|
| Status |
Public on Jun 16, 2019 |
| Title |
camta6_5_NaCl3 |
| Sample type |
SRA |
| |
|
| Source name |
pre-germinated seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: camta6 mutant
tissue: seedlings
treatment: 200 mM NaCl for 16 hrs
|
| Treatment protocol |
medium was supplemented with 0 (control) or 200 mM NaCl for 16 hours.
|
| Growth protocol |
Cold stratified seeds of wild-type (Col-0) and an allele of camta6 mutant (camta6-5) was sown on 0.25 X MS, agar-solidified medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the ZR Plant RNA MiniPrep™ kit (Zymo Research, USA).
Illumina HiSeq 2500; Illumina TruSeq RNA Library Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_6_5_NaCl3
|
| Data processing |
Adaptors were removed and quality values above phred33 were used for analysis (cutadapt version 1.9).
Mapping and alignment was performed using TopHat version 2.1.0 using Bowtie2 (v2.2.6) (reference genome TAIR10), followed by gene counting performed by HTseq-count version 0.6.1.
Values above 10 were used for normalization and gene expression analysis (DESeq2 version 1.10.0).
Genome_build: TAIR10
Supplementary_files_format_and_content: raw expression values
|
| |
|
| Submission date |
Jun 20, 2018 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Metsada Pasmanik-Chor |
| E-mail(s) |
[email protected]
|
| Organization name |
Tel Aviv University
|
| Department |
Biology
|
| Lab |
Bioinformatics Unit
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE116069 |
Calmodulin-binding transcription activator (CAMTA) 6 is a key regulator of Na+ homeostasis and salinity stress responses during early germination |
|
| Relations |
| BioSample |
SAMN09462099 |
| SRA |
SRX4277176 |
