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| Status |
Public on Aug 14, 2014 |
| Title |
Mut1 [small RNA-seq] |
| Sample type |
SRA |
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| Source name |
cKO retina
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
cKO replicate 1; isolated retinal small RNAs
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| 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
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| Submission date |
Feb 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaodong Bai |
| Organization name |
Case Western Reserve University
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| Department |
Center for RNA Molecular Biology
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| Street address |
10900 Euclid Avenue
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| City |
Cleveland |
| ZIP/Postal code |
44212 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02665390 |
| SRA |
SRX476182 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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