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Sample GSM1574325

Query DataSets for GSM1574325

Status

Public on Oct 12, 2015

Title

P1_Dicer_mut_n1

Sample type

SRA

Source name

sciatic nerves

Organism

Mus musculus

Characteristics

strain: mixed
genotype: dhhCre+/- Dicerfl/fl
age: postnatal day 1

Extracted molecule

total RNA

Extraction protocol

Sciatic nerves were freed from perineurial fibroblast layer and homogenized with a chilled pestle. Total RNA was subsequently extracted using Qiazol according to manufacturers description.
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were depleted of ribosomal RNA using Ribo Zero Gold (Epicentre¨) and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit¨ (1.0) Fluorometer and the Caliper GX LabChip¨ GX (Caliper Life Sciences, Inc.). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-HCl 10 mM (pH 8.5) with 0.1% Tween 20. The TruSeq PE Cluster Kit v3-cBot-HS or TruSeq SR Cluster Kit v3-cBot-HS (Illumina, Inc.) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing were performed on the Illumina HiSeq 2000 paired end at 2 X101 bp or single end 100 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc.)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Re-accessioned as GSM1581954

Data processing

the obtained raw reads were first cleaned by removing adapter sequences and trimming low quality ends. Sequence alignment of the resulting high-quality reads to the mouse reference genome (build mm10) and quantification of gene level expression was carried out using RSEM (Version 1.2.12).
The R software package from Bioconductor, DESeq2 (Version 1.4.5)33, was used to assess the statistical significance of differences in gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet include RPKM values, log2 fold changes and adjusted p-values

Submission date

Dec 29, 2014

Last update date

Jul 11, 2022

Contact name

Robert Blelloch

Organization name

UCSF

Department

Urology

Street address

35 Medical Center Way