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Sample GSM4114037 Query DataSets for GSM4114037
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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