|
| Status |
Public on Aug 23, 2021 |
| Title |
T_6h_005 |
| Sample type |
SRA |
| |
|
| Source name |
MDM_T_6h
|
| Organisms |
Haemophilus influenzae; Homo sapiens |
| Characteristics |
cell type: Monocyte-derived macrophage
treatment/time point: Infected (T, treated) sample at 6h (6h)
|
| Treatment protocol |
Samples from five biological replicates (indicated as numbers at end of sample names; 005, 016, 082, 104, 124) were either infected with NTHi (T, treated) or left uninfected (C, control) for 6h, with RNA extracted after a 90 min gentamicin wash (6h) or after a prolonged incubation until 24h (24)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy kit
ribosomal RNA (rRNA) was removed from all samples using Ribo-Zero™ Magnetic Kit and libraries were generated using the NEBNext®Ultra™ Directional RNA Library Prep Kit for Illumina®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Infected (T, treated) sample at 6h (6h) for sample ID 005 (005)
|
| Data processing |
The Spliced Transcripts Alignment to a Reference (STAR) software (version 2.5) was used to map reads to the human genome (hg38) and Bowtie (version 2.2.3) was used to map reads to the NTHi ST14 genome
Aligned reads were quantified using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for MDM or NTHi data
|
| |
|
| Submission date |
Jul 15, 2021 |
| Last update date |
Aug 23, 2021 |
| Contact name |
Jodie Ackland |
| E-mail(s) |
J.Ackland@soton.ac.uk
|
| Organization name |
University of Southampton
|
| Department |
Clinical and Experimental Sciences, Faculty of Medicine
|
| Street address |
Mail Point 810, Level F, South Block Southampton General Hospital, Tremona Road
|
| City |
Southampton |
| State/province |
Hampshire |
| ZIP/Postal code |
SO166YD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30396 |
| Series (1) |
| GSE180166 |
Dual RNASeq reveals NTHi-macrophage transcriptomic changes during intracellular persistence |
|
| Relations |
| BioSample |
SAMN20244288 |
| SRA |
SRX11454673 |
