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Sample GSM5566253 Query DataSets for GSM5566253
Status Public on Feb 14, 2023
Title Col-0 22°C H3K27me3 ChIP-seq IP (replicate 1)
Sample type SRA
 
Source name Seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: Seedling
genotype: WT
temperature: 22degreeC
age: 7 days
chip antibody: H3K27me3
Treatment protocol Plants were grown in short day (8-hour light, 16-hour dark) at 22°C or 27°C.
Growth protocol Tissue (7-day-old seedlings) was harvested for experiment at ZT-6.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments.
Library was prepared using NEB Illumina library preparation kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Col-0_22C_IP.bw
Data processing Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC.
After quality assessment, reads were aligned on TAIR10 genome using Bowtie2 for ChIP-seq.
SAM files generated from mapping were then converted into BAM files and sorted using Samtools.
For the gene counting bedtools program was used which generates raw count using BAM files.
Genome_build: TAIR10
Supplementary_files_format_and_content: .bw (IGV)
 
Submission date Sep 07, 2021
Last update date Feb 14, 2023
Contact name Sibum Sung
E-mail(s) sbsung@austin.utexas.edu
Organization name University of Texas at Austin
Street address NMS 5.110, Stop A5000
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL19580
Series (1)
GSE149686 Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis
Relations
BioSample SAMN21346731
SRA SRX12075519

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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