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Sample GSM7105837 Query DataSets for GSM7105837
Status Public on Sep 23, 2024
Title Embryonic meninges, E14.5, Foxc1 +/+, embryo 4
Sample type SRA
 
Source name meninges
Organism Mus musculus
Characteristics tissue: meninges
genotype: Foxc1 +/+
age: E14.5
Growth protocol The embryos carrying Foxc1 delta/delta null mutation were generated by deletion of the entire Foxc1 open reading frame by crossing Foxc1 flox/flox mice to EIIa-cre mice as described previously (Sasman et al., 2012, PMID: 22522965).
Extracted molecule total RNA
Extraction protocol Foxc1 null and wild-type embryos were harvested at E14.5 in cold PBS and dissected in RNALater solution (Thermo). RNA was isolated from meningeal tissue by RNeasy Mini Kit (Qiagen).
Library construction and sequencing was performed at the BRC Sequencing Core (University of British Columbia, Vancouver, BC). Sample quality was checked using the Agilent 2100 Bioanalyzer to ensure high RNA integrity. Samples were then prepped following the standard protocol for the NEBnext Ultra II Stranded mRNA (New England Biolabs).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 43bp x 43bp
Data processing Data de-multiplexed using Illumina's bcl2fastq2. Illumina BaseSpace FASTQ generation version 1.0.0.
De-multiplexed read sequences aligned to the Mus musculus (mm10) reference sequence using STAR aligner. Illumina BaseSpace workflow version 1.1.0.
Assembly and differential expression was estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub. Illumina BaseSpace Cufflinks Assembly & DE version 2.1.0.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample. Cuffdiff defferential expression analysis results provided as comma separated values file.
 
Submission date Mar 20, 2023
Last update date Sep 23, 2024
Contact name Serhiy Havrylov
E-mail(s) havrylov@ualberta.ca
Phone 7804928835
Organization name University of Alberta
Department Medical Genetics
Lab Ordan Lehmann
Street address 8-29 Medical Sciences Building
City Edmonton
State/province Alberta
ZIP/Postal code T6G2H7
Country Canada
 
Platform ID GPL19057
Series (1)
GSE227703 Gene expression changes associated with loss of Foxc1 in meningeal tissue of E14.5 mouse embryos
Relations
BioSample SAMN33829181
SRA SRX19730503

Supplementary file Size Download File type/resource
GSM7105837_W4.genes.fpkm_tracking.gz 670.5 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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