|
| Status |
Public on May 12, 2022 |
| Title |
mmlib_bubble_5min_1rep |
| Sample type |
SRA |
| |
|
| Source name |
mismatch library
|
| Organism |
synthetic construct |
| Characteristics |
base sequence: Widom 601 DNA
perturbation type: mismatch bubble
chd1 sliding: 5 min Chd1 sliding
|
| Treatment protocol |
nucleosomal DNA was photo-crosslinked site-specifically and cleavaged by alkaline treatment
|
| Growth protocol |
nucleosome libraries are reconstituted by salt-dialysis methods from synthetic DNA pools with Xenopus laevis histone octamers
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
phenol chloroform extraction of DNA
single-stranded 3’ end DNA fragments were converted into double-stranded DNA by Bst polymerase (NEB Bst 2.0 WarmStart). And NGS library was prepared with NEBUltraII kit (NEBNext Ultra II DNA Library Prep Kit) for Illumina sequecing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Trim Illumina adaptor using Trim Galore software
Merge the pair-end reads with FLASh software
Reads alignment with Bowtie2 software
Calling the sequence identity and DNA cleavage location by using custom python script
Data imputation by linear regression with custom python script
Supplementary files format and content: .data file including estimated nucleosome positioning scores and cleavage counts for each sequence in the library
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
May 12, 2022 |
| Contact name |
Taekjip Ha |
| Organization name |
Johns Hopkins University
|
| Street address |
3400 N. Charles Street
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE198440 |
Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex |
|
| Relations |
| BioSample |
SAMN26583015 |
| SRA |
SRX14439207 |
