|
Status |
Public on Sep 13, 2018 |
Title |
GapR_g80 |
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 in 0.3% xylose, 80 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.
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|
|
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
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|
|
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 |
SAMN07299084 |
SRA |
SRX2969632 |