Mus musculus Cranial Facial Atlas

Overview
Analysis NameMus musculus Cranial Facial Atlas
MethodNCBI GEO (GSE55966)
SourceMmus_cranialFacial_expression_FPKM_updated.txt
Date performed2017-07-05
Sample GSM1349577 Query DataSets for GSM1349577
Status Public on Mar 18, 2014
Title E10.5 dorsal control neural epithelium
Sample type SRA
 
Source name Mouse embryo_E10.5
Organism Mus musculus
Characteristics strain: CD1
Stage: E10.5
tissue: dorsal control neural epithelium
Extracted molecule total RNA
Extraction protocol RNA was purified using the ZR RNA MicroPrep kit (Zymo).
RNA-seq was carried out using 50b single end reads on the Illumina Hi-Seq 2500 machine according to Illumina protocols, with read depths > 40 million.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description E10.5 DCNE
Data processing RNA-seq data were analyzed by a combination of Bowtie, Tophat, and GeneSpring versions 7.3.1
RNA-seq BAM files generated using the Bowtie-Tophat2 pipeline were analyzed for the expression of known and unknown genes/transcripts using both Cufflinks2 and GeneSpring 12.6. Workflows included filtering to remove duplicate reads, and those with post-aligned read metrics mapping quality below 40, as well as the exclusion of samples that exhibited strong outlier 3’/5’ read distribution ratios.
Transcript/isoform and gene summarized expression tables were filtered to identify entities whose expression was at least 3 FPKM (Cufflinks) or 3 nRPKM (GeneSpring) in at least one sample.
The RNA-seq FPKM table was normalized using a baseline of 1 FPKM (a level of gene expression unlikely to be significant in these assays) followed by global median normalization to give a table of ratio values.
Genome_build: mm9
Supplementary_files_format_and_content: text files containing normalized expression values
 
Submission date Mar 17, 2014
Last update date Mar 18, 2014
Contact name Rebekah Karns
E-mail Rebekah.Karns@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Gastroenterology, Hepatology, & Nutrition
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45276
Country USA
 
Platform ID GPL17021
Series (2)
GSE55966 Gene expression of early craniofacial development through RNA-seq
GSE55967 A superseries of gene expression in early craniofacial development in mouse embryos at stages E8.5, E9,5, and E10.5.
Relations
BioSample SAMN02689892
SRA SRX494150

Supplementary file Size Download File type/resource
GSM1349577_E10.5_CNE.txt.gz 182.8 Kb (ftp)(http) TXT
SRX/SRX494/SRX494150 (ftp) SRA Experiment
Raw data provided as supplementary file
Processed data provided as supplementary file

Properties
Additional information about this analysis:
Property NameValue
Analysis expression organism id22
Analysis expression associated analysis id0
Analysis expression biosourceprovider id3
Analysis expression arraydesign id
Analysis expression assaydate2017-7-5 00:00:00
Analysis expression assay description
Analysis expression acquisitiondate2017-7-5 00:00:00
Analysis expression acquisition uri
Analysis expression quantificationdate2017-7-5 00:00:00
Analysis expression quantification uri
Analysis expression assay protocol id0
Analysis expression acquisition protocol id0
Analysis expression quantification protocol id0
Analysis expression assay operator id
Analysis expression quantification operator id
Analysis expression filetypemat
Analysis expression submit job1
Analysis expression fileext
Analysis expression filepath/var/other_data/organisms/mouse/Mmus/genomes/GRCm38/analysis/cranialfacial/Mmus_cranialFacial_expression_FPKM_updated.txt
Analysis expression re start
Analysis expression re end
Analysis expression feature uniquenamesuniq