|
| Status |
Public on Mar 15, 2011 |
| Title |
H3K4me3 ChIP-chip of THP1 cells after 1hr TNF-alpha treatment; array2of4 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3 ChIP DNA from THP1 with 1hr TNF-alpha treatment
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3
cell line: THP1
treatment: TNF-alpha
treatment duration: 1hr
|
| Treatment protocol |
Cells were treated with TNF-alpha (10ng/mL) for 1hr.
|
| Growth protocol |
THP1 cells were obtained from ATCC and cultured under recommended conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin were isolated from cells crosslinked with 1% formaldehyde, and chromatin immunoprecipitation was performed using specific antibodies. Resulting ChIP DNA and input DNA were isolated and amplified following NimbleGen protocol.
|
| Label |
Cy5
|
| Label protocol |
NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
Input DNA from THP1 with 1hr TNF-alpha treatment
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: none
cell line: THP1
treatment: TNF-alpha
treatment duration: 1hr
|
| Treatment protocol |
Cells were treated with TNF-alpha (10ng/mL) for 1hr.
|
| Growth protocol |
THP1 cells were obtained from ATCC and cultured under recommended conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin were isolated from cells crosslinked with 1% formaldehyde, and chromatin immunoprecipitation was performed using specific antibodies. Resulting ChIP DNA and input DNA were isolated and amplified following NimbleGen protocol.
|
| Label |
Cy3
|
| Label protocol |
NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
NimbleGen protocol.
|
| Scan protocol |
NimbleGen protocol.
|
| Description |
ChIP-chip mapping of H3K4me3 locations in THP1 cells treated with TNF-alpha for 1hr.
|
| Data processing |
Normalization was performed using the Model-based Analysis of 2-Color Arrays (MA2C) software package using default parameters (Robust C=2).
|
| |
|
| Submission date |
Jan 31, 2011 |
| Last update date |
Mar 15, 2011 |
| Contact name |
Fulai Jin |
| E-mail(s) |
fxj45@case.edu
|
| Phone |
2163681811
|
| Organization name |
Case Western Reserve University
|
| Lab |
Fulai Jin
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| State/province |
OH - OHIO |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL7879 |
| Series (2) |
| GSE26988 |
PU.1 and C/EBPalpha synergistically program distinct response to NF-kappaB activation through establishing monocyte-specific enhancers (ChIP-chip data) |
| GSE26994 |
PU.1 and C/EBPalpha synergistically program distinct response to NF-kappaB activation through establishing monocyte-specific enhancers |
|
