|
| Status |
Public on Jan 03, 2019 |
| Title |
DNA sequencing in mmi1(W112A) cells (REP 2) ChIP H3K9me2 |
| Sample type |
SRA |
| |
|
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: mmi1-W112A mutant
antibody: H3K9me2
|
| Treatment protocol |
Genomic deletion of erh1. Genomic mutation of mmi1(W112A).
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 32˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde at room temperature for 20 minutes. Cells were lysed using bead-beater method. Lysates were sonicated and immunoprecipitations were performed using H3K9me2 antibodies (ab115159). Reverse crosslinking was performed overnight at 65˚C, followed by treatment with RNase A and proteinase K. DNA was purified using QIAquick PCR purification kit (cat. no. 28014).
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina NextSeq 500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Alignment was done using BWA-MEM.
Reads per Genomic Content (RPGC) values were obtained using Deeptools suite
Genome_build: asm294v2.29
Supplementary_files_format_and_content: bigWig from Deeptools suite
|
| |
|
| Submission date |
Sep 06, 2018 |
| Last update date |
Jan 03, 2019 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE119604 |
Genome wide map of H3K9me2 in fission yeast Schizosaccharomyces pombe. |
|
| Relations |
| BioSample |
SAMN09986323 |
| SRA |
SRX4650530 |
