|
| Status |
Public on Dec 22, 2018 |
| Title |
Sth1_H2B_1_(20180116_SB_ScDmSp_Sth1_H2B) |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin immunocleavage and release followed by ChIP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: yeast
experiment: = Yeast nuclei; Sigma-Aldrich #F1804 (CUT&RUN); abcam #ab4626 (ChIP)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN.ChIP_protocol.pdf
PMID 29651053
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CUT&RUN with 3x FLAG-tagged protein Sth1 (RSC) followed by ChIP with epitope H2B; replicate 1
|
| Data processing |
Genome_build: UCSC sacCer3
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC sacCer3. 2. We extracted properly paired reads from the alignments. 3. We used mapped fragments in the length range of 121-200. 4. We computed the fraction of all aligned bases at each base pair and scaled it by the size of the sacCer3 genome = 121507105 (Supplementary file .121-200.bedgraph.gz).
|
| |
|
| Submission date |
Jul 10, 2018 |
| Last update date |
Dec 23, 2018 |
| 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) |
| GSE116853 |
RSC Defines MNase-sensitive Promoter Architecture in Yeast |
|
| Relations |
| BioSample |
SAMN09636016 |
| SRA |
SRX4373859 |
