|
| Status |
Public on Jun 02, 2020 |
| Title |
E16.5_oONL1 |
| Sample type |
SRA |
| |
|
| Source name |
E16.5 Outer Olfactory Nerve Layer
|
| Organism |
Mus musculus |
| Characteristics |
embryonic stage: E16.5
tissue: Outer Olfactory Nerve Layer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Olfactory and trigeminal nerve regions were isolated in situ by laser microdissection and RNA was extracted using the PicoPure RNA isolation kit (Arcturus). The SMART-seq V4 ultra low-input RNA kit for sequencing was used for cDNA synthesis and amplification using ~2000 pg of RNA.
1 ng of amplified cDNA was used for paired-end library preparation using the Nextera XT DNA library prep kit. Libraries were pooled to a final concentration of 4 nM and quantified using the KAPA Library Quantification Kit (ABI Prism) from Kapa Biosystems.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality of sequenced reads was assessed with FastQC and mapped to mm10 mouse genome using Tophat2 version 2.1.0.
Alignment files were sorted by name and a count matrix was produced using HTSeq. The FPKM and differential expression analysis were generated using DESeq2 version 3.7.
Deseq outputs were combined into one file using a custom perl script. Genes where FPKM was less than 1 in all samples were removed using a custom perl script.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx and DESeq outputs (differential expression analysis, FPKM based on counts table)
|
| |
|
| Submission date |
Oct 08, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Clare Baker |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Cambridge
|
| Department |
Dept. Physiology, Development & Neuroscience (PDN)
|
| Street address |
Downing Street
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 3DY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE138596 |
Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach |
|
| Relations |
| BioSample |
SAMN12994911 |
| SRA |
SRX6965726 |
