|
| Status |
Public on Sep 25, 2021 |
| Title |
Hep-G2-T5-NI-C2 |
| Sample type |
SRA |
| |
|
| Source name |
Human hepatocarcinoma cell line HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
treatment: control (non-infected)
time: 72h
|
| Treatment protocol |
Cells were uninfected or infected with Listeria at multiplicity of infection of 1-5. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.
|
| Growth protocol |
Listeria monocytogenes EGDe strain was grown in brain-heart infusion (BHI) at 37°C. Human HepG2 hepatocytes (ATCC HB-8065) were grown as recommanded by ATCC, on collagen-coated 6-well plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (Qiagen) and genomic DNA was removed using TURBO DNA-freeTM kit (Ambion), according to the manufacturer’s instructions. The integrity, purity and concentration of RNA samples was assessed on an RNA 6000 pico chip using the Agilent 2100 electrophoresis Bioanalyzer. RNA was quality checked an then store at -80°C.
RNA-seq libraries of infected and non-infected cell RNA were assembled using 500-1300 ng total RNA using the TruSeq® mRNA Stranded Library Prep kit (Illumina) which includes polyA-selection. The RNA-seq libraries were monitored for quality on the Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit. Libraries were pooled in equimolar proportions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Demultiplexing was performed (bcl2fastq2 V2.2.18.12) and adapters were trimmed with Cutadapt (v1.15); only reads longer than 10 bp were kept.
TopHat (version 2.1.1) was used for alignment on the reference genome
Data were evaluated through principal component analysis and hierarchical clustering after transformation of the count data using RLOG function.
Normalization and differential analysis were carried out using the DESeq2 package, with a pre-filter step to remove genes with low counts (sum of all replicates counts<10, in all conditions compared)
Genome_build: Ensembl-98 human genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Sep 23, 2021 |
| Last update date |
Sep 25, 2021 |
| Contact name |
Jouneau Luc |
| E-mail(s) |
luc.jouneau@inrae.fr
|
| Organization name |
INRA
|
| Lab |
VIM
|
| Street address |
Domaine de Vilvert
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
78352 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE184697 |
Transcriptome (RNA-seq) of HepG2 cells non-infected (NI) or infected (Inf.) with the pathogen Listeria monocytogenes (strain EGD-e) |
|
| Relations |
| BioSample |
SAMN21580685 |
| SRA |
SRX12314214 |
