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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 09, 2014 |
| Title |
Repeat elements study in pluripotent stem cells [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We surveyed RNA-Seq data to identify those TEs that are transcriptionally active uniquely in human pluripotent cells. We identified one endogenous retrovirus (HERV-H) family, uniquely found in primates as being unusually abundant in the transcriptome.
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| Overall design |
Poly(A)+ RNA extraction and further sequencing library construction was done for two types of cells (iPS, HFF-1) and hiPSC-derived embryoid bodies following Illumina TruSeq RNA Sample Preparation Kit protocol, which was further sequenced on Illumina HiSeq machine with single-end 101 cycles.
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| Contributor(s) |
Wang J, Xie G, Singh M, Ghanbarian AT, Raskó T, Szvetnik A, Cai H, Besser D, Prigione A, Fuchs N, Schumann G, Chen W, Lorincz MC, Ivics Z, Hurst LD, Izsvák Z |
| Citation(s) |
25317556 |
| Submission date |
Feb 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gangcai Xie |
| Organization name |
Nantong University
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| Department |
Medical school
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| Lab |
Gangcai Xie Lab
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| Street address |
Number 9, Se Yuan Road
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| City |
Nantong |
| State/province |
Jiangsu |
| ZIP/Postal code |
226019 |
| Country |
China |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE54726 |
Repeat elements study in pluripotent stem cells |
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| Relations |
| SRA |
SRP018848 |
| BioProject |
PRJNA191069 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE44646_Gene_Expression.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
| GSE44646_RepeatElements_Expression.tsv.gz |
107.5 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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