|
| Status |
Public on Aug 24, 2020 |
| Title |
epe1KO isolate D H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
log phase fission yeast culture
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: PAS525
genotype: epe1KO
chip antibody: H3K4me3
|
| Growth protocol |
50mL of cells were grown to OD=0.6-0.8 overnight from OD=0.025 in rich media (YES). Base on OD measurements, 300x10^6 cells per sample were fixed in 1% formaldehyde and flash frozen
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA was extracted using a bead beater and 0.5mm zirconia beads. Lysates were clarfied following shearing by sonication and then DNA/histone complexes were immunoprecipitated with antibody.
Libraries were constructed first with end repair via the Fast End Repair Kit (Thermo) then A-tailed using Klenow fragment (NEB). Illumina adaptors were ligated using Rapid T4 DNA Ligase (Enzymatics), followed by PCR amplification for 15 cycles, and size selection between 200-500bp by bead purification and gel extraction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
525D_K4me3
|
| Data processing |
ChIP-Seq reads were mapped to the S. pombe genome with with Bowtie2 version 2.3.4.2
Merge input files and wild-type H3K9me2 files were generated with samtools "merge" for normalization
Input or WT normalized signal tracks were generated using the MACS2 version 2.1.1.20160309 functions "callpeak" and "bdgcmp"
Genome_build: pombase.org September 2018 release
Supplementary_files_format_and_content: bigWig files for input and WT normalized ChIP-Seq data
|
| |
|
| Submission date |
Nov 07, 2019 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Bassem Al-Sady |
| E-mail(s) |
[email protected]
|
| Phone |
4158065708
|
| Organization name |
UC San Francisco
|
| Street address |
513 Parnassus Ave HSW1501
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL22682 |
| Series (1) |
| GSE140067 |
Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability |
|
| Relations |
| BioSample |
SAMN13229373 |
| SRA |
SRX7114666 |
