|
| Status |
Public on Dec 14, 2013 |
| Title |
Reb1_150mM_yeast_fly_mixed_1_IP_(20121214_7_12) |
| Sample type |
SRA |
| |
|
| Source name |
Native-ChIPped chromatin
|
| Organisms |
Saccharomyces cerevisiae; Drosophila melanogaster |
| Characteristics |
strain: Mixture of S. cerevisiae W1588-4C strain carrying Reb1-3XFLAG and Drosophila S2 cells
antibody: M2 anti-FLAG
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See ORGANIC_profiling_protocol.rtf for protocol with references. Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
(Replicate 1) Approximately equal numbers of nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 and nuclei from Drosophila S2 cells were mixed and subjected to MNase digestion for 10 minutes and chromatin was solubilized in 150 mM salt by needle extraction followed by native ChIP with anti-FLAG antibody.
|
| 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. We also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary files .bam) 2. We extracted properly paired reads that were only mapped to one organism (Supplementary files .bed).
|
| |
|
| Submission date |
Apr 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
|
| 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 |
GPL16939 |
| Series (1) |
| GSE45672 |
High-resolution mapping of transcription factor binding sites on native chromatin |
|
| Relations |
| SRA |
SRX263814 |
| BioSample |
SAMN02029000 |
