GSE61946
GSE GEOhESC-derived liver transcriptome analysis
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Summary
To characterize the transcriptional programs that underlie pancreas differentiation and identity, we have generated genome-scale expression profiles by RNA-seq from human embryonic stem cell derived liver progenitors and human fetal pancreatic tissue (days 54-57 post conception). These samples were compared to those already published transcriptomes (Xie et al., 2013). Together, these samples were used to perform principles compotent analysis. Once this was performed, we were able to identify transcription factors that were important in the identity of each cell type.
Overall Design
To generate genome-scale expression profiles by RNA-seq from human embryonic stem cell derived liver progenitors, total RNA was isolated from human embryonic stem cell derived liver progenitors. Libraries were sequenced and mapped to the hg19 version of the human genome. Gene expression was determined using Sailfish. These samples were compared to those already published transcriptomes (Xie et al., 2013). Together, these samples were used to perform principles compotent analysis.
Analysis (9 steps)
View Data Processing- 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).
Supplementary Files (1)
GEO Samples (2)
Dataset Citations (1)
SRA Experiments (2) and Runs (2)
Total: 3177 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1593955 | 27781131 | 2778113100 | 1567.38 | FGC0186_s_7_sequence.fastq.gz, SRR1593955 | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1593956 | 27896714 | 2789671400 | 1609.88 | FGC0186_s_8_sequence.fastq.gz, SRR1593956 | SRA |