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pmid:32784357

Phenylpropanoids Are Connected to Cell Wall Fortification and Stress Tolerance in Avocado Somatic Embryogenesis.

Carol A Olivares-García · Martín Mata-Rosas · Carolina Peña-Montes · Francisco Quiroz-Figueroa · Aldo Segura-Cabrera · Laura M Shannon · Victor M Loyola-Vargas · Juan L Monribot-Villanueva · Jose M Elizalde-Contreras · Enrique Ibarra-Laclette · Mónica Ramirez-Vázquez · José A Guerrero-Analco · Eliel Ruiz-May

International journal of molecular sciences · 2020 doi:10.3390/ijms21165679

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title
Phenylpropanoids Are Connected to Cell Wall Fortification and Stress Tolerance in Avocado Somatic Embryogenesis.
doi
10.3390/ijms21165679
pmid
32784357
authors array · 13 items
[0]
Carol A Olivares-García
[1]
Martín Mata-Rosas
[2]
Carolina Peña-Montes
[3]
Francisco Quiroz-Figueroa
[4]
Aldo Segura-Cabrera
[5]
Laura M Shannon
[6]
Victor M Loyola-Vargas
[7]
Juan L Monribot-Villanueva
[8]
Jose M Elizalde-Contreras
[9]
Enrique Ibarra-Laclette
[10]
Mónica Ramirez-Vázquez
[11]
José A Guerrero-Analco
[12]
Eliel Ruiz-May
journal
International journal of molecular sciences
year
2020
abstract
Somatic embryogenesis (SE) is a valuable model for understanding the mechanism of plant embryogenesis and a tool for the mass production of plants. However, establishing SE in avocado has been complicated due to the very low efficiency of embryo induction and plant regeneration. To understand the molecular foundation of the SE induction and development in avocado, we compared embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties using proteomic and metabolomic approaches. Although Criollo and Hass EC exhibited similarities in the proteome and metabolome profile, in general, we observed a more active phenylpropanoid pathway in EC than NEC. This pathway is associated with the tolerance of stress responses, probably through the reinforcement of the cell wall and flavonoid production. We could corroborate that particular polyphenolics compounds, including p-coumaric acid and t-ferulic acid, stimulated the production of somatic embryos in avocado. Exogen phenolic compounds were associated with the modification of the content of endogenous polyphenolic and the induction of the production of the putative auxin-a, adenosine, cellulose and 1,26-hexacosanediol-diferulate. We suggest that in EC of avocado, there is an enhanced phenylpropanoid metabolism for the production of the building blocks of lignin and flavonoid compounds having a role in cell wall reinforcement for tolerating stress response. Data are available at ProteomeXchange with the identifier PXD019705.
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Proteomics study in somatic embryogenesis in avocado
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The endogenous concentration of phenolic compounds (mg g−1 fresh weight) in embryogenic cultures of Criollo and Hass avocado treated with different concentrations of p-coumaric (1 and 10 µM) and trans-ferulic acid (10 and 100 µM) during 6 and 12 h, and 14 and 28 days. The analysis was carried out with dynamic multiple reaction monitoring (dMRM) study. Replicate values, error standard and statistic values are presented in Table S2. p-hydroxybenzoic acid (PHBA), vanillin (VA), p-coumaric acid (p-CA), trans-ferulic acid (t-FA), SA (Sinapic acid) and trans-cinnamic acid (t-CA). We indicated in bold and italic the values described in the text.
structure object · 5 fields
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PMC7460882
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2.4. The Improvement of the Production of Embryos in Avocado EC Is Associated with the Alteration of the Endogenous Content of Polyphenolic Compounds
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31
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Table 1
caption
The endogenous concentration of phenolic compounds (mg g−1 fresh weight) in embryogenic cultures of Criollo and Hass avocado treated with different concentrations of p-coumaric (1 and 10 µM) and trans-ferulic acid (10 and 100 µM) during 6 and 12 h, and 14 and 28 days. The analysis was carried out with dynamic multiple reaction monitoring (dMRM) study. Replicate values, error standard and statistic values are presented in Table S2. p-hydroxybenzoic acid (PHBA), vanillin (VA), p-coumaric acid (p-CA), trans-ferulic acid (t-FA), SA (Sinapic acid) and trans-cinnamic acid (t-CA). We indicated in bold and italic the values described in the text.
