|
| Status |
Public on Jan 25, 2022 |
| Title |
H3K56R_HP1_input_BMRC210004453-1A |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype/variation: H3K56R
antibody: HP1
|
| Growth protocol |
Conidia of indicated strains were inoculated in petri dishes with 50 mL minimal medium (1× Vogel's and 2% glucose) and cultured at 25°C in constant light until the exponential growth phase of mycelia. The mycelial mats were cut with a specific puncher for quantification. Then, these small mycelial disks were transferred to Erlenmeyer flasks with 50 mL minimal medium and were grown at 25°C with shaking for 18 hours under constant light.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated mycelia and histone-DNA complexes were isolated with antibody.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
software used for basecalling
ChIP-seq reads were aligned to the NC10 genome assembly using Bowtie 2 version 2.3.4.1 with the following configurations…
Data were filtered using the following specifications…
peaks were called using masc2 version 2.2 with the following setting
Genome_build: NC10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage 3.5.1
Supplementary_files_format_and_content: bedGraph files were generated using Bismark Version v0.23.1
|
| |
|
| Submission date |
Jan 05, 2022 |
| Last update date |
Jan 25, 2022 |
| Contact name |
Lu Zhang |
| Organization name |
YunNan University
|
| Street address |
WuJiaYing Street
|
| City |
KunMing |
| State/province |
YunNan |
| ZIP/Postal code |
650500 |
| Country |
China |
| |
|
| Platform ID |
GPL26551 |
| Series (1) |
| GSE193075 |
H3K56 deacetylation and H2A.Z deposition are required for aberrant heterochromatin spreading |
|
| Relations |
| BioSample |
SAMN24655626 |
| SRA |
SRX13618030 |
