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Sample GSM1967915 Query DataSets for GSM1967915
Status Public on Dec 11, 2015
Title in vitro ΔpinT 01 h R2
Sample type SRA
 
Source name in vitro infection model
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics infection agent: Salmonella Typhimurium SL1344
Treatment protocol Cells were washed twice with PBS and once with SPI-2 medium, diluted 1:50 in pre-warmed SPI-2 medium 24 (defined as t0) and grown further in SPI-2 medium in Erlenmeyer flasks for the indicated time periods.
Growth protocol To mimic the early stages of the infection of a host cell in vitro, the indicated Salmonella strains were grown in LB overnight, diluted 1:100 in LB and grown to an OD600 of 2.0 (i.e. a condition under which SPI-1 is highly induced).
Extracted molecule total RNA
Extraction protocol miRvana kit for total RNA (Ambion)
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description total RNA after rRNA depletion
Data processing Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0 (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition
 
Submission date Dec 08, 2015
Last update date May 15, 2019
Contact name Konrad U. Förstner
E-mail(s) foerstner@zbmed.de
Organization name ZB MED - Information Centre for Life Sciences
Department Information Services
Lab Förstner Lab
Street address Gleueler Str. 60
City Cologne
State/province North Rhine-Westphalia
ZIP/Postal code 50931
Country Germany
 
Platform ID GPL21220
Series (2)
GSE60144 Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains
GSE67949 Dual RNA-seq – Comparative RNA-seq (in vitro medium shift experiment)
Relations
SRA SRX1470901
BioSample SAMN04327102

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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