|
| Status |
Public on Oct 18, 2023 |
| Title |
Cla4_IP |
| Sample type |
SRA |
| |
|
| Source name |
genomic DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: genomic DNA
cell line: BY4741
chip antibody: FLAG (F1804-1MG; Sigma-Aldrich)
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Cells were grown in YPD medium until mid-log phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against FLAG (F1804-1MG; Sigma-Aldrich),
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Fastq files for chip-seq samples were generated with bcl2fastq 1.8.3 from Illumina.
ChIP-seq reads were trimmed from 5' end eith at least 6 bp until the final base had a quality score > 30, using Trim Galore , discarding reads left with < 70 bp
ChIP-seqdatawasalignedtosacCer3genomefromUCSCwithbowtie2(2.2.0)using-k1
bigWig files were created by using deeptool bamCompare command, normalizing to reads per kilomillion by multiplying by 1 kilomillion and dividing by the total number of alignments for each sample.
Peask were called by using Macs2 callpeak command with -g 1.2e-7 --nomodel AND with the significance cut-off q-value <=0.01
Assembly: sacCer3
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Oct 18, 2023 |
| Contact name |
Yu Qi |
| Organization name |
Hubei university
|
| Department |
College of life sciences
|
| Street address |
xujiapeng
|
| City |
wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430062 |
| Country |
China |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE229516 |
ChIP Seq Analysis of H3K4me3 in Wild Type and Set1 S228A S228E mutants |
|
| Relations |
| SRA |
SRX19945090 |
| BioSample |
SAMN34156631 |
