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| Status |
Public on Jun 30, 2020 |
| Title |
TY53 |
| Sample type |
SRA |
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| Source name |
axillary shoot
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| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: axillary shoot
treatment: topped plants after 5 days
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| Treatment protocol |
The flowering head and two leaves below the flag leaf were removed by topping
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 100 mg of shoot tissue using a reagent kit (Invitrogen, Germany) following the manufacturer's instructions
The RNAeSeq library was constructed using a NEBNext® Ultra™ RNA Library Prep Kit (Illumina,NEB, USA) following the manufacturer's recommendations, and index cards were added to attribute sequences to different samples.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw data (raw reads) in fastq format were cleaned by removing adaptor sequences, reads containing poly-N sequences, and low-quality reads.
The clean reads were mapped directly to the reference tobacco genome available from the 2017 genome website(ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/edwards_et_al_2017/annotation/).
The expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) was calculated based on the length of the gene and read counts mapped to the gene.
DEGs of both conditions were identified by the DEGSeq R package (v1.20.0).
The P-values were adjusted using the Benjamini and Hochberg method. A corrected P-value of 0.005 and a log2(fold change) of 1 were set as the threshold for significant differential expression.
Genome_build: Nicotiana_tabacum_Edwards2017_Scf.fa
Supplementary_files_format_and_content: FPKM values for each Sample
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| Submission date |
Jun 29, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Jing Lv |
| E-mail(s) |
lvjing@caas.cn
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| Organization name |
CAAS
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| Street address |
No.11, Keyuan Jingsi Road, Laoshan District
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| City |
Qingdao |
| State/province |
China |
| ZIP/Postal code |
266101 |
| Country |
China |
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| Platform ID |
GPL13760 |
| Series (1) |
| GSE153483 |
Transcriptomic analysis of topping-induced axillary shoot outgrowth in Nicotiana tabacum |
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| Relations |
| BioSample |
SAMN15398584 |
| SRA |
SRX8632267 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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