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Series GSE135406 Query DataSets for GSE135406
Status Public on May 01, 2020
Title Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia
Organisms Danio rerio; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Injury induces retinal Muller glia of non-mammalian, but not mammalian, vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia, we used bulk and single-cell RNA-seq and ATAC-seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish, chick and mice. This was conducted during glial development, following inner and outer retinal injury, as well as following treatment with extrinsic factors that induce glial reprogramming. Integration of these data, together with functional analysis of candidate genes, identified evolutionarily conserved and species-specific gene regulatory networks controlling glial quiescence, gliosis, and neurogenic competence. In zebrafish and chick, transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence, while in mice a dedicated network suppresses this transition and rapidly restores quiescence. These findings may help guide the design of cell-based therapies aimed at restoring retinal neurons lost to disease.
Overall design In this study, to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG, we profiled mRNA levels using bulk RNA-seq and chromatin accessibility using ATAC (Assay for Transposase-Accessible Chromatin) sequencing technology in zebrafish and mouse in response to multiple neuronal injury models, as well as growth factor treatment. In total, we generated 105 bulk RNA-Seq libraries (including 5 technical replicates) and 40 bulk ATAC-Seq libraries.
Contributor(s) Hoang T, Wang J, Boyd P, Wang F, Hyde DR, Qian J, Blackshaw S
Citation(s) 33004674, 35259089, 38123561
Submission date Aug 05, 2019
Last update date Jan 03, 2024
Contact name Jie Wang
Organization name Johns Hopkins University
Department Ophthalmology
Street address 400 N Broadway
City Baltimore
State/province Maryland
ZIP/Postal code 21231
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (145)
GSM4007729 mmRNAdevP60R1
GSM4007730 mmRNAdevP60R2
GSM4007731 mmRNAdevhP60R1
BioProject PRJNA558770
SRA SRP217505

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Supplementary file Size Download File type/resource
GSE135406_Fpkm_expression_values_of_all_RNA-seq_samples.xlsx 27.5 Mb (ftp)(http) XLSX
GSE135406_RAW.tar 44.8 Mb (http)(custom) TAR (of NARROWPEAK)
GSE135406_Table_1_Counts_of_open_chromatin_regions_in_zebrafish_and_mouse_Muller_glia_identified_by_ATAC-Seq.xlsx 50.0 Mb (ftp)(http) XLSX
GSE135406_Table_2_Transcription_factor_footprints_detected_in_open_chromatin_regions_of_zebrafish_and_mouse_Muller_glia.xlsx 50.5 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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