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Status |
Public on Sep 23, 2024 |
Title |
Embryonic meninges, E14.5, Foxc1 +/+, embryo 4 |
Sample type |
SRA |
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|
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).
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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.
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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 |