|
| Status |
Public on Apr 15, 2023 |
| Title |
CK-3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Leaf
treatment: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol kit (Qiagen). 1. ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Abclonal Mrna-seq Lib Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The data generated from Illumina (or BGI) platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology. The major software and parameters are as follows
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysi
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapp
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), DEGs with | log2FC | > 1 and Padj < 0.05 were considered to be significantly different expressed genes
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Apr 17, 2023 |
| Contact name |
Fang Liu |
| E-mail(s) |
liufang830318@126.com
|
| Phone |
+86-311-83014618
|
| Organization name |
Biology Institute, Hebei Academy of Sciences
|
| Department |
Biology Institute
|
| Street address |
46th, South Street of Friendship
|
| City |
Shijiazhuang |
| State/province |
HeBei |
| ZIP/Postal code |
050051 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
|
| Relations |
| SRA |
SRX19944220 |
| BioSample |
SAMN34156483 |
