|
Status |
Public on May 11, 2011 |
Title |
WT_IPvsInput |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
ChIP DNA from 19-day-old WT inflorescences using LFY antibody
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype/variation: wild type 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 |
WT Input DNA from 19-day-old inflorescences
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype/variation: wild type 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 |
WT 19-day-old inflorescences IP vs. Input, 5 biological reps
|
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 |
Supplementary file |
Size |
Download |
File type/resource |
GSM694045_WT_IP_Input.bed.gz |
9.8 Kb |
(ftp)(http) |
BED |
GSM694045_WT_IP_Input.fc.bar.gz |
17.9 Mb |
(ftp)(http) |
BAR |
GSM694045_WT_IP_Input.ma.bar.gz |
17.5 Mb |
(ftp)(http) |
BAR |
GSM694045_WT_IP_rep1.CEL.gz |
26.1 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_IP_rep2.CEL.gz |
27.1 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_IP_rep3.CEL.gz |
26.3 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_IP_rep4.CEL.gz |
26.2 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_IP_rep5.CEL.gz |
24.1 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_Input_rep1.CEL.gz |
28.9 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_Input_rep2.CEL.gz |
28.0 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_Input_rep3.CEL.gz |
28.7 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_Input_rep4.CEL.gz |
29.4 Mb |
(ftp)(http) |
CEL |
GSM694045_WT_Input_rep5.CEL.gz |
27.7 Mb |
(ftp)(http) |
CEL |
Processed data provided as supplementary file |