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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 08, 2014 |
| Title |
WT_S2_2.0_minus_TEX |
| Sample type |
SRA |
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| Source name |
wild typ_-TEX_OD=2.0
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| Organism |
Vibrio cholerae |
| Characteristics |
strain background: C6706
genotype/variation: wild type
tex: minus TEX
od600 at collection: 2.0
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| Treatment protocol |
When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)
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| Growth protocol |
V. cholerae was grown aerobically in LB at 37°C and samples were collected at OD600=0.1 and 2.0
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
WT HCD
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| 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
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| Submission date |
Oct 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
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| Organization name |
ZB MED - Information Centre for Life Sciences
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| Department |
Information Services
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| Lab |
Förstner Lab
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| Street address |
Gleueler Str. 60
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| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platform ID |
GPL19265 |
| Series (1) |
| GSE62084 |
Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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