|
| Status |
Public on Oct 21, 2013 |
| Title |
Mot1_IP_2.5min_MNase_(20121214_7_2) |
| Sample type |
SRA |
| |
|
| Source name |
Mot1 IP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell: nuclei
mutant: WT
strain: W1588-4C
genotype: MOT1-3FLAG-kanMX4
antibody: anti-FLAG beads (Sigma #8823)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mot1 IP, 2.5' MNase
|
| Data processing |
1. We used Novoalign (2.08.01 - Mar 14 2012) 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 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. 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 .bedGraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.
|
| |
|
| Submission date |
Feb 08, 2013 |
| 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 (1) |
| GSE44200 |
Mot1 redistributes TBP from TATA-containing to TATA-less promoters |
|
| Relations |
| SRA |
SRX235689 |
| BioSample |
SAMN01919668 |
