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Sample GSM8059070 Query DataSets for GSM8059070
Status Public on Mar 18, 2024
Title PEACH_FRUIT_3
Sample type SRA
 
Source name Immature fruits
Organism Prunus persica
Characteristics tissue: Immature fruits
cultivar: Early Gold
Growth protocol Field conditions, normally watered trees.
Extracted molecule total RNA
Extraction protocol Total RNA was extrated using the Maxwell RSC Plant RNA Kit and the Maxwell RSC instrument (Promega Corporation, Madison, WI, USA).
RNA libraries were prepared using TruSeq Stranded mRNA protocol and were sequenced on Illumina platform NewxSeq 500 (2x150 bp, Paired-end).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNA-sequencing
Data processing For general gene expression analysis, we used the methology described in Vendrell-Mir et al., 2020, with minor modifications.
For Allele-specific expression, SNPS between P0 and P1 phases were detected using paftools.js call from Minimap2. RNA-seq reads were mapped to P0 using Hisat2 . Allele-specific counts were obtained using ASEReadCounter from GATK.
Assembly: Phased almond genome (v.3.0); FASTA with transcript sequences is available on the series record.
Supplementary files format and content: Matrix table with read counts for every gene per sample
Supplementary files format and content: Matrix table with rlog normalized expression values for every gene per sample
Supplementary files format and content: Matrix table with read counts for every allele of gene per sample
Supplementary files format and content: Matrix table with rlog normalized expression values for every gene per sample
 
Submission date Feb 01, 2024
Last update date Mar 18, 2024
Contact name Carlos de Tomás
Organization name CRAG
Street address Carrer de la Vall Moronta
City Cerdanyola del Vallès
State/province Barcelona
ZIP/Postal code 08193
Country Spain
 
Platform ID GPL21993
Series (1)
GSE254853 A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous transposon insertions
Relations
BioSample SAMN39732750
SRA SRX23501748

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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