 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 14, 2020 |
| Title |
TNeq WT rep2 |
| 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 |
SAMN15230445 |
| SRA |
SRX8541182 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4615149_WT2_minusheader.wig.gz |
569.9 Kb |
(ftp)(http) |
WIG |
| GSM4615149_WT2_plusheader.wig.gz |
554.6 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
