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| Status |
Public on Jan 07, 2025 |
| Title |
Leaf, Cool, 477, rep 2 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Wahlenbergia ceracea |
| Characteristics |
tissue: Leaf
genotype: 477
treatment: Cool
tolerance: Sensitive
flowering state: Non-flowering
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| Treatment protocol |
Two weeks after transplantation, plants were subject to either cool (24/15 ºC day/night, optimal for growth and flowering of post-seedling plants; Arnold et al., 2022) or warm temperatures (30/20 ºC day/night). Plants grown at 30 ºC have reduced fitness (seed number and viability) but are not sterile nor undergo photoinhibition [Fv/Fm (maximum PSII efficiency) > 0.70; Notarnicola et al., 2021]. Experimental design: 12 lines x 3 replicates x 2 growth temperatures = 72 individuals (Figure S1). We let the plants grow for a further two weeks by which time they had produced new leaves acclimated to the respective temperature conditions. We took two ~1 mg leaf tissue per plant from the two youngest, fully-expanded, healthy leaves. Leaves were harvested in a randomized order between 11:00 and 16:30, and immediately flash-frozen in liquid nitrogen and stored at -80 ºC. Time of harvesting and developmental stage were recorded for each sample (‘nonflowering’ n = 56; ‘early bud’ n = 16).
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| Growth protocol |
F3 seeds were germinated in seed raising mix in 14 × 8.5 × 5 cm pots in the glasshouse under 28/20 ºC to maximise germination and establishment (Notarnicola et al., 2022; Arnold et al., 2022). Subsequently, plants were grown under controlled conditions (28/20 ºC, 60 % relative humidity, 14-hour photoperiod, 1200 µmol s-1 m-2) using a Growth Capsule GC (Photon Systems Instruments, Brno, Czech Republic). Individual plants were transplanted into individual pots (6.5 × 6.5 × 16 cm) and supplemented with slow-release fertilizer (Osmocote Plus, Scotts Australia). We randomly arranged three replicate plants for each line in three blocks (one replicate per block) that were equivalent in each of 2 capsules. Plants were bottom watered as needed and supplemented with liquid fertiliser every two weeks (Yates Thrive, Yates Australia).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from snap-frozen and ground leaf tissue using the Spectrum Plant Total RNA Kit (Merck, New Jersey, USA) with on-column DNase I digestion.
The construction of cDNA libraries was conducted with 250 ng RNA input using the Illumina stranded mRNA prep ligation protocol, as per manufacturer’s instructions except that reaction volumes were scaled by one-half and 12 PCR cycles were used for library amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads were trimmed for adapters and low-quality base calls (PHRED < 20) using Trim Galore! (Babraham Bioinformatics) with default settings.
Trimmed reads were inspected using MultiQC (Ewels et al., 2016).
An index was constructed with Kallisto using a fasta file of transcripts defined in our trancsriptome assembly. Transcript quantification was performed with Kallisto (Bray et al., 2016) on those transcripts.
Assembly: W. ceracea genome assembly will be uploaded on DRYAD upon manuscript submission
Supplementary files format and content: tsv: plaintext file of the abundance estimates. It does not contains bootstrap estimates.
Supplementary files format and content: h5: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: count_matrix.csv: csv file containing raw gene counts for each gene and each sample generated by the tximport R package and function with the 'lengthScaledTPM' algorithm.
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| Submission date |
Aug 15, 2024 |
| Last update date |
Jan 07, 2025 |
| Contact name |
Rocco Fabrizio Notarnicola |
| E-mail(s) |
roccofabrizio.notarnicola2@gmail.com
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| Organization name |
Adam Mickiewicz University
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| Department |
Evolutionary Biology
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| Street address |
ul, Uniwersytetu Poznańskiego 6
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| City |
Poznan |
| State/province |
Wielkopolskie |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
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| Platform ID |
GPL34820 |
| Series (1) |
| GSE274951 |
Transcriptional acclimation to warming temperatures in the Australian alpine herb Wahlenbergia ceracea |
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| Relations |
| BioSample |
SAMN43207048 |
| SRA |
SRX25717652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8462709_C05_S21_477.4C.h5 |
2.3 Mb |
(ftp)(http) |
H5 |
| GSM8462709_C05_S21_477.4C.tsv.gz |
614.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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