|
| Status |
Public on May 31, 2020 |
| Title |
WT_AfterCut_r2 |
| Sample type |
SRA |
| |
|
| Source name |
Excised hypocotyl from dark-grown seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia (Col-0)
genotype: wild type
time of sampling: within 15 minutes after excision
|
| Treatment protocol |
Hypocotyl explants (around 10mm long) were excised using a razor blade and incubated on CIM (Gamborg B5 medium with 0.25% Gelzan supplemented with 0.5 μg/ml 2,4-dichlorophenoxyacetic acid [2,4-D] and 0.05 μg/ml kinetin) for 4 days under constant light. Hypocotyl or root explants were then transferred to SIM (Gamborg B5 medium 0.25% Gelzan, 0.15ug/ml IAA and 0.5 ug/ml 2-IPA)
|
| Growth protocol |
22°C constant temperature in the dark vertically grown on 1%Sucrose 1X MS medium containing 0.6% Gelzan CM growth 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq for wild-type hypocotyl after cut replicate 2
|
| Data processing |
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 1.2.1 with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-delimited data with transcript CPM (counts per million mapped reads) values for each sample
|
| |
|
| Submission date |
Nov 29, 2019 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Duncan Peter Coleman |
| Organization name |
Riken
|
| Department |
CSRS
|
| Lab |
Cell Function Research
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE141188 |
Gene expression profile of Arabidopsis thaliana wild type and siz1-2 mutant during in vitro shoot regeneration on callus inducing media (CIM) and shoot inducing media (SIM) |
|
| Relations |
| BioSample |
SAMN13429466 |
| SRA |
SRX7241965 |
