NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5028849 Query DataSets for GSM5028849
Status Public on Nov 29, 2021
Title TM-1-leaf_rep1
Sample type SRA
 
Source name TM-1-leaf
Organism Gossypium hirsutum
Characteristics tissue: leaf
age: 20 days
Treatment protocol none
Growth protocol The allotetraploid cotton cultivar Gossypium hirsutum was used in this study. Cotton seeds were soaked in water for 24 h, then transferred to soil in pots to continue to grow in a greenhouse with 60 % humidity at 28/25°C and 16/8-h light/dark cycle. Two and three true leaves were collected from 20-old plants and ground into fine powder using liquid nitrogen
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared using Trizol followed by DNase I treatment and removal of majority of mRNAs with oligo(T)-conjugated magnetic beads.
The enriched mRNA was subse- quently used for RNA-seq library preparation following the standard protocol for preparing Illumina RNA-seq libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Raw reads of all sequencing data were trimmed using fastp (Chen et al., 2018b) based on the quality value (Q≥25) and read length (≥20 bp).
The trimmed reads RNA-seq data were mapped to the G. hirsutum reference genome with Hisat2 (Kim et al., 2015a).
Aligned reads with mapping quality (MapQ) less than 30 were removed using samtools (Li et al., 2009).
FPKM computed from StringTie (Pertea et al., 2015) was used to measure the expression level of each gene.
Genome_build: NBI_Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: FPKM files were generated from StringTie
 
Submission date Jan 21, 2021
Last update date Nov 29, 2021
Contact name Li Wen Zhang
E-mail(s) wzhang25@njau.edu.cn
Organization name Nanjing Agricultural University
Street address No.1 Weigang
City Nanjing
State/province Jiangsu
ZIP/Postal code 210095
Country China
 
Platform ID GPL29633
Series (2)
GSE165244 Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (RNA-Seq)
GSE165245 Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton
Relations
BioSample SAMN17469061
SRA SRX9908782

Supplementary file Size Download File type/resource
GSM5028849_TM-1-leaf_rep1.FPKM.txt.gz 442.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap