|
| Status |
Public on Mar 21, 2011 |
| Title |
H3K4me3_overexpHOTTIP_HOX_lung |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3 ChIP in HOTTIP overexpressing lung fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: input
genotype/variation: HOTTIP overexpressing
cell type: lung fibroblasts
|
| Growth protocol |
Cells for both ChIP and input Samples were grown in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA which was then subjected to one round of amplification with the sigma WGA2 kit. Amplification
|
| Label |
CY3
|
| Label protocol |
Input DNA labeled CY3, and ChIP DNA labeled CY5, Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with Klenow extension)
|
| |
|
| Channel 2 |
| Source name |
H3K4me3 ChIP in HOTTIP overexpressing lung fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me3
genotype/variation: HOTTIP overexpressing
cell type: lung fibroblasts
|
| Growth protocol |
Cells for both ChIP and input Samples were grown in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed on 4x10^6 fibroblast cells and Farnham ChIP protocol was used to derive ChIP DNA which was then subjected to one round of amplification with the sigma WGA2 kit. Amplification
|
| Label |
CY5
|
| Label protocol |
Input DNA labeled CY3, and ChIP DNA labeled CY5, Standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of cy labeled primers with Klenow extension)
|
| |
|
| |
| Hybridization protocol |
Standard Nimblegen hybridization kits and protocols were used, hybridization was performed in Nimblegene MAUI 12 bay machine
|
| Scan protocol |
Arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols
|
| Description |
H3K4me3 ChIP in HOTTIP overexpressing lung fibroblasts
|
| Data processing |
Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction
log2 ratio of ChIP/INPUT, using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction, log2 ratio created from two raw pair files
For each gff. File: columnA: Chromosome, columnD/E: probe start/stop site, columnF: log2 ratio of ChIP/INPUT
|
| |
|
| Submission date |
Jan 10, 2011 |
| Last update date |
Mar 21, 2011 |
| Contact name |
Kevin Wang |
| E-mail(s) |
kevwang@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Dermatology
|
| Street address |
269 Campus Drive CCSR 2142
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
| |
|
| Platform ID |
GPL5790 |
| Series (1) |
| GSE26540 |
ChIP-chip of siGFP- or siHOTTIP-treated foreskin fibroblasts with anti-H3K4me3, anti-H3K27me3, anti-H3K4me2, anti-histone, anti-MLL1, and anti-WDR5 antibodies on HOX tiling array |
|
