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pmid:31453303

Microarray data on the comparison of transcript expression between normal and Pt-Delta RNAi embryos in the common house spider Parasteatoda tepidariorum.

Hiroki Oda · Yasuko Akiyama-Oda

Data in brief · 2019 doi:10.1016/j.dib.2019.104350

Paper

complete

Experiment

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Data

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Analysis

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title
Microarray data on the comparison of transcript expression between normal and Pt-Delta RNAi embryos in the common house spider Parasteatoda tepidariorum.
doi
10.1016/j.dib.2019.104350
pmid
31453303
authors array · 2 items
[0]
Hiroki Oda
[1]
Yasuko Akiyama-Oda
journal
Data in brief
year
2019
abstract
We conducted a custom microarray experiment to detect the differences in the transcript expression levels between untreated (normal) and Pt-Delta-RNAi embryos at late stage 6 in the common house spider Parasteatoda tepidariorum. The array probes were designed based on accumulated EST and cDNA sequences. The microarray dataset has been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession GSE113064. The expression of the transcripts selected based on the detected differences was examined in embryos by whole-mount in situ hybridization.
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The quantitative data were subjected to Loess normalization. The microarray dataset deposited in the GEO Database at NCBI (GSE113064) consists of a data table showing the details of probe sequences for array spots (Platform: GPL24882) and that showing the ratio of [Pt-Delta RNAi]/[normal] for each array spot (Sample: GSM3095654).
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sections[6] "Microarray analysis" paragraph 2
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The quantitative data were subjected to Loess normalization.
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sections[3] "Data" paragraph 2
quote
The microarray dataset deposited in the GEO Database at NCBI (GSE113064) consists of a data table showing the details of probe sequences for array spots (Platform: GPL24882) and that showing the ratio of [Pt-Delta RNAi]/[normal] for each array spot (Sample: GSM3095654).
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The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3.
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The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3.
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The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3.
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The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3.
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Identification of genes whose expression is affected by Delta RNAi in spider embryos
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Values of the [Pt-Delta RNAi]/[normal] ratio from control probes in the microarray analysis.
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List of EST clones selected based on the [Pt-Delta RNAi]/[normal] ratio (<0.6) in the microarray analysis.
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Table 2
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List of EST clones selected based on the [Pt-Delta RNAi]/[normal] ratio (<0.6) in the microarray analysis.
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g58
[4]
LOC107440897
[5]
0.483
[6]
At_eW_022_C14*
[7]
[30] array · 8 items
[0]
At_eW_022_G16
[1]
10754
[2]
FY223437
[3]
g11061
[4]
LOC107457313
[5]
0.569
[6]
At_eW_022_G16*
[7]
ect (ptn)
[31] array · 8 items
[0]
At_eW_022_P10
[1]
11105
[2]
FY223640
[3]
g26989
[4]
LOC107440147
[5]
0.474
[6]
At_eW_022_P10*
[7]
cm
[32] array · 8 items
[0]
At_eW_025_H20
[1]
7926
[2]
FY224563
[3]
g23736
[4]
LOC107453117
[5]
0.572
[6]
At_eW_025_H20
[7]
[33] array · 8 items
[0]
eS7_SB_013_D07
[1]
10632
[2]
FY378703
[3]
g23736
[4]
LOC107453117
[5]
0.551
[6]
eS7_SB_013_D07*
[7]
end
[34] array · 8 items
[0]
eS7_001_G09
[1]
2121
