|
| Status |
Public on Jan 24, 2010 |
| Title |
H3K27 methylation in RL cells |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K27me3 ChIP DNA from RL cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RL
cell type: follicular lymphoma cells
genotype: t(14,18) gene rearrangement
chip antibody: H3K27Me3
|
| Treatment protocol |
Untreated.
|
| Growth protocol |
RL cells were cultured in RPMI media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were carried out using a Magna ChIP kit (Millipore, Billerica, MA) following the manufacturer’s suggested protocols. For each ChIP experiment, 5×106 RL cells were crosslinked with 10% formaldehyde at 37°C for 10 minutes. The following antibodies were used: anti-trimethyl-H3K27 (Upstate, no. 07-449), anti-trimethyl-H3K4 (Upstate, no. 04-745), and anti-Suz12 (Abcam, ab-12073).
|
| Label |
Cy5
|
| Label protocol |
For hybridization to the microarrays, 10ng each of Input and ChIP DNA samples was amplified using the GenomePlex WGA kit (Sigma-Aldrich, St. Louis, MO). The Input and ChIP samples were labeled with Cy3 and Cy5 fluorescent dye, respectively.
|
| |
|
| Channel 2 |
| Source name |
Input DNA from RL cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RL
cell type: follicular lymphoma cells
genotype: t(14,18) gene rearrangement
chip antibody: none
|
| Treatment protocol |
Untreated.
|
| Growth protocol |
RL cells were cultured in RPMI media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were carried out using a Magna ChIP kit (Millipore, Billerica, MA) following the manufacturer’s suggested protocols. For each ChIP experiment, 5×106 RL cells were crosslinked with 10% formaldehyde at 37°C for 10 minutes.
|
| Label |
Cy3
|
| Label protocol |
For hybridization to the microarrays, 10ng each of Input and ChIP DNA samples was amplified using the GenomePlex WGA kit (Sigma-Aldrich, St. Louis, MO). The Input and ChIP samples were labeled with Cy3 and Cy5 fluorescent dye, respectively.
|
| |
|
| |
| Hybridization protocol |
The Input and ChIP samples were co-hybridized onto the NimbleGen promoter microarray (Roche-NimbleGen, Madison, WI) according to manufacturer's protocols.
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| Description |
ChIP-chip, RL cells, H3K27me3.
|
| Data processing |
The array data were extracted according to standard operating procedures by NimbleGen Systems, Inc. The peaks were identified with a cut-off of false discovery rate (FDR) of <0.05 using NimbleGen SignalMap software.
|
| |
|
| Submission date |
Jan 23, 2010 |
| Last update date |
Jan 23, 2010 |
| Contact name |
Huidong Shi |
| E-mail(s) |
hshi@augusta.edu
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL7408 |
| Series (1) |
| GSE20019 |
ChIP-chip from the follicular lymphoma cell line RL with H3K4me3, H3K37me3 and Suz12 |
|
