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| Status |
Public on Sep 06, 2023 |
| Title |
Transcriptome analysis by RNA sequencing of the cortical brain in a mouse model of early life pain |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Preterm children are frequently exposed to various painful stimuli in the early days of life. Early-life-pain (ELP) may affect cortical development and reduce the fitness and resilience in during youth and adult life. We developed an optogenetic Cre/loxP mouse model of "early-life-pain" (ELP) using mice with transgenic expression of an improved channelrhodopsin-2 (ChR2)/Td-Tomato fusion protein under control of the advillin promoter, that drives expression of ChR2/td-Tomato specifically in primary somatosensory neurons of the dorsal root ganglia (Avil-ChR2 mice). Floxed ChR2/td-Tomato littermates (ChR2-flfl) were used as controls. Mice were exposed to blue light in a chamber once daily from postnatal day P1-P5. Cortical gene expression was analyzed at P7 via RNA-sequencing in eight biological replicates per group. Cortices were rapidly excised and snap froze in liquid nitrogen. Total RNA was extracted from with Qiagen RNeays spin columns and quantified on a Nanodrop. Sequencing libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit, and sequencing was performed on an Illumina NGS platform. The alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Sequence reads were normalized with EdgeR and analyzed in ArrayStar 17 (Lasergene). Differential gene expression was assessed with general linear models and adjusted according to Benjamini Hochberg.
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| Overall design |
RNA from the mouse cortex was analyzed by RNA sequencing of 8 biological replicates per group using an Illumina NextGen system (NS500213).
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| Contributor(s) |
Tegeder I |
| Citation(s) |
37635256 |
| |
| Submission date |
Apr 04, 2022 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Irmgard Tegeder |
| E-mail(s) |
itegeder@hotmail.com
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| Phone |
496963017621
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| Organization name |
Goethe University Frankfurt
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| Department |
Clinical Pharmacology
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| Lab |
Clinical Pharmacology
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| Street address |
Theodor Stern Kai 7
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| City |
Frankfurt |
| State/province |
Hessen |
| ZIP/Postal code |
60590 |
| Country |
Germany |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA823048 |
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