|
| Status |
Public on Nov 17, 2024 |
| Title |
A101 rRNA-free RNA |
| Sample type |
SRA |
| |
|
| Source name |
gingiva
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: gingiva
periondontitis: positive
redondoviridae infection: positive
fraction: rRNA-free RNA
|
| Treatment protocol |
Gingiva biopsy samples from the periodontitis patients were collected from the sulcular region that included the connective tissues and gingival epithelium facing towards the sulcus. For the control group participants, similar biopsy specimens of healthy gingiva were taken while extracting teeth that were either impacted or required extraction or for the orthodontic treatment. Two gingival samples (one for redondoviruses detection, and the other for RNA sequencing) were collected from each participant and were immediately frozen with liquid nitrogen, then stored at −80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
(rRNA-free RNA) Total RNA was extracted from cell or animal tissue by Trizol reagent(Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200(Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
(miRNA) Total RNA was extracted from cell or animal tissue by Trizol reagent(Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200(Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit(Qiagen) and the purification result was validated by Gel electrophoresis.
(rRNA-free RNA) RNA libraries were prepared for sequencing using standard Illumina protocols
(miRNA) RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
All.counts.exp_mRNA_lncRNA.txt/all.counts.exp_circRNA.txt
|
| Data processing |
(mRNA and lncRNA) We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20.
(mRNA and lncRNA) Hisat2 2.0.4 mapping to reference genome
(mRNA and lncRNA) count counting
(circRNA) Circular RNA was predicted based on the sequencing data with ACFS circRNA prediction pipeline. Unmapped Reads was collected utilizing BWA-mem(bwa mem -t 1 -k 16 -T 20) for circRNA identification: head-to-tail junction was identified and highest splicing strength score was calculated by MaxEntScan33 with a filtering criterion greater than or equal to 10. Base on the re-alignment of the unmapped reads on the circular RNA candidates, Reads that mapped to the circular RNA back splicing junction(with an overhang of at least 6 nt) were counted for each circRNA.
(circRNA) count counting
(miRNA) We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a) 10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
(miRNA) Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo Sapiens miRNA database and GRCH38 genome.
(miRNA) count counting
Genome_build: GRCh38 / miRBase 22.0
Supplementary_files_format_and_content: TXT files contain counts for each sample
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Nov 17, 2024 |
| Contact name |
Yu Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine
|
| Street address |
639 Zhizaoju Road, Shanghai, PR China
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE189022 |
Redondoviridae infection regulates circRNAome in periodontitis |
|
| Relations |
| BioSample |
SAMN23242584 |
| SRA |
SRX13156599 |
