|
| Status |
Public on Jun 06, 2021 |
| Title |
sig5-3 4C ZT27 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
temperature: 4C
time in ll (zt): 27
genotype: sig5-3
|
| Treatment protocol |
24 hours under constant light and then exposed to 19 °C or 4 °C starting at two different times of day (ZT 27 and ZT 45).
|
| Growth protocol |
11 days 12 h photoperiod 19°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from three samples of 10 seedlings each, using Macherey-Nagel Nucleospin II RNA extraction kits.
RNA sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA kit, according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DR-34-D1_R1_val
|
| Data processing |
Base calling by RTA 2.4.6 and FASTQ creator by BaseSpace.
Sequence data were trimmed for adaptor sequence and imported into Partek Genomics Suite version 6.6
Sequenced reads were mapped to TAIR11 using STAR - 2.5.3a
Quantification to annotated model was performed using Quantify to annotation model (Partek E/M) for strict paired-end settings.
Counts were normalized using the TMM with defaulst settings. Means <= 1.0 were excluded.
Genome_build: TAIR 11
Supplementary_files_format_and_content: tab-delimited text file with locus ID and counts per sample (columns)
|
| |
|
| Submission date |
Jun 06, 2018 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Antony N Dodd |
| E-mail(s) |
antony.dodd@bristol.ac.uk
|
| Phone |
+44 (0) 117 39 41176
|
| Organization name |
University of Bristol
|
| Department |
Life Sciences Building
|
| Street address |
24 Tyndall Avenue
|
| City |
Bristol |
| ZIP/Postal code |
BS8 1TQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE115428 |
Global transcriptomic response to chilling temperature in Col-0 wild type and sig5-3 (SALK_141383C) mutant Arabidopsis plants. |
|
| Relations |
| BioSample |
SAMN09375755 |
| SRA |
SRX4178370 |
