|
| Status |
Public on Jun 01, 2012 |
| Title |
T1D lymphocytes H3K4me3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3 ChIP with pooled type 1 diabetes samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood lymphocytes
disease status: type 1 diabetes
chip antibody: H3K4me3
antibody vendor: Millipore
antibody catalog #: 07-473
|
| Treatment protocol |
None.
|
| Growth protocol |
None.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood lymphocytes were freshly isolated from normal and T1D subjects and then crosslinked in 1% formaldehyde, sonicated to shear DNA, and immunoprecipitated with antibodies to histone PTMs. IP with no antibody was used as the Input control.
|
| Label |
Cy5
|
| Label protocol |
According to the standard NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
lymphocytes, no antibody control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood lymphocytes
disease status: type 1 diabetes
chip antibody: none
|
| Treatment protocol |
None.
|
| Growth protocol |
None.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood lymphocytes were freshly isolated from normal and T1D subjects and then crosslinked in 1% formaldehyde, sonicated to shear DNA, and immunoprecipitated with antibodies to histone PTMs. IP with no antibody was used as the Input control.
|
| Label |
Cy3
|
| Label protocol |
According to the standard NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
According to the NimbleGen kit.
|
| Scan protocol |
NimbleScan's default procedures using an Agilent Scanner.
|
| Description |
H3K4me3_T1D
H3K4me3 profile with pooled type 1 diabetes samples.
|
| Data processing |
Mean-centered log2 ratios (Cy5/Cy3) (NimbleScan).
|
| |
|
| Submission date |
Mar 09, 2012 |
| Last update date |
Jun 01, 2012 |
| Contact name |
Nancy Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
City of Hope
|
| Department |
Diabetes
|
| Street address |
1500 Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL7408 |
| Series (2) |
| GSE36402 |
ChIP-chip of lymphocytes using H3K9Ac, H3K4me3, H3K9me3, H3K27me3 and H4K16Ac antibodies |
| GSE36403 |
Profiles of Epigenetic Histone Post-translational Modifications at Type 1 Diabetes Susceptible Genes |
|
