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Sample GSM5266387 Query DataSets for GSM5266387
Status Public on Aug 03, 2022
Title Yanyan97_1h_rep1
Sample type SRA
 
Source name Yanyan97
Organism Nicotiana tabacum
Characteristics developmental stage: five-leaf stage
tissue: seedlings
treatment: 1h cold treatment at 4 degrees centigrade
genotype: Yanyan97
Treatment protocol Tobacco seedlings at the five-leaf stage were used for cold treatment at 4℃. Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.
Growth protocol Two cultivated tobacco (Nicotiana tabacum L.) varieties, Taiyan8 tobacco (TT) and Yanyan97 tobacco (YT), were used in this study. The seeds were sterilized in 75% ethanol for 30 s and washed with sterile water for five times. Sterilized seeds were germinated and grown in 1/2 MS medium in an illuminated incubator (16 h/8 h day/night light cycle, 22/20℃day/night temperature setting with 65% relative humidity).
Extracted molecule total RNA
Extraction protocol Leaves from CK and cold-treated plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The raw sequence data were processed to remove low-quality reads using FastQC (v0.11.5) and Trim_Galore (v0.6.4). The filtered high-quality reads were mapped on the Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/) using HISAT2 (v2.0.5) with default parameters.
Reads with a mapping quality below twenty were excluded from further analyses using SAMtools (v1.9).(-q 20)
StringTie (v1.3.4d) and FeatureCounts (v1.6.4) were used to obtain transcripts per million (TPM) and read counts for all annotated genes in the tobacco genome.
Genome_build: Nicotiana tabacum genome (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/ edwards_et_al_2017/assembly/)
Supplementary_files_format_and_content: tab-delimited text files include TPM (Transcripts Per Million) values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene read counts for every gene and every sample
 
Submission date Apr 26, 2021
Last update date Aug 03, 2022
Contact name zhenyu luo
E-mail(s) [email protected]
Organization name Nanjing Agricultural University
Department College of Agricuture
Lab Zhanglab
Street address Xuanwu
City Nanjing
State/province Jiangsu
ZIP/Postal code 210095
Country China
 
Platform ID GPL25653
Series (1)
GSE173352 Transcriptomic insights into differential cold tolerance of two tobacco cultivars
Relations
BioSample SAMN18872727
SRA SRX10681856

Supplementary file Size Download File type/resource
GSM5266387_Y-1-1A.q20.bw 26.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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