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Sample GSM4835615

Query DataSets for GSM4835615

Status

Public on Jan 01, 2023

Title

UV4 rep3

Sample type

SRA

Source name

UV4_leaf

Organism

Artemisia annua

Characteristics

cultivar: high-artemisinin cultivar, Huhao 1
developmetal stage/age: six-week-old A. annua seedlings
tissue: leaf
genotype: wild type
treatment/time point: 4h after exposure to UV-B radiation

Treatment protocol

For UV-B treatment, six-week-old A. annua seedlings growing under normal growth condition were supplemented with extra narrowband UV-B lamps (Philips TL20W/01RS; 1.5 μmol·m-2·s-1). The most recently expanded leaf for each A. annua seedling was collected at 0, 2, 4 and 6 hours after exposure to UV-B radiation and named as UV0, UV2, UV4 and UV6, respectively according to their harvest time. All samples were separately harvested from three independent individual seedlings as mix. Three biological repeats for each sample were measured.

Growth protocol

Artemisia annua used in this study is a high-artemisinin cultivar, ‘Huhao 1’, which has been selected and developed in Shanghai for several years. A. annua and Nicotiana benthamiana seeds were sown in pots filled with a 3:7 mixture of peat soil and vermiculite and placed in a greenhouse under the growth condition of 16-hour light/8-hour dark photoperiod at 23 ± 2°C and supplemented with regular water and fertilizer.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from three independent pools of leaves using RNAprep pure Plant Kit (Tiangen, Beijing, China), according to the manufacturer’s instructions. The concentration and integrity of each RNA sample was detected using a NanoDrop 2000 (Thermo Scientific, Waltham, MA, USA) and 1% agarose gels. The quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to txid35608 whole genome using Hisat2 version 2.1.0 with default parameters
Normalized gene expression levels were estimated using TPM (transcripts per million) value using Salmon software and differential expression levels were analyzed using the DESeq R package.
Genome_build: txid35608; https://www.ncbi.nlm.nih.gov/assembly/GCA_003112345.1
Supplementary_files_format_and_content: TPM values for each Sample

Submission date

Oct 19, 2020

Last update date

Jan 01, 2023

Contact name

yongp li

E-mail(s)

[email protected]

Organization name

shanghai jiaotong university

Street address

shanghai