microRNAs (miRNAs) are an abundant class of non-coding RNA species with important regulatory roles in gene expression at the posttranscriptional level. The helminth; Acanthocheilonema viteae; serves as model organism for research on parasitic filarial nematodes. Total RNA secreted or excreted; in vitro; by 1500 adult female and male; A. viteae; over 3 weeks was isolated from culture media previously processed by differential ultracentrifugation. miRNA sequencing revealed the presence of 360 unique miRNA candidates released by adult; A. viteae in vitro; . Among them, 74 high-confidence unique miRNAs; ,; as well as several potential novel miRNA candidates were discovered. A large proportion of the sequenced miRNA candidates appeared differentially expressed between the male and female samples based on normalized copy count. The presence of extracellular vesicles, often rich in miRNAs, could not be confirmed unambiguously by transmission electron microscopy

Endriss, Yvette

Marti, Hanspeter

Soichot, Julien

Tritten, Lucienne

English

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Data in brief 29 (2020) 105334Contents lists available at ScienceDirectData in briefjournal homepage: www.elsevier .com/locate/dibData ArticleSecreted microRNA data from the parasiticﬁlarial nematode Acanthocheilonema viteaeJulien Soichot a, Yvette Endriss b, Hanspeter Marti b,Lucienne Tritten a, *a Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerlandb Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051, Basel, Switzerlanda r t i c l e i n f oArticle history:Received 29 January 2020Accepted 18 February 2020Available online 25 February 2020Keywords:microRNAExcretory-secretoryExtracellular vesicleFilarial nematodeParasite* Corresponding author.E-mail address: lucienne.tritten@uzh.ch (L. Trithttps://doi.org/10.1016/j.dib.2020.1053342352-3409/© 2020 The Author(s). Published by Elsecreativecommons.org/licenses/by-nc-nd/4.0/).a b s t r a c tmicroRNAs (miRNAs) are an abundant class of non-coding RNAspecies with important regulatory roles in gene expression at theposttranscriptional level. The helminth Acanthocheilonema viteaeserves as model organism for research on parasitic ﬁlarialnematodes.Total RNA secreted or excreted in vitro by 1500 adult female andmale A. viteae over 3 weeks was isolated from culture mediapreviously processed by differential ultracentrifugation. miRNAsequencing revealed the presence of 360 unique miRNA candidatesreleased by adult A. viteae in vitro. Among them, 74 high-conﬁdence unique miRNAs, as well as several potential novelmiRNA candidates were discovered. A large proportion of thesequenced miRNA candidates appeared differentially expressedbetween the male and female samples based on normalized copycount.The presence of extracellular vesicles, often rich in miRNAs, couldnot be conﬁrmed unambiguously by transmission electronmicroscopy.© 2020 The Author(s). Published by Elsevier Inc. This is an openaccess article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).ten).vier Inc. This is an open access article under the CC BY-NC-ND license (http://Speciﬁcations TableSubject Immunology and Microbiology: ParasitologySpeciﬁc subject area microRNA sequencingType of data TableHow data were acquired Illumina HiSeq 2500Data format Raw (FASTQ) and processed data (excel)Parameters for data collection A. viteae adult females and malesDescription of data collection Female and male A. viteae secreted miRNAs extracted from ultracentrifuged culturemedia were sequenced and analyzed.Data source location Institute of Parasitology, University of ZurichZurichSwitzerlandData accessibility Repository name: Gene Expression Omnibus (NCBI)Data identiﬁcation number: GSE143793Direct URL to data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc¼GSE143793Value of the Data Excretory/secretory miRNAs from the model helminth Acanthocheilonema viteae could serve as potential biomarkers ofinfection with ﬁlarial nematodes and in comparative studies of host-parasite speciﬁcity. Excretory/secretory miRNAs from A. viteae, described here for the ﬁrst time, may represent a useful tool for helminthresearch. miRNAs may be species-speciﬁc or similar in sequence and function to those of their hosts. Hence, they may be a result ofthe evolutionary arms races underlying all host-helminth associations and contribute to the establishment of a successfulinfection.J. Soichot et al. / Data in brief 29 (2020) 10533421. Data descriptionApproximately 1500 adult worms were collected; males and females were separated and culturedin vitro for up to 3 weeks. Total RNA was used for library preparation, for female and male culturemedia, respectively. Analyzed data can be found in Supplementary Table 1. Across both samples, a totalof 360 unique putative mature miRNAs were