|
| Status |
Public on Nov 02, 2015 |
| Title |
t1_Hi726ctr_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Gram-negative bacteria
|
| Organism |
Haemophilus influenzae |
| Characteristics |
time: bacterial control
|
| Treatment protocol |
after 28 day of culture cells were infected with Hi176 at MOI of 100:1. NTHi strain 176,is an isolate obtained from the middle ear and was a part of a Finnish otitis media outbreak cohort study (kindly provided by Derek Hood, University Oxford, UK)
|
| Growth protocol |
Primary NHBE cells from single healthy donor were obtained from Clonetics-BioWhittaker, San Diego, CA. Briefly, cells were cultured on transwell membrane supports at ALI to trigger differentiation. At 28 d post-ALI, cultures which formed a pseudostratified mucociliary epithelium with beating cilia and mucus production
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Hi176 infected WD-NHBE cells at 1, 6, 24 and 72 h post infection using Trizol reagent, as well as mock-infected cells and Hi176 conditioned in infection medium for 1 h.
The strand-specific cDNA library was generated with ScriptSeq- Complete Gold Kit – Epidemiology, Low Input from Epicentre after ribosomal RNA depletion using Ribo-Zero Gold – Epidemiology kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq file were mapped using STAR version 2.3.1n
sam files were sorted using picard-tools-1.90
raw counts were generated with htseq-count version 0.6.0 and UCSC gtf file for hg19
raw counts were combined in a table using a R script
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file containing raw counts
|
| |
|
| Submission date |
Dec 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19560 |
| Series (1) |
| GSE63900 |
Dual RNA-sequencing of nontypeable Haemophilus influenzae and host cell transcriptomes reveals new aspects of host-pathogen interface |
|
| Relations |
| BioSample |
SAMN03265929 |
| SRA |
SRX810718 |
