|
| Status |
Public on Nov 22, 2010 |
| Title |
root_Fe_def_5d_2_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
wt
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole roots
growth protocol: 5d on -Fe media grown seedlings
genotype: wild type
antibody: anti-GFP
antibody manufacturer: ABCAM
antibody catalog #: ab290
lot #: 527131
|
| Treatment protocol |
Whole root tissue was fixed as described in Long et. al. 2010
|
| Growth protocol |
pye-1 / ProPYE:PYE:GFP and wildtype lines were germinated and grown on iron deficient media for 5 days as described in Long et. al. 2010
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation as described in Long et. al. 2010
|
| Label |
Cy3
|
| Label protocol |
DNA from the pye-1 / ProPYE:PYE: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 |
PYE:GFP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole roots
growth protocol: 5d on -Fe media grown seedlings
genotype: PYE:GFP
antibody: anti-GFP
antibody manufacturer: ABCAM
antibody catalog #: ab290
lot #: 527131
|
| Treatment protocol |
Whole root tissue was fixed as described in Long et. al. 2010
|
| Growth protocol |
pye-1 / ProPYE:PYE:GFP and wildtype lines were germinated and grown on iron deficient media for 5 days as described in Long et. al. 2010
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin Immunoprecipitation as described in Long et. al. 2010
|
| Label |
Cy5
|
| Label protocol |
DNA from the pye-1 / ProPYE:PYE: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 |
PYE: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 Long et al., 2010
|
| |
|
| Submission date |
May 03, 2010 |
| Last update date |
Nov 22, 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) |
| GSE21625 |
The novel transcription factor, POPEYE, regulates response to iron deficiency in Arabidopsis roots |
|
