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GSE61945

GSE GEO
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Human fetal pancreas transcriptome analysis

Organism: Homo sapiens
Platform: GPL9052
Samples: 2
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Oct 01 2014
Last Updated: May 15 2019
Status: Public on Aug 07 2015
Contact: Maike,,Sander (UC San Diego)

Relations

SubSeries of: GSE61948 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA262734 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP048556

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 and human fetal pancreatic tissue (days 54-57 post conception), total RNA was isolated from human embryonic stem cell derived liver progenitors and frozen human fetal pancreas. 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
Processing steps for GSE61945
  1. Quality Control.
  2. Quality of sequencing data is analyzed using the software FastQC v0.10.1.
  3. The results are examined to determine if samples are of questionable quality on an array of metrics.
  4. Mapping.
  5. Alignment of sequencing data to reference genomes is performed with the software RNA-Star 2.3.0e.
  6. Parameters are set to default and reads are mapped to references along with splice junction databases.
  7. Gene Expression Quantification.
  8. 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)

GSE61945_rpkm_table_Ensemble_annotated.txt.gz Download
GEO Samples (2)
GSM1517598 GSM1517599

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

SRA Experiments (2) and Runs (2)

Total: 6282 MB
SRX718110 SRP048556 RNA-Seq SINGLE
GSM1517598: human_fetal_panc_54to57dpc_RNAseq replicate 1; Homo sapiens; RNA-Seq
Sample: SRS713926
BioProject: PRJNA262734
BioSample: SAMN03085513
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: Human fetal pancreata
developmental stage: fetus
age: 54-57 days post conception (gestation)
tissue: pancreas
Original files (1)
Human fetal pancreata
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1593953 32342149 3266557049 1895.03 FGC0170_s_7_sequence.fastq.gz, SRR1593953 SRA
SRX718111 SRP048556 RNA-Seq SINGLE
GSM1517599: human_fetal_panc_54to57dpc_RNAseq replicate 2; Homo sapiens; RNA-Seq
Sample: SRS713927
BioProject: PRJNA262734
BioSample: SAMN03085514
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: Human fetal pancreata
developmental stage: fetus
age: 54-57 days post conception (gestation)
tissue: pancreas
Original files (1)
Human fetal pancreata
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR1593954 79103953 7910395300 4386.99 FGC0175_s_7_sequence.fastq, SRR1593954 SRA

Linked Publications (1)

A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
Cell reports · 2015

Data Files (2)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— FGC0170_s_7_sequence.fastq.gz RNA-Seq 1.9 GB link
— FGC0175_s_7_sequence.fastq RNA-Seq 4.3 GB link