cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100088
title: Genomic data for the Tibetan ground tit (<em>Pseudopoces humilis</em>).

description: Available here is the first draft genome sequence of the Tibetan ground tit (<em>Pseudopodoces humilis</em>) also known as Humes Groundpecker. This bird is native to the Qinghai-Tibet Plateau (QTP) or the roof of the world, which has become a focus for many biological studies due to the extreme environmental conditions, and the genetic mechanisms of high-altitude adaptation has never been studied. Controversy also exists regarding the ground tits phylogeny formerly thought to be part of the Corvidae family, recent phylogenetic analysis have determined this to not be the case. <br>A 1.04 Gb assembled draft genome sequence was generated that covered 95.4% of the whole genome. The scaffold N50 and contig N50 values were 16.3 Mb and 164.7 Kb respectively. High accuracy at the sequencing level was ensured, where the average sequencing depth of the ground tit assembly was 96×, and 99% of the assembly had at least 20× coverage. This data contributes to the study of avian evolutionary history and provides new insights into the tits adaptation to extreme environmental conditions.
DOI: 10.5524/100095
title: Supporting data for "Low coverage sequencing of two Asian elephant (<em>Elephas maximus</em>) genomes."

description: Three species of elephant exist, the Asian elephant (<em>Elephas maximus</em>) and two species of African elephant (<em>Loxodonta africana, Loxodonta cyclotis</em>). Populations of all species are dwindling, and are under threat due to factors such as habitat destruction and ivory hunting. The two species differ in many respects, including in their morphology and response to disease. The availability of elephant genome sequence data from both species will complement studies of behaviour, genetic diversity, evolution and disease resistance. 
<br>We present low-coverage Illumina sequence data from two Asian elephants, representing approximately 5X and 2.5X coverage respectively. Both raw and aligned data are available, using the African elephant genome as a reference. 
<br>The data presented here are an important addition to the available genetic and genomic information on Asian and African elephants.
DOI: 10.5524/100048
title: Quantitative proteomics and transcriptomics data from the anaerobic thermophilic eubacterium Thermoanaerobacter tengcongensis

description: Thermoanaerobacter tengcongensis (T. tengcongensis) is a thermophilic eubacterium isolated from Tengchong, China. It is an anaerobic, Gram-negative, rod-shaped bacterium, able to survive in temperatures ranging from 50 to 80 °C. The genome sequence of T. tengcongensis was decoded in 2001, comprising 2.69 Mb in length and containing 2,588 predicted proteins. Previous studies of the proteomic response to growth temperature changes and thermo-survival of T. tengcongensis have been carried out with 2DE and MALDI-TOF/TOF MS. However, due to limitations of the technique, only few proteins with semi-quantitative estimation for the differential 2DE spots responsive to temperature changes are obtained.

An improved iTRAQ-based quantification proteomics protocol has been developed, and using this method data produced to analyze the T. tengcongensis cultured at four temperatures: 55, 65, 75, and 80 oC. In order to obtain reproducible data, two biological replicates and multiple technical replicates (four times for the first sample preparation and three times for the second one) were carried out. Using the iTRAQ labeled sample analyzing procedure of high-pH RP HPLC coupled with LTQ Orbitrap Velos MS, 732,234 MS/MS spectra in total were obtained. The raw data were searched by Mascot 2.3, approximately 23% of the spectra were matched to peptides (FDR&lt;0.01), while 0.5% less of the identified peptides were absent with the reporter tags. In total, 1,589 proteins elicited from 13,223 unique peptides, were identified with quantitative information, which covered 61.4% of the 2,588 predicted proteins of the T. tengcongensis genome. To study the abundance correlation between protein and mRNA, RNA-seq was carried out to study the transcription of the different cultured samples. Using Illumina HiSeqTM 2000 sequencing and the analyzing the raw data using SOAP2, the RNA-seq data covered approximately 97% (2501/2588) of the predicted genes, with more than two reads for each gene. These two datasets help show that the temperature-dependent responses of transcription and translation can happen in synchrony.
DOI: 10.5524/100051
title: A test-retest functional MRI dataset for motor, language and spatial attention functions

