|
| Status |
Public on Oct 20, 2016 |
| Title |
Med17dmed15GCSM_30s_(20160115_SG_Sc_56_pSM_1) |
| Sample type |
SRA |
| |
|
| Source name |
Med17 ChEC-seq
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4705
genotype: dmed15::kanMX4 Med17-3FLAG-MNase-HIS3MX6
growth medium: GC-ile-val + 0.5 _g/mL SM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See Series supplementary file Zenter_protocol.rtf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 30 seconds after calcium addition
|
| Data processing |
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options -a -r Random 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 fragment ends mapped, and then multiplying by the total number of mapped base pairs (Supplementary file .wig). Generation and normalization of tracks was performed with https://github.com/zentnerlab/chec-seq/blob/master/pairs_single_end_sizes.pl.
|
| |
|
| Submission date |
May 10, 2016 |
| 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 |
GPL17342 |
| Series (1) |
| GSE81289 |
Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters |
|
| Relations |
| BioSample |
SAMN04977869 |
| SRA |
SRX1755654 |
