|
| Status |
Public on Nov 07, 2022 |
| Title |
porphyromonas gingivalis W83, wild type, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Porphyromonas gingivalis W83 |
| Characteristics |
strain: W83
cell type: bacteria
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 2μg of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq X TEN (2 × 150bp read length).
The processing of original images to sequences, base-calling, and quality value calculations were performed using the Illumina GA Pipeline (version 1.6). A Perl program was written to select clean reads by removing low-quality sequences, reads with more than 5% of N bases (unknown bases) and reads containing adaptor sequences.
Trimmed sequence reads were mapped to the reference genome of P. gingivalis W83 (PRJNA393092) through Bowtie2
Read count extraction and normalization were performed using RSEM.
Assembly: porphyromonas gingivalis w83 (PRJNA393092)
Supplementary files format and content: text files include TPM values for each Sample
|
| |
|
| Submission date |
Aug 06, 2022 |
| Last update date |
Nov 08, 2022 |
| Contact name |
renjie zou |
| E-mail(s) |
pellter_ju5144@126.com
|
| Organization name |
sichuan university
|
| Street address |
Chengdu City, Sichuan Province, Wuhou District people's South Road, three 17
|
| City |
chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610044 |
| Country |
China |
| |
|
| Platform ID |
GPL32551 |
| Series (1) |
| GSE210663 |
Effect of deletion of trkA on gene expression of Porphyromonas gingivalis W83 |
|
| Relations |
| BioSample |
SAMN30173406 |
| SRA |
SRX16930622 |
