|
| Status |
Public on May 11, 2011 |
| Title |
lfy6_IPvsInput (negative control) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ChIP DNA from 19-day-old lfy6 inflorescences using LFY antibody
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: Ify6
age: 19-day-old
tissue: inflorescences
chip antibody: LFY
|
| Growth protocol |
Seeds cold-treated for 7 days at 4°C were grown in inductive conditions (continuous light or 16 hour long-day light conditions) at 23°C at a fluence rate of 45 μmol/m2 sec on 0.5x Murashige and Skoog plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with an anti-LFY antibody (Wagner et al., 1999; PMID 10417387) essentially as described (Kwon et al., 2005) except that DNA was sonicated to an average size range of 300-500bp.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Affymetrix GeneChIP WT Double-Stranded DNA Terminal Labeling Kit.
|
| |
|
| Channel 2 |
| Source name |
lfy6 Input DNA from 19-day-old inflorescences
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: Ify6
age: 19-day-old
tissue: inflorescences
chip antibody: none
|
| Growth protocol |
Seeds cold-treated for 7 days at 4°C were grown in inductive conditions (continuous light or 16 hour long-day light conditions) at 23°C at a fluence rate of 45 μmol/m2 sec on 0.5x Murashige and Skoog plates
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with an anti-LFY antibody (Wagner et al., 1999; PMID 10417387) essentially as described (Kwon et al., 2005) except that DNA was sonicated to an average size range of 300-500bp.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Affymetrix GeneChIP WT Double-Stranded DNA Terminal Labeling Kit.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.
|
| Scan protocol |
Scanning was performed at the University of Pennsylvania Microarray Core Facility using standard Affymetrix protocols.
|
| Description |
lfy6 19-day-old inflorescences IP vs. Input, no replicates
|
| Data processing |
Data were quantile normalized and analyzed with CisGenome. Log2(IP/Input) fold changes (fc) and CisGenome moving average (ma) statistics were reported in BAR files. Significantly bound regions are reported in the .bed file.
Results file descriptions: fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. File WT_IP_Input.bed contains all 867 reported significantly bound regions. lfy6_IP.CEL.bar and lfy6_Input.CEL.bar contain processed probe-level signal intensities.
|
| |
|
| Submission date |
Mar 21, 2011 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Cara Michele Winter |
| E-mail(s) |
caramw@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Blvd.
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL10977 |
| Series (2) |
| GSE28061 |
LEAFY target genes reveal a link between flower development and biotic stimulus response (II) |
| GSE28063 |
LEAFY target genes reveal a link between flower development and biotic stimulus response |
|
| Relations |
| Reanalyzed by |
GSE136843 |
