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Sample GSM4056571 Query DataSets for GSM4056571
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

Supplementary file Size Download File type/resource
GSM4056571_S.tm_input_1.txt.gz 110.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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