|
| Status |
Public on Dec 31, 2020 |
| Title |
H. parainfluenzae coculture with S. mitis rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organisms |
Haemophilus parainfluenzae; Streptococcus mitis |
| Characteristics |
strain: H. parainfluenzae ATCC 33392 and S. mitis NCTC 12261
|
| Growth protocol |
H. parainfluenzae grown in mono or coculture with mitis aerobically for 22 hours on BHI-YE HP at 37.C, 5% CO2, transferred to fresh media for 4 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Beadbeating and trizol
RNAtag-Seq (Shishkin AA, Giannoukos G, Kucukural A, et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015;12(4):323-5.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
paired end alignment using bowtie2
counts generated using htseq-count with parameters -rev -a 1 -m intersection-nonempty
normalization and differential expression analysis carried out using DESeq2
automated workflow can be found at https://github.com/dasithperera-hub/RNASeq-analysis-toolkit
Genome_build: H. parainfluenzae ATCC 33392
Supplementary_files_format_and_content: csv file
|
| |
|
| Submission date |
Sep 30, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Dasith Perera |
| E-mail(s) |
dasithperera89@gmail.com
|
| Organization name |
University of Rhode Island
|
| Street address |
Flagg Rd
|
| City |
Kingston |
| State/province |
Rhode Island |
| ZIP/Postal code |
02881 |
| Country |
USA |
| |
|
| Platform ID |
GPL29208 |
| Series (1) |
| GSE158845 |
Gene expression of H. parainfluenzae in monoculture and coculture with S. mitis |
|
| Relations |
| BioSample |
SAMN16320229 |
| SRA |
SRX9221402 |
