|
| Status |
Public on Feb 15, 2022 |
| Title |
Col_17C_SIM4D_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Hypocotyl explant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
treatment: 4 days on CIM then 4 days on SIM
temperature: 17°C
replicate: 2
tissue: Hypocotyl explant
|
| Treatment protocol |
Explants were first incubated on CIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 7.5 g.L-1 Gellan gum, 0.1 mg.L-1 kinetin and 0.5 mg.L-1 2,4 D, for 4 days in continuous light conditions and at 17°C or 27°C. Explants were then transferred on SIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 2.5 g.L-1 Gellan gum, 0.5 mg.L-1 2-iP and 0.15 mg.L-1 IAA, for 4 days in continuous light conditions and at 17°C or 27°C.
|
| Growth protocol |
Plants were grown on nylon mesh over MS medium containing 1% sucrose and 0.6% (w/v) gelzan. Plates were placed vertically and kept in the dark at 22°C to induce hypocotyl elongation. 7-day-old etiolated seedlings were dissected with a razor blade to harvest hypocotyls explants located between ~3 mm above the root/hypocotyl junction and ~5 mm below the hypocotyl/shoot junction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
~100 hypocotyls explants harvested and frozen with liquid nitrogen. The samples were then ground using zirconia ceramic beads in a TissueLyser (QIAGEN) mixer mill. RNA was extracted using the RNeasy Plant Mini kit (QIAGEN) following the manufacturer's instructions.
Libraries for sequencing were prepared using the KAPA Stranded mRNA-seq Kit (Kapa Biosystems, Roche) with a mix of FastGene (Nippon Genetics) and NEBNext (New England Biolabs) adapters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing quality was first checked using FastQC (version 0.11.7).
Reads were then mapped to the TAIR10 Arabidopsis genome using Bowtie2 (version 2.3.4.3) with the "--no-1mm-upfront" option.
Resulting SAM files were converted to BAM using the samtools (version 1.9) function "view".
Duplicated reads were removed with samtools "rmdup".
Resulting BAM files were sorted and indexed with samtools "sort" and "index".
Read counts per gene were determined using the "multicov" function from bedtools (version 2.26.0) and were used to produce the Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed file.
Genome_build: TAIR10
Supplementary_files_format_and_content: Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed is a tab-delimited BED (~.txt) file containing the read counts for each TAIR10 genes in each sequencing sample.
|
| |
|
| Submission date |
Jun 04, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Alice Lambolez |
| Organization name |
The University of Tokyo
|
| Department |
Faculty of Science, Department of Biological Sciences
|
| Lab |
Kakutani Lab
|
| Street address |
7 Chome-3-1 Hongo
|
| City |
Bunkyo |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8654 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE176161 |
Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures |
|
| Relations |
| BioSample |
SAMN19572116 |
| SRA |
SRX11068487 |
