|
| Status |
Public on Feb 28, 2013 |
| Title |
Chd1 K407R N-ChIP-seq 2.5' MNase (K407R Chd1 FLAG 20120606 2) |
| Sample type |
SRA |
| |
|
| Source name |
Chd1 K407R ChIP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
sample type: nuclei
chip antibody: FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823, lot #041M6135)
strain: W1588-4C (congenic to W303-1A except RAD5+)
genotype: Chd1 K407R
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chd1 K407R native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chd1 K407R native chromatin immunoprecipitation after 2.5' micrococcal nuclease followed by sequencing
|
| Data processing |
1. We used Novoalign (2.07.00MT - Aug 5 2010) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file .sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Jul 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE39331 |
Dynamics of yeast ISWI and CHD chromatin remodeler genomic association |
| GSE39430 |
Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1) |
|
| Relations |
| SRA |
SRX160481 |
| BioSample |
SAMN01090677 |
