GSE61948
GSE GEOTranscriptome and cistrome analysis reveals synergistic roles for Sox9 and Pdx1 in lineage allocation of foregut progenitor cells
Organism:
Mus musculus
Platform:
GPL7202
Samples:
15
Experiment Types:
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by array
Submitted:
Oct 01 2014
Last Updated:
May 15 2019
Status:
Public on Aug 07 2015
Contact:
Maike,,Sander (UC San Diego)
Relations
SuperSeries of: GSE61945
SuperSeries of: GSE61946
SuperSeries of: GSE61947
SuperSeries of: GSE62023
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA262729
Summary
This SuperSeries is composed of the SubSeries listed below.
Overall Design
Refer to individual Series
Analysis (9 steps)
View Data Processing
Processing steps for GSE61948
- Quality Control.
- Quality of sequencing data is analyzed using the software FastQC v0.10.1.
- The results are examined to determine if samples are of questionable quality on an array of metrics.
- Mapping.
- Alignment of sequencing data to reference genomes is performed with the software RNA-Star 2.3.0e.
- Parameters are set to default and reads are mapped to references along with splice junction databases.
- Gene Expression Quantification.
- To obtain gene expression values, several quantification methods are used (Sailfish 0.6.3, Cufflinks 2.2.0).
Showing first 8 steps.
Supplementary Files (1)
GSE61948_RAW.tar
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Dataset Citations (1)
A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
PMID 26440894
· 2015
· Cell reports
Hung Ping Shih, Philip A Seymour, Nisha A Patel, Ruiyu Xie, Allen Wang, Patrick P Liu, Gene W Yeo, Mark A Magnuson, Maike Sander