|
| Status |
Public on Jun 01, 2007 |
| Title |
Embryo5_Replicate1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Anti-CTCF immunopurification
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Experimental Chromatin from 0-20hr immunopurified with rabbit anti-CTCF (Moon et al, 2005, EMBO Reports, 6:p165). Immunopurification as described in Birch-Machin et al (2005) Genome Biology 6:R63. Detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin purified as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Label |
Cy3
|
| Label protocol |
Enriched chromatin labelling as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| |
|
| Channel 2 |
| Source name |
Normal Rabbit Serum immunopurification
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Control Chromatin from 0-20hr immunopurified with noraml rabit serum. Immunopurification as described in Birch-Machin et al (2005) Genome Biology 6:R63. Detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin purified as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Label |
Cy5
|
| Label protocol |
Enriched chromatin labelling as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| |
|
| |
| Hybridization protocol |
As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Scan protocol |
As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/
|
| Description |
Identification of in vivo CTCF binding sites in the Drosophila genome.
|
| Data processing |
Spotfinding performed with Dapple (Buhler J. et al (2000). Dapple: improved techniques for finding spots on DNA microarrays. University of Washington technical report, UWTR 2000-08-05).
VSN normalisation of 4 slides in an experimental group - VALUE is the VSN normalised ratio of experimental (anti-CTCF-enriched to control). All other data are raw un-normalised values.
See www.flychip.org.uk for full details
|
| |
|
| Submission date |
Mar 23, 2007 |
| Last update date |
Mar 27, 2007 |
| Contact name |
Steve Russell |
| E-mail(s) |
s.russell@gen.cam.ac.uk
|
| Phone |
+44 (0) 1223 766929
|
| Fax |
+44 (0) 1223 333992
|
| Organization name |
University of Cambridge
|
| Department |
Department of Genetics
|
| Street address |
Downing Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 3EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5028 |
| Series (1) |
| GSE7351 |
In vivo genomic binding sites for the Drosophila CTCF Insulator |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
VSN Normalised ratio experimental/control |
| Status1 |
Spotfinding status for channel 1 (A=Accept, R=Reject, S=Suspect) |
| fgMedian1 |
foreground median pixel intensity of channel 1 |
| bgMedian1 |
background (local area around spot) median pixel intensity of channel 1 |
| fgAdjMAD1 |
foreground (spot) pixel intensity variability of channel 1 |
| bgAdjMAD1 |
background (local area around spot) pixel intensity variability of channel 1 |
| Status2 |
Spotfinding status for channel 2 (A=Accept, R=Reject, S=Suspect) |
| fgMedian2 |
f |
| bgMedian2 |
background (local area around spot) median pixel intensity of channel 2 |
| fgAdjMAD2 |
f |
| bgAdjMAD2 |
background (local area around spot) pixel intensity variability of channel 2 |
| fgN |
number of pixels in the foreground |
| bgN |
number of pixels in the background |
