|
| Status |
Public on Oct 07, 2015 |
| Title |
AtMYB12_fruit_breaker_input |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
chip antibody: input
ecotype: MicroTom
genotype: AtMYB12
tissue: pericarp
time point: 3-4 days after breaker
|
| Treatment protocol |
ChIP experiments were done using WT and AtMYB12 tomato fruit at 3-4 days after breaker (when the expression of AtMYB12 is strongly induced). To cross-link protein and DNA, fruit were sliced into small pieces and immersed in cross-linking buffer (0.4M Sucrose, 10 mM Tris- HCl pH8.0, 0.1% β-mercaptoethanol, 100μM PMSF, 1% formaldehyde and 1x protease inhibitor cocktail (Roche, http://www.roche.com/index.htm) and vacuum infiltrated two times, for 10 minutes each time. To terminate cross-linking, glycine was added to a final concentration of 0.125 M and samples were vacuum infiltrated for an additional 5 min. After cross-linking, samples were washed in ice-cold water and ground in liquid nitrogen.
|
| Growth protocol |
Tomato plants were grown in glasshouse under natural light. Temperature were maintained between 20-25 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation was performed using Honda buffer as previously described. ChIP was performed using anti-AtMYB12 polyclonal antibody (prepared in rabbit against peptide sequence: CLLDGDDEATIGNSN; GenScript USA Inc). DNA was recovered after immunoprecipitation.
Library construction was done using an Illumina ChIP-seq Sample Prep Kit following the manufacturer’s instructions and sequencing was undertaken on Illumina’s HiSeq platform (Beijing Genomics Institute (BGI), China)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The data we have received from BGI, has adapter reads deleted and the low quality reads (quality value <=20 is no less than 50% or the rate of “N” in a read is no less than 10%) were removed.
The quality filtered library was aligned to the Solanum lycopersicum chromosome sequences (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_genomic.fasta) using soap2.21. Only the aligments within 2 mismathches were considered in peak calling.
Whole genome peak scanning was performed using MACS-1.4.0. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads and the region with p-value <1e-5 were defined as a peak.
Genome_build: Tomato ITAG2.3
Supplementary_files_format_and_content: wig files were generated using MACS-1.4.0
|
| |
|
| Submission date |
Oct 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ghanasyam Rallapalli |
| E-mail(s) |
g.rallapalli@uea.ac.uk
|
| Organization name |
The Sainsbury Laboratory
|
| Street address |
Norwich Research Park
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE62462 |
Reprogramming of primary metabolism facilitates metabolic engineering of bioactives in tomato fruit (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN03114899 |
| SRA |
SRX734535 |
