|
| Status |
Public on Nov 01, 2023 |
| Title |
Ctrl, 1h, R1 |
| Sample type |
SRA |
| |
|
| Source name |
Jurkat cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat cells
cell type: T lymphoblast
treatment: -
time: 1h
|
| Treatment protocol |
Jurkat cells were exposed to sterile bacterial culture supernatants diluted in Jurkat cell culture medium. Concentrations were adjusted to 1% (v/v) and 20% (v/v) for S.aureus and E.coli derived supernatants, respectively. The cells were incubated at 37 °C and 5% CO2 for 1h and 6h.
|
| Growth protocol |
Jurkat cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 2 mM Ultraglutamine in humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB) with in-tube DNase treatment after elution of the RNA. The Monarch RNA Cleanup Kit (NEB) was used for subsequent purification of the RNA. Quality and quantity of the samples were evaluated on the Agilent Bioanalyzer using the Agilent RNA 6000 Nano Kit.
The NEBNext Ultra II Directional RNA Library Prep Kit (NEB) was used for library preparation following the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Ctrl_1h_R1
Raw_read_counts_All.txt
|
| Data processing |
The raw sequence data were demultiplexed to fastq data using Illumina's software bcl convert (version3.8.4).
Quality control was performed with FastQC (version0.11.9).
Adapter trimming and read filtering was performed with Trimmomatic (version0.38).
Reads were aligned to the reference genome (GRCh38.108) using HISAT2 (version2.2.1).
Aligned reads were sorted with the software SAMtools (version1.9).
Counting was performed with htseq-count (version 0.11.2).
Analysis of differential gene expression was performed with the R package DESeq2 (version1.38.1).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing raw read counts for all samples
Supplementary files format and content: Tab-delimited text files containing DESeq2 output (gene expression changes of 1h treatment vs 1h control and 6h treatment vs 6h control)
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Kari Lavinia vom Werth |
| E-mail(s) |
karilavinia.vomwerth@ukmuenster.de
|
| Organization name |
University Hospital Münster
|
| Department |
Institute of Hygiene
|
| Street address |
Robert-Koch-Str. 41
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE232159 |
Comparison of T cell response to S. aureus and E. coli derived virulence determinants using RNA sequencing |
|
| Relations |
| BioSample |
SAMN35025723 |
| SRA |
SRX20277586 |
