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| Status |
Public on Sep 29, 2021 |
| Title |
A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We employed in situ Hi-C with an auxin-inducible degron (AID) system to demonstrate the effect of chromatin remodeling on 3D genome organization in yeast.
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| Overall design |
IAA (Sigma, I2886) was added to a final concentration of 0.5 mM for degradation of target proteins and the same volume of 100% ethanol was used as a control. For G1 arrest, alpha-factor was added at a final concentration of 50 ng/ml to bar1Δ strains; after 2 h, 0.5 mM IAA was added and the cells were incubated for an additional 3 h. For S or G2/M arrest, alpha-factor was added at a final concentration of 50 ng/ml to bar1Δ strains; after 1.5 h, the yeast cells were transferred to fresh YPD medium containing 200 mM hydroxyurea (HU; Sigma, H8627) for S arrest or 15 ug/ml nocodazole (Sigma, M1404) for G2 arrest. At 1.5 h after HU/nocodazole treatment, 0.5 mM IAA was added and cells were incubated for an additional 3 h. For G2 arrest, an additional 10 ug/ml of nocodazole was applied along with the IAA.
Yeast cells (50 O.D.600) were cultured, fixed with 3% formaldehyde (Wako, 064-00406), quenched, pelleted, pre-incubated with β-ME buffer (20 mM EDTA and 0.7 M β-ME) for 10 min at 30℃, and then lysed with 2 mg of zymolase (US Biological, Z1004) in 2 ml lyticase buffer (1 M sorbitol, 50 mM Tris-Cl (pH 8.0), 5 mM β-ME) for 20 min at 30℃. The obtained spheroplasts were resuspended in 2 ml of ice-cold PBS. The isolated nuclear DNA was resuspended in 50 ul of 0.5% SDS, incubated for 10 min at 62℃, mixed with 170 ul of 1.47% TritonX-100 and incubated for 15 min at 37℃. The generated libraries were sequenced using 150-bp paired-end reads on an Illumina Novaseq6000 and/or HiSeqX.
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| Contributor(s) |
Jo H, Lee D |
| Citation(s) |
34737268 |
| |
| Submission date |
Sep 22, 2020 |
| Last update date |
Nov 30, 2021 |
| Contact name |
Hyelim Jo |
| E-mail(s) |
hyelimi@kaist.ac.kr
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| Organization name |
KAIST
|
| Department |
Biological science
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| Lab |
chromatin biology lab.
|
| Street address |
335 Gwahangno, Yuseong-Gu
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| City |
Daejeon |
| ZIP/Postal code |
305-701 |
| Country |
South Korea |
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| Platforms (2) |
| GPL26171 |
HiSeq X Ten (Saccharomyces cerevisiae) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
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| Samples (84)
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| Relations |
| BioProject |
PRJNA664936 |
| SRA |
SRP284851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE158336_1K_G1_CHD1ISW1_IAA.cool.gz |
50.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_CHD1ISW1_no.cool.gz |
48.4 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_CHD1_IAA.cool.gz |
54.8 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_CHD1_no.cool.gz |
48.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_ISW1_IAA.cool.gz |
49.1 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_ISW1_no.cool.gz |
49.4 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_K501R_IAA.cool.gz |
49.9 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_K501R_no.cool.gz |
48.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_SPT6_IAA.cool.gz |
51.0 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_SPT6_no.cool.gz |
47.1 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_SWR1_IAA.cool.gz |
54.4 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G1_SWR1_no.cool.gz |
55.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G2_CHD1_IAA.cool.gz |
35.9 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G2_CHD1_no.cool.gz |
31.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G2_SWR1_IAA.cool.gz |
38.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_G2_SWR1_no.cool.gz |
49.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_S_CHD1_IAA.cool.gz |
50.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_S_CHD1_no.cool.gz |
53.2 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_S_SWR1_IAA.cool.gz |
51.0 Mb |
(ftp)(http) |
COOL |
| GSE158336_1K_S_SWR1_no.cool.gz |
51.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_G1_IAA_5000.cool.gz |
18.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_G1_no_5000.cool.gz |
18.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_G2_IAA_5000.cool.gz |
18.1 Mb |
(ftp)(http) |
COOL |
| GSE158336_G2_no_5000.cool.gz |
18.1 Mb |
(ftp)(http) |
COOL |
| GSE158336_S_IAA_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_S_no_5000.cool.gz |
17.9 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_chd1_IAA_5000.cool.gz |
17.5 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_chd1_no_5000.cool.gz |
18.4 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_fun30_IAA_5000.cool.gz |
17.4 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_fun30_no_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_ino80_IAA_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_ino80_no_5000.cool.gz |
18.1 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_isw1_IAA_5000.cool.gz |
17.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_isw1_no_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_isw2_IAA_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_isw2_no_5000.cool.gz |
17.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_snf2_IAA_5000.cool.gz |
18.8 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_snf2_no_5000.cool.gz |
18.7 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_sth1_IAA_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_sth1_no_5000.cool.gz |
17.3 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_swr1_IAA_5000.cool.gz |
17.6 Mb |
(ftp)(http) |
COOL |
| GSE158336_all_Min_swr1_no_5000.cool.gz |
18.5 Mb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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