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| Status |
Public on Nov 16, 2023 |
| Title |
H3K9me2, lsd1 clr4 del set1 del, rep1 |
| Sample type |
SRA |
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| Source name |
whole cell
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
tissue: whole cell
strain: lsd1 clr4 del set1 del
chip antibody: H3K9me2
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| Treatment protocol |
FTP-tagged ChIP was performed using 50 µL IgG Sepharose (GE Healthcare) for 4-6 hours at 4o C. myc-ChIPs that were performed in FTP (Protein A-, TEV cleavage site, and Flag- double epitope-tag) backgrounds were modified.
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| Growth protocol |
Strains were cultured in 100 mL to the exponential growth phase, and protein-DNA crosslinking was performed with Paraformaldehyde with slow shaking for 30 minutes.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were incubated with 50 units of AcTEV protease (Invitrogen Corp. Catalog#: 12575015, Massachusetts, USA) and 50µL IgG Sepharose (GE Healthcare, Catalog#: 17096901, Illinois, USA) at 4 °C overnight. The next morning, pre-cleared whole cell extracts were collected after centrifugation at 17,530 × g for 10 min, followed by adding the antibody (Anti-myc, Abcam ab9132). Reverse cross-linking and elution were performed at 65o C overnight.
ChIP DNA was purified using DNA purification columns (Thermo Fisher, K0512), and quantified by quantitative-PCR (QuantStudio 3, Applied Biosystems) using SYBR Select Master Mix (Applied Biosystems, 4472908).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
C6_lsd1ftpclr4set1del_C1_wtbackground_log2_combined.bw
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| Data processing |
Reads were first trimmed of adapters using Trimmomatic v0.39 under the default settings using adaptors from TruSeq2-PE. Fa
DNA reads were then mapped to the S. pombe reference genome ASM294v2 55 using bwa mem v0.7.17
Narrow peaks for each strain were identified using MACS2 v2.2.7.1 using the default settings specifically for narrow peak detection
Differential binding was scrutinized first by using BEDTools v2.17.0 closestBed argument and the ASM294v2 annotated feature file
Log2 comparisons of each strain to the input were performed using the readCount scale factoring method in deepTools
Assembly: ASM294v2
Supplementary files format and content: bigwig
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| Submission date |
Oct 30, 2023 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Ke Zhang Reid |
| Organization name |
Wake Forest University
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| Street address |
1834 Wake Forest Rd
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| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27109 |
| Country |
USA |
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| Platform ID |
GPL28961 |
| Series (2) |
| GSE246596 |
The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe [ChIP-seq] |
| GSE246597 |
The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe |
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| Relations |
| BioSample |
SAMN38042087 |
| SRA |
SRX22288938 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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