description: The following data comes from the study A test-retest fMRI dataset for motor, language and spatial attention functions, which is a test-retest dataset acquired to validate functional magnetic resonance imaging (fMRI) tasks used in pre-surgical planning. Five task-related fMRI time series (finger, foot and lip movement, overt verb generation, covert verb generation, overt word repetition, and landmark tasks) were used to investigate which protocols gave reliable single-subject results. Ten healthy participants in their fifties were scanned twice using an identical protocol 2-3 days apart. In addition to the fMRI sessions, high-angular resolution diffusion tensor MRI (DTI), and high-resolution 3D T1-weighted volume scans were acquired.<br><br>Each subject was assigned a random, unique identifier using the DICOM confidential de-identification toolkit to replace their name and any other medical identification information. DICOM files for each scanning sequence were anonymized according to the Health Insurance Portability and Accountability Act guidelines, and DICOM to NIfTI conversion was performed using the dcm2nii tool. To prevent visual identification, the 3D T1-weighted volumes have been defaced using mri_deface. Seven NIfTI files are provided for each subject/session: five 4D fMRI, one 4D DTI, and one 3D T1-weighted volume scan.<br><br>Due to the fact that the overt language tasks were scanned using sparse sampling, we were able to record and analyze each subjects responses (not included due to privacy concerns). This analysis lead to exclusion of one session of one subject of the overt word repetition task, due to the fact that the subject failed to perform the task correctly. Data and its description are arranged according to the OpenfMRI layout. Together, this dataset provides a unique opportunity to investigate the reliability of different fMRI tasks, as well as methods and algorithms used to analyze, de-noise and combine fMRI, DTI and structural T1-weighted volume data.<br><br>Related code in GitHub: https://github.com/chrisfilo/2010-Reliability-Study
DOI: 10.5524/100053
title: Stress responsive proteins are actively regulated during rice (<em>Oryza sativa</em>) embryogenesis as indicated by quantitative proteomics analysis

description: Embryogenesis is the beginning of a plants life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2,165 unique proteins were identified in rice embryos by using the Q-Exactive Mass spectrometry, and the abundances of 867 proteins were actively changed based on statistical evaluation towards the quantitative MS/MS signals. The quantitative data were then confirmed by using multiple reactions monitoring (MRM) conducted on Qtrap 5500 Mass spectrometry. To make the study reproducible by others, all of the raw Q-Exactive and Qtrap 5500 data had been deposited in the GigaScience database (GigaDB).<br>By using the WENGOsoftware, we further analyze the GO distribution of the identified embryo proteins. In the molecular functional group, the identified proteins that work as metabolic enzymes, binding (protein binding, nucleotide binding) and transporter are ranked at the top of the category. In the biological process categorization, the proteins that participate in metabolic and response to stimulus process are at the top ratio in the identified embryo proteins.
DOI: 10.5524/100056
title: <em>Termitomyces</em> sp. J132 fungus genome assembly data.

description: <b>Background: </b><em>Termitomyces</em> is a genus of basidiomycete fungi domesticated by Macrotermitinae as food source and form obligate symbiosis with the termites. The fungal symbiont is thought to be the decomposer of lignocellulose, however, the exact function of the symbiont is still unclear.<br>
<b>Sampling:</b> The homokaryotic strain of <em>Termitomyces</em> was obtained using a standard protoplasting procedure of a heterokaryon isolated from a colony of <em>Macrotermes natalensis</em> (Mn105) in Mookgophong, South Africa (S24°4030.5 E28°4750.4, elevation 1045 m).<br>
<b>Finding:</b> The fungus genome assembly yielded a size of 83.7Mb sequence, with a scaffold N50 of 262Kb, upon which 11,556 genes were annotated.
<br>
DOI: 10.5524/100070
title: Data looking at methylation changes of intestinal genes in the neonatal period of preterm neonate pigs.

