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Series GSE165344 Query DataSets for GSE165344
Status Public on Feb 04, 2021
Title Cell-autonomous retinoic acid receptor signaling alters enteric nervous system development with stage-specific effects in mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Determine how blocking retinoic acid receptor (RAR) signaling within enteric neural crest-derived cells (ENCDC) from E11.5 stomach or E13.5 colon alters mRNA abundance. These ENCDC become the enteric nervous system.
Methods: Enteric nervous system precursors were isolated from mouse E11.5 stomach or E13.5 colon using fluorescence activated cell sorting to purify TdTomato or EYFP expressing cells respectively from fetal bowel. The RarαDN allele encodes a potent RAR dominant negative protein that is expressed after CRE-mediated DNA recombination. Tamoxifen-activated CRE-ERT2 was expressed from the Ret locus for E13.5 colon studies and mice were tamoxifen treated at E10.5 prior to cell sorting. The Wnt1Cre allele was employed for E11.5 stomach studies. RNA-SEQ was performed in quadruplicate using Illumina HiSeq 4000. Sequence reads that passed quality filters were aligned to remove repeat sequences and ribosomal RNA reads and then processed using RNA-Seq unified mapper (RUM) package. RUM files were visualized in the TessLA browser for subsequent analyses.
Results: Transcriptional profiling shows RarαDN differentially impacts gene expression in E11.5 stomach and E13.5 colon enteric neural crest-derived cells (ENCDC) that become the enteric nervous system.
Conclusions: Blocking of RAR signaling in ENCDC causes dramatic changes in gene expression during early development in a stage-specific manner.
 
Overall design Gene expression profiles for ENCDC that expressed a dominant negative RAR protein were compared to ENCDC that did not express this dominant negative RAR. All ENCDC expressed a fluorescent reporter (EYFP for E13.5 colon and TdTomato for E11.5 stomach ENCDC). Mice used for E13.5 colon studies had been tamoxifen-treated at E10.5.
 
Contributor(s) Heuckeroth RO, Gao T
Citation(s) 33848271
Submission date Jan 22, 2021
Last update date May 06, 2021
Contact name Robert O Heuckeroth
Organization name Children's Hospital of Philadelphia
Department Research Institute
Lab ARC Room 1116I
Street address 3615 Civic Center Blvd
City Philadelphia
State/province PENNSYLVANIA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (15)
GSM5031897 RETCre Control #1
GSM5031898 RETCre Control #2
GSM5031899 RETCre Control #3
Relations
BioProject PRJNA694135
SRA SRP302899

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
GSE165344_RNA_SEQ_Processed_Data.xls.gz 4.7 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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