|
| Status |
Public on Jan 21, 2015 |
| Title |
CD1 female OE |
| Sample type |
SRA |
| |
|
| Source name |
Olfactory Epithelium
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
genotype/variation: wildtype
gender: female
tissue/cell type: Olfactory Epithelium (OE)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Olfactory Epithelia were prepared and pooled from eight individuals for each condition. ORNs were obtained from OMP-GFP mice and enriched by FACS sorting. Subsequently RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer´s protocol including the optional on-column DNaseI digestion.
Libraries for NGS sequencing were prepared from RNA and subjected to DSN normalization by standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
tissue pool of eight adult animals
CD1OEfemale
|
| Data processing |
Illumina sequencing was performed on a Genome Analyzer IIx using single end 36-bp (OE) respectively 75-bp (ORNs) reads. In case of C57BL/6J mice and FACS-sorted mice (heterozygous) were sequenced on a HiSeq-2000 by standard Illumina protocols (101-bp, paired end).
RNA-Seq reads were aligned to version mm9 of mouse reference genome and transcriptome using TopHat (v2.0.7) which utilizes the ultra-fast short–read mapping program Bowtie to arrange the alignment
Aligned RNA-Seq reads for each sample were assembled into transcripts and their abundance was estimated by the program Cufflinks (v1.3.3) using the RefSeq mm9 reference transcriptome in Gene Transfer Format (GTF) obtained from the UCSC Genome Bioinformatics database (University of California Santa Cruz)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for sample
|
| |
|
| Submission date |
Jan 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ninthujah Kanageswaran |
| Organization name |
Ruhr-University Bochum
|
| Department |
Biology and Biotechnology
|
| Lab |
Cell Physiology
|
| Street address |
Universitätsstr. 150
|
| City |
Bochum |
| ZIP/Postal code |
44780 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE53793 |
Deep sequencing of the murine olfactory receptor neuron transcriptome |
|
| Relations |
| BioSample |
SAMN02567296 |
| SRA |
SRX404376 |
