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| Status |
Public on Oct 24, 2021 |
| Title |
WT3 |
| Sample type |
SRA |
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| Source name |
P. gingivalis W83
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| Organism |
Porphyromonas gingivalis |
| Characteristics |
genotype: W83 Wild-type
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| Growth protocol |
P. gingivalis W83 and DPG_RS08170 were cultured in anaerobic 37oC condition with 10% H2, and 10% CO2, 80% N2, and in brain-heart infusion (BHI) medium (Oxoid, Basingstoke, USA), supplemented with hemin (5 mg/ml), and menadione (1 mg/ml) (Sigma, St Louis, USA), 5% defibrinated sheep blood (Beiruite Biotechnology, Zhengzhou, China) on blood agar plate.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500) and 150 bp/125bp paired-end reads were generated.
Duplicated sequences, ambiguous reads, and low-quality reads (Q > 20) were removed and assembled from the raw reads. Then the clean reads were mapped to the reference genomes from NCBI for P. gingivalis W83. The numbers of reads were calculated by using Reads Per Kilobase per Million Mapped Reads (RPKM).
The Upper Quartile (UQ) normalization factors were applied to the samples and multiplied by the mean upper quartile by applying the FDR adjustment with the threshold of < 0.05 q-values to compare different experiments or samples using Rockhooper2.
Genome_build: reference genomes from NCBI for P. gingivalis W83
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Oct 22, 2021 |
| Last update date |
Oct 25, 2021 |
| Contact name |
Peiyao Wu |
| E-mail(s) |
13982763352@139.com
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| Organization name |
Sichuan University
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| Street address |
Renmin South road
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| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24653 |
| Series (1) |
| GSE186376 |
Porphyromonas gingivalis W83:Transcriptome profiling and functional verification of flavodoxin |
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| Relations |
| BioSample |
SAMN22503817 |
| SRA |
SRX12734457 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5646600_WT3.txt.gz |
8.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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