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Sample GSM1519470 Query DataSets for GSM1519470
Status Public on Dec 08, 2014
Title WT_S2_2.0_minus_TEX
Sample type SRA
Source name wild typ_-TEX_OD=2.0
Organism Vibrio cholerae
Characteristics strain background: C6706
genotype/variation: wild type
tex: minus TEX
od600 at collection: 2.0
Treatment protocol When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)
Growth protocol V. cholerae was grown aerobically in LB at 37°C and samples were collected at OD600=0.1 and 2.0
Extracted molecule total RNA
Extraction protocol Trizol Reagent followed by Dnase I treatment
The cDNA libraries were constructed as previously described (Dugar et al. 2013). For Illumina sequencing (HiSeq) of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a HiSeq 2000 machine (Illumina) in single-read mode and 100 cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description WT HCD
Data processing Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: NC_002505.1, NC_002506.1 and NC_001133.9, NC_001134.8, NC_001135.5, NC_001136.10, NC_001137.3, NC_001138.5, NC_001139.9, NC_001140.6, NC_001141.2, NC_001142.9, NC_001143.9, NC_001144.5, NC_001145.3, NC_001146.8, NC_001147.6, NC_001148.4, NC_001224.1
Supplementary_files_format_and_content: wiggle
Submission date Oct 06, 2014
Last update date May 15, 2019
Contact name Konrad U. Förstner
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 GPL19265
Series (1)
GSE62084 Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors
BioSample SAMN03097422
SRA SRX724853

Supplementary file Size Download File type/resource
GSM1519470_WT_S2_2.0_minus_TEX_div_by_6643865.0_multi_by_5191739.0_forward.wig.bz2 10.4 Mb (ftp)(http) WIG
GSM1519470_WT_S2_2.0_minus_TEX_div_by_6643865.0_multi_by_5191739.0_reverse.wig.bz2 10.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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