Click here to close Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly. We suggest using a current version of Chrome, FireFox, or Safari.
Return to search results

GEO Series: GSE137844

Title: Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons

Summary

Xenopus is uniquely suited for addressing the question of whether a core gene expression program for successful CNS axon regeneration exists, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed RNA-Seq after optic nerve and spinal cord injury to identify trauma-induced genes shared between two regenerative CNS regions, but not shared with a non-regenerative one. We provide these data as a resource for new avenues of investigation into the molecular basis of tissue regeneration.


Contributors: Ben Szaro, Ben Szaro, Kurt Gibbs, Jamie Belrose

Experiment Type: RNA-seq (30 million nominal reads per sample) was performed on 51 samples: operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at three different timepoints (3 days, 11 days, 3 weeks), plus surgiically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at three timepoints (3 days, 7 days, 3 weeks), with 5 pooled hindbrains for each sample; juvenile frog hindbrain after spinal cord transection at 3 timepoints (3 days, 7 days, 3 weeks), plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.

Phenotypes:
Xla Wt + optic nerve amputation + eye juvenile 11 day post amp. (RNA-Seq (RNA))

Article: XB-ART-57252, PubMed

Source: NCBI GEO, Xenbase Download

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
hindbrain 1 week post amp. - NF53 GSM4089669  GSM4089670  GSM4089671  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
   hindbrain + spinal cord amputation 1 week post amp. - NF53 DEG GSM4089663  GSM4089664  GSM4089665  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
hindbrain 3 week post amp. - NF53 GSM4089672  GSM4089673  GSM4089674  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
   hindbrain + spinal cord amputation 3 week post amp. - NF53 DEG GSM4089666  GSM4089667  GSM4089668  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
hindbrain 3 day post amp. - NF53 GSM4089657  GSM4089658  GSM4089659  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
   hindbrain + spinal cord amputation 3 day post amp. - NF53 DEG GSM4089660  GSM4089661  GSM4089662  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain NF stage 53  
hindbrain - juvenile GSM4089675  GSM4089676  GSM4089677  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain juvenile frog stage  
   hindbrain + spinal cord amputation 1 week post amp.- juvenile DEG GSM4089681  GSM4089682  GSM4089683  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain juvenile frog stage  
   hindbrain + spinal cord amputation 3 day post amp. - juvenile DEG GSM4089678  GSM4089679  GSM4089680  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain juvenile frog stage  
   hindbrain + spinal cord amputation 3 week post amp. - juvenile DEG GSM4089684  GSM4089685  GSM4089686  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   NF stage 53 spinal cord
Conditions:
Tissue Assay Stages ChIP Antibody
hindbrain juvenile frog stage  
eye 3 day post amp. - juvenile GSM4089693  GSM4089694  GSM4089695  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
   eye + optic nerve amputation 3 day post amp. - juvenile DEG GSM4089690  GSM4089691  GSM4089692  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   juvenile frog stage optic nerve
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
eye 11 day post amp. - juvenile GSM4089699  GSM4089700  GSM4089701  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
   eye + optic nerve amputation 11 day post amp. - juvenile DEG GSM4089696  GSM4089697  GSM4089698  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   juvenile frog stage optic nerve
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
eye 3 week post amp. - juvenile GSM4089705  GSM4089706  GSM4089707  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
   eye + optic nerve amputation 3 week post amp. - juvenile DEG GSM4089702  GSM4089703  GSM4089704  RNA-Seq
Background: Xla.B Strain albino
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
amputation/regeneration   juvenile frog stage optic nerve
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
eye - juvenile GSM4089687  GSM4089688  GSM4089689  RNA-Seq
Background: Xla.B Strain albino
Conditions:
Tissue Assay Stages ChIP Antibody
eye juvenile frog stage  
Select All DEG      Select All 
Xtr   
Xla 

Return to search results