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Sample GSM1335066 Query DataSets for GSM1335066
Status Public on Aug 14, 2014
Title WT3 [small RNA-seq]
Sample type SRA
 
Source name control retina
Organism Mus musculus
Characteristics strain background: Mixed C57BL/6J - SJL
genotype/variation: Dicerfl/fl, iCre75-
age: 4 Weeks
tissue: Retina
molecule subtype: Small RNAs/miRNA
Extracted molecule total RNA
Extraction protocol Mice were euthanized by cervical dislocation. Eyes were enucleated and retinas were dissected and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity.
Total RNA was isolated from a pool of 6 retinas per library. After removal of RNALater, Qiazol (Qiagen, Germantown, MD) was added and the tissue was disrupted using a Tissuelyser II bead mill. RNA was purified from the Qiazol homogenate using the Zymo Direct-zol (Zymo Research, Irvine, CA) protocol with on-column DNase I digestion. Libraries were made from 1 µg of total RNA utilizing the Illumina (San Diego, CA) Truseq Small RNA Sample Preparation kit, amplified with 11 rounds of PCR, and size selected for micro-RNA size inserts by gel purification. Each library was prepared to incorporate a unique index sequence which permitted multiplexing of all six libraries for sequencing. Final libraries were analyzed and quantified using the Bioanalzyer and pooled in equimolar proportions. The pooled libraries were sequenced as one 50 bp single-end run on an Illumina HiSeq 2500 instrument using a rapid-run flowcell.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description Control replicate 3; isolated retinal small RNAs
Data processing Base-calling was performed using the Illumina pipeline software ELAND v1.7
Reads were processed to remove Illumina adapter sequences and associated with samples based on the multiplex identifier. Identical reads were grouped into clusters before being mapped to mouse miRNA sequences from miRBASE (50) using the bowtie program (51)
Identical reads were grouped into clusters before being mapped to mouse miRNA sequences from miRBASE using the bowtie program
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
 
Submission date Feb 26, 2014
Last update date May 15, 2019
Contact name Xiaodong Bai
Organization name Case Western Reserve University
Department Center for RNA Molecular Biology
Street address 10900 Euclid Avenue
City Cleveland
ZIP/Postal code 44212
Country USA
 
Platform ID GPL17021
Series (2)
GSE55376 small RNAseq analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates
GSE55393 Analysis of the global retinal transcriptome of rod photoreceptor-specific Dicer1 conditional knockout mice and control littermates
Relations
BioSample SAMN02665391
SRA SRX476181

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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