[2]
FY376646
[3]
g2117
[4]
LOC107448180
[5]
0.598
[6]
eS7_SB_018_G10*
[7]
end
[35] array · 8 items
[0]
eS7_002_F12
[1]
5636
[2]
FY376729
[3]
g2859
[4]
LOC107449611
[5]
0.588
[6]
eS7_002_F12*
[7]
[36] array · 8 items
[0]
eS7_006_B01
[1]
7269
[2]
FY377014
[3]
g15364
[4]
LOC107448906
[5]
0.598
[6]
eS7_SB_046_H04*
[7]
end
[37] array · 8 items
[0]
eS7_008_B09
[1]
6413
[2]
FY377193
[3]
g7446
[4]
LOC107444045
[5]
0.597
[6]
eS7_008_B09*
[7]
end
[38] array · 8 items
[0]
eS7_012_A12
[1]
11123
[2]
FY377551
[3]
g3860
[4]
LOC107451189
[5]
0.570
[6]
eS7_012_A12*
[7]
end
[39] array · 8 items
[0]
eS7_012_C04
[1]
6762
[2]
FY377567
[3]
g9240
[4]
LOC107445106
[5]
0.512
[6]
eS7_SB_007_G10*
[7]
end
[40] array · 8 items
[0]
eS7_012_F02
[1]
12018
[2]
FY377596
[3]
g18588
[4]
LOC107445478
[5]
0.574
[6]
eS7_012_F02*
[7]
end
[41] array · 8 items
[0]
eS7_SB_001_H07
[1]
633
[2]
FY377714
[3]
g8636
[4]
LOC107456533
[5]
0.579
[6]
eS7_SB_001_H07*
[7]
end + ex
[42] array · 8 items
[0]
eS7_SB_008_B12
[1]
11074
[2]
FY378225
[3]
g15926
[4]
LOC107441456
[5]
0.553
[6]
eS7_SB_008_B12*
[7]
cm
[43] array · 8 items
[0]
eS7_SB_008_D04
[1]
9585
[2]
FY378241
[3]
g11817
[4]
LOC107436785
[5]
0.524
[6]
eS7_SB_008_D04*
[7]
[44] array · 8 items
[0]
eS7_SB_009_G06
[1]
11640
[2]
FY378373
[3]
g16253
[4]
LOC107441912
[5]
0.595
[6]
eS7_SB_009_G06*
[7]
[45] array · 8 items
[0]
eS7_SB_016_B10
[1]
12337
[2]
FY378949
[3]
g18790
[4]
LOC107445841
[5]
0.565
[6]
eS7_SB_016_B10*
[7]
end
[46] array · 8 items
[0]
eS7_SB_016_B10
[1]
7166
[2]
FY378949
[3]
g18790
[4]
LOC107445841
[5]
0.535
[6]
eS7_SB_016_B10*
[7]
end
[47] array · 8 items
[0]
eS7_SB_019_A02
[1]
12357
[2]
FY379131
[3]
g8457
[4]
LOC107456289
[5]
0.493
[6]
eS7_SB_019_A02*
[7]
[48] array · 8 items
[0]
eS7_SB_028_A08
[1]
8536
[2]
FY379919
[3]
g4630
[4]
LOC107452244
[5]
0.574
[6]
eS7_SB_028_A08*
[7]
[49] array · 8 items
[0]
eS7_SB_045_H12
[1]
11661
[2]
FY381390
[3]
g25109
[4]
LOC107455614
[5]
0.536
[6]
eS7_SB_045_H12*
[7]
end
locator
section[3]/table-wrap[2]#tbl2
gaps array · 2 items
[0]
asset:data:geo:GSE113064 not downloaded
[1]
asset:data:geo:GSE113064 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Loess normalization
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
reordered
quote
The quantitative data were subjected to Loess normalization. The microarray dataset deposited in the GEO Database at NCBI (GSE113064) consists of a data table showing the details of probe sequences for array spots (Platform: GPL24882) and that showing the ratio of [Pt-Delta RNAi]/[normal] for each array spot (Sample: GSM3095654).
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
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
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Loess normalization), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
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
reachable
true
accessions array · 1 item
[0]
GSE113064
resolved_accessions array · 1 item
[0]
GSE113064
statements array · 1 item
[0]
The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3.
basis
The paper names GSE113064 in Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
[0]
source:pmid:31453303
[1]
data:geo:GSE113064
[2]
asset:table:pmid:31453303:1
[3]
asset:table:pmid:31453303:2
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE113064
gaps array · 1 item
[0]
method:not_determinable
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:15:56Z
independence
single_reader
evidence_check object · 2 fields
method
reordered
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
8779
completion_tokens
1244
cached_tokens
792
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:31453303
type
paper
label
pmid:31453303
[1] object · 3 fields
id
source:pmid:31453303
type
manuscript
label
PMID 31453303 full text
[2] object · 3 fields
id
data:geo:GSE113064
type
dataset
label
GEO GSE113064
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:31453303
type
paper
label
pmid:31453303
[1] object · 3 fields
id
source:pmid:31453303
type
manuscript
label
PMID 31453303 full text
[2] object · 3 fields
id
data:geo:GSE113064
type
dataset