description: For this study, six term pigs were delivered close to full term (115116 days gestation, by cesarean section) from two pregnant sows (Large White × Duroc, Askelygaard, Denmark), serving as the 0d-term group. Within 6 hours of birth, these pigs were euthanized (sodium pentobarbitone, 200 mg/kg, intravenous), and mid small intestine was dissected out, snap frozen in liquid nitrogen and stored at -80°C.
<br>Under anesthesia, six preterm pigs were obtained from five pregnant sows (Large White × Duroc; Askelygaard, Denmark) by cesarean delivery at 90- 92% (104107 days) gestation. Six of these pigs were euthanized within 6 hours of birth without any feeding (0d-preterm group). The intestine was also dissected out and frozen at -80°C. The remaining 6 preterm pigs were reared individually in infant incubators (Air-Shields, Hatboro, PN) and fitted with orogastric catheters for PN and oro-gastric feeding tube. The pigs were given PN solution at a rate of 4 mL/(kg × h) on d1 and 6 mL/(kg × h) on d2 as well as minimal enteral nutrition: 24 mL/(kg × d) on d1 and 40 mL/(kg × d) on d2 with infant formula. The PN solution was based on a commercially available product (Kabiven, Fresenius Kabi) and adjusted in nutrient composition to meet the requirement of pigs. On d3, they were transferred to full enteral nutrition (EN) [120 mL/(kg × d)] for two more days before sacrifice. The mid intestine was also dissected out and frozen at -80°C. 
<br>Pigs were continuously monitored for clinical symptoms of Necrotizing enterocolitis (NEC) and at tissue collection the severity of NEC-like intestinal lesions was evaluated using scoring system. Six pigs remained healthy at the time of tissue collection on day 4 (4d-preterm) while six other pigs had significant NEC lesions identified in their intestines. Experimental and animal management procedures followed a high standard of veterinary care and were conducted in accordance with approval of institutional and national policies and guidelines. 
<br>For sanger sequencing, the processed sequence was aligned to the pig reference regions (all PCR regions) by the blast software. For HiSeq sequencing, the Illumina reads were post-processed and aligned to the pig reference regions (all PCR regions) using SOAP aligner (Version 2.01) with default parameters that excluded reads with more than five mismatched bases. Multiple reads mapping to the same position were counted only once to remove potential bias from PCR. Then we calculated the methylated level based on the effective data.
DOI: 10.5524/100071
title: Genomic data from the domestic yak (<em>Bos grunniens</em>).

description: Domestic yaks (<em>Bos grunniens</em>) provide meat and other necessities for Tibetans living at high altitude on the Qinghai-Tibetan Plateau and in adjacent regions. Here, we present the draft genome sequence of a female domestic yak generated using Illumina HiSeq 2000 technology at 65-fold coverage. <br>De novo assembly of 4.4 billion reads from paired-end libraries yielded a draft assembly with a total length of 2,657 Mb, and contig and scaffold N50 sizes of 20.4 kb and 1.4 Mb, respectively. Approximately 90% of the total sequence was covered by 2,083 scaffolds of &gt;307 kb, with the largest scaffold spanning 8.8 Mb.
DOI: 10.5524/100080
title: Genomic data of the domestic donkey (<em>Equus asinus</em>).

description: The domestic donkey is derived from the African Wild Ass. As with most domesticated species there are a wide variety of coat colours and sizes. They can live for upto 40years. <br>We sequenced the genome to a depth of approximately 19.4 X with short reads from a series of libraries with various insert sizes ( 800bp and 2kb) on a HiSeq 2000 sequencer.<br>The assembled scaffolds of high quality sequences total 48.6 Gb.
DOI: 10.5524/100082
title: Genomic data of the domestic goat (<em>Capra hircus</em>).

