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| Status |
Public on Mar 03, 2023 |
| Title |
Transcriptional analysis of murine cortical astrocytes with adeno-associated viral transduction with and without 4x6T miR cassette, vs transgenically labeled astrocytes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We generated adeno-associated Cre viral vectors with improved astrocyte-specific expression by including a cassette of miRNA targeting sequences (4x6T) to decrease off-target expression. We delivered these viruses in Ribotag mice using the PHP.eB serotype, either intracortically or systemically. We compared these samples with mice that received intracortical AAV2/5::GfaABC1D-Cre and transgenic Aldh1l1-CreERT2/Ribotag mice.
We sequenced whole-tissue RNA as well as ribosomally-loaded astrocyte-enriched mRNA to assess cell-type specificity of viruses as well as virus-related transcriptomic changes.
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| Overall design |
Four cohorts were generated: Aldh1l1-CreERT2/Ribotag transgenic mice (control mice with highly astrocyte-specific labeled ribosomes); AAV2/5::GfaABC1D-Cre intracortical injection mice (standard astrocyte-enriched virus); PHP.eB::GfaABC1D-Cre-4x6T intracortical injection mice; and PHP.eB::GfaABC1D-Cre-4x6T systemic injection mice. Each cohort included 4 mice, and each mouse had both input (whole-cortex) and immunoprecipitated (ribosomally loaded, astrocyte-enriched) mRNA samples.
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| Contributor(s) |
Gleichman AJ, Carmichael TS |
| Citation(s) |
37973910 |
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| Submission date |
Mar 01, 2023 |
| Last update date |
Dec 07, 2023 |
| Contact name |
Riki Kawaguchi |
| Organization name |
University of California, Los Angeles
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| Department |
Department of Psychiatry and Neurology Department of Psychiatry
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| Lab |
AMRF Functional Genomics Common Research Resource
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| Street address |
760 Westwood Plaza, Room 37-420
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1759 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (32)
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| GSM7073978 |
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 1 |
| GSM7073979 |
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 2 |
| GSM7073980 |
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 3 |
| GSM7073981 |
AAV2/5 GfaABC1D-Cre mouse, input RNA, rep 4 |
| GSM7073982 |
Aldh1l1-CreERT2 mouse, input RNA, rep 1 |
| GSM7073983 |
Aldh1l1-CreERT2 mouse, input RNA, rep 2 |
| GSM7073984 |
Aldh1l1-CreERT2 mouse, input RNA, rep 3 |
| GSM7073985 |
Aldh1l1-CreERT2 mouse, input RNA, rep 4 |
| GSM7073986 |
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 1 |
| GSM7073987 |
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 2 |
| GSM7073988 |
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 3 |
| GSM7073989 |
PHPeB GfaABC1D-Cre intracortical mouse, input RNA, rep 4 |
| GSM7073990 |
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 1 |
| GSM7073991 |
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 2 |
| GSM7073992 |
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 3 |
| GSM7073993 |
PHPeB GfaABC1D-Cre systemic mouse, input RNA, rep 4 |
| GSM7073994 |
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 1 |
| GSM7073995 |
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 2 |
| GSM7073996 |
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 3 |
| GSM7073997 |
AAV2/5 GfaABC1D-Cre mouse, immunoprecipitated mRNA, rep 4 |
| GSM7073998 |
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 1 |
| GSM7073999 |
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 2 |
| GSM7074000 |
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 3 |
| GSM7074001 |
Aldh1l1-CreERT2 mouse, immunoprecipitated mRNA, rep 4 |
| GSM7074002 |
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 1 |
| GSM7074003 |
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 2 |
| GSM7074004 |
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 3 |
| GSM7074005 |
PHPeB GfaABC1D-Cre intracortical mouse, immunoprecipitated mRNA, rep 4 |
| GSM7074006 |
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 1 |
| GSM7074007 |
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 2 |
| GSM7074008 |
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 3 |
| GSM7074009 |
PHPeB GfaABC1D-Cre systemic mouse, immunoprecipitated mRNA, rep 4 |
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| Relations |
| BioProject |
PRJNA940089 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE226366_Counts.xlsx |
6.9 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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