|
| Status |
Public on Nov 12, 2010 |
| Title |
root_UPB1_2_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
wt
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
growth protocol: whole roots from 6d on MS-media grown seedlings
tissue: whole roots
genotype: wt
antibody: anti-GFP
antibody manufacturer: ABCAM
antibody catalog #: ab290
lot #: 527131
|
| Treatment protocol |
Whole root tissue was fixed as described in Tsukagoshi et. al. 2010
|
| Growth protocol |
upb1-1 / ProUPB1:UPB1:GFP and wildtype lines were germinated and grown on MS media for 6 days as described in Tsukagoshi et. al. 2010
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation as described in Tsukagoshi et. al. 2010
|
| Label |
Cy3
|
| Label protocol |
DNA from the upb1-1 / ProUPB1:UPB1:GFP and wildtype ChIPs were blunted using T4 DNA polymerase, cleaned up with the Qiagen Reaction Cleanup Kit, amplified with 22 PCR cycles, and subsequently cleaned up according to the Agilent Mammalian ChIP-on-chip Kit protocol. 2ug of DNA was fragmented, and labeled with Cyanine 3-dUTP, and Cyanine 5-dUTP according to the Agilent Mammalian ChIP-on-chip Kit protocol.
|
| |
|
| Channel 2 |
| Source name |
ProUPB1:UPB1:GFP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
growth protocol: whole roots from 6d on MS-media grown seedlings
tissue: whole roots
genotype: ProUPB1:UPB1:GFP
antibody: anti-GFP
antibody manufacturer: ABCAM
antibody catalog #: ab290
lot #: 527131
|
| Treatment protocol |
Whole root tissue was fixed as described in Tsukagoshi et. al. 2010
|
| Growth protocol |
upb1-1 / ProUPB1:UPB1:GFP and wildtype lines were germinated and grown on MS media for 6 days as described in Tsukagoshi et. al. 2010
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation as described in Tsukagoshi et. al. 2010
|
| Label |
Cy5
|
| Label protocol |
DNA from the upb1-1 / ProUPB1:UPB1:GFP and wildtype ChIPs were blunted using T4 DNA polymerase, cleaned up with the Qiagen Reaction Cleanup Kit, amplified with 22 PCR cycles, and subsequently cleaned up according to the Agilent Mammalian ChIP-on-chip Kit protocol. 2ug of DNA was fragmented, and labeled with Cyanine 3-dUTP, and Cyanine 5-dUTP according to the Agilent Mammalian ChIP-on-chip Kit protocol.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the Agilent Mammalian ChIP-on-chip Kit protocol
|
| Scan protocol |
Scanner G2565BA with protocoll CGH-v4_95_Feb07
|
| Description |
ProUPB1:UPB1:GFP transcription factor ChIP sample v wildtype control (no GFP) ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis
|
| Data processing |
Signal extraction and initial data processing were done using the Agilent feature extraction software. Additional analysis as described in Tsukagoshi et. al. 2010
|
| |
|
| Submission date |
May 07, 2010 |
| Last update date |
Nov 02, 2010 |
| Contact name |
Wolfgang Busch |
| E-mail(s) |
wolfgang.busch@duke.edu
|
| Phone |
919-613-8202
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Benfey Lab
|
| Street address |
124 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL10326 |
| Series (1) |
| GSE21741 |
Transcriptional regulation of ROS controls the transition from proliferation to differentiation in the root |
|
