|
| Status |
Public on Dec 01, 2023 |
| Title |
HT-29 SGM replicate b |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
cell line: HT-29
cell type: adenocarcinoma
treatment: SGM
|
| Treatment protocol |
Stationary phase bacteria were scratched from fresh THY plates (o.n. culture) and washed with sterile phosphate buffered saline, pH 7.4 (PBS). The bacteria are diluted in DMEM (Gibco, Ref. 12320032, low glucose, pyruvate, HEPES) to obtain the desired concentration of: (i) SGM of 6,5x10’5 CFU/ml and (ii) SGG UCN34 of 6,5x10’4 CFU/ml. Cells are washed once with DMEM and then infected with the medium containing the bacteria by adding 2 ml of bacterial suspension per well of 6-well plate. For NT conditions only 2 ml of fresh media was added.
|
| Growth protocol |
The human normal colon epithelial cell lines, FHC (ATCC: CRL-183132) and CCD 841 CoN (ATCC CRL-1790) were cultured in DMEM/F12 medium (Gibco, France) supplemented with 10% heat-inactivated calf serum and additional factors (25 mM HEPES; 10 ng/mL cholera toxin; 0.005 mg/mL insulin; 0.005 mg/mL transferrin; 100 ng/mL hydrocortisone; EFG 20 ng/mL; 10% SVF) to sustain their growth and could be passed 5-10 times only. The human cancerous cell lines HT-29 (ATCC: HTB-38 33) were cultivated in DMEM with 10% heat-inactivated calf serum and supplemented with 25 mM HEPES. The cells were cultured in ventilated T75 flasks at 37 °C and 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell monolayers with the RNeasy Plus Mini kit (Qiagen, USA), according to the manufacturer's instructions.
Illumina TruSeq Stranded mRNA Sample preparation kit
Directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on DNA 1000 chips (Bioanalyzer, Agilent)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.
Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a with default parameters was used for the alignment on the reference genome ().
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0.
Assembly: Human genome hg38 from Ensembl
Supplementary files format and content: Count data from featureCounts
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Hugo Varet |
| Organization name |
Institut Pasteur
|
| Street address |
28 rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE232211 |
Transcriptional response to gut pathobiont Streptococcus gallolyticus subsp. gallolyticus infection of huham colon cells |
|
| Relations |
| BioSample |
SAMN35027482 |
| SRA |
SRX20280938 |
