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Sample GSM3374694 Query DataSets for GSM3374694
Status Public on Jan 05, 2019
Title WI: WT EHEC with 500µM indole
Sample type SRA
Source name EHEC
Organism Escherichia coli O157:H7
Characteristics strain: 86 24
genotype: WT
treatment: indole
Treatment protocol 500µM of indole or only methanol in a dilution ratio of 1:1000 was added to the low gluocse DMEM before starting the experiment
Growth protocol WT and △tnaA EHEC strains were grown in low gluocse DMEM until late log phase with either methanol or 500µM indole in three biological replicates. Samples were checked for similar O.D and then samples were harvested by centrfugation. The RNA was extracted from the pellet fraction using Ribopure RNA extraction kit (Ambion).
Extracted molecule total RNA
Extraction protocol RNA was extracted using Ribopure RNA extraction kit (Ambion)
12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Our 12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
Sequencing run: Our 12 RNA libraries were run on illumine HiSeq 2500 sequencer with SE-50.
Raw data was processed using DNAStar Lasergene software as per the instructions provided on the DNAStar website
Genome_build: sakai genome downloaded from ncbi was used as a reference genome (NC_002695.1)
Supplementary_files_format_and_content: tab delimited text file includes the RKPM values for all samples under the conditions tested above.
Supplementary_files_format_and_content: .astar files can be accessed using DNAStar Lasergene software
Submission date Sep 04, 2018
Last update date Jan 05, 2019
Contact name Aman Kumar
Organization name UT Southwestern Medical Center
Department Microbiology
Street address 5323 Harry Hines Blvd.
City Dallas
State/province Texas
ZIP/Postal code 75390-9048
Country USA
Platform ID GPL25528
Series (1)
GSE119440 Indole signaling at the host-microbiota-pathogen interface
BioSample SAMN09951430
SRA SRX4637977

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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