sequenced, including 74 high-conﬁdence unique maturemiRNAs (assigned to groups 1 and 2a, see methods; the top 10 can be found in Table 1). Another 25sequences mapped to the A. viteae genome as well as non-nematode miRNAs in miRBase (group 2b).Another 221 mature sequences mapped to miRBase entries, but not to the current A. viteae genome(group 3). Finally, 41 predicted candidates mapped to the A. viteae genome but to no other miRNAregistered inmiRBase and hence, represent novel miRNA candidates (group 4). A total of 192 sequencesappeared differentially expressed between the female and male sample, log2 fold change 1 or -1, p-value < 0.05 (Supplementary Table 2). We failed to identify EVs unambiguously in A. viteae culturesupernatants using transmission electron microscopy.2. Experimental design, materials, and methods2.1. Animal infectionsEthical clearance was obtained from the Cantonal Veterinary Ofﬁce of Basel (permit number 2802).All experiments were conducted in accordance with the Swiss cantonal and national regulations onanimal experimentation. Brieﬂy, 30 male Syrian golden hamsters (Mesocricetus auratus) were inocu-lated subcutaneously with 250 A. viteae third stage larvae obtained from infected ticks (Ornithodorosmoubata), as described [1]. Hamsters were euthanized after 8 weeks and adult A. viteaewere collectedfrom the subcutaneous tissue of the back and neck region.Table 1Top 10 high conﬁdence miRNA candidates in secretions from A. viteae females and males. High conﬁdence miRNAs are thosesequences assigned to groups 1 and 2a (see methods).Rank A. viteae females A. viteae malesName Normalized counts Name Normalized counts1 bma-miR-100a_Rþ1 66,324 bma-miR-36c-3p_R-1_1ss20GA 48422 bma-miR-100d_Rþ1 61,458 bma-miR-100a_Rþ1 45503 bma-miR-36c-3p_R-1_1ss20GA 45,502 bma-miR-100d_Rþ1 40514 asu-miR-81a 11,637 bma-miR-279_Rþ1 22865 bma-miR-100b_Rþ1 11,596 asu-miR-81a 17266 asu-miR-86-5p 8020 asu-lin-4-5p_1ss19TC 16227 bma-miR-100c_Rþ2_1ss12CT 7865 bma-miR-71_Rþ4 11728 bma-miR-279_Rþ1 6178 bma-miR-2c_Rþ1_1ss1CT 11459 bma-miR-71_Rþ4 5456 asu-let-7-5p 108410 bma-miR-36a_Rþ1_1ss20TC 4955 bma-miR-100b_Rþ1 1082J. Soichot et al. / Data in brief 29 (2020) 105334 32.2. In vitro culture, media processing, and extraction of total RNAFemales and males were separated and cultured for up to 3 weeks at 1e2 worms per ml RPMI-1640containing 200 U/ml penicillin, 200 mg streptomycin, and 4 mM L-glutamine, at 37 C, 5% CO2. Mediafrom the ﬁrst 24 h served as initial ‘wash’ and were discarded. Worms were checked for viability(movement) and transferred to fresh media every 1e2 days. Those showing poor or no motility wereremoved. Collected culture media were spun at 1000g for 30 min at 4 C, ﬁltered through 0.22 mmpores, and frozen at 20 C for several weeks. Upon thawing, media were concentrated over a 3 kDAultraﬁltration cellulose membrane (Millipore PLBC06210). Concentrated media were further spun 45min at 12,000g and ultracentrifuged in a Beckman system (Optima L-80 XP), using a SW40Ti rotorand Ultra-Clear thinwall tubes (14  95 mm, Beckman 344060) as follows: 2 h at 100,000g, 4 C; thepellet was washed once with 12 ml ice cold sterile PBS (Gibco), and centrifuged again for 2h at100,000g, 4 C, as described [2,3].Total RNA was extracted from the ‘pellet’ in 0.5 ml PBS using the blood protocol of a total RNApuriﬁcation kit (Norgen Biotek 17200) and shipped to LC Sciences (Houston, TX, USA) for miRNAsequencing and analysis.2.3. miRNA sequencing and analysisThe total RNA quality and quantity were determined using a Bioanalyzer 2100 (Agilent, CA, USA)with RIN number >7.0. The library was prepared following Illumina's TruSeq small-RNA-samplepreparation protocols. Single-end sequencing with 50 bp reads was performed on Illumina's HiSeq2500 sequencing system. Raw reads were subjected to LC Sciences' proprietary program, ACGT101-miR(LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNAfamilies (rRNA, tRNA, snRNA, snoRNA) and repeats. Unique sequences in length of 18e26 nucleotideswere mapped to the A. viteae genome (https://parasite.wormbase.org/Acanthocheilonema_viteae_prjeb1697/Info/Index) by BLAST search and to nematode and all miRNAs/pre-miRNAs in miRBasev22.0 [4] to identify known miRNAs and novel 3p- and 5p-derived miRNAs. Length variation at both 30and 50 ends and one mismatch inside of the sequence were allowed in the alignment. Sequences weremapped to the nematode and all miRNA precursors collection in miRBase v22.0 by BLAST search, andthe mapped pre-miRNAs were further BLASTed to determine their genomic locations. The unmappedsequences were BLASTed against the A. viteae genome, and the hairpin RNA structures containingsequences were predicted from the ﬂanking 80 nt sequences using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi). The criteria for secondary