label
GEO GSE113064
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-31453303
type
extraction
used array · 1 item
[0]
source:pmid:31453303
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE113064
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE113064
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:31453303
parent_hash
sha256:3b1f16204e48cc15677499ce1671d689f783b14bb55d2a93d4b28eb0e2733343
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE113064 licence not read
[1]
asset:data:geo:GSE113064 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
Microarray data on the comparison of transcript express
[1]
We conducted a custom microarray experiment to detect the differences in the
[2]
d on accumulated EST and cDNA sequences. The microarray dataset has been deposited in the Gene Expre
[3]
in P. tepidariorum embryos [2]. Flow of the microarray experiment is schematically shown in Fig. 1.
order_basis
paper_text_order:0
id
assay:1
Complete file
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The array probes were designed based on accumulated EST and cDNA sequences. The microarray dataset has been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession GSE113064. The expression of the transcripts selected based on the detected differences was examined in embryos by whole-mount in situ hybridization.", "claims": [{"id": "claim-method", "statement": "The quantitative data were subjected to Loess normalization. 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"Ratio (mean ± s.d.)c"], ["At_eW_003_D02", "alpha-catenin", "1719/4149/8989/11508", "AB433907", "g13984", "LOC107439705", "0.880 ± 0.039"], ["At_eW_003_D02", "alpha-catenin", "623/6036/6733/11968", "AB433907", "g13984", "LOC107439705", "0.950 ± 0.265"], ["eS7_003_G08", "elongation factor 1-alpha", "1697/2124/4972", "AB433908", "g27264", "LOC107441347", "1.163 ± 0.040"], ["eS7_003_G08", "elongation factor 1-alpha", "6130/9614/11011", "AB433908", "g27264", "LOC107441347", "1.061 ± 0.072"], ["eS7_SB_037_C01", "histone H3", "565/1580/1610/4874", "AB433909", "g1955", "LOC107447866", "0.965 ± 0.074"], ["eS7_SB_037_C01", "histone H3", "946/6236/6382/9005", "AB433909", "g1955", "LOC107447866", "0.834 ± 0.085"], ["At_O091", "Delta", "3003/6080/9491/10203", "AB287420", "g25248", "LOC107456525", "1.022 ± 0.099"], ["At_O091", "Delta", "3364/10373/10432/12130", "AB287420", "g25248", "LOC107456525", "1.164 ± 0.212"], ["At_O034", "caudal", "4150/6419/9162/12485", "AB096075", "g12643", "LOC107437910", "0.379 ± 0.068"], ["At_O034", "caudal", "6936/8225/8858/10344", "AB096075", "g12643", "LOC107437910", "0.358 ± 0.026"], ["At_O035", "caudal", "3904/4818/8215/10264", "AB096075", "g12643", "LOC107437910", "0.150 ± 0.009"], ["At_O045", "twist", "6351/7485/7754/9334", "AB167807", "g14287", "LOC107440133", "1.464 ± 0.098"], ["At_O045", "twist", "1481/3243/7334/10872", "AB167807", "g14287", "LOC107440133", "1.058 ± 0.074"], ["At_O046", "twist", "2538/3783/7509/8625", "AB167807", "g14287", "LOC107440133", "1.070 ± 0.095"], ["At_O029", "hedgehog", "3925/5404/11012/11143", "AB125742", "g4322", "LOC107451809", "0.436 ± 0.037"], ["At_O029", "hedgehog", "432/865/4215/4950", "AB125742", "g4322", "LOC107451809", "0.623 ± 0.102"], ["At_O030", "hedgehog", "2406/4772/4944/7704", "AB125742", "g4322", "LOC107451809", "0.905 ± 0.053"], ["At_O032", "orthodenticle", "1941/5594/10660/11559", "AB096074", "g9172", "LOC107457189", "0.298 ± 0.040"], ["At_O032", "orthodenticle", "838/3555/8545/9265", "AB096074", "g9172", "LOC107457189", "0.878 ± 0.155"], ["At_O071", "odd-paired", "6865/9525/9551/11052", "AB605264", "g12202", "LOC107437305", "0.716 ± 0.023"], ["At_O071", "odd-paired", "347/3228/4356/10492", "AB605264", "g12202", "LOC107437305", "1.021 ± 0.161"]], "row_count": 22, "column_count": 7, "numeric_cells": 128, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:31453303:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:70fcddb1da9815cfc8424e521b6ae053a9ade1bb3dd526f11aea5ac71188790f", "bytes": 4800, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#tbl2", "version": null, "note": "List