|
Status |
Public on Jan 20, 2020 |
Title |
S.tm_input_1 |
Sample type |
SRA |
|
|
Source name |
Salmonella Typhimurium
|
Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
Characteristics |
cell type: Salmonella enterica serovar Typhimurium (SL1344), constitutively expressing GFP precursor: Salmonella enterica serovar Typhimurium (SL1344)
|
Treatment protocol |
Cells were stimulated with Salmonella enterica serovar Typhimurium, added to the apical side (MOI 10, 24 h)
|
Growth protocol |
intestinal tissue model in a trans-well setting, with natural porcine intestinal collagen matrix. Caco2 cells (apical), endothelial cells (basolateral) and peripheral blood cells (basolateral) were cultured in MEM (apical) and Vasculife / X-Vivo15 (basolateral) medium.
|
Extracted molecule |
total RNA |
Extraction protocol |
Cells were washed once with PBS and flow-sorted (endothelial and Caco2 cells were disattached by Accutase treatment and scraping). RNA was extracted using the Mirvana microRNA isolation kit, with the total RNA isolation protocol. Strand-specific libraries were prepared following rRNA depletion (Ribo-Zero Gold rRNA Removal Kit (Epidemiology)), by Vertis Biotech AG, according to the companies protocols strand-dpecific rRNA-depleted totalRNA-Seq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Salmonella pre-infection inoculum
|
Data processing |
RTA version 1.18.66.4 was used for basecalling bcl2fastq version 1.8.4. was used for demultiplexing Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 GENCODE human genome annotation, fused to the S. Typhimurium SL1344 annotation (Vogel lab) with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8. RPKMs were calculated for genes using the CLC genomics worbench version 10.01 Genome_build: hg38 Supplementary_files_format_and_content: Tab-delimited text-files including gene ID, chromosome, gene type, genomic position, unique read number, RPKM
|
|
|
Submission date |
Sep 02, 2019 |
Last update date |
Jan 20, 2020 |
Contact name |
Leon Nicolas Schulte |
E-mail(s) |
[email protected]
|
Organization name |
Philipps-Universität Marburg
|
Department |
Institute for Lung Research
|
Lab |
Schulte
|
Street address |
Hans-Meerwein-Str. 2
|
City |
Marburg |
State/province |
Hessen |
ZIP/Postal code |
35043 |
Country |
Germany |
|
|
Platform ID |
GPL20056 |
Series (1) |
GSE136717 |
An advanced intestinal tissue model reveals host and pathogen strategies during Salmonella infection |
|
Relations |
BioSample |
SAMN12672542 |
SRA |
SRX6789992 |