|
| Status |
Public on Jul 25, 2024 |
| Title |
gi-2 RNAseq ZT0 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
genotype: gi-2
|
| Growth protocol |
Seedlings were grown on 0.5x MS plates under short day photoperiods (8 h light, 16 h dark) at a light intensity of 80 umol m-2 s-1 and a constant temperature of 22 °C for 7 d. Samples were collected at ZT0 by snap-freezing in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the GeneJET Plant RNA Purification Kit (Thermo Scientific) and digested with DNase Max (Qiagen).
Preparation of RNA library (non-directional 250~300 bp insert cDNA library (NEB))
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
gi0_rep3
|
| Data processing |
Raw reads were aligned to the TAIR10 genome using STAR (v2.5.5) (Dobin et al. 2013) with the method of Maximal Mappable Prefix (MMP).
Mapped reads were counted by HTSeq v0.6.1 and then FPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression was performed using the DESeq2 R package (2_1.6.3) (Anders and Huber 2010).
Genes with adjusted p-value < 0.05 and |log2(FoldChange)| > 0 were considered as differentially expressed.
Assembly: TAIR10
Supplementary files format and content: txt file includes read counts for each sample
|
| |
|
| Submission date |
Jul 18, 2023 |
| Last update date |
Jul 25, 2024 |
| Contact name |
Maria A Nohales |
| E-mail(s) |
manozaf@ibmcp.upv.es
|
| Organization name |
IBMCP (CSIC/UPV)
|
| Street address |
Ingeniero Fausto Elio s/n
|
| City |
Valencia |
| ZIP/Postal code |
46022 |
| Country |
Spain |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE237670 |
Effect of the gi-2 mutation on Arabidopsis thaliana gene expression |
|
| Relations |
| BioSample |
SAMN36521181 |
| SRA |
SRX21063797 |
