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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).
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|
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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
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|
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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 |