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Sample GSM2690552 Query DataSets for GSM2690552
Status Public on Sep 13, 2018
Title WT grown in glucose 6h
Sample type SRA
 
Source name Caulobacter crescentus NA1000
Organism Caulobacter vibrioides NA1000
Characteristics growth stage: exponential phase
genotype: wild type
media: PYE + 0.2% glucose
Growth protocol Caulobacter crescentus was grown to OD 0.2-0.4 before treatment or harvest
Extracted molecule total RNA
Extraction protocol Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with either Phusion (NEB) or Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 250-600 bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mRNA
RNA was extracted by hot trizol lysis and Direct-zol RNA MiniPrep (Zymo). rRNAs were removed using the Ribo-Zero Kit for Gram-negative bacteria (Illumina) and mRNAs were then fragmented with RNA fragmentation reagents (Ambion). First-strand cDNA synthesis was performed with random primers (Invitrogen) and Superscript III. After purifying cDNAs by phenol:chloroform:isoamyl alcohol extraction and precipitation, second-strand synthesis occurred with dUTP (Promega) instead of dTTP and RNase H (NEB), E.coli DNA ligase (NEB), and DNA Pol I (NEB). Sequencing libraries were built as with other libraries, except that the second strand was digested with USER (NEB) after the addition of Y-adaptors.
Data processing Reads were aligned to Caulobacter NC_011916.1 (NA1000) with bowtie (single-end reads) or bowtie2 (paired end reads) allowing for 1 mismatch
Bowtie alignments were converted to wiggle files by mapping the center of each read.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: wig files were generated using custom python scripts, tab delimited files, first column represents genome position, second column represents value of position
 
Submission date Jun 29, 2017
Last update date May 15, 2019
Contact name Monica S Guo
E-mail(s) msguo@uw.edu
Organization name University of Washington
Department Microbiology
Lab Guo
Street address 750 Republican St
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL18276
Series (1)
GSE100657 A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication
Relations
BioSample SAMN07299075
SRA SRX2969617

Supplementary file Size Download File type/resource
GSM2690552_WT_glu_f.wig.gz 15.6 Mb (ftp)(http) WIG
GSM2690552_WT_glu_r.wig.gz 15.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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