|
| Status |
Public on May 24, 2012 |
| Title |
HP1g HCT116 RenLab ENCODE PCR tiling array replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Chromatin immunoprecipitated DNA from HCT116 cells using HP1g antibody
|
| Organism |
Homo sapiens |
| Characteristics |
fraction: Chromatin immunoprecipitated DNA
cell line: HCT116
antibody: HP1g
antibody vendor: Millipore
antibody catalog number: 05-690
antibody lot numbers: 1501782 and 17908001
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Kim et al., 2005a; Li et al., 2003). Briefly, 2 ug of specific antibodies were bound to Dynal magnetic secondary beads for 6 hours. After washing, 200 ug of sonicated chromatin was incubated with the bead bound antibody overnight. Beads were washed and enriched DNA was isolated.
|
| Label |
Cy5
|
| Label protocol |
One microgram of immunoprecipitated LM-PCR DNA was annealed with Cy5 end labeled random prime nonamer oligonucleotides.
|
| |
|
| Channel 2 |
| Source name |
Input DNA from HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
fraction: Input DNA
cell line: HCT116
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Kim et al., 2005a; Li et al., 2003). Briefly, 2 ug of specific antibodies were bound to Dynal magnetic secondary beads for 6 hours. After washing, 200 ug of sonicated chromatin was incubated with the bead bound antibody overnight. Beads were washed and enriched DNA was isolated.
|
| Label |
Cy3
|
| Label protocol |
One microgram of input genomic LM-PCR DNA was annealed with Cy3 end labeled random prime nonamer oligonucleotides.
|
| |
|
| |
| Hybridization protocol |
Enriched DNA from ChIP experiments were prepped for hybridization to Roche Nimblegen microarrays as previously described (Kim et al., 2005b). Briefly, one microgram each of immunoprecipitated or input genomic LM-PCR DNA was annealed with Cy5 and Cy3 end labeled random prime nonamer oligonucleotides. Annealed DNA was then incubated with DNA polymerase Klenow fragment and dNTPs for 2 hours at 370C. The labeled samples were isolated by ethanol precipitation. Equal amounts of Cy5 labeled IP’d DNA and Cy3 labeled input DNA were mixed and hybridized to Nimblegen HD2 economy tiling arrays (hg18 Nimblegen-Roche) using the MAUI Hybridization Station (BioMicro Systems Inc.) at 420C for 16-20 hours. The hybridized slides were washed twice in Wash buffer 1 (0.2X SSC, 0.2% SDS, and 0.1 mM DTT), and once each in buffer 2 (0.2X SSC and 0.1 mM DTT) and buffer 3 (0.05% SSC and 0.1 mM DTT) then dried.
|
| Scan protocol |
The arrays were scanned on an Axon GenePix 4000B scanner (Axon Instruments Inc.) at 532nm for Cy3 and 635nm for Cy5.
|
| Description |
ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
|
| Data processing |
The arrays were scanned on an Axon GenePix 4000B scanner (Axon Instruments Inc.) at 532nm for Cy3 and 635nm for Cy5. Raw data only. Processed/normalized data not generated for this record.
|
| |
|
| Submission date |
Mar 15, 2011 |
| Last update date |
May 24, 2012 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL1454 |
| Series (1) |
| GSE28115 |
CBX3 Regulates Efficient RNA Processing Genome Wide |
|