rows array · 31 items
[0] array · 10 items
[0]
Cultivar Time
[1]
Treatment
[2]
PHBA
[3]
VA
[4]
p-CA
[5]
Quercetin 3,4’-di-O-glucoside
[6]
t-FA
[7]
SA
[8]
Naringin
[9]
t-CA
[1] array · 10 items
[0]
Criollo 0 h
[1]
0 µM Control
[2]
0.11 ± 0.01
[3]
0.11 ± 0.01
[4]
0.42 ± 0.01
[5]
0.02 ± 0.01
[6]
0.23 ± 0.01
[7]
0
[8]
0.07 ± 0.01
[9]
0.02 ± 0.01
[2] array · 9 items
[0]
1 µM p-CA
[1]
0.11 ± 0.01
[2]
0.11 ± 0.01
[3]
0.42 ± 0.01
[4]
0.02 ± 0.01
[5]
0.23 ± 0.01
[6]
0
[7]
0.07 ± 0.01
[8]
0.02 ± 0.01
[3] array · 9 items
[0]
1 µM t-FA
[1]
0.11 ± 0.01
[2]
0.11 ± 0.01
[3]
0.42 ± 0.01
[4]
0.02 ± 0.01
[5]
0.23 ± 0.01
[6]
0
[7]
0.07 ± 0.01
[8]
0.02 ± 0.01
[4] array · 10 items
[0]
Hass 0 h
[1]
0 µM Control
[2]
0.21 ± 0.01
[3]
0.03 ± 0.03
[4]
0.66 ± 0.02
[5]
0.01 ± 0.01
[6]
0.09 ± 0.01
[7]
0
[8]
0
[9]
0.04 ± 0.01
[5] array · 9 items
[0]
10 µM p-CA
[1]
0.21 ± 0.01
[2]
0.03 ± 0.03
[3]
0.66 ± 0.02
[4]
0.01 ± 0.01
[5]
0.09 ± 0.01
[6]
0
[7]
0
[8]
0.04 ± 0.01
[6] array · 9 items
[0]
100 µM t-FA
[1]
0.21 ± 0.01
[2]
0.03 ± 0.03
[3]
0.66 ± 0.02
[4]
0.01 ± 0.01
[5]
0.09 ± 0.01
[6]
0
[7]
0
[8]
0.04 ± 0.01
[7] array · 10 items
[0]
Criollo 6 h
[1]
0 µM Control
[2]
0.58 ± 0.01 ***
[3]
0.22 ± 0.01 ***
[4]
0.85 ± 0.01 ***
[5]
1.66 ± 0.07 ***
[6]
1.12 ± 0.01 ***
[7]
0.7 ± 0.01 ***
[8]
0.34 ± 0.01 ***
[9]
0.06 ± 0.01 **
[8] array · 9 items
[0]
1 µM p-CA
[1]
0.64 ± 0.05 ***
[2]
0.06 ± 0.01 **
[3]
0.29 ± 0.01 **
[4]
0 *
[5]
0.12 ± 0.01 **
[6]
0 **
[7]
0 **
[8]
0.4 ± 0.01 ***
[9] array · 9 items
[0]
1 µM t-FA
[1]
0.38 ± 0.01 **
[2]
0.05 ± 0.01 **
[3]
0.18 ± 0.01 **
[4]
0.03 ± 0.04 **
[5]
0.28 ± 0.01 **
[6]
0 **
[7]
0 **
[8]
0.11 ± 0.01 ***
[10] array · 10 items
[0]
Hass 6 h
[1]
0 µM Control
[2]
0.29 ± 0.01 *
[3]
0.06 ± 0.01 *
[4]
0.62 ± 0.01 *
[5]
0.33 ± 0.05 *
[6]
1 ± 0.01 **
[7]
0.86 ± 0.02 ***
[8]
0.06 ± 0.01 *
[9]
0.03 ± 0 *
[11] array · 9 items
[0]
10 µM p-CA
[1]
0.25 ± 0.01 *
[2]
0.05 ± 0.001 *
[3]
0.7 ± 0.01 **
[4]
0.02 ± 0.03 **
[5]
0.13 ± 0.01 *
[6]
0 *
[7]
0 *
[8]
0.29 ± 0.01 *
[12] array · 9 items
[0]
100 µM t-FA
[1]
0.32 ± 0.01 *
[2]
0.24 ± 0.01 ***
[3]
1.39 ± 0.01 ***
[4]
0.62 ± 0.02 ***
[5]
10.6 ± 0.22 ***
[6]
0.64 ± 0.02 **
[7]
0.18 ± 0.02 ***
[8]
0.98 ± 0.02 ***
[13] array · 10 items
[0]
Criollo 12 h
[1]
0 µM Control
[2]
0.21 ± 0.01 **
[3]
0.15 ± 0.01 ***
[4]
0.61 ± 0.01 ***
[5]
0.62 ± 0.04 ***
[6]
0.52 ± 0.01 ***
[7]
0.72 ± 0.02 ***
[8]
0.05 ± 0.01 ***
[9]
0.02 ± 0.01 **
[14] array · 9 items
[0]
1 µM p-CA
[1]
0.25 ± 0.01 ***
[2]
0.06 ± 0.01 **
[3]
0.46 ± 0.01 **
[4]
0 **
[5]
0.26 ± 0.01 **
[6]
0 **
[7]
0 ***
[8]
0.15 ± 0.01 ***
[15] array · 9 items
[0]
1 µM t-FA
[1]
0.18 ± 0 *
[2]
0.04 ± 0.01 *
[3]
0.18 ± 0.01 *
[4]
0 **
[5]
0.12 ± 0.01 *
