|
| Status |
Public on Jul 31, 2020 |
| Title |
△Ioc3_1 [MNase-seq] |
| Sample type |
SRA |
| |
|
| Source name |
△Ioc3
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4742
genotype/variation: {delta}Ioc3
epitop tag: FLAG
|
| Growth protocol |
Yeast strains were grown in YPD to an OD 600 of approximately 0.7-0.9 in three independent biological replicates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Strains with IOC3-FLAG and ioc3ΔcHLB-FLAG were grown as three biological replicates at 30˚C in YPD to an OD600 of 0.8. Samples were incubated with 1% formaldehyde for 20 min and quenched with glycine (125 mM final) for 5 min (Henikoff, 2015 ). Cells were harvested and converted to spheroplasts using 2 mg/ml zymolase (United Biologicals). Spheroplasts were digested with micrococcal nuclease (NEB M0247S) until ~70% of chromatin was converted into mononucleosomes. Samples were incubated overnight at 65°C with proteinase K (80 g/l, Roche 03115879001) and RNase A (30 g/l, Thermo Scientific EN 0531), and nucleosomal DNA isolated by phenol:chloroform extraction. DNA was analyzed on a 1.5% agarose gel with mononucleosomal DNA excised and purified using a Qiaquick gel extraction kit (Qiagen 28706).
Libraries were prepared using standard Illumina protocols
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
dIOC3_Merged_Nucleosome_Calls_MNase_seq
|
| Data processing |
DNA libraries for Illumina paired-end sequencing of nucleosomal DNA was performed as described previously (Zentner et al., 2013). The samples were sequenced using high throughput paired-end sequencing with a Illumina HiSeq 2000 Illumina sequencer. Paired-end sequence reads were mapped to the sacCer3 reference genome using Bowtie 2.0 (Langmead and Salzberg, 2012). Reads that mapped to the repetitive rRNA locus (chrXII: 451275 -469084) were filtered out (Gossett and Lieb, 2012). Dyad density maps were obtained for the mapped reads by considering the center of the paired sequence reads after normalizing to the mean genome wide coverage. Stereotypic nucleosome positions were identified using a greedy algorithm as described for Gene Track (Albert et al., 2008). These nucleosome calls include the nucleosome dyad position, standard deviation of the dyad and nucleosome occupancy values.
Genome_build: SacCer3
Supplementary_files_format_and_content: Excel file containing nucleosome calls
|
| |
|
| Submission date |
May 19, 2020 |
| Last update date |
Jul 31, 2020 |
| Contact name |
Blaine Bartholomew |
| E-mail(s) |
[email protected]
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Bartholomew
|
| Street address |
1808 Park Road 1C
|
| City |
Smithville |
| ZIP/Postal code |
78957 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE150827 |
The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [MNase-Seq] |
| GSE150829 |
The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription |
|
| Relations |
| BioSample |
SAMN14970860 |
| SRA |
SRX8362536 |
