|
| Status |
Public on Dec 25, 2011 |
| Title |
2G ddm1 385K_ChIP_1 rep1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
5meC ChIP DNA from 2G ddm1 mutant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: ddm1(2G-generation after plants became homozygous)
tissue: leaves
generation: 2nd
chip antibody: anti 5meC antibody
chip antibody manufacturer: Calbiochem
chip antibody catalog #: NA81
chip antibody lot#: D00062056
genetic background: Col-0
|
| Growth protocol |
2G ddm1 plants were grown on soil at 22°C in 16h-8h light-dark condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from leaves with the Illustra Nucleon Phytopure Genomic DNA Extraction Kits (GE Healthcare).
|
| Label |
Cy5
|
| Label protocol |
Immunoprecipitated DNA was amplified using GenomePlex Complete Whole Genome Amplification Kit (SIGMA) and purified using QIA Quick PCR Purification Kit (QIAGEN). 2μg of amplified DNA and input DNA were labeled with Cy5 and Cy3, respectively.
|
| |
|
| Channel 2 |
| Source name |
Input DNA from 2G ddm1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: ddm1(2G-generation after plants became homozygous)
tissue: leaves
chip antibody: none, input DNA
generation: 2nd
genetic background: Col-0
|
| Growth protocol |
2G ddm1 plants were grown on soil at 22°C in 16h-8h light-dark condition
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from leaves with the Illustra Nucleon Phytopure Genomic DNA Extraction Kits (GE Healthcare).
|
| Label |
Cy3
|
| Label protocol |
Immunoprecipitated DNA was amplified using GenomePlex Complete Whole Genome Amplification Kit (SIGMA) and purified using QIA Quick PCR Purification Kit (QIAGEN). 2μg of amplified DNA and input DNA were labeled with Cy5 and Cy3, respectively.
|
| |
|
| |
| Hybridization protocol |
According to standard NimbleGen protocols (www.nimblegen.com).
|
| Scan protocol |
Used Agilent Microarray Scanner.
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. This chip covers entire chromosome 1 and part of chromosome 2 of A. thaliana. Scaling is performed by subtracting the bi-weight mean for the IP/input log2 ratio values for chromosome 1 from each log2 ratio value.
|
| |
|
| Submission date |
Dec 07, 2011 |
| Last update date |
Dec 25, 2011 |
| Contact name |
Taku Sasaki |
| E-mail(s) |
[email protected]
|
| Organization name |
Gregor Mendel Institute
|
| Street address |
Dr. Bohr-gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL14974 |
| Series (1) |
| GSE34222 |
Methyl DIP-chip from self-pollinated ddm1 mutant and ddm1 kyp double mutant |
|
