of deaths, the University Medical Centre Hamburg-Eppendorf and BGI-Shenzhen worked together to sequence the bacterium and assess its human health risk.<br><br>The bacteriums genome was first sequenced using Life Technologies; Ion Torrent sequencing platform. According to the results of the draft assembly, the estimated genome size of this new <em>E. coli</em> strain is about 5.2 Mb. Sequence analysis indicated this bacterium is an EHEC serotype O104 <em>E. coli</em> strain. Comparative analysis showed that this bacterium has 93% sequence similarity with the EAEC 55989 <em>E. coli</em> strain, which was isolated in the Central African Republic and known to cause serious diarrhea. This strain of <em>E. coli</em>, however, has also acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome. The acquisition of these genes may have occurred through horizontal gene transfer.<br><br>To maximize its utility to the research community and aid those fighting the epidemic, this genomic data was released into the public domain under a CC0 license.<br><br>To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to genomic data from the 2011 <em>E. coli</em> outbreak. This work is published from China.