|
Status |
Public on Dec 22, 2018 |
Title |
Sth1_H2B_2_(20170801_SB_ScDm_Sth_H2B_0713) |
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 2
|
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 |
SAMN09636015 |
SRA |
SRX4373860 |