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| Status |
Public on Jan 01, 2022 |
| Title |
The effect of curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to compare NGS-derived gingiva transcriptome profiling (RNA-seq) of rats with or without experimental periodontitis and to explore the effect of curcumin/ZNPs hydrogel on the transcription of gingiva in rats with periodontitis.
Methods: Six-week-old male Sprague-Dawley rats weighing 250–300 g (Dashuo company, China) were randomly divided into five groups (n = 5 per group): i) healthy control (Sham); ii) experimental periodontitis (EP); iii) experimental periodontitis treated by curcumin hydrogel (EP+Cur); iv) experimental periodontitis treated by ZNPs hydrogel (EP+ZNPs); v) experimental periodontitis treated by curcumin/ZNPs hydrogel (EP+Cur/ZNPs). Animals were anesthetized with isoflurane (5% induction, 2% maintenance, sealed until euthanized) and intramuscularly administered 0.1 mL penicillin (40,000 U/mL) for 7 days. EP was established by ligature with 4–0 silk thread around the bilateral maxillary first molars. Three days after ligature, P. gingivalis ATCC 33277 (107 CFU/mL) was smeared onto silk twice. Rats in the EP+Cur group were treated by curcumin hydrogel (Dalian Meilun Biotech Co., Ltd), EP+ZNPs group were treated by ZNPs hydrogel (Shanghai aladdin Biochemical Technology Co., Ltd), and EP+Cur/ZNPs group were treated by curcumin/ZNPs hydrogel. Total RNA was extracted with TRIzol® reagent (Thermo Fisher Scientific, Inc.). The TruSeq Stranded total RNA with RiboZero Plus kit (IIlumina, San Diego, CA) was used to obtain a sequencing library from 1μg of total RNA. Eukaryotic mRNA sequencing was performed on Illumina Novaseq 6000 by Shanghai Majorbio Bio-pharm Technology Co., Ltd. Raw gene counts with a minimum of two counts per million in at least one sample were used for downstream analyses. Differentially expressed genes were determined by the DESeq2 Bioconductor/R package. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: Transcriptome analysis of 25 samples was completed in this project, and a total of 184.45 Gb Clean Data was obtained. The Clean Data of each sample reached 5.92 Gb and above, and the Q30 base percentage was above 92.75%. The Clean Reads of each sample were compared with the designated reference genome, and the comparison rate ranged from 93.38% to 95.1%. A total of 26188 expressed genes were detected in this analysis, including 22736 known genes and 3452 new genes; 57,961 expressed transcripts, including 29332 known transcripts and 28629 new transcripts.
Conclusions: Our study represents the first detailed analysis of gingival transcriptomes of rats treated by Cur/ZnO gel, with biologic replicates, generated by RNA-seq technology.
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| Overall design |
Gingival mRNA profiles of six-week old Sprague-Dawley rats in Sham, EP, EP+Cur, EP+ZnO and EP+Cur/ZnO groups.
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| Contributor(s) |
Liu C |
| Citation(s) |
38549147 |
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| Submission date |
Oct 01, 2021 |
| Last update date |
Apr 04, 2024 |
| Contact name |
CHENGCHENG LIU |
| E-mail(s) |
liuchengchengsc@gmail.com
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| Organization name |
Sichuan University
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| Street address |
No. 14, Section 3, Renminnan Road
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| City |
CHENGDU |
| State/province |
SICHUAN |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (25)
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| Relations |
| BioProject |
PRJNA767816 |
| SRA |
SRP339642 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE185147_Gene_count-each_sample_and_each_gene.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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