NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4615148 Query DataSets for GSM4615148
Status Public on Jun 14, 2020
Title TNseq WT rep1
Sample type SRA
 
Source name Bacterial cells
Organism Caulobacter vibrioides NA1000
Characteristics strain: NA1000
growth: exponential
age: outgrowth
genotype: wild type
Treatment protocol No special treatments.
Growth protocol Grown in PYE medium.
Extracted molecule genomic DNA
Extraction protocol See methods for details. RNAseq was rRNA depleted with Ribozero from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols. Tnseq was prepared by arbitrary priming and counting.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Library strategy: Tn-seq
Base calling was done via Illumina Nextseq 500.
RNAseq: Reads were mapped to the Caulobacter NA1000 genome using BWA, sorted with Samtools and the resulting BAM files were used as input with bedtools map and a bedfile consisting of the all gene features to count the number of reads per gene
Tnseq:, single end 75 base reads were first demultiplexed by index, each library was concatenated and the molecular modifier added in the second PCR was clipped using Je (Girardot et al., 2016). Clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC_011916.1) using BWA (Li and Durbin, 2010), sorted with Samtools (Li et al., 2009). Duplicate transposon reads introduced by PCR were removed using Je (Girardot et al., 2016) and indexed with Samtools (Li et al., 2009). For ease of data visualization, the 5’ insertion sites of each transposon were converted to a wiggle file (.wig) and visualized using Integrative Genomics Viewer (IGV) (Robinson et al., 2011). Specific hits for each library were determined by calculating per position numbers of 5' sites for unique inserts across the entire genome using bedtools (Quinlan and Hall, 2010) genomecov, then counting the number of unique 5' insertions within the middle 80% of each gene using custom bedfiles with truncated ORFs and bedtools map. For statistical comparison, a quasi-likelihood F-test (glmQLFit) from the edgeR package in the Bioconductor suite (Robinson et al., 2009) was used to determine the false discovery rate adjusted p-values.
Genome_build: Caulobacter vibrioides NA1000
Supplementary_files_format_and_content: tab-delimited text files include counts for wt and dlon samples.
Supplementary_files_format_and_content: Wig files of insertion distributions for wt and dlon libraries for visualization.
 
Submission date Jun 13, 2020
Last update date Jun 15, 2020
Contact name Rilee D Zeinert
E-mail(s) rzeinert@umass.edu
Phone 9206366963
Organization name UMass Amherst
Lab Chien Lab
Street address 240 Thatcher Way
City Amherst
State/province MA
ZIP/Postal code 01003
Country USA
 
Platform ID GPL26188
Series (1)
GSE152426 The Lon protease links nucleotide metabolism with proteotoxic stress
Relations
BioSample SAMN15230446
SRA SRX8541181

Supplementary file Size Download File type/resource
GSM4615148_WT1_minusheader.wig.gz 580.4 Kb (ftp)(http) WIG
GSM4615148_WT1_plusheader.wig.gz 559.8 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap