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Sample GSM7681026 Query DataSets for GSM7681026
Status Public on Dec 01, 2023
Title B73_White_2
Sample type SRA
 
Source name leaf
Organism Zea mays
Characteristics tissue: leaf
developmental stage: 7 DAY OLD
genotype: Wild-type
treatment: white light
Treatment protocol treat with or without UVB treatment 1 hour
Growth protocol 7 days of B73 and zmuvr8-1 seedlings grown in low white light
Extracted molecule total RNA
Extraction protocol total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat(version:2.2.1)
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: B73_RefGen_v4_gramene_63
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Aug 04, 2023
Last update date Dec 01, 2023
Contact name Zhao Zhiwei
E-mail(s) zwzhao@cemps.ac.cn
Phone +8618817395284
Organization name CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology
Street address 300 Feng Lin Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL25410
Series (1)
GSE240077 Next Generation Sequencing Facilitates Quantitative Analysis of B73 and zmuvr8-1 mutant in low white with or without UVB treat Transcriptomes
Relations
BioSample SAMN36839242
SRA SRX21250290

Supplementary file Size Download File type/resource
GSM7681026_B73_White_rep2.xlsx 2.4 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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