|
| Status |
Public on Aug 03, 2023 |
| Title |
CTCF_10:1_2uM_ACF_75min_biolrep2_techrep1 |
| Sample type |
SRA |
| |
|
| Source name |
CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled
|
| Organism |
unidentified plasmid |
| Characteristics |
remodeler: ACF
remodeler concentration: 2 uM
remodeling turnover_conditions: single-turnover
remodeling time: Long
remodeling atp/adp_conditions: plus ATP
histone: dna ratio: 10:1 ratio
ecogii methylation: EcoGII Methylated
sample type: in vitro (plasmid insert)
|
| Treatment protocol |
N/A (in vitro samples)
N/A (in vitro samples)
|
| Growth protocol |
N/A (in vitro samples)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
PacBio SMRTbell® library preparation
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel II |
| |
|
| Description |
Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.
|
| Data processing |
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular concensus sequences (CCS) using ccs
Aligning subreads to nonanucleosomal molecule reference
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Library strategy: SAMOSA
|
| |
|
| Submission date |
Dec 14, 2022 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Megan Ostrowski |
| E-mail(s) |
megan.ostrowski@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institutes
|
| Lab |
Ramani
|
| Street address |
1700 Owens
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL29466 |
| Series (1) |
| GSE197979 |
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler |
|
| Relations |
| BioSample |
SAMN32227410 |
| SRA |
SRX18756317 |