[6]
0 **
[7]
0 ***
[8]
0.03 ± 0.01 **
[16] array · 10 items
[0]
Hass 12 h
[1]
0 µM Control
[2]
0.6 ± 0.01 ***
[3]
0.11 ± 0.01 *
[4]
0.94 ± 0.02 ***
[5]
0.18 ± 0.02 ***
[6]
0.86 ± 0.07 ***
[7]
0.42 ± 0.01 ***
[8]
0.21 ± 0.01 ***
[9]
0.12 ± 0.01 **
[17] array · 9 items
[0]
10 µM p-CA
[1]
0.2 ± 0 *
[2]
0.03 ± 0.001 *
[3]
0.24 ± 0.01 *
[4]
0.04 ± 0.01 **
[5]
0.13 ± 0.01 *
[6]
0 *
[7]
0 *
[8]
0.08 ± 0.01 *
[18] array · 9 items
[0]
100 µM t-FA
[1]
0.4 ± 0 *
[2]
0.17 ± 0.01 ***
[3]
0.48 ± 0.01 *
[4]
0.05 ± 0.04 **
[5]
0.39 ± 0.01 *
[6]
0 *
[7]
0.22 ± 0.01 ***
[8]
0.08 ± 0.01 *
[19] array · 10 items
[0]
Criollo 14 days
[1]
0 µM Control
[2]
1.12 ± 0.02 ***
[3]
0.06 ± 0.001 ***
[4]
1.28 ± 0.02 ***
[5]
0.3 ± 0.01 ***
[6]
0.23 ± 0.01 *
[7]
0.03 ± 0.02 ***
[8]
0 ***
[9]
0.01 ± 0.02 ***
[20] array · 9 items
[0]
1 µM p-CA
[1]
0.09 ± 0.001 *
[2]
0.05 ± 0.01 **
[3]
0.39 ± 0.01 *
[4]
0 **
[5]
0.28 ± 0.02 **
[6]
0 **
[7]
0 ***
[8]
0.01 ± 0.02 ***
[21] array · 9 items
[0]
1 µM t-FA
[1]
0.12 ± 0.01 **
[2]
0.02 ± 0.01 *
[3]
1.18 ± 0.08 **
[4]
0 **
[5]
0.56 ± 0.03 ***
[6]
0.02 ± 0.01 *****
[7]
0 ***
[8]
0.02 ± 0.01 ***
[22] array · 10 items
[0]
Hass 14 days
[1]
0 µM Control
[2]
0.09 ± 0.01 *
[3]
0.03 ± 0.01 ***
[4]
0.69 ± 0.03 ***
[5]
0 *
[6]
0.4 ± 0.01 **
[7]
0.01 ± 0.01 **
[8]
0 ***
[9]
0.02 ± 0.01 ***
[23] array · 9 items
[0]
10 µM p-CA
[1]
0.11 ± 0.01 **
[2]
0.03 ± 0.01 ***
[3]
0.24 ± 0.02 *
[4]
0.06 ± 0.01 **
[5]
0.55 ± 0.03 **
[6]
0.1 ± 0.02 ***
[7]
0 ***
[8]
0.01 ± 0.01 **
[24] array · 9 items
[0]
100 µM t-FA
[1]
0 *
[2]
0 *
[3]
0 *
[4]
0 *
[5]
7.06 ± 3.63 ***
[6]
0 **
[7]
0 ***
[8]
0 *
[25] array · 10 items
[0]
Criollo 28days
[1]
0 µM Control
[2]
0.62 ± 0.01 *
[3]
0.05 ± 0.01 **
[4]
0.96 ± 0 ***
[5]
0 ***
[6]
0.72 ± 0.01 ***
[7]
0.23 ± 0.01 **
[8]
0 ***
[9]
0.5 ± 0 ***
[26] array · 9 items
[0]
1 µM p-CA
[1]
3.56 ± 0.06 ***
[2]
0 *
[3]
0.05 ± 0.04 *
[4]
0 ***
[5]
0 *
[6]
0 *
[7]
0 ***
[8]
0 *
[27] array · 9 items
[0]
1 µM t-FA
[1]
1.35 ± 0.02 **
[2]
0.08 ± 0 ***
[3]
0.74 ± 0.01 **
[4]
0.02 ± 0.04 ***
[5]
0.12 ± 0.10 **
[6]
1.55 ± 0.12 ***
[7]
0 ***
[8]
0.03 ± 0 **
[28] array · 10 items
[0]
Hass 28 days
[1]
0 µM Control
[2]
0.4 ± 0 *
[3]
0.05 ± 0 **
[4]
1.14 ± 0.01 ***
[5]
0 ***
[6]
0.78 ± 0.01 **
[7]
0.04 ± 0.01 ***
[8]
0 ***
[9]
0.01 ± 0 ***
[29] array · 9 items
[0]
10 µM p-CA
[1]
1.36 ± 0.03 ***
[2]
0 *
[3]
0.02 ± 0.02 *
[4]
0 ***
[5]
7.75 ± 4.43 ***
[6]
0 *
[7]
0 ***
[8]
0 **
[30] array · 9 items
[0]
100 µM t-FA
[1]
1.12 ± 0.01 **
[2]
0.03 ± 0 *
[3]
0.16 ± 0.01 *
[4]
0 ***
[5]
0.08 ± 0 **
[6]
0.01 ± 0.01 **
[7]
0 ***
[8]
0 **
row_count
31
column_count
10
numeric_cells
281
header_rows
1
locator
section[6]/table-wrap[1]#ijms-21-05679-t001
