|
| Status |
Public on Oct 22, 2014 |
| Title |
Expression_pht1D |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: pht1Δrad21-K1
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C or 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: WT; mat1Msmto leu1-32 ade6-216 Psc3-GFP::kanMX
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C or 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Master Pure Yeast RNA purification kit (Epicenter) according manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Ribosomal RNA was depleted with RiboMinus kit (Invitrogen) and total RNA reverse-transcribed and labeled using SuperScript Indirect cDNA labeling kit (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Equal amounts of Cy5-labeled mutant cDNA and Cy3-labeled wild-type cDNA were mixed and combined with human Cot1DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
|
| Data processing |
Data were extracted using Agilent Feature Extraction Software (GE2-v5_95_Feb07 protocol) and subjected to combined rank consistency filtering with LOWES intensity normalization. Background signal was estimated as a median processed signal of 152 oligonucleotides with no homology to S. pombe genome.
|
| |
|
| Submission date |
Apr 29, 2014 |
| Last update date |
Mar 11, 2016 |
| 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 |
GPL8908 |
| Series (2) |
| GSE56849 |
High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture |
| GSE57159 |
High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [Expression Array] |
|
