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Series GSE176435 Query DataSets for GSE176435
Status Public on Nov 17, 2021
Title Effect of Environmental Enrichment on Transcriptomic Profile and Chromatin Accessibility of Cortical Neurons
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Wildtype Swiss webster mice were exposed to four weeks of either standard housing (SH) or environmental enrichment (EE) starting at one month of age. EE chambers were large mouse cages containing two nesting/burrowing materials, a running wheel, and toys that were changed every 3-4 days for novelty and exploration. By contrast, SH control mice were housed with an equal number of littermates in smaller, standard cages containing only one nesting material and no toys or running wheel. We used an antibody for Rbfox3 (NeuN) to sort neuronal nuclei from the dissociated frontal cortices of male mice reared in EE and SH conditions. Isolated neuronal nuclei were then subjected to ATAC-seq or nuclear RNA isolation (random hexamer priming) as per published protocols.
 
Overall design Examination of ATAC-seq and nuclear RNA-seq signal from cortical neurons after enrichment
 
Contributor(s) Tsai L, Raju RM, Barker SJ
Citation(s) 34731014
Submission date Jun 09, 2021
Last update date Feb 16, 2022
Contact name Ravikiran Raju
E-mail(s) Ravikiran.Raju@childrens.harvard.edu
Phone 9086723259
Organization name MIT
Department Picower Institute
Lab Li-Huei Tsai
Street address 15A Maple Ave
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (43)
GSM5365486 Female standard housed (SH) cortical neurons - ATACseq - rep1
GSM5365487 Female standard housed (SH) cortical neurons - ATACseq - rep2
GSM5365488 Female standard housed (SH) cortical neurons - ATACseq - rep3
Relations
BioProject PRJNA736242
SRA SRP323333

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Supplementary file Size Download File type/resource
GSE176435_160718Tsa_Female_EEvsSH_ATACseq_countmatrix.txt.gz 3.1 Mb (ftp)(http) TXT
GSE176435_171030TsaA_Male_EEvsSH_ATACseq_countmatrix.txt.gz 5.7 Mb (ftp)(http) TXT
GSE176435_171107Tsa_Male_EEvsSH_RNAseq_countmatrix.txt.gz 641.2 Kb (ftp)(http) TXT
GSE176435_180821TsaA_Female_EEvsSH_RNAseq_CountMatrix.txt.gz 1.3 Mb (ftp)(http) TXT
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