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| Status |
Public on Nov 28, 2015 |
| Title |
Affymetrix Human Exon 1.0 ST Array data for human induced pluripotent stem cells (hiPSCs) and human fibroblasts |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Human genomic variations are associated with several phenotypic traits, such as facial features or hereditary diseases. These variations can be, for example, single nucleotide polymorphisms (SNPs) or copy number variations (CNVs). Several genome-wide studies detecting the correlations between genomic variants and gene expression levels have been performed. In this study, we have studied human embryonic stem cells and human induced pluripotent stem cells and computationally identified the associations between SNPs and expression levels of exons, transcripts and genes as well as associations between CNVs and gene expression levels. We have identified SNP genotypes and gene copy numbers with genome wide Affymetrix SNP arrays and expression levels are measured with Affymetrix Exon arrays. For identifying SNPs that reliably correlate with expression levels, we filtered out the values that may cause variability to the expression values, such as the values measured with probes locating in SNP-areas. Additionally, we perform downstream analyses such as transcription factor binding site analysis and enrichment analysis. Further, we detected the genes that could be associated both with CNVs and SNPs and as expected according to earlier studies, we identify a few of this kind of genes. Overall, we could find several CNVs that correlated with gene expression levels while only few cases of SNPs that correlated with expression levels could be found as the sample size was small. However, as stem cells are hoped to be used in personalized disease treatments, our findings are important and provide a useful test set for experimental laboratory studies. In addition, our results open an interesting future direction to study how our findings correlate with the diversity of stem cell lines such as the variation in their differentiation potential.
In the study, data from GEO Series GSE15097 and Series GSE26173 was also used.
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| Overall design |
Eight human induced pluripotent stem cell samples and three fibroblasts were hybridized to exon arrays.
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| Contributor(s) |
Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 29, 2012 |
| Last update date |
Nov 29, 2015 |
| Contact name |
Reija Autio |
| Organization name |
Tampere University of Technology
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| Department |
SGN
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| Street address |
Korkeakoulunkatu 1
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| City |
Tampere |
| ZIP/Postal code |
33101 |
| Country |
Finland |
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| Platforms (3) |
| GPL8238 |
[HuEx10stv2_Hs_ENSG] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1] |
| GPL16340 |
[HuEx10stv2_Hs_ENST] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1] |
| GPL16341 |
[HuEx10stv2_Hs_ENSE] Affymetrix Human Exon 1.0 ST Array [Brainarray Version 11.0.1] |
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| Samples (33)
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| GSM1046229 |
Parental Fibroblast line MRC5, passage 19 ENSG |
| GSM1046230 |
Parental Fibroblast line HFF, passage 11 ENSG |
| GSM1046231 |
Parental Fibroblast line IMR90, passage 14 ENSG |
| GSM1046232 |
hiPSC line FiPS1-14, passage 13 ENSG |
| GSM1046233 |
hiPSC line FiPS2-10, passage 16 ENSG |
| GSM1046234 |
hiPSC line FiPS2-13, passage 12 ENSG |
| GSM1046235 |
hiPSC line FiPS3-12, passage 19 ENSG |
| GSM1046236 |
hiPSC line FiPS5-3, passage 12 ENSG |
| GSM1046237 |
hiPSC line FiPS5-7, passage 10 ENSG |
| GSM1046238 |
hiPSC line FiPS6-3, passage 14 ENSG |
| GSM1046239 |
hiPSC line FiPS6-12, passage 14 ENSG |
| GSM1046240 |
Parental Fibroblast line MRC5, passage 19 ENST |
| GSM1046241 |
Parental Fibroblast line HFF, passage 11 ENST |
| GSM1046242 |
Parental Fibroblast line IMR90, passage 14 ENST |
| GSM1046243 |
hiPSC line FiPS1-14, passage 13 ENST |
| GSM1046244 |
hiPSC line FiPS2-10, passage 16 ENST |
| GSM1046245 |
hiPSC line FiPS2-13, passage 12 ENST |
| GSM1046246 |
hiPSC line FiPS3-12, passage 19 ENST |
| GSM1046247 |
hiPSC line FiPS5-3, passage 12 ENST |
| GSM1046248 |
hiPSC line FiPS5-7, passage 10 ENST |
| GSM1046249 |
hiPSC line FiPS6-3, passage 14 ENST |
| GSM1046250 |
hiPSC line FiPS6-12, passage 14 ENST |
| GSM1046251 |
Parental Fibroblast line MRC5, passage 19 ENSE |
| GSM1046252 |
Parental Fibroblast line HFF, passage 11 ENSE |
| GSM1046253 |
Parental Fibroblast line IMR90, passage 14 ENSE |
| GSM1046254 |
hiPSC line FiPS1-14, passage 13 ENSE |
| GSM1046255 |
hiPSC line FiPS2-10, passage 16 ENSE |
| GSM1046256 |
hiPSC line FiPS2-13, passage 12 ENSE |
| GSM1046257 |
hiPSC line FiPS3-12, passage 19 ENSE |
| GSM1046258 |
hiPSC line FiPS5-3, passage 12 ENSE |
| GSM1046259 |
hiPSC line FiPS5-7, passage 10 ENSE |
| GSM1046260 |
hiPSC line FiPS6-3, passage 14 ENSE |
| GSM1046261 |
hiPSC line FiPS6-12, passage 14 ENSE |
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| Relations |
| BioProject |
PRJNA182371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42625_RAW.tar |
936.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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