|
| Status |
Public on Feb 01, 2011 |
| Title |
JIL-1, rep1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Input DNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Schneider line2 (S2) cells
chip antibody: none, input DNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cells were grown in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).
|
| Label |
Cy3
|
| Label protocol |
performed by imaGenes (www.imagenes-bio.de)
|
| |
|
| Channel 2 |
| Source name |
JIL1 IP DNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Schneider line2 (S2) cells
chip antibody: JIL1, R70 (custom rabbit anti JIL-1 antibody)
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Cells were grown in Schneider Medium supplemented with 10% FCS, penicillin and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the ‘high’ setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).
|
| Label |
Cy5
|
| Label protocol |
performed by imaGenes (www.imagenes-bio.de)
|
| |
|
| |
| Hybridization protocol |
performed by imaGenes (www.imagenes-bio.de)
|
| Scan protocol |
performed by imaGenes (www.imagenes-bio.de)
|
| Description |
Chip-chip S2 cells JIL-1
|
| Data processing |
raw signals of all channels in all replicate arrays were log2 transformed and quantile normalized in R/Bioconductor (normalize.quantiles in preprocessCore package).
|
| |
|
| Submission date |
Jun 29, 2010 |
| Last update date |
May 03, 2011 |
| Contact name |
Tobias Straub |
| E-mail(s) |
tstraub@med.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center, Bioinformatics
|
| Street address |
Großhadener Str. 9
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7107 |
| Series (2) |
| GSE22618 |
JIL kinase – marker of active chromatin and sensor of dosage compensation |
| GSE22621 |
Chromosomal kinase JIL-1 in Drosophila S2 Cells |
|
