|
| Status |
Public on Jun 15, 2016 |
| Title |
RNA sequencing in wild type cells |
| Sample type |
SRA |
| |
|
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: wild type cells (Smt0)
|
| Treatment protocol |
Genomic deletion of CCR4 and ERH1.
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 30˚C to OD600=~0.2 and then shifted to 37˚C for 5 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (epicentre)
ScriptSeq v2 RNA-Seq Library Preparation Kit was used according to manufacturer's recommendation. Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks
|
| |
|
| Submission date |
Dec 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16192 |
| Series (2) |
| GSE76112 |
Expression profiling of fission yeast strains: wild-type, erh1∆, and ccr4∆ |
| GSE76114 |
Expression profiling and ChIP-chip of Schizosaccharomyces pombe strains wildtype, erh1∆, and ccr4∆ |
|
| Relations |
| BioSample |
SAMN04348730 |
| SRA |
SRX1489432 |
