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Series GSE164044 Query DataSets for GSE164044
Status Public on Dec 31, 2020
Title Nucleome Dynamics during Retinal Development [scRNA-seq/scATAC-seq_Mm]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Single cell RNA-sequencing shows cell type specific expression of genes in the retina. Single cell ATAC-sequencing of the wild type retina revealed that chromatin in the Vsx2 CRC SE, a stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene, was only open in bipolar cells. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina, which was confirmed by scRNA-sequencing of Vsx2SEKO mice.
Overall design Single cell RNA sequencing from adult WT and VSX2SE KO mouse retina and single cell ATAC-sequencing from WT mouse retina.
Please note that the scRNA-seq processed data was generated from multiple samples as indicated in the corresponding sample description field and thus, is linked to the Series records.
Contributor(s) Norrie J, Dyer M
Citation(s) 31493975
Submission date Dec 30, 2020
Last update date Jan 02, 2021
Contact name Michael A Dyer
Organization name St. Jude Children's Research Hospital
Department DNB
Street address 262 Danny Thomas
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (5)
GSM4995561 scRNA_Retina_WT_Rep1
GSM4995562 scRNA_Retina_WT_Rep2
GSM4995563 scRNA_Retina_VSX2SEKO_Rep1
This SubSeries is part of SuperSeries:
GSE87064 The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
BioProject PRJNA688704
SRA SRP299803

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE164044_RAW.tar 908.0 Mb (http)(custom) TAR (of BED, MTX, TSV)
GSE164044_scRNA_WT_VSX2-SEKO_barcodes.tsv.gz 115.6 Kb (ftp)(http) TSV
GSE164044_scRNA_WT_VSX2-SEKO_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE164044_scRNA_WT_VSX2-SEKO_matrix.mtx.gz 72.6 Mb (ftp)(http) MTX
GSE164044_scRNA_WT_barcodes.tsv.gz 56.1 Kb (ftp)(http) TSV
GSE164044_scRNA_WT_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE164044_scRNA_WT_matrix.mtx.gz 37.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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