Data from: Permissive and instructive Hox codes govern limb positioning
Data files
Apr 08, 2026 version files 104.86 MB
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dominant-negative.zip
48.73 MB
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fig.3C-genes.csv
2.17 KB
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over-expression.zip
27.89 MB
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README.md
3.93 KB
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RNAseq-raw_data.csv
28.23 MB
Abstract
The positioning of limbs along the anterior-posterior axis varies widely across vertebrates. The mechanisms controlling this feature remain to be fully understood. For over 30 years, it has been speculated that Hox genes play a key role in this process, but evidence supporting this hypothesis has been largely indirect. In this study, we employed loss- and gain-of-function Hox gene variants in chick embryos to address this issue. Using this approach, we found that Hox4/5 genes are necessary but insufficient for forelimb formation. Within the Hox4/5 expression domain, Hox6/7 genes are sufficient for reprogramming of neck lateral plate mesoderm to form an ectopic limb bud, thereby inducing forelimb formation anterior to the normal limb field. Our findings demonstrate that the forelimb program depends on the combinatorial actions of these Hox genes. We propose that during the evolutionary emergence of the neck, Hox4/5 provide permissive cues for forelimb formation throughout the neck region, while the final position of the forelimb is determined by the instructive cues of Hox6/7 in the lateral plate mesoderm.
Dataset DOI: 10.5061/dryad.cz8w9gjk5
Description of the data and file structure
The first zip file (dominant-negative) includes the images related to the wing buds with dominant-negative Hox gene (Hox4/5/6/7) expression in the forelimb region(Fig.1c and Fig.1A-T), showing that the wing bud was not able to grow as distally as the normal buds.
The second zip file (over-expression) is concluding the images related to the wing buds with Hox gene (Hox4/5/6/7) over-expression in the neck region, showing overexpression of Hox gene induced ectopic bud(Fig.2b-e and Fig.2A-T).
Other csv files are named to indicate their information, showing the final images for publication and related analysis data. Any empty cells represent data not available and #N/A represent not determined.
Files and variables
File: dominant-negative.zip
Description: information for Fig.1(Fig.1c and Fig.1A-T) with wing buds' images
File: fig.3C-genes.csv
Description: the list for 221 genes related to Fig.3C
File: over-expression.zip
Description: the information for Fig.2(Fig.2b-e and Fig.2A-T) with wing buds' images
File: RNAseq-raw_data.csv
Description:
Variables
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Count:16666
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Name: gene name
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Chromosome: which chromosome the gene is located on
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Region: Specific genomic coordinates (start–end position).
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Identifier: Unique gene ID
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neck LPM vs. ori limbbud - Log fold change
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neck LPM vs. ori limbbud - Fold change
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neck LPM vs. ori limbbud - P-value
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neck LPM vs. ori limbbud - FDR p-value
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neck LPM vs. ori limbbud - Bonferroni
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A6 over vs. ori limbbud - Log fold change
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A6 over vs. ori limbbud - Fold change
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A6 over vs. ori limbbud - P-value
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A6 over vs. ori limbbud - FDR p-value
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A6 over vs. ori limbbud - Bonferroni
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A6 over vs. neck LPM - Log fold change
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A6 over vs. neck LPM - Fold change
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A6 over vs. neck LPM - P-value
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A6 over vs. neck LPM - FDR p-value
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A6 over vs. neck LPM - Bonferroni
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Feature ID
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Database
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Database identifier
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Database symbol
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Qualifier:
The following are the Gene Ontology annotations:
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GO biological process: biological activity
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GO cellular component: where in the cell the gene product acts
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GO molecular function: molecular activity
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Database object name
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Synonym: Alternative gene names
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Database object type:
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Taxon ID: Species identifier
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Date: annotation date
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Assigned by:
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Annotation extension:
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Probe type:
The following are the expression measurements (Reads Per Kilobase Million, Transcripts Per Million, Raw count, Counts Per Million)
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387-1_S1 (GE) - Total counts
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387-1_S1 (GE) - RPKM
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387-1_S1 (GE) - TPM
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387-1_S1 (GE) - CPM
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387-2_S2 (GE) - Total counts
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387-2_S2 (GE) - RPKM
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387-2_S2 (GE) - TPM
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387-2_S2 (GE) - CPM
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387-3_S3 (GE) - Total counts
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387-3_S3 (GE) - RPKM
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387-3_S3 (GE) - TPM
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387-3_S3 (GE) - CPM
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387-4_S4 (GE) - Total counts
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387-4_S4 (GE) - RPKM
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387-4_S4 (GE) - TPM
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387-4_S4 (GE) - CPM
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387-17_S9 (GE) - Total counts
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387-17_S9 (GE) - RPKM
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387-17_S9 (GE) - TPM
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387-17_S9 (GE) - CPM
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387-18_S10 (GE) - Total counts
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387-18_S10 (GE) - RPKM
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387-18_S10 (GE) - TPM
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387-18_S10 (GE) - CPM
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387-19_S11 (GE) - Total counts
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387-19_S11 (GE) - RPKM
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387-19_S11 (GE) - TPM
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387-19_S11 (GE) - CPM
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387-20_S12 (GE) - Total counts
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387-20_S12 (GE) - RPKM
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387-20_S12 (GE) - TPM
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387-20_S12 (GE) - CPM
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387-11_S5 (GE) - Total counts
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387-11_S5 (GE) - RPKM
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387-11_S5 (GE) - TPM
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387-11_S5 (GE) - CPM
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387-13_S6 (GE) - Total counts
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387-13_S6 (GE) - RPKM
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387-13_S6 (GE) - TPM
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387-13_S6 (GE) - CPM
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387-15_S7 (GE) - Total counts
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387-15_S7 (GE) - RPKM
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387-15_S7 (GE) - TPM
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387-15_S7 (GE) - CPM
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387-16_S8 (GE) - Total counts
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387-16_S8 (GE) - RPKM
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387-16_S8 (GE) - TPM
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387-16_S8 (GE) - CPM