DOI: 10.5281/zenodo.15081326
title: Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica)

description: Zenodo

FPKM expression matrices of data from (Shi and Ge et al.) which contains Malus domestica RNA-SEQ data

In details, data are labelled as follows:

FPKM of bud break stage.txt



Type of data:The FPKM matrix representing gene expression profiles in of multiple apple rootstock cultivars at bud breaking stage.

Label of samples: A1d_0_1\A1d_0_2\A1d_0_3 :phloem of A1d at bud break stage replicate; PYTC_0_1\PYTC_0_2\PYTC_0_3: Phloem of PYTC at bud break stage replicate; QZ1_0_1\QZ1_0_2\QZ1_0_3: Phloem of QZ1 at bud break stage replicate.

Origin of the data: NCBI Accession numbers: GSE276181: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE276181


FPKM of axillary buds.txt



Type of data :The FPKM matrix representing gene expression profiles in of multiple apple rootstock cultivars at bud breaking stage.

Label of samples : MB1\MB2\MB3: Multi-branched lateral buds in the ungerminated state; MB4\MB5\MB6: Multi-branched lateral buds in the sprouted state; WT1\WT2\WT3: Wild-type lateral bud in ungerminated state.

Origin of the data : NCBI Accession numbers: PRJNA801073 https://www.ncbi.nlm.nih.gov/bioproject/?term=%20PRJNA801073; Ge H, Li G, Wan S, Zhao A, Huang Y, Ma R, Zhang R, Song Y, and Sha GJG. 2022. Whole genome re-sequencing and transcriptome reveal an alteration in hormone signal transduction in a more-branching mutant of apple.  818:146214.


FPKM of 4 samples -60DABB



Type of data : The FPKM matrix representing gene expression profiles in phloem tissues of multiple apple rootstock cultivars at 60 Days After Bud Break (DABB).

Label of samples: A1d: dwarfing Apple rootstock; B9: dwarfing Apple rootstock phloem 60dabb; dwarfing Apple rootstock M9 phloem 60dabb; control vigorous :PYTC phloem 60dabb.Two biological replicates of each sample; M. sylvestris:M. sylvestris phloem at 60dabb; two biological replicates.

Origin of the data: NCBI SRA, accession numbers: GSE253335: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE253335


FPKM of AF vs PF.tab.xls



Type of data: The FPKM matrix representing gene expression profiles of fuji6 scions grafted on different kinds of apple rootstocks.

Label of samples: AF: RNA-Seq of fuji6 new shoots grafted on dwarfing A1d stock. PF: RNA-Seq of fuji6 new shootsgrafted on vigorous PYTC stock.

Origin of the data: NCBI SRA under Accession: PRJNA826123 https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA826123


FKPM of Root.txt



Type of data: The FPKM matrix representing Root of WT Malus spectabilis ‘Bly114’ or its multibranching mutant (MB).

Label of samples: WR: Root of WT Malus spectabilis ‘Bly114’ grafted on M. robusta; MR: Root of WT Malus spectabilis ‘Bly114’ grafted on M. robusta.

Origin of the data: NCBI accession numbers: SRR3095691  https://www.ncbi.nlm.nih.gov/sra/?term=SRR3095691; Li G, Ma J, Tan M, Mao J, An N, Sha G, Zhang D, Zhao C, and Han MJBG. 2016. Transcriptome analysis reveals the effects of sugar metabolism and auxin and cytokinin signaling pathways on root growth and development of grafted apple.  17:1-17.


FKPM of stem_leaves_flower.txt





Type of data: The FPKM matrix representing stem\leaves and flower of WT Malus spectabilis ‘Bly114’ or its multibranching mutant (MB).




Label of samples: WS: stem of WT Malus spectabilis ‘Bly114’ grafted on M. robusta; MS: stem of MB grafted on M. robusta; WL: leaves of WT Malus spectabilis ‘Bly114’ grafted on M. robusta; MB: leaves of WB grafted on M. robusta. Three replicates per sample.M3: receptacle of WT Malus spectabilis ‘Bly118’ grafted on M. robusta; T3: receptacle of WB grafted on M. robusta.




Origin of the data: NCBI Gene Expression Omnibus (GEO): GSE274104 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE274104. Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica) (ongoing submission);