|
| Status |
Public on Jul 01, 2024 |
| Title |
Col_2 |
| Sample type |
SRA |
| |
|
| Source name |
Shoot rossette leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue type: third and fourth rosette leaves
cell type: Shoot tissue cell
salt stress: Mock
genotype/variation: wildtype, Columbia-0 background Rep2
|
| Treatment protocol |
The detached leaves at 16 DAE were floated on 3 mM MES (pH5.8) containing 100 mM NaCl and placed on 22°C under a 16-h light/8-h dark photoperiod for 1 day.
|
| Growth protocol |
Arabidopsis thaliana plants (Col ecotype) were grown in a growth room at 22°C under a 16-h light/8-h dark photoperiod. To generate Arabidopsis transgenic plants that overexpress ERF34, the coding sequence (CDS) of ERF34 was amplified by RT-PCR, subcloned into the pCR-CCD-F vector (Kim et al., 2013), and then recombined into the pCsVMV Gateway binary vector with the CsVMV promoter and N-terminal GFP tag by LR recombination (Invitrogen, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-seq experiments were performed in three independent biological replicates of the Col and ERF34-OX#1 plants. RNA was isolated using WelPrepTM (WelGENE, Korea). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 7.8.
Poly(A) mRNA was isolated from the RNA (2 µg) and fragmented using Illumina Truseq™ Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads. After the cDNA synthesis from the RNA fragments by using Superscript II reverse transcriptase (Life Technologies), the strand-specific cDNA libraries were generated with adaptor-ligation and sequenced by Illumina HiSeq 2500 system, according to the Illumina Directional RNA-Seq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
normalized_in_TMM_ERF34.txt
Sample 8
|
| Data processing |
Alignment of the resulting reads to the Arabidopsis thaliana genome (TAIR10; Lamesch et al., 2012) was performed using TopHat (Trapnell et al., 2009) with the default option
the abundance was calculated as the fragments per kilobase per million mapped reads (FPKMs) for each transcript using Cufflinks
TMM normalization
Genome_build: Arabidopsis_thaliana.TAIR10.31
Supplementary_files_format_and_content: Tab-delimited text file including TMM values for the individual samples
|
| |
|
| Submission date |
Jul 14, 2021 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Hyunsu Park |
| E-mail(s) |
qop814@dgist.ac.kr
|
| Organization name |
DGIST
|
| Department |
New biology
|
| Lab |
Plant Molecular Communications Lab
|
| Street address |
E4-620, 333, Techno jungang-daero
|
| City |
Hyeonpung-eup |
| State/province |
Dalseong-gun, Daegu |
| ZIP/Postal code |
42988 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE180096 |
Ethylene Responsive Factor 34 (ERF34) negatively mediates salt stress-induced leaf senescence by regulating the expression of salt stress-responsive genes in Arabidopsis |
|
| Relations |
| BioSample |
SAMN20209563 |
| SRA |
SRX11439591 |
