21 Works

Quantitative proteomics data using mTRAQ/MRM looking at human AKR family members in cancer cell lines

S Zhang, B Wen, B Zhou, L Yang, C Cha, S Xu, X Qiu, Q Wang, H Sun, X Lou, J Zi, Y Zhang, L Lin & Liu S
Members of the human aldo-keto reductase(AKR)superfamily 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...

Genomic data from Triticum urartu - the progenitor of wheat A genome

H-Q Ling, S Zhao, C Zhang, Y Tao, C Gao, Q Liang, D Wang, A Zhang & J Wang
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...

Genomic data from Aegilops tauschii - The Progenitor of Wheat D Genome

J Jia, S Zhao, W He, Y Tao, C Zhang, C Gao, D Li, L Mao & J Wang
A spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n=14, DD) with cultivated tetraploid wheat Triticum turgidum (2n=4x=28, AABB) 8,000~10,000 years ago in the Fertile Crescent resulted in the bread wheat (Triticum aestivum; 2n=6x=42, AABBDD), one of the earliest cultivated crops in modern agriculture. We sequenced the 4.36-gigabase (Gb) genome of Ae. tauschii by generating ~90x genome coverage of short reads from a series of libraries with various insert sizes. The assembled scaffolds of...

Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis

J Zi, J Zhang, Q Wang, B Zhou, J Zhong, C Zhang, X Qiu, B Wen, S Zhang, X Fu, L Lin & S Liu
Embryogenesis is the beginning of a plant’s 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...

CEGMA gene predictions for Assemblathon 2 entries

KR Bradnam, JN Fass & IK Korf
Assemblathon 2 genome assemblies were assessed for their genic content. This was done by using published tool (CEGMA) that looks for the presence of nearly full-length genes within a single scaffold sequence. Such genes must match HMMs made from a set of 458 highlyconserved genes that are presumed to be conserved in all eukaryotes.

Assembled Fosmid sequences used for assessment of Assemblathon 2 entries

JN Fass, IK Korf, KR Bradnam, ED Jarvis, J Howard, J Shendure, J Hiatt & JO Kitzman
Assemblathon 2 genome assemblies for bird and snake were assessed using high-confidence regions of assembled Fosmid sequences. These validated Fosmid regions (VFRs) were included as an additional file as part of the Assemblathon 2 manuscript. This file contains the complete assembled Fosmid sequences for both species (47 sequences for bird, 29 for snake).

Holobiomic division of labor in fungus-farming termites

M Poulsen, H Hu, C Li, J.J Boomsma & G Zhang
Termites, Macrotermes natalensis, rely on gut symbionts to decompose organic matter, but the derived Macrotermitinae domesticated Termitomyces fungi to produce their food. This transition to fungiculture led to a change in the ancestral gut symbionts towards a novel gut microbiome, but the complementary roles of the major components of this obligate symbiosis have remained enigmatic. Here we obtained the genomes of a Macrotermes natalensis termite, its Termitomyces fungus cultivar, as well as community gut microbiomes...

A test-retest functional MRI dataset for motor, language and spatial attention functions

KJ Gorgolewski, A Storkey, ME Bastin, IR Whittle, JM Wardlaw & CR Pernet
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...

Raw data, assembly and annotation results for: “Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification”

X Zhou, Y Li, S Liu, Q Yang, X Su, L Zhou, M Tang, R Fu & J Li
The following data comes from the study “Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification”, which is the first systematic meta-barcoding study sequencing the total DNA from insect communities independent of PCR amplification. Following mitochondrial enrichment using differential centrifugation, a preliminary sample and a formal sample are achieved respectively with 2.2G and 13.2G from the Illumina HiSeq 2000 platform using 100 bp paired-end (PE) sequencing, following manufacturer’s instructions. The...

GigaGalaxy workflows and histories from “Galaxy tools to study genome diversity”

OC Bedoya-Reina, A Ratan, R Burhans, HL Kim, B Giardine, C Riemer, Q Li, TL Olson, , BM VonHoldt, GH Perry, SC Schuster & W Miller
Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data. A suite of tools for the Galaxy web server have been created aimed at...

De novo high-coverage sequencing and annotated assemblies of the budgerigar genome

JT Howard, S Koren, A Phillippy, S Zhou, D Schwartz, M Schatz, R Aboukhalil, JM Ward, J Li, B Li, O Fedrigo, L Bukovnik, T Wang, G Wray, I Rasolonjatovo, R Winer, J R Knight, W Warren, G Zhang & ED Jarvis
Background: Parrots are considered one of the most behaviorally advanced vertebrate groups. They have an advanced ability of vocal learning. Parrots can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, very little is known about the genetics of these traits. In order to understand the molecular and genetic basis of these traits we need whole genome sequencing and a robust assembly of...

Assemblathon 2 assemblies

KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, S Boisvert, JA Chapman, G Chapuis, R Chikhi, H Chitsaz, J Corbeil, C Del Fabbro, TR Docking, R Durbin, D Earl, S Emrich, P Fedotov, NA Fonseca, G Ganapathy, RA Gibbs, S Gnerre, É Godzaridis, S Goldstein, M Haimel … & IF Korf
Assemblathon 2 is a genome assembly contest where participating teams attempted to assemble genomes for three vertebrate species using a mixture of next-generation sequencing data. In total, 43 assemblies were submitted for three species (15 for bird, 16 for fish, and 12 for snake). These assemblies were assessed using a wide variety of statistical approaches as well as using experimental data from Fosmid sequences and optical maps.

