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Sample GSM2791495 Query DataSets for GSM2791495
Status Public on Aug 16, 2018
Title no_MMC_fragmented
Sample type SRA
Source name no_MMC_total bacterial RNA
Organism Caulobacter vibrioides NA1000
Characteristics genotype/variation: wild type
internal stock id: KFS_0006
Treatment protocol Samples were collected prior to treatment (OD660 of 0.4) and after 4h of treatment with mitomycinC (0.1 ug/mL)
Growth protocol Caulobacter crescentus was grown aerobically at 30C in PYE medium
Extracted molecule total RNA
Extraction protocol RNA was extracted with the HotPhenol method and digested with DNaseI
For the depletion of processed transcripts, equal amounts of RNA were incubated with Terminator 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020) as previously described (Sharma et al., 2010). The transcripts were not fragmented in order to get mainly sequencing reads of the 5'-end of the transcripts. Libraries for Illumina sequencing of cDNA were constructed by vertis Biotechnology AG, Germany (, as described previously for eukaryotic microRNAs (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis. Equal amounts of RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'-triphosphates were removed by applying tobacco acid pyrophosphatase (TAP) resulting in 5'-monophosphat. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Quality trimming with fastq_quality_trimmer (fastx 0.11.2)
Read mapping with READemption (0.4.3) and segemehl (0.2.)
Coverage plote generation with READemtpoin
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wiggle of normalized coverages
Submission date Sep 25, 2017
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 GPL21317
Series (1)
GSE104186 Identification of small RNAs expressed in Caulobacter crescentus in response to DNA damage
BioSample SAMN07692730
SRA SRX3210368

Supplementary file Size Download File type/resource
GSM2791495_no_MMC_fragmented_div_by_7452139.0_multi_by_1000000.0_forward.wig.gz 11.2 Mb (ftp)(http) WIG
GSM2791495_no_MMC_fragmented_div_by_7452139.0_multi_by_1000000.0_reverse.wig.gz 11.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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