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Sample GSM6012606 Query DataSets for GSM6012606
Status Public on Sep 06, 2023
Title Avil-ChR2 mouse#37
Sample type SRA
 
Source name Brain Cortex
Organism Mus musculus
Characteristics strain: C57BL6
tissue: Cortex
age: 7 days
gender: female
genotype: Advillin-ChR2 positive
treatment: blue light
Treatment protocol Mice were exposed to blue light in a chamber from postnatal day p1 to p5, once daily for 1h. Tissue was dissected on p7.
Growth protocol does not apply
Extracted molecule total RNA
Extraction protocol Cortices were removed, flash frozen on dry ice, and total RNA was extracted using Qiagen RNeasy spin columns. Illumina TruSeq mRNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 02_AvilChR05_37
Data processing Sample quality was assessed with demultiplexed fastq.gz files and subsequently 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.
Results were displayed with ArrayStar 17 (Lasergene) including the amount of mapped reads, target length, source length and position, strand, genes and gene IDs, annotated according to the mm10 assembly. The reads were normalized according to EdgeR.
Normalized reads were analyzed with ArrayStar 17, which uses general linear models to assess differential expression.
Genes were filtered for at least 12 valid values (EdgeR log2 > -5) out of 16 samples to exclude low expression genes.
Assembly: mm10
Supplementary files format and content: ELP_EdgeR_36930_allgenes.txt (tab delimited txt file with EdgeR normalized counts for each biological replicate i.e. mouse )
ELPassembly_EdgeR_Valid21695.txt (tab delimited txt file with EdgeR normalized counts of the biological replicates, i.e. mice of filtered valid genes)
 
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
 
Platform ID GPL19057
Series (1)
GSE200140 Transcriptome analysis by RNA sequencing of the cortical brain in a mouse model of early life pain
Relations
BioSample SAMN27292806
SRA SRX14732620

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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