[3] object · 16 fields
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jats-table
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read_table
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section[31]/table-wrap[1]#array1
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structure object · 5 fields
pmcid
PMC7460882
section_index
31
section_title
Abbreviations
row_count
32
column_count
2
table object · 8 fields
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null
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null
rows array · 32 items
[0] array · 2 items
[0]
ALH2C4
[1]
Aldehyde dehydrogenase family 2-member C4
[1] array · 2 items
[0]
c-CA
[1]
cis-cinnamic acid
[2] array · 2 items
[0]
p-CA
[1]
p-coumaric acid
[3] array · 2 items
[0]
t-CA
[1]
trans-cinnamic acid
[4] array · 2 items
[0]
CAD9
[1]
Cinnamyl alcohol dehydrogenase 9
[5] array · 2 items
[0]
BSA
[1]
Bovine serum albumin
[6] array · 2 items
[0]
CCoAOMT
[1]
Caffeoyl-CoA O-methyltransferase
[7] array · 2 items
[0]
CCoAOMT1
[1]
Caffeoyl-CoA O-methyltransferase 1
[8] array · 2 items
[0]
C4H/ CYP73A5
[1]
Cinnamic acid 4-hydroxylases
[9] array · 2 items
[0]
4CL1
[1]
4-coumarate: CoA ligase 1
[10] array · 2 items
[0]
EC
[1]
Embryogenic callus
[11] array · 2 items
[0]
EMSN
[1]
Extracellular matrix surface Network
[12] array · 2 items
[0]
EP
[1]
Embryogenic potency
[13] array · 2 items
[0]
t-FA
[1]
trans-ferulic acid
[14] array · 2 items
[0]
GLM
[1]
General linear model
[15] array · 2 items
[0]
LDOX
[1]
Leucoanthocyanidin dioxygenase
[16] array · 2 items
[0]
MS
[1]
Murashige and Skoog
[17] array · 2 items
[0]
MSP
[1]
Murashige and Skoog medium supplemented with 0.1 mg L−1 picloram
[18] array · 2 items
[0]
NEC
[1]
Non-embryogenic callus
[19] array · 2 items
[0]
OMT1
[1]
Flavone 3’-O-methyltransferase 1
[20] array · 2 items
[0]
PAL1
[1]
Phenylalanine ammonia-lyase 1
[21] array · 2 items
[0]
PCA
[1]
Principal component analysis
[22] array · 2 items
[0]
PHBA
[1]
p-hydroxybenzoic acid
[23] array · 2 items
[0]
POX52
[1]
Peroxidase 52
[24] array · 2 items
[0]
PP
[1]
Phenylpropanoid pathway
[25] array · 2 items
[0]
ROS
[1]
Reactive oxygen species
[26] array · 2 items
[0]
SA
[1]
Sinapic acid
[27] array · 2 items
[0]
SE
[1]
Somatic embryogenesis
[28] array · 2 items
[0]
TCEP
[1]
tris (2-carboxyethyl) phosphine
[29] array · 2 items
[0]
TMT
[1]
Tandem mass tags
[30] array · 2 items
[0]
VBE
[1]
Vanillyl benzyl ether
[31] array · 2 items
[0]
VA
[1]
Vanillin
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32
column_count
2
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13
header_rows
0
locator
section[31]/table-wrap[1]#array1
gaps array · 2 items
[0]
asset:data:geo:PXD019705 not downloaded
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method-1
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differential_expression
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limma_voom
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Differential expression analysis
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normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
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count_matrix_with_condition
evidence object · 3 fields
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LIMMA
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method-2
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null
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Mann–Whitney U-test
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missing_operations array · 0 items
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evidence object · 3 fields
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1
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quote
“The statistical analysis of the endogenous content of phenolic compounds was carried out with a Mann–Whitney U-test (n = 3, p < 0.05).”
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gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
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capability_id
capability:computational_analysis
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Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
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differential_expression
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gwas
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owned
tier_unlocked
R1
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Automated Assays Laravel application and simulated adapters
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readiness object · 8 fields
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complete
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R1
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none
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nothing:replicable_now
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normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
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The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
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true
accessions array · 1 item
[0]
PXD019705
resolved_accessions array · 1 item
[0]
PXD019705
statements array · 1 item
[0]
Data are available at ProteomeXchange with the identifier PXD019705.
