|
| Status |
Public on Jul 21, 2016 |
| Title |
WT H3K36me3 antibody replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
yeast, wt, H3K36me3 ip, rep1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: wt
ip antibody: H3K36me3 antisera (5uL)
|
| Treatment protocol |
Immunoprecipitation was performed with 5 uL of antibody
|
| Growth protocol |
Cells were grown to an OD600 of 0.8-1 in YPD at 30 degrees.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Immune complexes were eluted at 65C for 30min with 1% SDS in TE supplemented with 250mM NaCl. Samples were treated with RNaseA followed by Proteinase K and crosslinks were reversed overnight at 65C. DNA was recovered by phenol chloroform isoamyl alcohol extraction followed by ethanol precipitation.
|
| Label |
Cy5
|
| Label protocol |
Input was labeled with Cy3 dye, while immunoprecipitated samples were labeled with Cy5 dye.
|
| |
|
| Channel 2 |
| Source name |
yeast, wt, H3K36me3 input, rep1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: wt
ip antibody: none (input)
|
| Treatment protocol |
Immunoprecipitation was performed with 5 uL of antibody
|
| Growth protocol |
Cells were grown to an OD600 of 0.8-1 in YPD at 30 degrees.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Immune complexes were eluted at 65C for 30min with 1% SDS in TE supplemented with 250mM NaCl. Samples were treated with RNaseA followed by Proteinase K and crosslinks were reversed overnight at 65C. DNA was recovered by phenol chloroform isoamyl alcohol extraction followed by ethanol precipitation.
|
| Label |
Cy3
|
| Label protocol |
Input was labeled with Cy3 dye, while immunoprecipitated samples were labeled with Cy5 dye.
|
| |
|
| |
| Hybridization protocol |
A mass of 5ug cy labeled samples with specific activity of greater than 15 pmol/ug were combined for each channel and hybridized according to the “Agilent Yeast ChIP-on-chip Analysis protocol Version 9.2, Mat 2007”. Hybridization occurred in an Agilent Rotisserie Hybridization Oven set to 20RPM at 65C for 40 hours.
|
| Scan protocol |
Scanning was performed on the Agilent DNA Microarray Scanner (Agilent Technologies, Model#G2505B)
|
| Description |
wt_h3k36me3_rep1
|
| Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used to quantify images. Data was read into R and normalized using median normalization.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
Jul 21, 2016 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL4130 |
| Series (1) |
| GSE68181 |
Rtr1 regulates global levels of RNA Polymerase II CTD phosphorylation during transcription elongation |
|
