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Sample GSM4812004 Query DataSets for GSM4812004
Status Public on Dec 31, 2020
Title H. parainfluenzae monoculture rep1
Sample type SRA
 
Source name Bacterial culture
Organism Haemophilus parainfluenzae
Characteristics strain: H. parainfluenzae ATCC 33392
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 GPL29207
Series (1)
GSE158845 Gene expression of H. parainfluenzae in monoculture and coculture with S. mitis
Relations
BioSample SAMN16320216
SRA SRX9221400

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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