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Sample GSM6779200 Query DataSets for GSM6779200
Status Public on Jun 07, 2023
Title Stra6_VAD_rep2
Sample type SRA
 
Source name C57BL/6
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Stra6-/-
treatment: diet: Vitamin A deficient diet
treatment: time_on_diet: 12 weeks
tissue type: RPE-choroid
Treatment protocol After weaning, Stra6 knockout and WT mice were maintained on a diet deficient (0 IU/g) or sufficient (4 IU/g) in vitamin A for 12 weeks
Growth protocol Before weaning (~28 days), the pups were kept with dams maintained on a standard rodent chow diet.
Extracted molecule total RNA
Extraction protocol RNA was harvested using TRIzol and Rneasy mini plus kit (Qiagen). At least 1 ug of total RNA was used for the construction of sequencing libraries (Novogene).
Library preparation and construction were performed by Novogene.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Sample SD2
Data processing The paired-end reads, provided by the fastq files, were aligned to to GRCm38/mm10 genome (UCSC genome source, 2011) using STAR (version 2.5.3a). An average of 87.4% of reads was uniquely mapped to the reference genome. The correlated annotation file (GTF) was applied and the gene expression level was determined by RSEM (version 1.2.30) quantification. Count normalization and differential gene expression was carried out using DESeq2 version 1.32.0. The Wald test was used for comparisons between treatment groups. To account for multiple testing, the FDR cutoff was set at 0.05. gProfiler was used for Gene Ontology and pathway analyses. An overrepresentation test was applied for significant changes in gene expression.
Assembly: mm10
Supplementary files format and content: comma separated values files include normalized counts produced by DESeq2
 
Submission date Dec 02, 2022
Last update date Jun 07, 2023
Contact name Johannes von Lintig
E-mail(s) jxv99@case.edu
Phone 2163683528
Organization name Case Western Reserve University
Department Pharmacology
Street address 2109 Adelbert Road
City Cleveland
ZIP/Postal code 44106
Country USA
 
Platform ID GPL24247
Series (1)
GSE219252 Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet
Relations
BioSample SAMN31997618
SRA SRX18471294

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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