Data Downloads

Li et al.  (DETONATE - 2014 submitted): 

RSEM-Eval-guided Juvenile Axolotl Blastema Transcriptome Assembly

Gzip'd Fasta Assembly (Trinity v201203 ; RSEM-EVAL v1.4):
RSEM-Eval-guided Juvenile Axolotl Blastema Transcriptome Assembly
 
Raw Input Reads (3 RNA-Seq runs ; 605M total reads): Run100301  Run100309   Run100330

Filtered Input Reads (3 RNA-Seq runs ; 345M total reads ; Trinity was run against this dataset):
Axolotl Timecourse Filtered Reads

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Stewart et al.  (2013):

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

Gene Expression
Gene Expression Across Time Course
Gene Expression All Contigs
Embryonic Stem (ES), Induced Pluripotent Stem(iPS) Cell Foreskin (FS) Expression Data

Differentially Expressed (DE) Genes
Upregulated Genes with a False Discovery Rate (FDR) < 0.05
Downregulated Genes with an FDR < 0.05
2 way cluster heatmap of ALL DE Genes
Heatmap of ALL DE Contigs

Gene Ontology (GO) Enrichment
GO Enrichment Lists for Upregulated Genes  (BP and MF, level 5)
Background set of human genes identified by axolotl reads
GO Enrichment Files from DAVID

Assembly
Assembly (Rascon/Tanaka)
Axolotl Timecourse Raw Reads (2 RNA-Seq runs ; 420M reads) Run100309 Run100330
Axolotl Timecourse Filtered Reads (2 RNA-Seq runs ; 210M reads)
Axolotl Timecourse Pre-RSEM Mapped Reads ; README.txt
Axolotl Timecourse Contigs To Which Reads Were Mapped
Axolotl Timecourse Mappings of the Contigs To The Human Genome ; README.txt

Other Files
List of Human Transcription Factors
 

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Campbell et al. (2011).
"Gene expression profile of the regeneration epithelium during axolotl limb regeneration." Developmental Dynamics 240, 1826-1840.
Regenerative Epithelium

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Monaghan et al. (2009).
"Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration." BMC Biology 7, 1. [Nerve Dependent Data]
Nerve-dependent Limb Regeneration (Supplemental Info)
Nerve-Dependent Limb Regeneration (.CEL files)

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Rao et al. (2009).
"Proteomic analysis of blastema formation in regenerating axolotl limbs." BMC Biology 7, 83.
Proteomics