|
| Status |
Public on Jul 06, 2010 |
| Title |
Yarrowia lipolytica genome-wide nucleosome data |
| Sample type |
SRA |
| |
|
| Source name |
in vivo cells
|
| Organism |
Yarrowia lipolytica |
| Characteristics |
strain: CLIB 89
|
| Treatment protocol |
Formaldehyde crosslink, shearing with MNase, isolation of mononucleosomal DNA using gel purification of DNA band ~150bp.
|
| Growth protocol |
Overnight cultures for each species were grown in 450ml of media at 220 RPM in a New Brunswick Scientific air-shaker at 30°C until reaching mid log-phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to standard Illumina instructions. Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 19 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Mnase digestion and gel purification of mononucleosomal DNA
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Mnase digested DNA and size selected for mononucleosomes (~150bp)
|
| Data processing |
Read Extended Nucleosome Map: Each uniquely mapped read was then extended to a length of 100bp. To generate a genomic nucleosome occupancy landscape, we cumulatively summed all extended reads covering each base pair. The *.wig files use the WIGGLE fixed_step format.
Alignment: Sequence reads were mapped to the appropriate reference genome (fasta file attached) using BLAT. All reads mapping to a unique location in the genome with 4 or fewer mismatches were retained. *.read files are tab delimited text files containing each uniques reads chromosomal coordinates. The files have 4 columns and the following headers: readChrom, readStart, readStop, onForwardStrand (1=forward strand or +, 0=reverse strand or -).
Genomes: The version of the species' genomic sequences used in this study are attached as fasta files (*.fsa).
|
| |
|
| Submission date |
Jun 08, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex M Tsankov |
| E-mail(s) |
atsankov@mit.edu
|
| Phone |
6172532442
|
| Fax |
6172532442
|
| Organization name |
MIT
|
| Street address |
155 Bay State
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL10512 |
| Series (2) |
| GSE21960 |
The role of nucleosome positioning in the evolution of gene regulation |
| GSE22211 |
Genome-wide nucleosome position data for 12 yeast species |
|
| Relations |
| SRA |
SRX023130 |
| BioSample |
SAMN00016910 |
