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| Status |
Public on Dec 31, 2023 |
| Title |
Breaker + 7day stage of slnor WT rep3 |
| Sample type |
SRA |
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| Source name |
Breaker + 7day stage of slnor WT
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| Organism |
Solanum lycopersicum |
| Characteristics |
Stage: B7 (Breaker + 7day stage)
genotype: WT
tissue: Fruits
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| Growth protocol |
Wild type tomato (Solanum lycopersicum) Ailsa Craig (AC), NAC-NOR CRISPR mutant (slnor) plants (AC background) were grown in a condition-controlled greenhouse (16 h:8 h, 25 ℃:20 ℃, light:dark cycle).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was performed according to a previous published protocol (Gao et al., 2020).
Total RNA samples were sent to LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China) for library construction and sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
B7_WT_3
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| Data processing |
Prior to assembly, the low quality reads (1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
The cleaned reads were mapped to the reference genome SL4.0 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG4.0_release) using HISAT package (Kim et al., 2015).
UMI-tools ( Smith et al., 2017) was used for removing sequence-dependent bias and amplification noise.
The mapped reads of each sample were assembled using StringTie (Pertea et al., 2015).
All transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – edgeR (M.D.Robinson et al., 2010).
Genome_build: SL4.0
Supplementary_files_format_and_content: counts files
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| Submission date |
Feb 10, 2022 |
| Last update date |
Dec 31, 2023 |
| Contact name |
yujing lin |
| E-mail(s) |
linyujing20@cemps.ac.cn
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| Phone |
+8618259081781
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| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
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| Street address |
No. 2, Yard 1, Beichen West Road, Chaoyang District, Beijing
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL25655 |
| Series (1) |
| GSE196474 |
RNA-seq of Wild type (WT) tomato (Solanum lycopersicum, cultivar Ailsa Craig) and NAC-NOR CRISPR mutant (slnor, AC background) |
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| Relations |
| BioSample |
SAMN25829052 |
| SRA |
SRX14127066 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5884827_B7_WT_3.txt.gz |
153.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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