Microarray Analysis of microRNA Expression during Axolotl Limb Regeneration
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ABSTRACT:
ORGANISM(S): Gorilla gorilla Bos taurus Mus musculus Rattus norvegicus Human gammaherpesvirus 8 Pan troglodytes JC polyomavirus Betapolyomavirus macacae Human immunodeficiency virus 1 Homo sapiens Monodelphis domestica Human betaherpesvirus 5 Ateles sp. Human alphaherpesvirus 1 Danio rerio Betapolyomavirus hominis Lemur catta human gammaherpesvirus 4 Ambystoma mexicanum Gallus gallus
PROVIDER: GSE29727 | GEO | 2012/11/06
SECONDARY ACCESSION(S): PRJNA141103
REPOSITORIES: GEO
Similar Datasets
Project description:The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis. LC Sciences arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Three arrays were hybridized comparing two paired samples each time. Biological dye-swaps were made by labeling bl samples once with Cy3 and twice with Cy5; st samples were labeled accordingly twice with Cy5 and once with Cy3. Multiple arrays averaged into a single Sample record. Supplementary files: GSE29727_LC_MultiArray_SimpleNormalizedData.txt.gz GSE29727_LC_signal_ratio_mean_SD.txt.gz GSE29727_LC_t-Test_st-vs-bl.txt.gz Exiqon arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Six arrays were hybridized comparing each sample labeled with Hy3 against a common reference sample made by pooling all the samples and labeling it with Hy5. Multiple arrays not averaged, represented as multiple Sample records. Supplementary file: GSE29727_Exiqon_matrix_complete.txt
2012-11-06 | E-GEOD-29727 | biostudies-arrayexpress
Project description:Blastema formation is a hallmark of limb regeneration that requires proliferation and migration of progenitors derived from many tissues to the amputation plane. To better understand the genetic programs that initiate limb regeneration, we reasoned that blastemal progenitors would be among early proliferating cells in the stump following amputation. Here we separately profiled dividing and non-dividing stump tissues, as well as the wound epidermis, during early axolotl limb regeneration to examine transcriptional programs of blastemal progenitors. We provide a description of the changes in gene expression specific to early dividing cells at the site of amputation, inclusive of progenitors for the regenerating limb. This work collectively demonstrates differential suppression/activation of core developmental signaling pathways in subsets of the early regenerating limb and further suggests that interleukin-8 (il-8) signaling is important for regeneration.
2019-01-01 | GSE111213 | GEO
Project description:The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information. The experiment includes two time course data sets. One is from mouse digit amputation, another is from Axolotl digit amputation
2013-09-01 | E-GEOD-34394 | biostudies-arrayexpress
Project description:Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we identified expression patterns that explain PD duplication including upregulation of proximal homeobox gene expression and silencing of distal-associated genes whereas limb truncation was associated with disrupted skeletal differentiation. Overall, mechanisms were identified that regulate RAR’s multifaceted roles in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.
2017-01-10 | GSE93303 | GEO
Project description:Here we report the results of a robust microarray experiment that examined the first 28 days of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1m of heterogeneous tissue collected from the distal limb tip. The distal 1.0mm of heterogeneous tissue from regenerating limb tip were removed and used for RNA extraction. 10 samples were collected for each of 20 time points.
2015-04-20 | E-GEOD-67118 | biostudies-arrayexpress
Project description:The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information.
2013-09-01 | GSE34394 | GEO
Project description:Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed ‘positional identity’. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/RARRES1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting HoxA13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.
2022-01-30 | GSE184948 | GEO
Project description:The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program. We performed Differential Gene expression analysis using data obtained from RNA-seq of two mature limb segments (mature arm vs hand). Therefore, we performed libraries from the mature arm and 5, 9, 13 dpa regenerating arm blastema.
2023-04-10 | GSE217593 | GEO
Project description:Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. Connective tissue (CT) – skeleton, periskeleton, tendon, dermis, interstitial cells – contributes the vast majority of cells that populate the blastema, however it is unclear how individual CT cells may reprogram their fate in order to rebuild the tetrapod limb. Here we use a combination of Cre-loxP reporter lineage tracking and single-cell (sc) RNA-seq to molecularly track, for the first time, adult CT cell heterogeneity and its transition to a limb blastema state. We uncover a multi-phasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that participates in inflammation and extracellular matrix disassembly prior to proliferation, establishment of positional information, and ultimately re-differentiation. While the early regeneration transcriptome states are unique to the blastema, the later stages recapitulate embryonic limb development. Notably, we do not find evidence of a pre-existing blastema-like precursor nor limb bud-like progenitors in the uninjured adult tissue. However, we find that distinct CT subpopulations in the adult limb differentially contribute to proximal and distal portions of the regenerated limb. Together, our data illuminates molecular and cellular reprogramming during complex organ regeneration in a vertebrate.
2018-09-27 | GSE106269 | GEO
Project description:Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013): https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration.
2016-12-15 | GSE92429 | GEO