Contributors: Margo Maex, Dag Treer, Henri De Greve, Paul Proost, Ines Van Boxclaer, Franky Bossuyt
... We investigated the evolutionary trajectory of a series of 15 kDa proteins – termed persuasins – that were co-opted more recently alongside the ancient sodefrin precursor-like factor (SPF) courtship pheromone system in salamanders. Expression, genomic and molecular phylogenetic analyses show that persuasins originated from a gene that is expressed as a multi-domain protein in internal organs where it has no pheromone function, but underwent gene duplication and neofunctionalisation. The subsequent evolution combined domain-loss and the introduction of a proteolytic cleavage site in the duplicated gene to give rise to two-domain cysteine rich proteins with structural properties similar to SPF pheromones In the absence of an NCBI database for sequences assembled by third party analyses (assembly of publicly available reads, RNA sequencing), we deposited nucleotide and amino acid sequences of persuasin and DUF-persuasin transcripts assembled from publicly available short reads (NCBI: SRA) on the Mendeley Data repository. Sources of publicly available SRA datasets are cited in the main article and supplemental information (Maex et al. (2018) Exaptation as a mechanism for functional reinforcement of an animal pheromone system).
Contributors: Luis F. Cadavid, Alejandra Zárate-Potes, Iván Ocampo
... Hydractinia symbiolongicarpus colonies were collected in Woods Hole, MA (USA), and were cultured in 40 L aquaria with recirculating artificial sea water (Instant Ocean Sea Salt) at of 20 ± 2°C and a relative density of 1,022, and water replacement of 25% every three days. In order to increase the representation of both inducible and repressible immune-related transcripts, two types of samples were used to construct cDNA libraries for sequencing; one sample was challenged with live bacteria whereas the other was left without immune challenge. For the bacterially challenged sample, a male colony (HWB103) was starved for three days and subsequently incubated with 108 cells/ml of a LB stationary phase co-culture of a Gram-positive (Microbacterium sp.) and a Gram-negative (Vibrio sp.) bacterium, for one hour at room temperature. After the bacterial challenge, the colony was washed with sterile artificial seawater, and tissue samples were collected in TRIzol Reagent (Invitrogen) for total RNA extraction. In order to increase the chances of sequencing cDNAs from inducible transcripts with different transcriptional times, samples were collected at 1, 3, 6, 12, 24 and 36 hours post-exposure. Total RNA was isolated from approximately 0,2 g of each tissue sample using TRizol Reagent (Invitrogene). Three types of RNA samples were prepared to construct the cDNA libraries as follows: i) early time post-challenge (ET) RNA, by pooling RNA samples from 1, 3 and 6 hours after bacterial challenge, ii) late time post-challenge (LT) RNA, by pooling RNA samples from 12, 24 and 36 hours after challenge, and iii) RNA from a non-challenged sample (C). cDNAs were synthesized from poly-A transcripts in each RNA class. They were subsequently fragmented by sonication, and fragments of about 300 bp long were gel-purified to add Illumina adaptors, tags, and primers. The resulting three libraries were sequenced in a single HiSeq 2000 Illumina PET indexed lane at the Canada’s Michael Smith Genome Sciences Center - British Columbia Cancer Agency, Canada. Quality of raw sequence data was evaluated using the FastQC software V. 0.10.1. Illumina adaptors and bases with a Phred score under 20 at the 3’ ends were trimmed out using the FastXToolkit (http://hannonlab.cshl.edu/ fastx_toolkit/index.html), and only reads longer than 30 bp were selected for further analysis. Ribosomal sequence depletion was performed using the RiboPicker software (Schmieder et al., 2011), based on the ribosomal sequence databases Silva (Quast et al., 2013), GreenGenes (DeSantis et al., 2006), RDP (Maidak et al., 2000), Rfam (Griffiths-Jones et al., 2003), and the NCBI. To reduce redundancy and the noise created by sequencing errors the data was digitally normalized using the Diginorm tool. The resulting raw sequences from the three cDNA libraries (ET, LT, and C) were combined to assemble the H. symbiolongicarpus transcriptome using the Trinity software (Grabherr et al., 2011).
Contributors: oliver purcell
... This is a genbank file containing the 16 plasmids used in the publication: "Encryption and Steganography of Synthetic Gene Circuits".
Data: Host migration strategy and blood parasite infections of three sparrow species sympatrically breeding in Southeast Europe
Contributors: Tamara Emmenegger, Silke Bauer, Dimitar Dimitrov, Juanita Olano Marin, Pavel Zehtindjiev, Steffen Hahn
... Appendix A: Field and infection data used for models Appendix B: Detailed results of models ran in R FASTA file: Cytochrome b sequences of Haemosporidian parasites
chloroplast DNA sequences (trnH-psbA, rpl16 intron and trnL-trnF) from Zingiber kawagoii and Z. shuanglongensis
Contributors: Bing-Hong Huang
... Alinged fasta format of chloroplast DNA sequences (trnH-psbA, rpl16 intron and trnL-trnF) from Zingiber kawagoii and Z. shuanglongensis.
Data for: Performance Metrics for Targeted Next Generation Sequencing Panels Using Reference Materials
Contributors: Megan Cleveland, Justin Zook
... This is NGS data (VCF files) for targeted sequencing panels (Illumina Inherited Disease Panel and Ion Torrent AmpliSeq Inherited Disease Panel) performed on NIST RMs 8398, 8392 and 8393 (NA12878, GM24149, GM24143, GM24385, GM24631).
Contributors: Jon Bråte
... Alignments used in the phylogenetic analyses of Bråte et al. 2018. Unicellular origin of the animal microRNA machinery. Current Biology.
Integrating bioacoustics, DNA barcoding and niche modeling for frog conservation – the threatened balloon frogs of Sri Lanka: audio, 16S & maps
Contributors: Madhava Meegaskumbura, Nayana Wijayathilaka, Gayani Senevirathne
... This data is associated with the following paper: Integrating bioacoustics, DNA barcoding and niche modeling for frog conservation – the threatened balloon frogs of Sri Lanka: audio, 16S & maps.
Contributors: Vladimir Svetlov
... Starting structures and unambiguous distance restraints from in vivo XL-MS, top docking model (HADDOCK)
Nr4a receptors regulate development and death of labile Treg precursors to prevent generation of pathogenic self-reactive cells
Contributors: Takashi Sekiya
... The data are original, un-manipulated data that were published in the paper entitled "Nr4a receptors regulate development and death of labile Treg precursors to prevent generation of pathogenic self-reactive cells". Each data appear in the paper were deposited in the folders which were labeled with the corresponding figure number.