basis
The paper names PXD019705 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 3 items
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normalise_counts
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differential_expression_fit
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fdr_bh
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[0]
source:pmid:32784357
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asset:table:pmid:32784357:1
[3]
asset:table:pmid:32784357:2
steps array · 1 item
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run_analysis
must_build object · 5 fields
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data:geo:PXD019705
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review object · 5 fields
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partial
machine_critique object · 5 fields
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extraction_review
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MiniMax-M3.1-Flash
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minimax
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minimax
read_at
2026-10-31T18:21:46Z
independence
single_reader
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reordered
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62498
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extraction
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pmid:32784357
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paper
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pmid:32784357
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source:pmid:32784357
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manuscript
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data:geo:PXD019705
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GEO PXD019705
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pmid:32784357
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source:pmid:32784357
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GEO PXD019705
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agent:corpus-assay-engine
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source:pmid:32784357
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used array · 1 item
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data:geo:PXD019705
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agent:corpus-assay-engine
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agent:corpus-assay-engine
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agent:minimax-reader
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343fb30756ba6ec3
capability_table_fingerprint
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sha256:0a8c1298c2ff176e207a7356b7dda73a6747032673e776211c0d1bdfb035d7f6
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for quantification of relative expression by qPCR, Data S1: Differential proteins identified i
[1]
ic acid for 28 days, Figure S6: Quantitative real-time PCR validation of for genes involved in phenylpr
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paper_text_order:3037
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Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32784357", "kind": "science-record", "revision": 7, "content_hash": "sha256:c201d6f60d14ad76a086f846a9acfa407db19b94c2078b0d80bf2d3970d91c37", "created_at": "2026-11-01T15:41:07Z", "updated_at": "2026-11-01T22:02:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Phenylpropanoids Are Connected to Cell Wall Fortification and Stress Tolerance in Avocado Somatic Embryogenesis.", "doi": "10.3390/ijms21165679", "pmid": "32784357", "authors": ["Carol A Olivares-García", "Martín Mata-Rosas", "Carolina Peña-Montes", "Francisco Quiroz-Figueroa", "Aldo Segura-Cabrera", "Laura M Shannon", "Victor M Loyola-Vargas", "Juan L Monribot-Villanueva", "Jose M Elizalde-Contreras", "Enrique Ibarra-Laclette", "Mónica Ramirez-Vázquez", "José A Guerrero-Analco", "Eliel Ruiz-May"], "journal": "International journal of molecular sciences", "year": 2020, "abstract": "Somatic embryogenesis (SE) is a valuable model for understanding the mechanism of plant embryogenesis and a tool for the mass production of plants. However, establishing SE in