of EST clones selected based on the [Pt-Delta RNAi]/[normal] ratio (<0.6) in the microarray analysis.", "structure": {"pmcid": "PMC6702388", "section_index": 3, "section_title": "Data", "row_count": 50, "column_count": 8}, "table": {"label": "Table 2", "caption": "List of EST clones selected based on the [Pt-Delta RNAi]/[normal] ratio (<0.6) in the microarray analysis.", "rows": [["EST clone", "Spot position number in MAa", "Sequence accession", "AUGUSTUS gene modelb", "NCBIGeneID", "Ratio", "WISH probec", "Exp.d"], ["At_eW_000_A15", "10599", "FY216311", "g9542", "LOC107437620", "0.597", "At_eW_000_A15*", "end"], ["eS7_SB_035_H06", "7990", "FY380468", "g9542", "LOC107437620", "0.550", "eS7_SB_035_H06", ""], ["eS7_SB_035_H06", "12394", "FY380468", "g9542", "LOC107437620", "0.556", "eS7_SB_035_H06", ""], ["At_eW_000_E06", "8245", "FY216397", "g15506", "LOC107449884", "0.453", "At_eW_000_E06*", "ect (ptn)"], ["At_eW_000_J22", "11227", "FY216533", "g15506", "LOC107449884", "0.506", "At_eW_000_J22", "ect (ptn)"], ["At_eW_000_J22", "9441", "FY216533", "g15506", "LOC107449884", "0.519", "At_eW_000_J22", "ect (ptn)"], ["At_eW_002_J21", "2951", "FY217255", "g6063", "LOC107454132", "0.554", "At_eW_002_J21*", "ect (ptn)"], ["At_eW_002_J21", "4632", "FY217255", "g6063", "LOC107454132", "0.508", "At_eW_002_J21*", "ect (ptn)"], ["At_eW_003_J01", "4517", "FY217568", "g12522", "LOC110282483", "0.592", "At_eW_003_J01*", "mes"], ["At_eW_005_P09", "6960", "FY218402", "g12522", "LOC110282483", "0.581", "eS7_SB_032_G07", "mes"], ["At_eW_004_F14", "12040", "FY217823", "g27319", "LOC107441543", "0.559", "eS7_SB_044_A09*", ""], ["At_eW_007_I04", "12305", "FY218925", "g18068", "LOC107444748", "0.494", "eS7_SB_013_G01*", ""], ["At_eW_007_I04", "6439", "FY218925", "g18068", "LOC107444748", "0.582", "eS7_SB_013_G01*", ""], ["At_eW_008_L13", "11956", "FY219308", "g16765", "n/a", "0.591", "At_eW_008_L13*", ""], ["At_eW_008_M14", "7886", "FY219331", "g19785", "LOC107447481", "0.516", "At_eW_008_M14*", ""], ["At_eW_012_A08", "3184", "FY220282", "g15726", "LOC107451427", "0.574", "At_eW_012_A08*", "end + ex"], ["At_eW_012_L16", "11579", "FY220479", "g3986", "LOC107451377", "0.588", "At_eW_012_L16*", ""], ["At_eW_013_K13", "9406", "FY220732", "g16422", "n/a", "0.599", "At_eW_013_K13*", ""], ["At_eW_013_M09", "5434", "FY220762", "g13957", "LOC107439672", "0.535", "At_eW_013_M09*", ""], ["At_eW_014_I18", "2396", "FY220952", "g27732", "LOC107442734", "0.599", "At_eW_014_I18*", "end"], ["At_eW_016_P19", "9236", "FY221580", "g27732", "LOC107442734", "0.576", "At_eW_016_P19", "end"], ["eS7_SB_012_D04", "8294", "FY378611", "g27733", "LOC107442734", "0.524", "eS7_SB_012_D04", "end"], ["eS7_SB_012_D04", "6032", "FY378611", "g27733", "LOC107442734", "0.567", "eS7_SB_012_D04", "end"], ["At_eW_016_B19", "4625", "FY221307", "g1624", "LOC107447145", "0.498", "At_eW_016_B19*", ""], ["At_eW_016_C08", "10970", "FY221318", "g17631", "n/a", "0.562", "At_eW_016_C08*", ""], ["At_eW_017_E05", "11338", "FY221647", "g7733", "LOC107447731", "0.589", "At_eW_017_E05*", ""], ["At_eW_021_K03", "11455", "FY223147", "g25961", "LOC107436162", "0.577", "eS7_SB_047_G11*", ""], ["At_eW_022_C14", "7174", "FY223344", "g58", "LOC107440897", "0.552", "At_eW_022_C14*", ""], ["At_eW_022_C14", "5932", "FY223344", "g58", "LOC107440897", "0.483", "At_eW_022_C14*", ""], ["At_eW_022_G16", "10754", "FY223437", "g11061", "LOC107457313", "0.569", "At_eW_022_G16*", "ect (ptn)"], ["At_eW_022_P10", "11105", "FY223640", "g26989", "LOC107440147", "0.474", "At_eW_022_P10*", "cm"], ["At_eW_025_H20", "7926", "FY224563", "g23736", "LOC107453117", "0.572", "At_eW_025_H20", ""], ["eS7_SB_013_D07", "10632", "FY378703", "g23736", "LOC107453117", "0.551", "eS7_SB_013_D07*", "end"], ["eS7_001_G09", "2121", "FY376646", "g2117", "LOC107448180", "0.598", "eS7_SB_018_G10*", "end"], ["eS7_002_F12", "5636", "FY376729", "g2859", "LOC107449611", "0.588", "eS7_002_F12*", ""], ["eS7_006_B01", "7269", "FY377014", "g15364", "LOC107448906", "0.598", "eS7_SB_046_H04*", "end"], ["eS7_008_B09", "6413", "FY377193", "g7446", "LOC107444045", "0.597", "eS7_008_B09*", "end"], ["eS7_012_A12", "11123", "FY377551", "g3860", "LOC107451189", "0.570", "eS7_012_A12*", "end"], ["eS7_012_C04", "6762", "FY377567", "g9240", "LOC107445106", "0.512", "eS7_SB_007_G10*", "end"], ["eS7_012_F02", "12018", "FY377596", "g18588", "LOC107445478", "0.574", "eS7_012_F02*", "end"], ["eS7_SB_001_H07", "633", "FY377714", "g8636", "LOC107456533", "0.579", "eS7_SB_001_H07*", "end + ex"], ["eS7_SB_008_B12", "11074", "FY378225", "g15926", "LOC107441456", "0.553", "eS7_SB_008_B12*", "cm"], ["eS7_SB_008_D04", "9585", "FY378241", "g11817", "LOC107436785", "0.524", "eS7_SB_008_D04*", ""], ["eS7_SB_009_G06", "11640", "FY378373", "g16253", "LOC107441912", "0.595", "eS7_SB_009_G06*", ""], ["eS7_SB_016_B10", "12337", "FY378949", "g18790", "LOC107445841", "0.565", "eS7_SB_016_B10*", "end"], ["eS7_SB_016_B10", "7166", "FY378949", "g18790", "LOC107445841", "0.535", "eS7_SB_016_B10*", "end"], ["eS7_SB_019_A02", "12357", "FY379131", "g8457", "LOC107456289", "0.493", "eS7_SB_019_A02*", ""], ["eS7_SB_028_A08", "8536", "FY379919", "g4630", "LOC107452244", "0.574", "eS7_SB_028_A08*", ""], ["eS7_SB_045_H12", "11661", "FY381390", "g25109", "LOC107455614", "0.536", "eS7_SB_045_H12*", "end"]], "row_count": 50, "column_count": 8, "numeric_cells": 340, "header_rows": 1, "locator": "section[3]/table-wrap[2]#tbl2"}}], "gaps": ["asset:data:geo:GSE113064 not downloaded", "asset:data:geo:GSE113064 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Loess normalization", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "The quantitative data were subjected to Loess normalization. The microarray dataset deposited in the GEO Database at NCBI (GSE113064) consists of a data table showing the details of probe sequences for array spots (Platform: GPL24882) and that showing the ratio of [Pt-Delta RNAi]/[normal] for each array spot (Sample: GSM3095654)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Loess normalization), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE113064"], "resolved_accessions": ["GSE113064"], "statements": ["The microarray dataset has been deposited in the Gene Expression Omnibus database at NCBI under the accession GSE113064. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE113064The image data have been deposited in the Mendeley Data repository. https://doi.org/10.17632/r79vg2ctr2.3."], "basis": "The paper names GSE113064 in Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31453303", "data:geo:GSE113064", "asset:table:pmid:31453303:1", "asset:table:pmid:31453303:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE113064"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:56Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 8779, "completion_tokens": 1244, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31453303", "type": "paper", "label": "pmid:31453303"}, {"id": "source:pmid:31453303", "type": "manuscript", "label": "PMID 31453303 full text"}, {"id": "data:geo:GSE113064", "type": "dataset", "label": "GEO GSE113064"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31453303", "type": "paper", "label": "pmid:31453303"}, {"id": "source:pmid:31453303", "type": "manuscript", "label": "PMID 31453303 full text"}, {"id": "data:geo:GSE113064", "type": "dataset", "label": "GEO GSE113064"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31453303", "type": "extraction", "used": ["source:pmid:31453303"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE113064", "type": "accession_resolution", "used": ["data:geo:GSE113064"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:31453303", "parent_hash": "sha256:3b1f16204e48cc15677499ce1671d689f783b14bb55d2a93d4b28eb0e2733343", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE113064 licence not read", "asset:data:geo:GSE113064 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Microarray data on the comparison of transcript express", "We conducted a custom microarray experiment to detect the differences in the", "d on accumulated EST and cDNA sequences. 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