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| Status |
Public on Feb 09, 2024 |
| Title |
LP, warm, 28d, rep3 |
| Sample type |
SRA |
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| Source name |
Floral bud
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| Organism |
Prunus persica |
| Characteristics |
tissue: Floral bud
genotype: KV021779
treatment: Warm (22 C)
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| Treatment protocol |
Peach cuttings were kept in chilling condition (4℃) for 1000 h, and then moved to warm condition (22℃) for 20 d for JB and 28 for LFP until they started to bloom.
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| Growth protocol |
Peach cuttings (shoots with floral buds attached) were kept with the base submersed in water, which was changed periodically.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extract from the floral buds using a RNA Isolation Kit (Norgen BiotecK Corp, Ontario, Canada)
Truseq Stranded mRNA Library Prep Kit (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina paired-end bisulfite sequences were evaluated for quality using FastQC (version 0.11.9)
Trim reads with Trimmomatic to remove adapter sequence or poor quality sequence from raw reads
FASTQ files were aligned to Prunus persica NCBIv2 genome (Cheng et al. 2017) using the STAR (v2.6.0) software
Mapped read counts were transformed to Counts per Million (CPM) using the Bioconductor package edgeR (Robinson et al., 2010
Differentially expressed genes (DEGs) were identified on genes with false discovery rate (FDR) < 0.05 and log fold-changes (logFC) > 1.5 between LFP and JB at each time point.
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| Submission date |
Oct 03, 2023 |
| Last update date |
Feb 09, 2024 |
| Contact name |
Jianyang Liu |
| E-mail(s) |
jianyang.liu@usda.gov
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| Organization name |
USDA-ARS
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| Street address |
2217 Wiltshire Road
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| City |
Kearneysville |
| State/province |
WV |
| ZIP/Postal code |
25430 |
| Country |
USA |
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| Platform ID |
GPL25275 |
| Series (1) |
| GSE244570 |
euAP2a, a Key Gene that Regulates Flowering Time with a Novel Mechanism in Peach (Prunus persica) |
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| Relations |
| BioSample |
SAMN37666433 |
| SRA |
SRX21980771 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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