|
| Status |
Public on Sep 23, 2015 |
| Title |
Recon_MNase-Exo_less-digested-1 |
| Sample type |
SRA |
| |
|
| Source name |
nucleosome core particles (MNase +ExoIII)
|
| Organism |
Synthetic plasmid |
| Characteristics |
genotype/variation: n/a
plasmid: plasmid pRS-ARG1-B
mnase or exoiii: MNase digest with ExoIII trimming
|
| Growth protocol |
Both strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were prepared from unfixed yeast cells and then digested with a range of MNase concentrations at two different ExoIII concentrations. In vitro reconstitutions were performed by mixing recombinant yeast histone octamers with purified plasmid pRS-ARG1-B DNA followed by salt dialysis. In both cases, mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Recombinant yeast histones and pRS-ARG1-B
Biological replicate 1
|
| Data processing |
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie2 with default settings. Bowtie2 was also used to align the reconstituted nucleosome sequences to the plasmid sequence (supplied here).
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535.
The processed data were converted to the bigwig files supplied here (using all sequences).
Genome_build: SacCer2 for in vivo data. In vitro reconstitutions: the plasmid sequence (pRS-ARG1-B.fa) is provided here; the S. cerevisiae ARG1 locus (from -1283 to +2936 relative to the start codon) was inserted into pRS414. See paper for more details.
Supplementary_files_format_and_content: yeast strains (in vivo data): bigwig files showing nucleosome occupancy (all reads included). Reconstituted nucleosomes on plasmid pRS-ARG1B: text files showing nucleosome occupancy at each plasmid coordinate (all lengths).
Supplementary_files_format_and_content: pRS-ARG1-B_688.fa (the plasmid sequence used to align nucleosome reads in the reconstitution experiments).
|
| |
|
| Submission date |
Feb 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Johannes Clark |
| E-mail(s) |
clarkda@mail.nih.gov
|
| Phone |
3014966966
|
| Organization name |
NICHD, NIH
|
| Department |
DDB
|
| Lab |
SCGE
|
| Street address |
6 Center Drive Bldg 6A Rm 2A02
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19776 |
| Series (1) |
| GSE65889 |
Novel nucleosomal particles containing core histones and linker DNA but no histone H1 |
|
| Relations |
| BioSample |
SAMN03342155 |
| SRA |
SRX876100 |
