|
Status |
Public on Mar 15, 2016 |
Title |
Time Point 4 - RNA_Seq |
Sample type |
SRA |
|
|
Source name |
CEN.PK
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
time: 110 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 |
SAMN04461205 |
SRA |
SRX1563217 |