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Sample GSM7819423 Query DataSets for GSM7819423
Status Public on Feb 09, 2024
Title JB, chill, 600h, rep1
Sample type SRA
 
Source name Floral bud
Organism Prunus persica
Characteristics tissue: Floral bud
genotype: John Boy
treatment: Chilling (4 C)
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.
Growth protocol Peach cuttings (shoots with floral buds attached) were kept with the base submersed in water, which was changed periodically.
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
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.
 
Submission date Oct 03, 2023
Last update date Feb 09, 2024
Contact name Jianyang Liu
E-mail(s) jianyang.liu@usda.gov
Organization name USDA-ARS
Street address 2217 Wiltshire Road
City Kearneysville
State/province WV
ZIP/Postal code 25430
Country USA
 
Platform ID GPL25275
Series (1)
GSE244570 euAP2a, a Key Gene that Regulates Flowering Time with a Novel Mechanism in Peach (Prunus persica)
Relations
BioSample SAMN37666504
SRA SRX21980700

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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