|
| Status |
Public on Mar 07, 2014 |
| Title |
Nr35 +GlcN |
| Sample type |
SRA |
| |
|
| Source name |
total RNA from liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: 108 weeks of age
agent: 10 g / kg GlcN in Diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Nr35
|
| Data processing |
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v1.4.1); C. elegans samples were mapped vs. the C. elegans genome (ce10); M. musculus samples were mapped vs. the M. musculus genome (mm10)
For counting the reads per gene (raw counts) the Python package HTSeq was used in mode ‘union’ together with the Ensembl gene annotation. Only uniquely mapable reads were regarded.
Genome_build: ce10
Genome_build: mm10
Supplementary_files_format_and_content: Nr01-12_25-36_counts_ce_mm.xls
|
| |
|
| Submission date |
Feb 10, 2014 |
| 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) |
| GSE54853 |
RNA-seq of C.elegans and M.musculus in the presence and absence of D-Glucosamine (GlcN) |
|
| Relations |
| BioSample |
SAMN02639724 |
| SRA |
SRX469132 |
