|
| Status |
Public on Nov 30, 2018 |
| Title |
set1_DD_K4_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype/variation: set1
harvest time: DD24
antibody: H3K4me3(Abcam)
|
| Treatment protocol |
For DD24 cultures were grown in the light for 24 hours then transferred to constant dark for 24 hours and harvested. The LP30 were grown in a similar fashion but just prior to harvesting the cultures were placed in constant light for 30 min prior to harvesting. The tissue was immediately snap frozen.
|
| Growth protocol |
For the growth, Neurospora conidia were inoculated in 2% liquid culture media (2% LCM) and grown in 100-mm Petri dishes overnight at 30 °C to generate mycelia mats. Plugs were cut from the mycelia and used to inoculate flasks containing 100 ml of 2% LCM and grown for a total of 2 days at 25 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was crosslinked with 1% formaldehyde.
The purified DNA was sent to Beijing Genome Institute (BGI) for library preparation and sequencing. The samples were sequenced to a depth of 50 million 50-bp single-end read.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were mapped to NC12 genome using Burroghs Wheeler Aligner (BWA) . The resulting Bam files were processed using macs2 to call peaks (broad peaks function was used for H3K9me3).
Genome_build: NC12
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
William J. Belden |
| E-mail(s) |
beldenwj@scarletmail.rutgers.edu
|
| Phone |
848-932-5617
|
| Organization name |
Rutgers, The State University of New Jersey
|
| Department |
Animal Sciences
|
| Lab |
Belden Lab
|
| Street address |
59 Dudley Rd
|
| City |
New Brunswick |
| State/province |
NJ |
| ZIP/Postal code |
08091 |
| Country |
USA |
| |
|
| Platform ID |
GPL20705 |
| Series (2) |
| GSE121333 |
Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci [ChIP-seq] |
| GSE121356 |
Context dependent Histone H3 Lysine 4 methylation is necessary for repression and is a requisite modification for facultative heterochromatin at distinct loci |
|
| Relations |
| BioSample |
SAMN10247576 |
| SRA |
SRX4893321 |
