|
| Status |
Public on Jan 08, 2018 |
| Title |
Ohr21B |
| Sample type |
SRA |
| |
|
| Source name |
total RNA extracted from skin (ear)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
age: 29.5 months
age_category: old
tissue: skin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from was extracted as described (Baumgart et al., 2012; PMID:22487494)
Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit v2 following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ohr21B
|
| Data processing |
Illumina Casava v1.8.4 software used for extraction of FASTQ files
Reads were mapped using Tophat (v2.1.0) to the genome taken the annotation into account: -p 4 -g 1 –no-coverage-search –library-type fr-unstranded
Counting of reads per gene was done using htseq-count (0.6.1p1): htseq-count --stranded=no -m=union -a 20 -t exon
Genome_build: UCSC mm10, Gencode vM6
Supplementary_files_format_and_content: tab separated file contains read counts per gene and sample
|
| |
|
| Submission date |
Feb 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marco Groth |
| E-mail(s) |
cfngs@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE78130 |
Deep sequencing of mRNA from Mus musculus at two different timepoints in skin (ear clip) |
|
| Relations |
| BioSample |
SAMN04505014 |
| SRA |
SRX1594745 |
