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| Status |
Public on Aug 27, 2022 |
| Title |
Ginseng, hairy roots, Ro stress, rep1 (mRNA-seq) |
| Sample type |
SRA |
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| Source name |
hairy roots
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| Organism |
Panax ginseng |
| Characteristics |
tissue: hairy roots
genotype: tissue
stress: Ro
dose: Ro-0.5 mg/L
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| Treatment protocol |
It was found that ginseng hairy roots grew significantly under Ro-0.5 mg/L stress.
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| Growth protocol |
This study took ginseng hairy roots as the research object, exogenously added ginsenoside Ro to regulate the growth of hairy roots, and measured the changes in its physiological and saponin content.
Place the germination paper with the seeds into a 2-gallon plastic container (a plastic bucket works fine). Fill bucket with tap water so it reaches up to 1/4 of the paper height. Incubate in a growth chamber for 6 days with a light-dark cycle of 16 hr light at 27°C and 8 hr dark at 24°C, and ~50% humidity
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA-seq:We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Be1
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| Data processing |
Firstly, fastp and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was also verified using fastp. including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'.
The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene). All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.kegg.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND[3] with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM.
Assembly: NA
Supplementary files format and content: genes_expression
Supplementary files format and content: Trinity.gene.fasta
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| Submission date |
Aug 26, 2022 |
| Last update date |
Aug 27, 2022 |
| Contact name |
yanyong cao |
| E-mail(s) |
zhangxingrui126@126.com
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| Organization name |
Henan Academy of Agricultural Sciences
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| Street address |
No. 116, Huayuan Road
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| City |
Zhengzhou |
| State/province |
henan |
| ZIP/Postal code |
450000 |
| Country |
China |
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| Platform ID |
GPL32600 |
| Series (1) |
| GSE212097 |
RNA sequencing of the regulatory network of ginsenoside biosynthesis under Ro stress in the hairy roots of Panax ginseng |
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| Relations |
| BioSample |
SAMN30521753 |
| SRA |
SRX17220002 |
| 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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