avocado has been complicated due to the very low efficiency of embryo induction and plant regeneration. To understand the molecular foundation of the SE induction and development in avocado, we compared embryogenic (EC) and non-embryogenic (NEC) cultures of two avocado varieties using proteomic and metabolomic approaches. Although Criollo and Hass EC exhibited similarities in the proteome and metabolome profile, in general, we observed a more active phenylpropanoid pathway in EC than NEC. This pathway is associated with the tolerance of stress responses, probably through the reinforcement of the cell wall and flavonoid production. We could corroborate that particular polyphenolics compounds, including p-coumaric acid and t-ferulic acid, stimulated the production of somatic embryos in avocado. Exogen phenolic compounds were associated with the modification of the content of endogenous polyphenolic and the induction of the production of the putative auxin-a, adenosine, cellulose and 1,26-hexacosanediol-diferulate. We suggest that in EC of avocado, there is an enhanced phenylpropanoid metabolism for the production of the building blocks of lignin and flavonoid compounds having a role in cell wall reinforcement for tolerating stress response. Data are available at ProteomeXchange with the identifier PXD019705.", "claims": [{"id": "claim-data-access", "statement": "Data are available at ProteomeXchange with the identifier PXD019705.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32784357", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available at ProteomeXchange with the identifier PXD019705."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32784357"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD019705"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD019705"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32784357", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms21165679", "sha256": "sha256:a870edbb62ae0782acf760cf0708a8c4a21426a7ad42171e6736d599fc548194", "bytes": 75472, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms21165679", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7460882", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD019705", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD019705", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD019705", "version": null, "note": "Data are available at ProteomeXchange with the identifier PXD019705.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available at ProteomeXchange with the identifier PXD019705.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics study in somatic embryogenesis in avocado", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32784357:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a039f3a484077aa4d138c1bdd05f25dcc87d9a9043547bdcd12d48cc2c517243", "bytes": 5060, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#ijms-21-05679-t001", "version": null, "note": "The endogenous concentration of phenolic compounds (mg g−1 fresh weight) in embryogenic cultures of Criollo and Hass avocado treated with different concentrations of p-coumaric (1 and 10 µM) and trans-ferulic acid (10 and 100 µM) during 6 and 12 h, and 14 and 28 days. The analysis was carried out with dynamic multiple reaction monitoring (dMRM) study. Replicate values, error standard and statistic values are presented in Table S2. p-hydroxybenzoic acid (PHBA), vanillin (VA), p-coumaric acid (p-CA), trans-ferulic acid (t-FA), SA (Sinapic acid) and trans-cinnamic acid (t-CA). We indicated in bold and italic the values described in the text.", "structure": {"pmcid": "PMC7460882", "section_index": 6, "section_title": "2.4. The Improvement of the Production of Embryos in Avocado EC Is Associated with the Alteration of the Endogenous Content of Polyphenolic Compounds", "row_count": 31, "column_count": 10}, "table": {"label": "Table 1", "caption": "The endogenous concentration of phenolic compounds (mg g−1 fresh weight) in embryogenic cultures of Criollo and Hass avocado treated with different concentrations of p-coumaric (1 and 10 µM) and trans-ferulic acid (10 and 100 µM) during 6 and 12 h, and 14 and 28 days. The analysis was carried out with dynamic multiple reaction monitoring (dMRM) study. Replicate