|
| Status |
Public on Aug 06, 2024 |
| Title |
Negatively supercoiled pBR322 DNA cleaved by gyrase with cip replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Synthetic plasmid
|
| Organism |
Cloning vector pBR322 |
| Characteristics |
tissue: Not applicable
supercoiling: neg
treatment: 10 uM cip
|
| Growth protocol |
Supercoiled pBR322 DNA was treated with no enzyme, E. coli gyrase, or E. coli topo IV.
|
| Extracted molecule |
other |
| Extraction protocol |
Qiagen PCR Clean-up Kit
NEBNext Ultra II PCR-free Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1)
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Trimmomatic to trim adapters from reads
BWA-MEM to align the reads to the reference sequence
SAMtools to index the reads
Pysam to extract reads, count enzyme-cleaved DNA ends, and normalize counts by spikein reads
Assembly: pBR322_plus_spikes.fa
Supplementary files format and content: TXT file with number and location of enzyme-cleaved DNA ends from forward and reverse reads
Library strategy: SHAN-seq
|
| |
|
| Submission date |
May 09, 2024 |
| Last update date |
Aug 06, 2024 |
| Contact name |
Ian L Morgan |
| E-mail(s) |
[email protected]
|
| Organization name |
National Heart Lung and Blood Institute
|
| Street address |
50 Center Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL34464 |
| Series (1) |
| GSE267149 |
Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq |
|
| Relations |
| BioSample |
SAMN41314111 |
| SRA |
SRX24513716 |
