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Sample GSM3263649 Query DataSets for GSM3263649
Status Public on Oct 01, 2018
Title 983-LW-8
Sample type SRA
 
Source name WT_retina
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: wild type
age: 3 months old
treatment: naïve
tissue: retina
Treatment protocol Naïve mice aged 3 months with no additional treatment.
Growth protocol Tissue extracted from animals.
Extracted molecule total RNA
Extraction protocol Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 983-LW-8-TAATGCGC-TATAGCCT_S392
Data processing DNase-treated total RNA quality was assessed using the 2100 Bioanalyzer (Agilent). Samples with a RNA integrity number greater than 6 were used to generate polyA (mRNA) enriched libraries using stranded mRNA sample kits with indexed adaptors (New England BioLabs).
Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).
Pooled libraries were subjected to 100 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). 
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
Reads were aligned to the GENCODE GRCm38.p5 genome using STAR v2.5.3a. 
GENCODE vM12 gene annotations were provided to STAR to improve the accuracy of mapping. Quality control on raw reads was performed using FastQC.
featureCounts v1.15.2 was used to count the number of mapped reads to each gene.
Significantly differential expressed genes with adjusted p-value < 0.05 and absolute fold change > 2 were detected by DESeq2 v1.14.
Genome_build: GENCODE GRCm38.p5 
Supplementary_files_format_and_content: counts
 
Submission date Jul 11, 2018
Last update date Oct 01, 2018
Contact name Lauren Katie Wareham
E-mail(s) lauren.wareham@vanderbilt.edu
Phone 8575408019
Organization name Vanderbilt University Medical Center
Department Vanderbilt Eye Institute
Lab Sappington Lab
Street address 2213 Garland Avenue, MRBIV 11435a
City Nashville
State/province Tennessee
ZIP/Postal code 37232
Country USA
 
Platform ID GPL24247
Series (1)
GSE116916 RNAseq quantitative analysis of naïve wild type and interleukin-6 knockout mice
Relations
BioSample SAMN09642192
SRA SRX4378904

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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