NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7854034 Query DataSets for GSM7854034
Status Public on Oct 01, 2024
Title nrpd1_2,replicate2,sRNA-seq
Sample type SRA
 
Source name 21 DAF embryo
Organism Solanum lycopersicum
Characteristics tissue: 21 DAF embryo
cultivar: Micro-Tom
genotype: SlNRPD1 knockout
Growth protocol The tomato cultivar S. lycopersicum L. cv. Micro-Tom was grown in a climate-controlled chamber under a 16-h light/26°C and 8-h dark/22°C cycle with a light intensity of 100~200 μmol m-2 s-1.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated from tomato embryos of 21 DAF using TRIzol reagent (Invitrogen, 15596026).
Libraries for sRNA-seq were generated using NEB Next® Multiplex Small RNA Library Prep Set for Illumina® (NEB E7300L).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Description nrpd1_shortstack_Results.txt
Data processing Adapters and low-quality reads were removed and 18-30 bp long clean reads were mapped without mismatches on the tomato reference genome (ITAG 4.0) (Tomato Genome, 2012) using bowtie.
Then all reads mapping to tRNAs, snRNAs, rRNAs, or snoRNAs were removed according to the ncRNA annotation information of the tomato.
Mapped reads from three biological replicates were pooled together and remapped to the tomato reference genome using the ShortStack software v3.8.5 (--mismatches 0 --mmap f) to annotate and quantify sRNA.
Assembly: SL4.0
Supplementary files format and content: ShortStack output
 
Submission date Oct 23, 2023
Last update date Oct 01, 2024
Contact name Ling Tong Liu
E-mail(s) ltliu@ibcas.ac.cn
Organization name Institute of Botany, Chinese Academy of Sciences
Street address No.20 Nanxincun, Xiangshan
City Beijing
ZIP/Postal code 100093
Country China
 
Platform ID GPL27957
Series (2)
GSE246017 RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation [sRNA-seq]
GSE246018 RNA polymerase IV is essential for tomato embryo development through mediating non-CG methylation
Relations
BioSample SAMN37926097
SRA SRX22174187

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.