|
| Status |
Public on Dec 31, 2010 |
| Title |
W2C ChIP |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
[test]: ChIP DNA from pBZR1::BZR1-CFP tissue (W2C is the name of BZR1-CFP transgenic line)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
sample type: test
ecotype: Columbia
age: 4-week-old
tissue: rosette
chip antibody: Polyclonal anti-YFP
chip antibody source: home-made
|
| Treatment protocol |
100nM Brassinolide, 2 hours
|
| Growth protocol |
Light-grown rosettes. 16 hour light 8 hour dark cycle, 4 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rosette tissue was cross-linked by 1% formaldehyde. Chromatin immunoprecipitation using anti-YFP antibodies and qPCR was performed according to our protocol (He et al., 2005).The precipitated DNA was amplified by Whole Genome Amplification Kit following the manufacturer’s instruction (Sigma), and fragmented to an average of 50-100 bps with DNase I (Cat. No. 18068-015 Invitrogen) at 30°C for 10 minutes.
|
| Label |
biotin
|
| Label protocol |
The fragmented DNA was labeled by TdT according to Affymetrix Chromatin Immunoprecipitation Protocol.
|
| |
|
| Channel 2 |
| Source name |
[ctrl]: ChIP DNA from wild type tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
sample type: control
ecotype: Columbia
age: 4-week-old
tissue: rosette
chip antibody: Polyclonal anti-GFP
chip antibody source: home-made
|
| Treatment protocol |
100nM Brassinolide, 2 hours
|
| Growth protocol |
Light-grown rosettes. 16 hour light 8 hour dark cycle, 4 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rosette tissue was cross-linked by 1% formaldehyde. Chromatin immunoprecipitation using anti-YFP antibodies and qPCR was performed according to our protocol (He et al., 2005).The precipitated DNA was amplified by Whole Genome Amplification Kit following the manufacturer’s instruction (Sigma), and fragmented to an average of 50-100 bps with DNase I (Cat. No. 18068-015 Invitrogen) at 30°C for 10 minutes.
|
| Label |
biotin
|
| Label protocol |
The fragmented DNA was labeled by TdT according to Affymetrix Chromatin Immunoprecipitation Protocol.
|
| |
|
| |
| Hybridization protocol |
The labeled DNA was hybridized to the Affymetrix GeneChip Arabidopsis Tiling 1.0R array according to affymetrix's Eukaryotic Target Protocol.
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G Scanner
|
| Description |
BZR1-CFP ChIP biologic repeat with control 1-3 assayed on Affymetrix GeneChip Arabidopsis Tiling array.
W2C is the name of BZR1-CFP transgenic line used for this experiment.
|
| Data processing |
Data was analyzed by two Tiling Analysis Software: TAS (version 1.1, Affymetrix) and Tilemap (Ji and Wong, 2005). Arabidopsis genome version/build: TAIR7.
With TAS software, the analysis was performed using the “two sample comparison analysis” option. Probes were analyzed using signal from both PerfectMatch and MisMatch with a bandwidth 250 bps, and the enriched intervals were defined by p<0.001 and signal ratio > 2, maximum gap 100 bps and minimum run 100 bps.
The analysis using Tilemap was performed using HMM option with posterior probability 0.5 and maximum gap 100 bps.
Results files descriptions:
The pvalue.bar file contains the p value of each probe generated by TAS, signal.bar file contains the signal value of each probe generated by TAS. W2C_tile.txt file contains the p value of each probe generated by tilemap.
TileGroup full set_p30.bed: The binding region identified by TAS software at P<0.001. TileGroup PM-MM_signal_1.bed: The binding region identified by TAS at signal> 2 fold. Both files are generated using signal from perfectMatch-MisMatch with a bandwidth of 250bps, maximum gap 100bps and minimum run 100bps. W2C_tile_hmm0.5.bed: The binding region identified by Tilemap at posterior probability >0.5 using HMM option and maximum gap 100bps.
|
| |
|
| Submission date |
Aug 24, 2010 |
| Last update date |
Dec 31, 2010 |
| Contact name |
Yu Sun |
| E-mail(s) |
yusun05@gmail.com
|
| Organization name |
Carnegie Institution of Washington
|
| Department |
plant biology
|
| Lab |
Zhiyong wang
|
| Street address |
260 panama street
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL8416 |
| Series (2) |
| GSE23774 |
Genome wide BZR1 binding site analysis in Arabidopsis |
| GSE25135 |
Brassinosteroid (BR) plant hormone signaling |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM586804_At35b_MR_v04_2_TIGRv5.bpmap.gz |
58.6 Mb |
(ftp)(http) |
BPMAP |
| GSM586804_Col_1_At35b_MR_v04.CEL.gz |
21.5 Mb |
(ftp)(http) |
CEL |
| GSM586804_Col_2_At35b_MR_v04.CEL.gz |
19.5 Mb |
(ftp)(http) |
CEL |
| GSM586804_Col_3_At35b_MR_v04.CEL.gz |
23.6 Mb |
(ftp)(http) |
CEL |
| GSM586804_TileGroup_PM-MM_signal_1.bed.gz |
133.9 Kb |
(ftp)(http) |
BED |
| GSM586804_TileGroup_full_set_p30.bed.gz |
20.8 Kb |
(ftp)(http) |
BED |
| GSM586804_TileGroup_full_set_pvalue.bar.gz |
18.6 Mb |
(ftp)(http) |
BAR |
| GSM586804_TileGroup_full_set_signal.bar.gz |
14.0 Mb |
(ftp)(http) |
BAR |
| GSM586804_W2C_1_At35b_MR_v04.CEL.gz |
23.7 Mb |
(ftp)(http) |
CEL |
| GSM586804_W2C_2_At35b_MR_v04.CEL.gz |
21.0 Mb |
(ftp)(http) |
CEL |
| GSM586804_W2C_3_At35b_MR_v04.CEL.gz |
25.6 Mb |
(ftp)(http) |
CEL |
| GSM586804_W2C_tile.txt.gz |
44.0 Mb |
(ftp)(http) |
TXT |
| GSM586804_W2C_tile_hmm0.5.bed.gz |
49.7 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
