|
| Status |
Public on Nov 08, 2023 |
| Title |
shoot+N_INPUT_Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
shoot
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: M82
tissue: shoot
treatment: shoot+N
|
| Treatment protocol |
Twenty-two day old plants were transferred to nitrogen free media for four days and then either replenished with fresh nitrogen free media (-N condition) or resupply of media containing nitrate (+N condition). After 6 hours of treatment, -N and +N samples were harvested.
|
| Growth protocol |
Plants were germinated on 1/2 strength MS plates and then transferred to a hydroponic system under greenhouse conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Two grams of tissues were fixed with 1% formaldehyde by applying vacuum at 700 mmHg for 25 min. Fixation was terminated by adding 2M glycine to a final concentration of 0.125M and vacuum application for 5 minutes. Formaldehyde-fixed tissues were ground in liquid nitrogen and nuclei were isolated. Isolated nuclei were sonicated using Bioruptor to prepare chromatin samples with single nucleosomes.
Chromatin immunoprecipitated using Protein A dynabeads with antibodies against histone marks or input chromatin was recovered and reverse-crosslinked. Libraries were prepared using NEBNext dual index library kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
shoot_SICER_df_K9.tar.gz
|
| Data processing |
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were convereted to fragments and dynamic islands were called using SICER-df.
Assembly: SL4.0
|
| |
|
| Submission date |
Sep 24, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Ryan Patrick |
| Organization name |
Purdue University
|
| Street address |
625 Agriculture Mall Dr
|
| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL27957 |
| Series (1) |
| GSE196887 |
Histone code dynamics during nitrogen response in tomato |
|
| Relations |
| BioSample |
SAMN37526326 |
| SRA |
SRX21870615 |
