|
| Status |
Public on Mar 02, 2021 |
| Title |
CK1 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Chrysanthemum x morifolium |
| Characteristics |
strain: tissue
tissue: leaves
age: 1-month-old
treatment: control
|
| Treatment protocol |
The buds raised from tissue-cultured seedlings were grown on MS medium (16 h photoperiod, 25 °C/22 °C day/night temperature) for thirty days. Then thirty-day old chrysanthemum seedlings were transferred to pots filled with a 1:1 mixture of peat and perlite, and acclimated for five days at normal condition. Then the seedlings were subjected to following treatments: (CK) normal condition as control, (T) 4 °C for 24 h, followed by − 4 °C for 4 h. Each treatment collected a mixture of three biologically replicated leaves, then samples rapidly frozen with liquid nitrogen and stored at − 80 °C. There were two samples in total used for RNA-Seq.
|
| Growth protocol |
Chrysanthemum “jinba” grown in the greenhouse (16 h photoperiod, 23±2℃ temperature)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chrysanthemums' leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
The Iso-Seq library was prepared according to the Isoform Sequencing protocol (Iso-Seq) using the Clontech SMARTer PCR cDNA Synthesis Kit and the BluePippin Size Selection System protocol as described by Pacific Biosciences
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 17, 2018 |
| Last update date |
Mar 02, 2021 |
| Contact name |
Zhenyu Bai |
| E-mail(s) |
1980592576@qq.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
211 Huimin Road, Wenjiang District
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL23798 |
| Series (1) |
| GSE117262 |
Study on Low temperature Mechanism via SMRT-based RNA-seq in Chrysanthemum leaves |
|
| Relations |
| BioSample |
SAMN09684173 |
| SRA |
SRX4401493 |
