|
| Status |
Public on Nov 08, 2023 |
| Title |
shoot-N_INPUT, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
shoot
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: M82
tissue: shoot
treatment: -N
chip antibody: none
|
| 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.tar.gz
|
| Data processing |
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were converted to fragments and dynamic islands were called using SICER-df.
RNA-Seq data was trimmed using CutAdapt and aligned using TopHat2. The gene counts were generated from mapped reads using htseq and counts were normalized with EDAseq, while differentially expressed genes were determined using DESeq2.
Genome_build: SL4.0
Supplementary_files_format_and_content: raw_counts.txt, SICER-df output files
|
| |
|
| Submission date |
Feb 16, 2022 |
| 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 |
SAMN25997956 |
| SRA |
SRX14204922 |
