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Series GSE217593 Query DataSets for GSE217593
Status Public on Apr 10, 2023
Title Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [RNA-seq]
Organism Ambystoma mexicanum
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Comparative gene expression profiling analysis of RNA-seq data for mature UA vs Hand, and mature UA vs UA BLs in different time points.
 
Contributor(s) Kawaguchi A, Wang J, Knapp D, Murawala P, Nowoshilow S, Masselink W, Taniguchi-Sugiura Y, Fei J, Tanaka EM
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Submission date Nov 09, 2022
Last update date Oct 04, 2023
Contact name Jingkui Wang
E-mail(s) jingkui.wang@imp.ac.at
Organization name Research Institute of Molecular Pathology (IMP)
Lab Tanaka
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (2)
GPL27159 Illumina NovaSeq 6000 (Ambystoma mexicanum)
GPL32846 NextSeq 2000 (Ambystoma mexicanum)
Samples (16)
GSM6722195 smartseq2_Mature_Hand_161517
GSM6722196 smartseq2_Mature_Hand_161514
GSM6722197 smartseq2_Mature_UA_161512
This SubSeries is part of SuperSeries:
GSE217594 Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration
Relations
BioProject PRJNA899787

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Supplementary file Size Download File type/resource
GSE217593_RAW.tar 724.6 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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