Raw Illumina Sequencing Data for “VEGF Signaling Promotes Blastema Growth…” (Savage et al., 2025)

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Savage, Aaron, 2025, "Raw Illumina Sequencing Data for “VEGF Signaling Promotes Blastema Growth…” (Savage et al., 2025)", https://doi.org/10.7910/DVN/VY3J77, Harvard Dataverse, V3
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This folder contains the data which were used in the publication "VEGF signaling promotes blastema growth and proliferation of vascular and non-vascular cells during axolotl limb regeneration" https://doi.org/10.1016/j.ydbio.2025.05.030 . This also is directly related to https://github.com/Whited-Lab/project-axolotl-vegf-limb-regeneration for downstream analysis. Additionally, a singularity file "kallisto_ubuntu-22.04.sif" is included as it is too large for github upload and is utilized in the pipeline. To replicate RNAseq analysis, download the Github locally and run the scripts - data contained in this dataverse will populate and the full pipeline should run without issues! (2025-06-05)
Subject Medicine, Health and Life Sciences
Related Publication Is Supplement To: Aaron M. Savage, Alexandra C. Wagner, Ryan T. Kim, Paul Gilbert, Hani D. Singer, Erica Chen, Elane M. Kim, Noah Lopez, Kelly E. Dooling, Julia C. Paoli, S.Y. Celeste Wu, Sebastian Böhm, Tim Froitzheim, Rachna Chilambi, Steven J. Blair, Connor Powell, Adnan Abouelela, Anna G. Luong, Kara N. Thornton, Noora Harake, Alparslan Karabacak, Benjamin Tajer, Duygu Payzin-Dogru, Jessica L. Whited, VEGF signaling promotes blastema growth and proliferation of vascular and non-vascular cells during axolotl limb regeneration, Developmental Biology, 2025, , ISSN 0012-1606, https://doi.org/10.1016/j.ydbio.2025.05.030. (https://www.sciencedirect.com/science/article/pii/S0012160625001538) Abstract: Salamanders are capable of regenerating whole limbs throughout life, a feat that is unmatched by other tetrapods. Limb regeneration is dependent upon the formation of a blastema containing progenitor cells which give rise to most tissues of the regenerated limb. Many signaling pathways, including FGF, BMP and Wnt, are required for regeneration, but the role of VEGF signaling during salamander limb regeneration is not well understood, particularly outside of angiogenesis. Here we show that VEGF signaling is essential for limb regeneration and that blastema cells and limb fibroblasts display impaired proliferation in the absence of VEGF signaling. Loss of VEGF signaling reduces expression of EMT-associated genes, suggesting VEGF signaling promotes expression of EMT-associated transcription factors, including Snai2, during axolotl limb regeneration. These findings highlight potential roles for VEGF signaling during regeneration which may extend beyond its expected pro-angiogenic function.doi: https://doi.org/10.1016/j.ydbio.2025.05.030
Notes Three replicates were collected for each condition as follows (note that DAPT samples are removed from analysis) : DAPT treated = "A01v1_A2_S1", "B01v1_C2_S2", "C01v1_D2_S3" AV951 treated = "D01v1_F2_S4", "E01v1_G2_S5", "F01v1_I2_S6" Control = "G01v1_M2_S7", "H01v1_N2_S8", "A02v1_O2_S9"
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kallisto_ubuntu-22.04.sif
Unknown - 147.0 MB
Published Jun 11, 2025
2 Downloads
MD5: f7546209cc7a30495d208a926ff25452
kallisto singularity image v0.48.0 used in analysis (too large for github upload)
P476_ASava18465_A01v1_A2_S1_R1_001.fastq.gz
Gzip Archive - 1.7 GB
Published Jun 10, 2025
1 Download
MD5: a8132b884eb07cb044ada4a0846c9201
FASTQ sequencing data
Sequencing Data
P476_ASava18465_A01v1_A2_S1_R2_001.fastq.gz
Gzip Archive - 1.8 GB
Published Jun 10, 2025
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MD5: 76ae88146466b86d4acd1efb2186d76e
FASTQ sequencing data
Sequencing Data
P476_ASava18465_A02v1_O2_S9_R1_001.fastq.gz
Gzip Archive - 1.6 GB
Published Jun 10, 2025
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MD5: b9c731b909f7686a9c784d6cdcb5f108
FASTQ sequencing data
Sequencing Data
P476_ASava18465_A02v1_O2_S9_R2_001.fastq.gz
Gzip Archive - 1.7 GB
Published Jun 10, 2025
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MD5: 75ffe9e02af41de94f5d29bd7ba7aebe
FASTQ sequencing data
Sequencing Data
P476_ASava18465_B01v1_C2_S2_R1_001.fastq.gz
Gzip Archive - 1.9 GB
Published Jun 10, 2025
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MD5: bf7282861882eb19fd69cd53f7e3543d
FASTQ sequencing data
Sequencing Data
P476_ASava18465_B01v1_C2_S2_R2_001.fastq.gz
Gzip Archive - 1.9 GB
Published Jun 10, 2025
0 Downloads
MD5: 2797db1609af0163dc334d5d92f15aea
FASTQ sequencing data
Sequencing Data
P476_ASava18465_C01v1_D2_S3_R1_001.fastq.gz
Gzip Archive - 1.8 GB
Published Jun 10, 2025
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MD5: dcc3887891b8816d6385ea17c3244937
FASTQ sequencing data
Sequencing Data
P476_ASava18465_C01v1_D2_S3_R2_001.fastq.gz
Gzip Archive - 1.8 GB
Published Jun 10, 2025
0 Downloads
MD5: 6f3e01b0dba6eb88aaa34dd48505ca84
FASTQ sequencing data
Sequencing Data
P476_ASava18465_D01v1_F2_S4_R1_001.fastq.gz
Gzip Archive - 1.8 GB
Published Jun 10, 2025
1 Download
MD5: a1b16be0368e1f542f080cf41c8dc4fb
FASTQ sequencing data
Sequencing Data
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