|
| Status |
Public on Apr 13, 2021 |
| Title |
Paracoccus denitrificans ATCC19367-florfenicol-treated-2 |
| Sample type |
SRA |
| |
|
| Source name |
Paracoccus denitrificans ATCC19367-florfenicol-treated-2
|
| Organism |
Paracoccus denitrificans |
| Characteristics |
agent: florfenicol
strain: ATCC19367
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Paracoccus denitrificans was collected by centrifugation, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard IIIuminia protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
L2
|
| Data processing |
Bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Paracoccus denitrificans ASM406373v1 whole genome using bowtie2 (v2.2.6).
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi and Williams, Nature methods, 2008.
Genome_build: Paracoccus denitrificans ASM406373v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Apr 13, 2021 |
| Contact name |
Mei Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
South China Agricultural University
|
| Department |
College of Veterinary Medicine
|
| Street address |
483 Wushan Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL29732 |
| Series (1) |
| GSE166910 |
Transcriptome sequencing of Paracoccus denitrificans ATCC19367 with florfenicol exporsure |
|
| Relations |
| BioSample |
SAMN17936456 |
| SRA |
SRX10117156 |
