|
| Status |
Public on Mar 15, 2016 |
| Title |
Time Point 1 - RNA_Seq |
| Sample type |
SRA |
| |
|
| Source name |
CEN.PK
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
time: 0 minutes
|
| Growth protocol |
Yeast Metabolic Cycle (Minimal Media)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the hot phenol method
RNA from each time-point was extracted by utilizing the hot phenol method, and libraries were generated with the NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer’s instructions (Catalog #E7530L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
alignment - bowtie2
nucleosome peak calling - iNPS_V1.1.2
RPKM values were generated using in house created software. RPKM = (ReadsWithinORF) / ( ORFLength/1000 x TotalNumReads/1,000,000 )
Genome_build: R64-1-1
Supplementary_files_format_and_content: wig files for nucleosome data were generated with iNPS
|
| |
|
| Submission date |
Feb 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Iestyn Whitehouse |
| E-mail(s) |
whitehoi@mskcc.org
|
| Organization name |
Sloan-Kettering Institute
|
| Department |
Molecular Biology
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE77631 |
Nucleosome Positioning Dynamics Through the Yeast Metabolic Cycle |
|
| Relations |
| BioSample |
SAMN04461202 |
| SRA |
SRX1563214 |
