|
| Status |
Public on Jan 23, 2020 |
| Title |
ML3174 (Pxyl-dcas9(Sth3) Pconstitutive-sgRNA(Sth3)_ctrA) in glucose |
| Sample type |
SRA |
| |
|
| Source name |
Caulobacter crescentus CB15N
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
growth stage: exponential phase
strain: ML3174
media: PYE + 0.2% glucose
|
| Growth protocol |
Caulobacter crescentus was grown in PYE+0.2% glucose to OD ~ 0.05-0.1. Cultures were split and 0.3% xylose was added to to one flask to induce the CRISPR system. RNA was harvested after 2hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as previously reported (Culviner and Laub, 2018).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Strains were grown in PYE + supplements to OD600~0.2 and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).
|
| Data processing |
Reads were aligned to Caulobacter NC_011916.1 (NA1000) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
The change in gene expression was calculated by taking log2-RPKM ratio of each gene from the experimental condition to the control condition (dcas9 grown in xylose / dcas9 grown in glucose; sgRNA-ctrA grown in xylose / sgRNA-ctrA grown in glucose).
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position. For RNA-seq, two files are provided, one for forward and reverse strand.
|
| |
|
| Submission date |
Oct 28, 2019 |
| Last update date |
Jan 23, 2020 |
| 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 |
GPL24555 |
| Series (1) |
| GSE139521 |
A CRISPRi system for efficient and rapid gene knockdown in Caulobacter crescentus |
|
| Relations |
| BioSample |
SAMN13150828 |
| SRA |
SRX7067018 |
