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Sample GSM5903665 Query DataSets for GSM5903665
Status Public on Nov 08, 2023
Title shoot+N_INPUT, Rep2
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 SAMN25997954
SRA SRX14204924

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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