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| Status |
Public on Jan 29, 2009 |
| Title |
H3K27met3 Day 45 |
| Sample type |
genomic |
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| Source name |
liver, Day 45
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| Organism |
Mus musculus |
| Characteristics |
C57BL/6
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| Treatment protocol |
No treatments
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| Growth protocol |
C57 BL/6 breeding pairs were purchased from Charles River Laboratories (Wilmington, MA). Mice were housed according to the American Animal Association Laboratory Animal Care guidelines, and were bred under standard conditions in Lab Animal Resources building in the University of Kansas Medical Center. Body weights of the female mice were recorded every day to monitor pregnancy status. Tissues from male offspring were collected at day -2 (17-days gestation), 1, 5, and 45 after birth. Tissues were frozen immediately in liquid nitrogen after harvest, and stored at -80℃ for further analysis.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To determine DNA and histone methylation, a combination of immunoprecipitation of methylated DNA fragments with an antibody against 5-methyl-cytosine (ab51552; Abcam Inc. Cambridge, MA) anti-H3K4me2 (Millipore 07-030) and anti-H3k27me3 (Millipore 07-449) and hybridization of the precipitated DNA fragments to the GeneChip array were used. Genomic DNA from the liver tissues was isolated by a ChargeSwitch gDNA Mini Tissue Kit (Invitrogen, Carlsbad, CA), following the manufacturer’s protocol. The purified ChIP-enriched fragments were amplified by random priming. A fixed sequence of 17 bases containing 9 random bases at the 3' end was first used in four linear amplification reactions with Sequenase (USB, Cleveland, OH). Following purification, the randomly primed ChIP DNA was amplified for 30 cycles using a fixed sequence primer. The resulting amplified DNA was purified, quantified, and tested by Q-PCR at the same genomic regions as the original immunoprecipitated DNA to assess quality of the amplification reactions
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| Label |
biotin
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| Label protocol |
Amplified DNAs were fragmented, labeled using the DNA Terminal Labeling Kit according to the standard Affymetrix protocol. (http://www.affymetrix.com/products/arrays/specific/mouse_tiling_2.affx).
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| Hybridization protocol |
Labeled products (12 µg) were hybridized to the Affymetrix mouse tiling 2.0R array. DNA without immunoprecipitation was used as control (input) for background hybridization.
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| Scan protocol |
Arrays were washed and scanned by GeneChip ® HT Array Plate Scanner according to standard procedures.
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| Description |
ChIP
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| Data processing |
Standard Affymetrix protocol
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| Submission date |
Jan 28, 2009 |
| Last update date |
Jan 28, 2009 |
| Contact name |
Steven Hart |
| E-mail(s) |
shart3@kumc.edu
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| Phone |
913-588-9020
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| Organization name |
University of Kansas Medical Center
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| Department |
Pharmacology, Toxicology & Therapeutics
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| Lab |
Zhong Lab
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| Street address |
3901 Rainbow Blvd
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| City |
Kansas City |
| State/province |
KS |
| ZIP/Postal code |
66160 |
| Country |
USA |
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| Platform ID |
GPL6448 |
| Series (1) |
| GSE14620 |
Ontoepigenetic profile of mouse liver reveals dynamic regulation of chromatin during development |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM365190.CEL.gz |
25.7 Mb |
(ftp)(http) |
CEL |
| GSM365190.bar.gz |
28.9 Mb |
(ftp)(http) |
BAR |
| Processed data provided as supplementary file |
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