|
| Status |
Public on Aug 23, 2018 |
| Title |
SD_ZT4_2 |
| Sample type |
SRA |
| |
|
| Source name |
SD_ZT4, 2 trifoliate leaves
|
| Organism |
Medicago truncatula |
| Characteristics |
accession: Jester
age: 15 days
condition: SD
timepoint: ZT4
tissue: 2 trifoliate leaves
|
| Growth protocol |
Seeds were scarified and germinated overnight at 15°C in gently shaking tubes of water and dark conditions for 24 hours. Germinated seeds were then vernalised in damp petri dishes at 4°C for a further 25 days. The seedlings were subsequently planted in seed raising mix (Daltons Ltd., NZ) in individual cell pots and grown in growth cabinets at 22°C under 240μM/m/sec cool white fluorescent light. Soil was was kept moist with a complete liquid nutrient media. Plants were grown in SD conditions (8 hours light/16 hour dark) for 10 days and then transferred to LD conditions (16 hours light/8 hour dark) where the timing of lights on (ZT0) was kept the same, but lights off occurred 8 h later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In the first experiment, sampling occurred from SD and LD shifted plants when the plants were 13 days old at ZT0 and two hours later at ZT2 and in the second experiment sampling occurred at ZT4 when the plants were 15 days old. Three biological replicates were taken each consisting of two pooled trifoliate leaves from different non-adjacent plants. Only the first trifoliate leaf to unfurl was sampled from a given plant. Samples were immediately frozen in liquid nitrogen. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, Germany) following the manufacturer's instructions.
Library construction was performed by the Otago Genomics Facility using ScriptSeq Complete Kit (Plant) (Illumina Inc., USA) in the first experiment while the second experiment (ZT4 samples) used TruSeq Stranded mRNA Kits (Illumina Inc., USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
second experiment
|
| Data processing |
Read trimming using the BBDuk tool in the BBTools suite (v37.54) with Phred = 20) and retaining only reads which were at least 36 bases in length. Read pairs lacking one of the pair were discarded.
Transcripts were quantified using Salmon (v0.8.2) using the Mt4.0v2 transcriptome.
Count tables were then imported into R using the tximport package (v1.4.0).
Genome_build: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary_files_format_and_content: CSV files containing the GeneID (gene), either the raw counts or normalized abundances in Transcripts per Million (counts or TPM), growth condition (condition), time of sampling (time) and replicate number (replicate)
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Aug 23, 2018 |
| Contact name |
Geoffrey Owen James Thomson |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Auckland
|
| Department |
School of Biological Sciences
|
| Lab |
Flowering Lab
|
| Street address |
Private Bag 92019
|
| City |
Auckland |
| ZIP/Postal code |
1142 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL17491 |
| Series (1) |
| GSE118893 |
The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula |
|
| Relations |
| BioSample |
SAMN09878737 |
| SRA |
SRX4594585 |
