|
| Status |
Public on Jun 13, 2019 |
| Title |
ChIPseq_H3_KO2 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741
|
| Organism |
Saccharomyces cerevisiae BY4741 |
| Characteristics |
strain: NKI4713
antibody: H3
|
| Growth protocol |
Yeast strains were grown in YEPD.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked for 20 min with of the volume of freshly prepared Fix Solution containing 1% formaldehyde. Cells were washed once in cold TBS with 0.2 mM PMSF and lysed by bead beating in 200 μl breaking buffer with Zirconia/silica beads. The lysate was washed twice in FA buffer and sonicated using the Bioruptor PICO for 10 min.
Libraries were prepared using the KAPA HTP Library Preparation Kit (Illumina), using Illumina-provided adapters at 200nM. After eleven PCR cycles, cleanup and pooling was as described above. After 11 PCR cycles, a size selection cleanup was performed using 0.5X Agencourt AMPure XP PCR Purification beads to get rid of large fragments due to crosslinking DNA. The supernatant of the 0.5X cleanup was used to catch the smaller fragments; this supernatant was cleaned up 2 times with 1X beads to remove primers present in the libraries.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mapping of the reads to reference genome
filter for mapping quality < 37
merge BAM files of replicate samples
extend each read with 150 bp
normalize for sequencing depth
convert to bigwig
Genome_build: R64-2-1
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Nov 24, 2017 |
| Last update date |
Jun 13, 2019 |
| Contact name |
Fred van Leeuwen |
| E-mail(s) |
fred.v.leeuwen@nki.nl
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Gene Regulation
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18330 |
| Series (1) |
| GSE107331 |
Genome-wide maps of H3K79me and H2Bub states |
|
| Relations |
| BioSample |
SAMN08097792 |
| SRA |
SRX3421881 |
