|
| Status |
Public on Oct 12, 2015 |
| Title |
P4_n2 |
| Sample type |
SRA |
| |
|
| Source name |
sciatic nerves
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild-type
age: postnatal day 4
|
| 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.
After RNA quality assessment with a Bioanalyzer 2100 (Agilent), the fraction of 15-35 nt was purified using gel electrophoresis and linked to Illumina TruSeq adapters. For multiplexing, barcodes were introduced during PCR amplification. Sequencing was performed using the Illumina HiSeq 2000 platform with a read length of 50 bp
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA pipeline v.1.8 was used for the base-calling of this run.
The ncPRO pipeline was used to map the reads against the mouse genome (version mm9) and the rat genome (version rn4). We used Bowtie with default options (but -m 5000 and -e 50).
The miRNA quantities were normalized by the number of mapped reads from the corresponding library and then multiplied by 1000000 to obtain the unit in reads per million (RPM).
The R software package DESeq R (Version 1.14.0) was used to assess the statistical significance of differences in gene expression.
Genes showing altered expression with adjusted p-value < 0.05 (Benjamini and Hochberg method) were considered as differentially expressed.
Genome_build: mm9 (rn4 for primary SC)
Supplementary_files_format_and_content: Tab delimited read count
|
| |
|
| 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
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE64561 |
Small RNA expression in wild-type sciatic nerves during myelination |
| GSE64562 |
Sequencing analysis of sciatic nerves during myelination |
|
| Relations |
| BioSample |
SAMN03273750 |
| SRA |
SRX825354 |
