Data set of differentially expressed microRNAs in sanguinarine-treated Caenorhabditis elegans and its F3 progeny

This article presents small RNA sequencing data of Caenorhabditis elegans consist of P0 control worms (untreated), P0 worms treated with a plant alkaloid, sanguinarine, and its F3 offspring. The data were analyzed to identify microRNAs that were differentially expressed in both the sanguinarine-treated P0 and its descendants F3 worms. Targets of the identified miRNAs, gene function annotations and their functional clusters are shown. The data presented here will facilitate comparison with data from other researchers who are working on miRNAs profiling of xenobiotic-treated C. elegans.


a b s t r a c t
This article presents small RNA sequencing data of Caenorhabditis elegans consist of P0 control worms (untreated), P0 worms treated with a plant alkaloid, sanguinarine, and its F3 offspring. The data were analyzed to identify microRNAs that were differentially expressed in both the sanguinarine-treated P0 and its descendants F3 worms. Targets of the identified miRNAs, gene function annotations and their functional clusters are shown. The data presented here will facilitate comparison with data from other researchers who are working on miRNAs profiling of xenobiotic-treated C. elegans.
& 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Subject area
Molecular biology More specific subject area miRNAs in Caenorhabditis elegans Type of data The data set generated for control, sanguinarine-treated and its F3 generation offspring of the Caenorhabditis elegans helps in identifying differentially expressed genes and related cellular pathways, and provides an insight to the epigenetic inheritance of miRNAs in the offspring of alkaloid-treated worms.
The data set can be used by researchers for comparison to other studies about xenobiotic effects on miRNA expressions.

Data
This article contains analysis from small RNA sequencing data of Caenorhabditis elegans consist of P0 control worms (untreated), P0 worms treated with a plant alkaloid, sanguinarine, and its F3 offspring. Fig. 1 shows the number of identified miRNAs in sanguinarine-treated P0 (SP0) whereby the number of up-regulated and down-regulated miRNAs indicates Z 2 fold-change differential expression compared with control P0 worms. Sequences that correspond to the predicted mature miRNAs were listed in Tables 1 and 2. The data were further analyzed to identify microRNAs that were differentially expressed in both the sanguinarine-treated P0 and its descendants F3 worms (Fig. 2). The interaction of differentially expressed miRNAs with their target genes were plotted using Cytoscape open source software ( Figs. 3 and 4). Data of differentially expressed miRNAs were analyzed using DAVID analysis software to obtain the miRNAs target gene function annotations (for biological Fig. 1. Number of annotated miRNAs found in sanguinarine-treated P0 worms. Up-regulated and down-regulated miRNAs refers to differential expression for Z 2 fold-change compared to P0 control.  Three miRNAs up-regulated in SP0 and SF3 worms were: miR-79-3p; miR-58a-3p; miR-786-5p. Eight miRNAs down-regulated in SP0 and SF3 worms were: let7-3p; miR-243-3p: miR-57-5p; miR-74-5p; miR230-3p; miR-230-5p; miR-90-5p; miR-228-3p.

Worm culture
Wild-type N2 (Bristol) worms were maintained on nematode growth media (NGM) at 20°C according to standard culture methods [1].

Worm treatment
L4 larval stage worms were treated with 10 μM sanguinarine or distilled water (as control) for 48 h at 20°C, 180 rpm (for aeration) in liquid S-Medium with Escherichia coli OP50 as food source in 24-well plates. After 48 h, control worms and sanguinarine-treated worms were collected, rinsed in M9 buffer and pelleted for RNA extraction as previously reported [2]. 20 worms from the sanguinarine-treated group were randomly picked and transferred to fresh NGM plates with OP50 and allowed to lay eggs. The procedure was repeated until F3 worms reached adult stage (at the same growth stage as P0 worms) and were collected for RNA extraction.

RNA samples
Total RNA was extracted with Sepasol-RNA I Super G (Nacalai Tesque), purified with an RNeasy Mini Kit (Qiagen). The concentration and purity of the RNA was determined using NanoDrop Spectrophotometer (Thermo Scientific 2000). The integrity of the extracted RNA was analyzed on a Bioanalyzer (Agilent Technologies 2100). P0 Control, sanguinarine-treated P0 and its F3 offspring RNA samples with RNA integrity numbers: 8.6, 10, 10 respectively, were used for library preparation. Sequencing was carried out using Illumina HiSeq. 2000 platform, single-end, 50 basepair read length.

Differentially expressed miRNAs
The differentially expressed miRNAs between P0 control and P0 sanguinarine-treated were determined using log 2 fold change and results with Z 2.0 fold change versus control were used for further analysis. The data were aligned to miRBase database (www.mirbase.org) and target predictions were obtained from TargetScanWorm database (www.targetscan.org). Interaction of the miR-NAs with their target genes were plotted using Cytoscape v. 3.4.0 software [3].

Functional annotation clustering and enrichment scores
Only the miRNAs that are both up-regulated or both down-regulated in P0 sanguinarine-treated and F3 of sanguinarine-treated P0 versus P0 control were analyzed. Functional annotation clustering (medium stringency) and gene ontology (biological processes) enrichment scores were processed using DAVID v. 6.8 system [4].   Table 4 Functional annotation clustering of down-regulated genes by DAVID system.