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Series GSE200140 Query DataSets for GSE200140
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
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.
 
Overall design RNA from the mouse cortex was analyzed by RNA sequencing of 8 biological replicates per group using an Illumina NextGen system (NS500213).
 
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
Phone 496963017621
Organization name University Hospital Frankfurt
Department Clinical Pharmacology
Lab Clinical Pharmacology
Street address Theodor Stern Kai 7
City Frankfurt
State/province Hessen
ZIP/Postal code 60590
Country Germany
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (16)
GSM6012594 ChR2-flfl mouse #26
GSM6012595 ChR2-flfl mouse #27
GSM6012596 ChR2-flfl mouse #32
Relations
BioProject PRJNA823048

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
GSE200140_ELP_EdgeR_36930_allgenes.txt.gz 5.6 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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