|
| Status |
Public on Jan 01, 2021 |
| Title |
A Light-Inducible Strain for Genome-Wide Histone Turnover Profiling in Neurospora crassa |
| Organism |
Neurospora crassa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Histones are not statically embedded, but are constantly exchanged outside of DNA replication. This study reports the characterization and validation of a histone turnover reporter strain of Neurospora crassa, and the method employed. This strain utilizes FLAG-tagged histone H3 under the control of a light-inducible promoter. This study also preliminarily explores histone turnover defects at constitutive heterochromatin with the loss of the heterochromatin proteins DIM-2, HDA-1, DIM-5, and HPO.
|
| |
|
| Overall design |
ChIP-seq: We analyzed incorporated FLAG-tagged histone H3 in Neurospora crassa strains in wild-type, ∆dim-2, ∆hda-1, ∆dim-5, and ∆hpo backgrounds by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.
|
| |
|
| Contributor(s) |
Storck WK, Bicocca VT, Rountree M, Selker EU |
| Citation(s) |
32357961 |
| |
| Submission date |
Jan 14, 2020 |
| Last update date |
Apr 02, 2021 |
| Contact name |
Eric U Selker |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oregon
|
| Department |
Biology, Institute of Molecular Biology
|
| Lab |
Selker
|
| Street address |
1229 University of Oregon; 1318 Franklin Blvd.
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL23150 |
Illumina HiSeq 4000 (Neurospora crassa) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA601092 |
| SRA |
SRP241885 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143603_HOMER_Merged_WT_IP.bigwig |
101.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_WT_IP_1.bigwig |
64.7 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_WT_IP_2.bigwig |
56.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_merged_dim2_IP.bigwig |
91.8 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_merged_dim5_IP.bigwig |
79.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_merged_hda1_IP.bigwig |
82.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_HOMER_merged_hpo_IP.bigwig |
98.6 Mb |
(ftp)(http) |
BIGWIG |
| GSE143603_NormalizeWTexpression_25-50_.bed.gz |
29.4 Kb |
(ftp)(http) |
BED |
| GSE143603_NormalizeWTexpression_50-75_.bed.gz |
29.5 Kb |
(ftp)(http) |
BED |
| GSE143603_NormalizeWTexpression_Highest_25_.bed.gz |
29.6 Kb |
(ftp)(http) |
BED |
| GSE143603_NormalizeWTexpression_Lowest_25_.bed.gz |
28.9 Kb |
(ftp)(http) |
BED |
| GSE143603_WT_H3K9me3_domains_SICER_corrected.bed.gz |
2.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...