RNA sequencing data of human periodontal ligament cells treated with continuous and intermittent compressive force

Mechanical force regulates numerous biological functions. Application of different force types leads to different cell responses. This data article describes RNA sequencing data identifying gene expression of human periodontal ligament cells (hPDLs) treated with the continuous or intermittent compressive force. These data could be further utilized to investigate the controlling pathways that regulate hPDLs’ behaviors by the different force types. Raw RNA sequencing data were deposited in the NCBI Sequence Read Archive (SRP136155) and NCBI Gene Expression Omnibus (GSE112122).


a b s t r a c t
Mechanical force regulates numerous biological functions. Application of different force types leads to different cell responses. This data article describes RNA sequencing data identifying gene expression of human periodontal ligament cells (hPDLs) treated with the continuous or intermittent compressive force. These data could be further utilized to investigate the controlling pathways that regulate hPDLs' behaviors by the different force types. Raw RNA sequencing data were deposited in the NCBI Sequence Read Archive (SRP136155) and NCBI Gene Expression Omnibus (GSE112122).
© 2019 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
Mechanical force regulates numerous cell functions [1,2]. Application of different force types leads to the different cell responses [2]. Periodontal ligament is always subjected to mechanical force during normal function for example chewing. This data article described the gene expression profiles of human periodontal ligament cells (hPDLs) after treating with the continuous or intermittent compressive force using RNA sequencing technique. The isolated RNA demonstrated the high intact and quality RNA input as shown by RNA integrity number higher than 9.0 ( Fig. 1). After library preparation, average library concentration and size of samples were in the range of 89e231 nM and 248e293 base pair, respectively ( Table 2). Library quality assurance was conducted using bioanalyzer (Fig. 2). RNA sequencing was performed using NextSeq500 (Illumina). Ninety four percent of reads exhibited Q score higher than 30 (Table 3). Average number of reads was ranged from 30. 6  Value of the Data Gene expression data could be further investigated to reveal the regulatory pathways and mechanisms related to the influence of mechanical force on hPDLs' behaviors. Researchers in orthodontics and periodontics related areas may utilize these data to identify regulatory mechanism(s) by which force controls hPDLs' functions and responses. Specific pathways can be identified to determine different regulatory mechanism of different force types on hPDLs' biological responses. Meta-analysis can be performed with other related databases to increase statistical power of the investigation for identification of genes regulated by mechanical force. million reads (75 bp; single-end). Reads exhibited total alignment percentage higher than 96% and base calling error rate was as low as 0.21% (Table 4).

Experimental design, materials and methods
Methods described in the following section are expanded version from our related work [3].

Cell isolation and culture
Experiment was approved by the Human Ethics Committee, Faculty of Dentistry, Chulalongkorn University (Study code HREC-DCU 2018-001). Periodontal tissues were gently scraped from the middle area of the tooth's root. Cell isolation was performed by the explant protocol. Growth medium was Dulbecco's Modified Eagle's Medium (Gibco, Carlsbad, CA, USA) with the addition of with 10% fetal bovine serum (Gibco), 2mM L-glutamine (Invitrogen, Carlsbad, CA, USA), 100 Units/ml penicillin (Invitrogen), 100 mg/ml streptomycin (Invitrogen), and 250 ng/ml amphotericin B (Invitrogen). The isolated cells were cultured at 37 C in a humidified 5% CO 2 atmosphere.

Compressive force treatment
Cell were subjected to mechanical compressive force using a computer-controlled apparatus [1,4]. Briefly, cells (37,500 cells/cm 2 ) were plated in 6-well tissue culture plates and maintained in growth medium for 24 h. After the serum starvation for 8 h, cells were treated to continuous or intermittent compressive force, according to previous publications [1,4]. In brief, cells were continuously loaded with 1.5 g/cm 2 force for a continuous force treatment. For intermittent compressive force application, cells were loaded with 1.5 g/cm 2 force at frequency of 0.23 Hz.

RNA preparation and sequencing
Cells were loaded with the continuous or intermittent compressive force in serum free culture condition for 24 h. The unloaded cells were employed as the control. Total cellular RNA was extracted using a RNeasy Plus Mini Kit with DNaseI treatment (Qiagen, USA). Each group consisted of the samples from three independent individuals (Table 1). RNA sequencing and bioinformatic analyses were performed and evaluated at the Omics Science and Bioinformatics Center, Faculty of Science,  Chulalongkorn University. RNA quality and quantity were determined using a Nanodrop and a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA). Nanodrop analysis revealed that the extracted RNA exhibited an OD260/280 ratio of 2.06e2.09 and the OD260/230 ratio ranged from 1.58 to 1.91. The RNA concentration ranged from 141.9 to 165.5 ng/ml. Further, mRNA library was prepared using the TrueSeq mRNA stranded library preparation kit (Illumina, San Diego, CA, USA). TrueSeq adapter-index was ligated to cDNA libraries and subsequently library enrichment was performed using polymerase chain reaction amplification for 8 cycles. Bioanalyzer was employed to determine RNA integrity number (RIN) (Fig. 1) and sequencing library quality (Fig. 2). Qubit 3.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) was used to evaluate library size and concentration (Table 2). NextSeq500 (Illumina) was employed for sequencing analysis.

Quality validation and read mapping
RTA2 software was used to analyze base calling and Q scoring. A bcl2fastq software was employed for file conversion and demultiplexing. FastQC and Trimmomatic were utilized to check read quality [5,6]. Trimmomatic was also employed for read trimming and filtering [5,6]. Homo sapiens UCSC hg38 was used as the reference for read mapping by HISAT2 [7]. Transcript quantification was performed using HTseq count [8]. The NextSeq run summary was shown in Table 3. Total alignment of each samples was demonstrated in Table 4. The distribution of raw read count was demonstrated ( Fig. 3A  and B). Variance was determined using principle component analysis ( Fig. 3C and D). Further, the differential gene expression was determined using EdgeR [9,10]. Genes that exhibited the Log2 fold change 1.0 or 1.0 were included. Significant difference was considered when FDR <0.05. Fig. 4 illustrated the volcano plots of up-and down-regulated genes in the continuous and intermittent compressive force treated cells compared with the control.