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Sample GSM6829429 Query DataSets for GSM6829429
Status Public on Oct 12, 2023
Title cs_RNAi4_rnaseq
Sample type SRA
 
Source name spikelets at booting stage (Feeke 10)
Organism Triticum aestivum
Characteristics cultivar: Fielder
tissue: spikelets at booting stage (Feeke 10)
genotype: RLG_7.3_enh_RNAi
Extracted molecule total RNA
Extraction protocol The spikelets at booting stage (Feeke 10) were harvested and frozen in liquid nitrogen for RNA isolation. More than 2 μg total RNA was used to prepare each sequencing sample.
Libraries were constructed and sequenced by Hanyubio Co. Ltd. (Shanghai, China) to produce 150-bp paired-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing For RNA-sequencing data, The sequencing reads were trimmed with the Trim Galore(version 0.6.4) and cutadapt ,clean reads were aligned with HISAT2 program(version 2.1.0) . SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount program of was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly(version 1.1).
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: tab-delimited text files include FPKM values for each RNA-seq sample
 
Submission date Dec 14, 2022
Last update date Oct 12, 2023
Contact name yijing zhang
E-mail(s) zhangyijing@fudan.edu.cn
Organization name Fudan University
Department Biochemistry
Lab Functional Epigenomics Group
Street address 2005 Songhu Road
City shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL25409
Series (1)
GSE198284 Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development
Relations
BioSample SAMN32218672
SRA SRX18690910

Supplementary file Size Download File type/resource
GSM6829429_cs_RNAi4_rnaseq_FPKM.txt.gz 597.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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