|
| Status |
Public on Jun 16, 2013 |
| Title |
HEK293-YY2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
YY2 ChIP DNA from HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
chip antibody: YY2
chip antibody manufacturer: Santa Cruz Biotechnology
chip antibody catalog #: SC-47637
|
| Treatment protocol |
HEK293 cells are an established cell line
|
| Growth protocol |
HEK293 cells were cultured in DMEM media for 3 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with the ChIP Assay Kit (Catalog # 17-295; Upstate) according to manufacturer’s protocol. 10 µg of anti-YY2 (SC-47637; Santa Cruz Biotechnology) antibody was added to immunoprecipitation samples. Incubation with no antibody served as negative control. After ChIP, DNA was purified with the QIAquick PCR Purification Kit (Qiagen). To reach a higher yield of DNA for ChIP-Chip, GenomePlex® Complete Whole Genome Amplification (WGA) Kit was (Catalog # WGA2; SIGMA) used after manufacturer’s recommendations. DNA was purified with the QIAquick PCR Purification Kit.
|
| Label |
Cy5
|
| Label protocol |
standard NimbleGen protocol, performed by imaGenes GmbH Campus Berlin-Buch Robert-Rössle-Str. 10 Erwin-Negelein-Haus (Building 79) 13125 Berlin Germany
|
| |
|
| Channel 2 |
| Source name |
Input DNA from HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
chip antibody: none, input DNA
|
| Treatment protocol |
HEK293 cells are an established cell line
|
| Growth protocol |
HEK293 cells were cultured in DMEM media for 3 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with the ChIP Assay Kit (Catalog # 17-295; Upstate) according to manufacturer’s protocol. 10 µg of anti-YY2 (SC-47637; Santa Cruz Biotechnology) antibody was added to immunoprecipitation samples. Incubation with no antibody served as negative control. After ChIP, DNA was purified with the QIAquick PCR Purification Kit (Qiagen). To reach a higher yield of DNA for ChIP-Chip, GenomePlex® Complete Whole Genome Amplification (WGA) Kit was (Catalog # WGA2; SIGMA) used after manufacturer’s recommendations. DNA was purified with the QIAquick PCR Purification Kit.
|
| Label |
Cy3
|
| Label protocol |
standard NimbleGen protocol, performed by imaGenes GmbH Campus Berlin-Buch Robert-Rössle-Str. 10 Erwin-Negelein-Haus (Building 79) 13125 Berlin Germany
|
| |
|
| |
| Hybridization protocol |
standard NimbleGen protocol, performed by imaGenes GmbH Campus Berlin-Buch Robert-Rössle-Str. 10 Erwin-Negelein-Haus (Building 79) 13125 Berlin Germany
|
| Scan protocol |
standard NimbleGen protocol, performed by imaGenes GmbH Campus Berlin-Buch Robert-Rössle-Str. 10 Erwin-Negelein-Haus (Building 79) 13125 Berlin Germany
|
| Description |
ChIP-chip HEK293 cells YY2
|
| Data processing |
standard NimbleGen protocol, performed by imaGenes GmbH Campus Berlin-Buch Robert-Rössle-Str. 10 Erwin-Negelein-Haus (Building 79) 13125 Berlin Germany
The log2-ratio is computed and scaled to centerthe ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.
|
| |
|
| Submission date |
Jun 28, 2010 |
| Last update date |
Jun 16, 2013 |
| Contact name |
David Drews |
| Organization name |
Charite
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10616 |
| Series (1) |
| GSE22599 |
ChIP-chip from HEK293 cells with YY2-antibody |
|
