|
| Status |
Public on Jun 25, 2015 |
| Title |
BY4741-37C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast_BY4741-37C
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
treatment: 37C, 90min
media: YPD
|
| Treatment protocol |
Yeast cells were fixed with 3% formaldehyde for 15 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted, spheroplasted with Zymolyase, and treated with a level of MNase yielding >95% mononucleosom. After stopping MNase, chromatin supernatant was dephosphorylated using Antarctic phosphatase. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Crosslinked chromatin was diluted into 10 mL and treated with T4 DNA ligase. After heat inactivation, chromatin was concentrated to 250uL, and treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated for 65 C overnight.
|
| Growth protocol |
100mL yeast culture were grown to midlog phase ~OD 0.55 in YPD media at 30 C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 65
processed data file: Micro-C interactions vs. distance for all datasets.xlsx
NDR-spanning reads for all replicates.xlsx
Gene compaction scores for temperature-sensitive dataset.xlsx
|
| Data processing |
library strategy: Micro-C
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to sacCer3 genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate interaction matrix.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: readme.txt file contains additional description of how each processed data file was generated.
|
| |
|
| Submission date |
Apr 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xavier Darzacq |
| E-mail(s) |
darzacq@berkeley.edu
|
| Phone |
510-642-0884
|
| Organization name |
University of California, Berkeley
|
| Department |
Molecular and Cell Biology
|
| Lab |
Darzacq Lab
|
| Street address |
475D Li Ka Shing Center
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE68016 |
Mapping nucleosome resolution chromosome folding in yeast by Micro-C |
|
| Relations |
| BioSample |
SAMN03490879 |
| SRA |
SRX999284 |
