|
| Status |
Public on Feb 27, 2024 |
| Title |
ZT83 Senescent bio rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole flag leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: whole flag leaf
cultivar: Mace
treatment: Senescent leaf
time: ZT83
|
| Treatment protocol |
When plants had concurrently reached the mature and senescent developmental stages, at dawn (Zeitgeber Time 0; ZT0), the growth room was set to continuous light and temperature (20ºC) and whole flag leaves from the primary tiller of four plants were collected every 2 h from ZT45 to ZT91 (48 h).
|
| Growth protocol |
Seeds were chilled at 4°C for 48 h and sown in a mix of sterilised potting soil with 4.5 g/L Osmocote 6-9 month slow-release fertiliser. Growth room was set to 12 h light (200-280 µmol m-2 s-1, 20ºC), 12 h dark (15ºC) prior to switch to continuous conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen leaf tissue was ground to a fine powder in liquid nitrogen-cooled mortar and pestles. Lysate buffer was added to the tissue (350 µL per 100 mg of tissue) and the mixture was vortexed immediately. RNA was extracted using ISOLATE II RNA Plant Kit (Meridian Bioscience). RNA from two individual leaf samples was equally pooled to provide two replicates for sequencing.
Library preparation and RNA-sequencing was performed by a commercial provider (Azenta). Library preparations were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs; NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
processed data file:
senescence_counts.tsv
senescence_fpkm.tsv
ZT83_S_R2
|
| Data processing |
bcl2fastq 2.17. Raw data was filtered as follows: (1) Discard pair-end reads with adapter; (2) Discard pair-end reads when the content of N bases is more than 10% in either read; (3) Discard pair-end reads when the ration of bases of low quality (Q<20) is more than 0.5 in either read.
STAR. Filtered reads were mapped to the T. aestivum cv. Mace (PGSBv2.1) genome sequence and annotation using STAR with default parameters
Cufflinks. Mapped reads were quantified and normalised using the cuffquant and cuffnorm modules of Cufflinks with default parameters
Assembly: Triticum aestivum cv. Mace. Genbank assembly ID: GCA_903994175.1
Supplementary files format and content: tab-delimited text file includes raw counts for mature samples
Supplementary files format and content: tab-delimited text file includes raw counts for senescent samples
Supplementary files format and content: tab-delimited text file includes fpkm for mature samples
Supplementary files format and content: tab-delimited text file includes fpkm for senescent samples
|
| |
|
| Submission date |
Feb 27, 2024 |
| Last update date |
Feb 29, 2024 |
| Contact name |
Christopher Robert Buckley |
| E-mail(s) |
buckley.c@unimelb.edu.au
|
| Organization name |
University of Melbourne
|
| Street address |
School of BioSciences, Level 3, Building 184, The University of Melbourne
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23509 |
| Series (1) |
| GSE259431 |
A circadian transcriptional sub-network and EARLY FLOWERING 3 control timing of senescence and grain nutrition in bread wheat |
|
| Relations |
| BioSample |
SAMN40180292 |
| SRA |
SRX23772862 |
