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Sample GSM4508972 Query DataSets for GSM4508972
Status Public on Feb 14, 2023
Title Col-0 22°C RNA-seq (replicate 2)
Sample type SRA
 
Source name Seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: 14 days old seedling
genotype: wildtype
temperature: 22degreeC
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 total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Col22.1
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 SAMN14789669
SRA SRX8241067

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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