|
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.
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|
|
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)
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|
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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 |