|
| Status |
Public on May 02, 2012 |
| Title |
delta_chd1_K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
delta_Chd1 yeast (FM391,delta Chd1)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: delta_Chd1 (FM391,delta Chd1)
chip antibody: anti-trimethylated H3K4 antibody (developed by our lab)
|
| Treatment protocol |
deletion of Chd1
|
| Growth protocol |
Chromatin immunoprecipitations (ChIPs) were performed with cell lysates prepared from exponentially growing wild-type and CHD1 deleted strains to OD600nm of 1.0 and the cells were cross-linked by formaldehyde treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We followed the modified ChIP protocol described previously (Wood et al., 2005) and used anti-trimethylated H3K4 and H3K79 antibodies for immunoprecipitation.; anti-trimethylated H3K4 was developed by our lab; and the anti-trimethylated H3K79 antibody was purchased from Abcam (ab2621). 10 ng of DNA prepared from each ChIP was amplified using LMPCR and subjected to single read sequencing on a HiSeq2000 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling: Casava 1.8
Alignment: Bowtie 0.12.7 -m 10 -v 2 for ChIP-seq; TopHat 1.3.1 -g 1 with Ensembl 63 GTF for RNA-seq
Genome_build: UCSC sacCer2
Supplementary_files_format_and_content: UCSC BED
|
| |
|
| Submission date |
Mar 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE36334 |
Co-dependency of H2B monoubiquitination and nucleosome re-assembly on Chd1 |
|
| Relations |
| SRA |
SRX127921 |
| BioSample |
SAMN00809252 |