description: The domestic goat is one of the most important livestock species in the world, especially in China, India and other developing countries. Goats not only serve as an important source of meat, milk, fiber and pelts, and have fulfilled agricultural, economic, cultural and even religious roles from very early times in human civilization, but also are now used as animal models for biomedical research and transgene production of protein medicines.We would like to share all the genome data of goat. We hope the genome sequence of goat can provide a new resource for biological research and breeding of goat and other small ruminants.<br>
We sequenced the 2.92 Gb genome to a depth of approximately 65.6 X with short reads from a series of libraries with various insert sizes ( 170 bp, 350 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.<br>
The assembled scaffolds of high quality sequences total 191.5 Gb, with the contig and scaffold N50 values of 18.7 kb and 2.21 Mb respectively. We identified 22,175 protein-coding genes.
In addition, we also provide the restriction-enzyme fragment maps derived from the whole genome mapping (WGM) technology developed by the Argus System (method described in this paper).<br>
Scaffolds derived from de novo assembly of next-generation sequencing data are converted into restriction maps by in silico restriction enzyme digestion. Then, the distance between restriction enzyme sites in the sequencing-derived scaffolds are matched to the lengths of the optical fragments in the single-molecule WGM restriction maps. Matches allow the scaffolds to be extended and linked into super-scaffolds.
DOI: 10.5524/100043
title: Bisulfite-PCR combined with cloning Sanger sequencing data for validating DNA methylation level in <em>Trichinella spiralis</em>.

description: <em>Trichinella spiralis</em> is the smallest nematode parasite of humans and is also infectious in the rat, pig and bear species. Responsible for the disease trichinosis, it is often referred to as the pork worm due to infection usually being caused by the consumption of undercooked pork products. Adults mature in the intestines of an intermediate host, and each female produces batches of larvae that bore through the intestinal wall and the lymphatic system. They are then carried to striated muscle where they encyst.

To date 5'-cytosine methylation (5mC) has not been reported in <em>Caenorhabditis elegans</em>, and using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) the existence of DNA methylation in <em>T. spiralis</em> was detected, making it the first 5mC reported in any species of nematode. Technological advances now enable the high-resolution detection of 5'-cytosine methylation, providing a stronger basis for examining the role of DNA methylation in eukaryotic genomes such as these. 

Using MethylC-seq, here we present the first comprehensive study that confirms the existence of DNA methylation in the parasitic nematode, <em>T. spiralis</em> and we characterised the methylomes during the three life-cycle stages of this food-borne infectious parasite of humans. We generated 61.65, 23.52 and 55.77 million raw reads, almost all of which (96.36%, 91.30% and 99.27%, respectively) were able to be aligned to the <em>T. spiralis</em> reference sequence, yielding 2.91, 1.05 and 2.71 Gb of DNA sequence data for the three life-cycle stages. To further validate the DNA methylation level we randomly selected genomic regions and performed Bisulfite-PCR combined with cloning Sanger sequencing. This additional data further supports the existence of DNA methylation in the parasitic nematode, <em>T. spiralis</em>.
DOI: 10.5524/100044
title: Software and supporting material for “SOAPdenovo2: An empirically improved memory-efficient short read <em>de novo</em> assembly”

description: SOAPdenovo2 is the latest <em>de novo</em> genome assembly package from BGIs SOAP (short oligonucleotide analysis package) suite of tools (homepage here: http://soap.genomics.org.cn/). Compared to SOAPdenovo1, this new version has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closure, and is optimized for large genomes.<br> Using new sequencing data from the YH (<em>Homo sapiens</em>) diploid genome the first sequenced Han Chinese individual, an updated assembly was produced (see dataset here: doi:10.5524/100038), with the N50 scores for the contig and scaffold being 3-fold and 50-fold longer, respectively, than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 times lower during the point of largest memory consumption. <br> Benchmarking with Assemblathon1 and GAGE datasets shows that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo1 and is competitive to other assemblers on both assembly length and accuracy.
<br>
In order to facilitate readers to repeat and recreate these findings, configured packages with the compressed pipelines containing all of the necessary shell scripts and tools are available from the BGI FTP server (ftp://public.genomics.org.cn/BGI/SOAPdenovo2).
<br>
The latest version of SOAPdenovo2 is available from Sourceforge: http://soapdenovo2.sourceforge.net/
<br>
These pipelines are available from our data platform as Galaxy workflows: http://galaxy.cbiit.cuhk.edu.hk/
DOI: 10.5524/100047
title: Quantitative proteomics data using mTRAQ/MRM looking at human AKR family members in cancer cell lines