values, error standard and statistic values are presented in Table S2. p-hydroxybenzoic acid (PHBA), vanillin (VA), p-coumaric acid (p-CA), trans-ferulic acid (t-FA), SA (Sinapic acid) and trans-cinnamic acid (t-CA). We indicated in bold and italic the values described in the text.", "rows": [["Cultivar Time", "Treatment", "PHBA", "VA", "p-CA", "Quercetin 3,4’-di-O-glucoside", "t-FA", "SA", "Naringin", "t-CA"], ["Criollo 0 h", "0 µM Control", "0.11 ± 0.01", "0.11 ± 0.01", "0.42 ± 0.01", "0.02 ± 0.01", "0.23 ± 0.01", "0", "0.07 ± 0.01", "0.02 ± 0.01"], ["1 µM p-CA", "0.11 ± 0.01", "0.11 ± 0.01", "0.42 ± 0.01", "0.02 ± 0.01", "0.23 ± 0.01", "0", "0.07 ± 0.01", "0.02 ± 0.01"], ["1 µM t-FA", "0.11 ± 0.01", "0.11 ± 0.01", "0.42 ± 0.01", "0.02 ± 0.01", "0.23 ± 0.01", "0", "0.07 ± 0.01", "0.02 ± 0.01"], ["Hass 0 h", "0 µM Control", "0.21 ± 0.01", "0.03 ± 0.03", "0.66 ± 0.02", "0.01 ± 0.01", "0.09 ± 0.01", "0", "0", "0.04 ± 0.01"], ["10 µM p-CA", "0.21 ± 0.01", "0.03 ± 0.03", "0.66 ± 0.02", "0.01 ± 0.01", "0.09 ± 0.01", "0", "0", "0.04 ± 0.01"], ["100 µM t-FA", "0.21 ± 0.01", "0.03 ± 0.03", "0.66 ± 0.02", "0.01 ± 0.01", "0.09 ± 0.01", "0", "0", "0.04 ± 0.01"], ["Criollo 6 h", "0 µM Control", "0.58 ± 0.01 ***", "0.22 ± 0.01 ***", "0.85 ± 0.01 ***", "1.66 ± 0.07 ***", "1.12 ± 0.01 ***", "0.7 ± 0.01 ***", "0.34 ± 0.01 ***", "0.06 ± 0.01 **"], ["1 µM p-CA", "0.64 ± 0.05 ***", "0.06 ± 0.01 **", "0.29 ± 0.01 **", "0 *", "0.12 ± 0.01 **", "0 **", "0 **", "0.4 ± 0.01 ***"], ["1 µM t-FA", "0.38 ± 0.01 **", "0.05 ± 0.01 **", "0.18 ± 0.01 **", "0.03 ± 0.04 **", "0.28 ± 0.01 **", "0 **", "0 **", "0.11 ± 0.01 ***"], ["Hass 6 h", "0 µM Control", "0.29 ± 0.01 *", "0.06 ± 0.01 *", "0.62 ± 0.01 *", "0.33 ± 0.05 *", "1 ± 0.01 **", "0.86 ± 0.02 ***", "0.06 ± 0.01 *", "0.03 ± 0 *"], ["10 µM p-CA", "0.25 ± 0.01 *", "0.05 ± 0.001 *", "0.7 ± 0.01 **", "0.02 ± 0.03 **", "0.13 ± 0.01 *", "0 *", "0 *", "0.29 ± 0.01 *"], ["100 µM t-FA", "0.32 ± 0.01 *", "0.24 ± 0.01 ***", "1.39 ± 0.01 ***", "0.62 ± 0.02 ***", "10.6 ± 0.22 ***", "0.64 ± 0.02 **", "0.18 ± 0.02 ***", "0.98 ± 0.02 ***"], ["Criollo 12 h", "0 µM Control", "0.21 ± 0.01 **", "0.15 ± 0.01 ***", "0.61 ± 0.01 ***", "0.62 ± 0.04 ***", "0.52 ± 0.01 ***", "0.72 ± 0.02 ***", "0.05 ± 0.01 ***", "0.02 ± 0.01 **"], ["1 µM p-CA", "0.25 ± 0.01 ***", "0.06 ± 0.01 **", "0.46 ± 0.01 **", "0 **", "0.26 ± 0.01 **", "0 **", "0 ***", "0.15 ± 0.01 ***"], ["1 µM t-FA", "0.18 ± 0 *", "0.04 ± 0.01 *", "0.18 ± 0.01 *", "0 **", "0.12 ± 0.01 *", "0 **", "0 ***", "0.03 ± 0.01 **"], ["Hass 12 h", "0 µM Control", "0.6 ± 0.01 ***", "0.11 ± 0.01 *", "0.94 ± 0.02 ***", "0.18 ± 0.02 ***", "0.86 ± 0.07 ***", "0.42 ± 0.01 ***", "0.21 ± 0.01 ***", "0.12 ± 0.01 **"], ["10 µM p-CA", "0.2 ± 0 *", "0.03 ± 0.001 *", "0.24 ± 0.01 *", "0.04 ± 0.01 **", "0.13 ± 0.01 *", "0 *", "0 *", "0.08 ± 0.01 *"], ["100 µM t-FA", "0.4 ± 0 *", "0.17 ± 0.01 ***", "0.48 ± 0.01 *", "0.05 ± 0.04 **", "0.39 ± 0.01 *", "0 *", "0.22 ± 0.01 ***", "0.08 ± 0.01 *"], ["Criollo 14 days", "0 µM Control", "1.12 ± 0.02 ***", "0.06 ± 0.001 ***", "1.28 ± 0.02 ***", "0.3 ± 0.01 ***", "0.23 ± 0.01 *", "0.03 ± 0.02 ***", "0 ***", "0.01 ± 0.02 ***"], ["1 µM p-CA", "0.09 ± 0.001 *", "0.05 ± 0.01 **", "0.39 ± 0.01 *", "0 **", "0.28 ± 0.02 **", "0 **", "0 ***", "0.01 ± 0.02 ***"], ["1 µM t-FA", "0.12 ± 0.01 **", "0.02 ± 0.01 *", "1.18 ± 0.08 **", "0 **", "0.56 ± 0.03 ***", "0.02 ± 0.01 *****", "0 ***", "0.02 ± 0.01 ***"], ["Hass 14 days", "0 µM Control", "0.09 ± 0.01 *", "0.03 ± 0.01 ***", "0.69 ± 0.03 ***", "0 *", "0.4 ± 0.01 **", "0.01 ± 0.01 **", "0 ***", "0.02 ± 0.01 ***"], ["10 µM p-CA", "0.11 ± 0.01 **", "0.03 ± 0.01 ***", "0.24 ± 0.02 *", "0.06 ± 0.01 **", "0.55 ± 0.03 **", "0.1 ± 0.02 ***", "0 ***", "0.01 ± 0.01 **"], ["100 µM t-FA", "0 *", "0 *", "0 *", "0 *", "7.06 ± 3.63 ***", "0 **", "0 ***", "0 *"], ["Criollo 28days", "0 µM Control", "0.62 ± 0.01 *", "0.05 ± 0.01 **", "0.96 ± 0 ***", "0 ***", "0.72 ± 0.01 ***", "0.23 ± 0.01 **", "0 ***", "0.5 ± 0 ***"], ["1 µM p-CA", "3.56 ± 0.06 ***", "0 *", "0.05 ± 0.04 *", "0 ***", "0 *", "0 *", "0 ***", "0 *"], ["1 µM t-FA", "1.35 ± 0.02 **", "0.08 ± 0 ***", "0.74 ± 0.01 **", "0.02 ± 0.04 ***", "0.12 ± 0.10 **", "1.55 ± 0.12 ***", "0 ***", 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