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Sample GSM6062555 Query DataSets for GSM6062555
Status Public on Apr 23, 2024
Title Col-0 rep 1
Sample type SRA
Source name Col-0
Organism Arabidopsis thaliana
Characteristics cell line: Col-0
cell type: seedlings
genotype: WT
treatment: white light 5 days
time: Day 5
Growth protocol Col-0 and csu6-2 mutant seedlings were grown in white light for 5 d
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the NovaSeq protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing We mapped RNA-seq reads to the TAIR10 genome using HISAT2. Only uniquely mapped reads were retained for subsequent analyses. Differential expression between samples was statistically assessed using the R/Bioconductor package edgeR (V3.0.8) [65], and normalization was performed by trimmed mean of M values (TMM). Genes with pvalue < 0.05 and he absolute foldchange more than 1.5 by edgeR were identified as differentially expressed.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Submission date Apr 24, 2022
Last update date Apr 23, 2024
Contact name Xuncheng Wang
Organization name Peiking University
Street address 5 Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
Platform ID GPL26208
Series (1)
GSE201389 COP1 SUPPRESSOR 6 promotes photomorphogenesis by repressing the transcription and activity of PIF4 and PIF5
BioSample SAMN27753449
SRA SRX14984361

Supplementary file Size Download File type/resource
GSM6062555_Col-1.txt.gz 138.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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