|
| Status |
Public on Dec 14, 2013 |
| Title |
Reb1_600mM_2_IP_(20121109_8_4) |
| Sample type |
SRA |
| |
|
| Source name |
Native-ChIPped chromatin
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: S. cerevisiae W1588-4C strain carrying Reb1-3XFLAG
antibody: M2 anti-FLAG
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
See ORGANIC_profiling_protocol.rtf for protocol with references. Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 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 2) Nuclei from S. cerevisiae strain carrying FLAG-tagged Reb1 were subjected to MNase digestion for 10 minutes and chromatin was solubilized in 600 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. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 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 |
Apr 01, 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) |
| GSE45672 |
High-resolution mapping of transcription factor binding sites on native chromatin |
|
| Relations |
| SRA |
SRX263800 |
| BioSample |
SAMN02028986 |
