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Sample GSM4508999 Query DataSets for GSM4508999
Status Public on Feb 14, 2023
Title arp6vil1 22°C H2AZ ChIP-seq IP (replicate 1)
Sample type SRA
 
Source name Seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: 14 days old seedling
genotype: arp6vil1
temperature: 22degreeC
antibody: H2AZ
Treatment protocol Tissue (14 days old seedlinds) was harvested for experiment at ZT-6
Growth protocol Plants were grown in long day (16-hour light, 8-hour dark) and short day (8-hour light, 16-hour dark) at 22°C or 27°C.
Extracted molecule genomic DNA
Extraction protocol Total RNAs were extracted by using TRIzol (Invitrogen) and treated with DNase I enzyme (Promega) to eliminate traces of genomic DNA
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 arp6vil1_H2AZ_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 HISAT2 for RNA-seq and 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
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample
Supplementary_files_format_and_content: .bw (IGV)
 
Submission date May 01, 2020
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 SAMN14789655
SRA SRX8241094

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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