description: Members of the human aldo-keto reductaseAKRsuperfamily have been reported to be involved in cancer progression, and to investigate their role further a quantitative method to measure human AKR proteins in cells using mTRAQ-based multiple reaction monitoring (MRM) has been developed. AKR peptides with multiple transitions were carefully selected upon tryptic digestion of the recombinant AKR proteins, while AKR proteins were identified by SDS-PAGE fractionation coupled with LC MS/MS. Utilizing mTRAQ triplex labeling to produce the derivative peptides, calibration curves were generated using the mixed lysate as background, and no significantly different quantification of AKRs was elicited from the two sets of calibration curves under the mixed and single lysate as background. This approach was employed to quantitatively determine the 6 AKR proteins, AKR1A1, AKR1B1, AKR1B10, AKR1C1/C2, AKR1C3 and AKR1C4 in 7 different cancer cell lines, and for the first time to obtain the absolute quantities of all the AKR proteins in each cell. The cluster plot revealed that AKR1A and AKR1B were widely distributed in most cancer cells with relatively stable abundances, whereas AKR1Cs were unevenly detected among cells demonstrating diverse dynamic abundances. The AKR quantitative distribution in different cancer cells, and may enable further insight on the role of AKR proteins are involved in tumorigenesis.
DOI: 10.5524/100049
title: Metacellulosomics data demonstrating synergism in a soil-derived cellulose-degrading microbial community.

description: Currently available enzyme technology is insufficient to economically degrade plant biomass, and presumably will remain so until we reach a comprehensive understanding of how nature solves this problem. Here we show that a microbial consortium enriched from soil establishes collaborative relationships to enable efficient hydrolysis of plant polysaccharides. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in the consortium show that these microbes cooperate in both cellulose-degrading and other important metabolic processes. Experimental evidence for cellulolytic inter-species synergies came from the discovery of cellulosome structures composed of subunits from different phylotypes. Oxygen consumption by specific phylotypes enables anaerobic saccharification, whereas inferred utilization of the resulting metabolites by non-cellulolytic phylotypes negates their accumulation and associated negative effects towards cellulose degradation. These collaborative microbial actions illustrate that efficient biomass conversion in nature relies on a high level of microbial community organization.
DOI: 10.5524/100050
title: Genomic data from Triticum urartu - the progenitor of wheat A genome

description: The wheat A genome, as a basic genome of bread wheat and other polyploid wheats, is centrally important to the evolution, domestication, and genetic improvement of wheat. The progenitor of the A genome is the diploid wild einkorn wheat Triticum urartu. Here, we sequenced T. urartu (accession G1812) using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform, and assembled the genome using SOAPdenovo2 with 448.49 Gb of filtered high-quality sequence data. The genome assembly reached 3.92 Gb (without Ns) with a contig N50 length of 3.42 kb and 4.66 Gb (with Ns) with a scaffold N50 length of 63.69 kb . To facilitate gene prediction, we generated a 116.65 Mb transcriptome of T. urartu with 67.14 Gb RNA-Seq data from eight different tissues and treatments, and 49,935 assembled transcripts from six tissues using the Roche 454 sequencing platform. In total, we predicted 34,879 protein-coding gene models. The average gene size was 3,207 bp, with a mean of 4.7 exons per gene.
DOI: 10.5524/100002
title: Genomic data from the Chinese Rhesus macaque (<em>Macaca mulatta lasiota</em>).

description: The Chinese rhesus macaque (<em>Macaca mulatta lasiota</em>) is a subspecies of rhesus macaques that mainly resides in western and central China. Due to their anatomical and physiological similarity with human beings, macaques are a common laboratory model. Also, as several macaques species have been sequenced, such as the Indian rhesus macaque and the crab-eating macaque, examination of the Chinese rhesus macaque (CR) genome offers interesting insights into the entire <em>Macaca</em> genus.

The DNA sample for data sequencing and analyses was obtained from a five-year old female CR from southwestern China. The genome was sequenced on the IlluminaGAIIx platform, from which 142-Gb of high-quality sequence, representing 47-fold genome coverage for CR. The total size of the assembled CR genome was about 2.84 Gb, providing 47-fold on average. Scaffolds were assigned to the chromosomes according to the synteny displayed with the Indian rhesus macaque and human genome sequences. About 97% of the CR scaffolds could be placed onto chromosomes.