structure predictionwere: (1) number ofnucleotides in one bulge in stem region (12), (2) number of base pairs in the stem region of thepredicted hairpin (16), (3) free energy cutoff (kCal/mol  -15), (4) length of hairpin (up and downstems þ terminal loop 50) (5) length of hairpin loop (20), (6) number of nucleotides in one bulgein mature region (8), (7) number of biased errors in one bulge in mature region (4), (8) numberJ. Soichot et al. / Data in brief 29 (2020) 1053344of biased bulges in mature region (2), (9) number of errors in mature region (7), (10) number of basepairs in the mature region of the predicted hairpin (12), (11) percent of mature in stem (80). Uniquereads were further analyzed in order to identify conserved and novel A. viteae miRNAs. Brieﬂy, readswhich mapped to miRNAs/pre-miRNAs of speciﬁc species in miRBase and for which pre-miRNAsfurther mapped to the A. viteae genome and EST were assigned to group 1. Reads from group 2awere mapped to miRNAs/pre-miRNAs of selected species in miRBase and the mapped pre-miRNAswere not further mapped to the genome, but the reads (and the miRNAs of the pre-miRNAs) weremapped to genome; the extended genome sequences from the genome loci may form hairpins. Ingroup 2b, reads were mapped to miRNAs/pre-miRNAs of selected species in miRBase and the mappedpre-miRNAs were not further mapped to the A. viteae genome, but the reads (and the miRNAs of thepre-miRNAs) weremapped to the genome; the extended genome sequences from the genome loci maynot form hairpins. Those reads which were (i) mapped to miRNAs/pre-miRNAs of selected species inmiRBase, (ii) for which the mapped pre-miRNAs were not further mapped to the A. viteae genome, and(iii) failed to map to the genome, were classiﬁed as group 3. Reads in group 4 were not mapped to pre-miRNAs of selected species in miRBase, but the reads were mapped to the A. viteae genome and theextended genome sequences may form hairpins. Normalization of sequence counts in each sample wasachieved by dividing the counts by a library size parameter of the corresponding sample, as in Ref. [5].AcknowledgmentsLT is supported by the Swiss National Science Foundation under Grant PZ00P3_168080.Conﬂict of InterestThe authors declare that they have no known competing ﬁnancial interests or personal relation-ships that could have appeared to inﬂuence the work reported in this paper.Appendix A. Supplementary dataSupplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2020.105334.References[1] R. Lucius, G. Textor, Acanthocheilonema viteae: rational design of the life cycle to increase production of parasite materialusing less experimental animals, Appl. Parasitol. 36 (1) (1995) 22e33.[2] C. Thery, S. Amigorena, G. Raposo, A. Clayton, Isolation and characterization of exosomes from cell culture supernatants andbiological ﬂuids, Curr. Protoc. Cell Biol. 3 (2006) 3.22, https://doi.org/10.1002/0471143030.cb0322s30. Editor. Board JuanBonifacino Al.[3] J. Sotillo, et al., Extracellular vesicles secreted by Schistosoma mansoni contain protein vaccine candidates, Int. J. Parasitol. 46(1) (2016) 1e5, https://doi.org/10.1016/j.ijpara.2015.09.002.[4] A. Kozomara, M. Birgaoanu, S. Grifﬁths-Jones, miRBase: from microRNA sequences to function, Nucleic Acids Res. 47 (D1)(2019) D155eD162, https://doi.org/10.1093/nar/gky1141.[5] L. Tritten, D. Clarke, S. Timmins, T. McTier, T.G. Geary, Diroﬁlaria immitis exhibits sex- and stage-speciﬁc differences inexcretory/secretory miRNA and protein proﬁles, Vet. Parasitol. 232 (2016) 1e7, https://doi.org/10.1016/j.vetpar.2016.11.005.

Secreted microRNA data from the parasitic filarial nematode Acanthocheilonema viteae

microRNAs (miRNAs) are an abundant class of non-coding RNA species with important regulatory roles in gene expression at the posttranscriptional level. The helminth Acanthocheilonema viteae serves as model organism for research on parasitic filarial nematodes. Total RNA secreted or excreted in vitro by 1500 adult female and male A. viteae over 3 weeks was isolated from culture media previously processed by differential ultracentrifugation. miRNA sequencing revealed the presence of 360 unique miRNA candidates released by adult A. viteae in vitro. Among them, 74 high-confidence unique miRNAs, as well as several potential novel miRNA candidates were discovered. A large proportion of the sequenced miRNA candidates appeared differentially expressed between the male and female samples based on normalized copy count. The presence of extracellular vesicles, often rich in miRNAs, could not be confirmed unambiguously by transmission electron microscopy

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Secreted microRNA data from the parasitic filarial nematode Acanthocheilonema viteae

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