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Sample GSM7510690 Query DataSets for GSM7510690
Status Public on Jun 29, 2023
Title RNA-Seq of T-9 leaves
Sample type SRA
 
Source name leaf
Organism Triticum aestivum
Characteristics tissue: leaf
treatment: Control
Treatment protocol No treatment was applied
Growth protocol The wheat seedlings were grown under optimum growth conditions
Extracted molecule total RNA
Extraction protocol RNA was extracted using EasyPure Plant RNA Kit (ER301-01) following manufacturer instructions
mRNAs were isolated and fragmented from total RNA using the oligo (dT) method for cDNA synthesis. The single-end sequencing libraries were constructed, and sequencing was performed on BGISEQ-500 using standard protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description RNA-Seq using single end sequencing library
Data processing Adapters with unknown bases (N’s > 5%) and low quality were removed from raw reads to produce ‘clean data’ as FastQ data files
High quality single-end reads were mapped to the reference genome of bread wheat
Alignment of the reference sequence with reads was performed
Quantification of the reads was performed using featureCounts software program and differentially expressed genes (DEGs) were identified using DeSEQ2
Assembly: IWGSC, INSDC AssemblyGCA_900519105.1
Supplementary files format and content: tab delimited text files include gene counts of each sample
Supplementary files format and content: tab delimited text files include tpm values of each sample
 
Submission date Jun 26, 2023
Last update date Jun 29, 2023
Contact name Saman Maqbool
Organization name Quaid-i-Azam University, Islamabad
Department Plant Sciences
Lab Plant Biology Lab
Street address Shahdra Road
City Islamabad
ZIP/Postal code 45320
Country Pakistan
 
Platform ID GPL26077
Series (1)
GSE235844 Leveraging RNA-seq of bread wheat transcriptome to reveal diversity of RSA-related transcripts and their expression in contrasting environments
Relations
BioSample SAMN30032953
SRA SRX16727215

Supplementary file Size Download File type/resource
GSM7510690_counts-T9-leaf.txt.gz 924.2 Kb (ftp)(http) TXT
GSM7510690_tpm-T9-rep1L.txt.gz 755.6 Kb (ftp)(http) TXT
GSM7510690_tpm-T9-rep2L.txt.gz 760.9 Kb (ftp)(http) TXT
GSM7510690_tpm-T9-rep3L.txt.gz 767.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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