|
| Status |
Public on Sep 13, 2018 |
| Title |
GapR_2hr_g0 |
| Sample type |
SRA |
| |
|
| Source name |
Caulobacter crescentus NA1000
|
| Organism |
Caulobacter vibrioides NA1000 |
| Characteristics |
growth stage: exponential phase
genotype: delta-gapR Pxyl-gapR
media: PYE + 0.2% glucose
growth treatment: grown 2hr in 0.2% glucose, 0 mins post synchrony in 0.2% glucose
|
| Growth protocol |
Caulobacter crescentus was grown to OD 0.2-0.4 before treatment or harvest
|
| Extracted molecule |
genomic DNA |
| 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
gDNA
Cells were lysed with lysozyme and SDS, and proteins were removed by Proteinase K. CTAB was added and DNAs were extracted by phenol:chloroform:isoamyl alcohol and precipitated. DNA was sheared to 300-800 bp fragments using a Bioruptor Plus sonicator (Diagenode). RNase A (Qiagen) was added and the fragments were electrophoresed, and 300-600 bp fragments were size selected, purified with Gel Extraction Kit (Qiagen), and resuspended in 50 µL EB. Sequencing reads were aligned to NC_011916.1 offset by 1 MB.
|
| 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 |
SAMN07299083 |
| SRA |
SRX2969633 |
