|
Status |
Public on Mar 31, 2011 |
Title |
HBEC H3K4me3 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
H3K4me3 ChIp DNA from HBEC
|
Organism |
Homo sapiens |
Characteristics |
cell type: human bronchial epitelia cells genotype/variation: HBEC immortalized with hTERT and CDK4 cell line: HBEC enrichment procedure: ChIp H3K4me3 antibody vendor/catalog number: Millipore #17-614 antibody lot#: DAM1612220
|
Treatment protocol |
no treatment
|
Growth protocol |
cells were cultured in K-SFM media (Invitrogen, Carlsbad, CA).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For UMC, sonicated DNA was treated according to the manufacturer’s instructions for the UMC kit (Active Motif), purified and amplified by using LM-PCR. For ChIP-chip experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by 0.125 M glycine. 8 µg of sonicated chromatin was incubated with appropriate antibodies overnight and captured with A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR.
|
Label |
Cy5
|
Label protocol |
According to standard NimbleGen Protocol
|
|
|
Channel 2 |
Source name |
Input DNA from HBEC
|
Organism |
Homo sapiens |
Characteristics |
cell type: human bronchial epitelia cells cell line: HBEC genotype/variation: HBEC immortalized with hTERT and CDK4 enrichment procedure: none, Input
|
Treatment protocol |
no treatment
|
Growth protocol |
cells were cultured in K-SFM media (Invitrogen, Carlsbad, CA).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For UMC, sonicated DNA was treated according to the manufacturer’s instructions for the UMC kit (Active Motif), purified and amplified by using LM-PCR. For ChIP-chip experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by 0.125 M glycine. 8 µg of sonicated chromatin was incubated with appropriate antibodies overnight and captured with A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR.
|
Label |
Cy3
|
Label protocol |
According to standard NimbleGen Protocol
|
|
|
|
Hybridization protocol |
According to NimbleGen Kit
|
Scan protocol |
Follow NimbleScan's default using Agilent Scanner
|
Description |
ChIp-ChIp HBEC H3K4me3
|
Data processing |
Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean
|
|
|
Submission date |
Dec 14, 2010 |
Last update date |
Mar 31, 2011 |
Contact name |
Xiwei Wu |
E-mail(s) |
xwu@coh.org
|
Organization name |
City of Hope National Medical Center
|
Department |
Computational and Quantitative Medicine
|
Street address |
1500 E. Duarte Rd.
|
City |
Duarte |
State/province |
CA |
ZIP/Postal code |
91010 |
Country |
USA |
|
|
Platform ID |
GPL11313 |
Series (2) |
GSE26020 |
Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription |
GSE26040 |
Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks |
|