|
| Status |
Public on Sep 29, 2021 |
| Title |
Isw1+IAA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Isw1+IAA_rep1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: 0.5mM IAA
strain: ISW1-AID
|
| Treatment protocol |
Final conc. 0.5mM of auxin (+IAA) or same volume of 100% ethanol(Con.) was treated.
|
| Growth protocol |
After 3hr of pre-incubation step, the yeast culture was diluted to 0.2 O.D. and treat auxin (+IAA) or ethanol and incubate for 3hr at 30℃.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total 50 O.D.600 of final 3% formaldehyde fixed yeast cells was cultured and pre-incubated with β-ME buffer (20mM EDTA, 0.7M β-ME) for 10min at 30℃. The yeast cell pellet permeabilized with 2mg of zymolyase (USbiological, Z1004) with 2ml lyticase buffer (1M sorbitiol, 50mM Tris-Cl (pH 8.0), 5mM β-ME) for 20min at 30℃. The obtained spheroplast was re-suspended into 2ml of ice-cold PBS.
in situ Hi-C library preparation was performed as previously reported (PMID:25497547), with some modifications in yeast nucleus isolation steps. The generated libraries sequenced using 150bp paired-end reads on Novaseq6000 and/or HiSeqX.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Hi-C
all_Min_isw1_IAA_5000.cool
|
| Data processing |
HiCPro pipeline (PMID26619908)
Convert .cool format using HiCExplorer (PMID29335486)
Genome_build: SaCcer3
Supplementary_files_format_and_content: 5kb resolution cool matrix
|
| |
|
| Submission date |
Sep 22, 2020 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Hyelim Jo |
| E-mail(s) |
hyelimi@kaist.ac.kr
|
| Organization name |
KAIST
|
| Department |
Biological science
|
| Lab |
chromatin biology lab.
|
| Street address |
335 Gwahangno, Yuseong-Gu
|
| City |
Daejeon |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE158336 |
A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast |
|
| Relations |
| BioSample |
SAMN16237498 |
| SRA |
SRX9171774 |
