|
| Status |
Public on Mar 17, 2008 |
| Title |
Acetyl H4 IP 30C vs Genomic set2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Acetyl H4 IP from unstressed cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
mid-log growth at 30 degree C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction.
|
| Label |
Cy5
|
| Label protocol |
Cy5 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)
|
| |
|
| Channel 2 |
| Source name |
Sonicated Genomic DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Sonicated genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by lysis of cells, phenol extraction, precipitation of DNA and sonication to less than 1 kb using a sonicator
|
| Label |
Cy3
|
| Label protocol |
Cy3 fluorophores were incorporated according to published protocol (Iyer 2003 In DNA microarrays: a molecular cloning manual (ed. D.B.a.J. Sambrook), pp. 453–463. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.)
|
| |
|
| |
| Hybridization protocol |
The Cy3 and Cy5 labeled DNA were combined,5 ?g of tRNA, 10 ?g of polyA were added, 20x SSC was added to a final concentration of 3.5x and SDS was added to a final concentration of 0.25%. The mixture was denatured at 100°C for 2 min, cooled down to room temperature and hybridized onto microarrays for 6 hrs to over night at 65°C. Arrays were washed once each in wash solution I (0.57x SSC, 0.028% SDS) and wash solution II (0.057X SSC), dried by centrifuging at 600 rpm for 5 min at room temperature in a table top centrifuge.
|
| Scan protocol |
The arrays were scanned with the Axon 4000B scanner (Axon Instruments) and quantitated using GenePix Pro 5.1 software. The data was uploaded into Acuity microarray informatics software 4.037 (Axon Laboratory), and filtered to remove spots with bad signal intensity and passed though other quality control thresholds.
|
| Description |
Immnoprecipitation of Acetyl H4 using anti Acetyl H4 antibody
|
| Data processing |
normalized log2 ratio
|
| |
|
| Submission date |
Apr 30, 2007 |
| Last update date |
Mar 17, 2008 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
iyerlab@gmail.com
|
| Phone |
5122327833
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway Dr. MBB 3.212
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL5076 |
| Series (1) |
| GSE7665 |
Stress-dependent dynamics of chromatin remodeling in yeast: Dual roles for SWI/SNF in heat shock stress response |
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