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Sample GSM6012607

Query DataSets for GSM6012607

Status

Public on Sep 06, 2023

Title

Avil-ChR2 mouse#38

Sample type

SRA

Source name

Brain Cortex

Organism

Mus musculus

Characteristics

strain: C57BL6
tissue: Cortex
age: 7 days
gender: male
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_AvilChR06_38

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

Goethe University Frankfurt