Whole-Genome Sequences of DA and F344 Rats with Different Susceptibilities to Arthritis, Autoimmunity, Inflammation and Cancer

X Guo, M Brenner & PS. Gulko
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...

Genomic and transcriptomic data from the Brandt's bat (Myotis brandtii)

I Seim, X Fang, Z Xiong, AV Lobanov, Z Huang, S Ma, Y Yue Feng, AA Turanov, Y Zhu, TL Lenz, MV Gerashchenko, D Fan, SH Yim, X Yao, D Jordan, Y Xiong, Y Ma, AN Lyapunov, G Chen, OI Kulakova, Y Sun, SG Lee, RT Bronson, AA Moskalev, Sunyaev … & VN Gladyshevb
Brandt's bat (Myotis brandtii) is a species of vesper bat in the family Vespertilionidae. It is found throughout most of Europe and parts of Asia. It is known for its extreme longevity quotient, approximately twice that of humans. A whole-genome shotgun strategy was applied to sequence the genome of an adult male Brandt’s bat (M. brandtii) from the Obvalnaya cave in Russia. We also sequenced liver, kidney and brain transcriptomes of hibernating and summer-active M....

Genomic data from the Black Flying Fox (Pteropus alecto)

G Zhang, C Cowled, Z Shi, Z Huang, KA Bishop-Lilly, X Fang, JW Wynne, Z Xiong, ML Baker, W Zhao, M Tachedjian, Y Zhu, P Zhou, X Jiang, J Ng, L Yang, L Wu, J Xiao, Y Feng, Y Chen, X Sun, Y Zhang, GA Marsh, G Crameri, CC Broder … & J Wang
The black flying fox, Pteropus alecto, is a megabat in the family Pteropodidae. Members of the genus Pteropus include the largest bats in the world. The Pteropus genus currently has about 57 recognised species. The genus is primarily an island taxon, with 55 species having some or all of their distribution on islands. We applied a whole genome shotgun strategy and next-generation sequencing technologies using an Illumina HiSeq 2000 platform to sequence the genome of...

Genomic data from the Insectivorous bat (Myotis davidii)

G Zhang, C Cowled, Z Shi, Z Huang, KA Bishop-Lilly, X Fang, JW Wynne, Z Xiong, ML Baker, W Zhao, M Tachedjian, Y Zhu, P Zhou, X Jiang, J Ng, L Yang, L Wu, J Xiao, Y Feng, Y Chen, X Sun, Y Zhang, GA Marsh, G Crameri, CC Broder … & J Wang
The microbats constitute the suborder Microchiroptera within the order Chiroptera (bats). They are most often referred to by their scientific name. Other English names are "insectivorous bats", "echolocating bats", "small bats" or "true bats". All these names are somewhat inaccurate, because not all microbats feed on insects, and some of them are larger than small megabats. We applied a whole genome shotgun strategy and next-generation sequencing technologies using an Illumina HiSeq 2000 platform to sequence...

Software and supporting material for: “Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification”

X Zhou, Y Li, S Liu, Q Yang, X Su, L Zhou, M Tang, R Fu, J Li & Q Huang
The software is a pipeline for mitochondrial protein annotation in mixed bulk samples. The pipeline annotates mitochondrial genes using homolog prediction with TBLASTN based on known complete mitochondrial genomes from GenBank RefSeq. The BLAST results were then used to determine gene ontology (e.g., mRNA and coding sequence regions) using Genewise. Annotation results include gff format annotation file, DNA and protein sequences of annotated genes. Compared to other mitochondrial annotation pipelines, the MT_annotation_BGI pipeline is easier...

Transcriptomic, DNA barcoding, and micro-CT imaging data from an advanced taxonomic description of a novel centipede species (Eupolybothrus cavernicolus Komerički Stoev, sp n)

N Akkari, J Hostens, AM Weigand, X Zhou, P Stoev, A Komerički, S Liu, D Porco & L Penev
The species description of a cave-dwelling centipede , Eupolybothrus cavernicolus Komerički Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia. This is the first eukaryotic species for which, in addition to traditional morphological description, a fully sequenced transcriptome, DNA barcode (i.e., mitochondrial Cytochrome C Oxidase Subunit I gene; COI), and detailed anatomical X-ray microtomography (micro-CT) scan has been provided. This project illustrates a workflow of producing, storing, publishing and...

Genomic data from the domestic yak (Bos grunniens)

Q Qiu, G Zhang, T Ma, W Qian, J Wang, Z Ye, C Cao, Q Hu, J Kim, DM Larkin, L Auvil, B Capitanu, J Ma, H.A Lewin, X Qian, Y Lang, R Zhou, L Wang, K Wang, J Xia, S Liao, S Pan, X Lu, H Hou, Y Wang … & J Liu
Domestic yaks (Bos grunniens) 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. 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...

Example files and supporting material for \"EMPeror: An interactive analysis and visualization tool for high throughput microbial ecology datasets.\"

Y Vázquez-Baeza, M Pirrung, A Gonzalez & R Knight
EMPeror is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets. Due to it's tailor-made graphical user interface, delving into a new dataset to elucidate the patterns hidden in the data, has never been easier. EMPeror brings a rich set of customizations and modifications that can be integrated into any QIIME compliant dataset; with lightweight data files and hardware accelerated graphics, constitutes itself as the state of...

Quantitative proteomics and transcriptomics data from the anaerobic thermophilic eubacterium Thermoanaerobacter tengcongensis

Z Chen, B Wen, Q Wang, W Tong, J Guo, X Bai, J Zhao, Y Sun, Q Tang, Z Lin, L Lin & Liu
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,...

Registration Year

  • 2013
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  • Dataset
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