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| Status |
Public on Oct 09, 2014 |
| Title |
EB |
| Sample type |
SRA |
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| Source name |
EB
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| Organism |
Homo sapiens |
| Characteristics |
tissue: hiPSC-derived embryoid bodies
passages: 10
clone: 7
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| Growth protocol |
For spontaneous differentiation through embryoid body formation, hiPSCs cultured in one well of the geltrex-coated 6-well plate, were dissociated with collogenase IV (1 mg/ml) for 5 min, and then split into small cell clumps. The small cell clumps were transferred into three 10-cm low-attached dishes fed with EB medium (knockout DMEM, 20% knockout serum replacement, 1 mM L-Glutamine, 1% nonessential amino acids, 0.1 mM 2-Mercaptoethanol and primocin). The medium was changed every two days. The embryoid bodies were culture for ten days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from embryoid bodies using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using TURBO DNA-free™ Kit (Ambion) and a second RNA extraction with TRIzol was performed.
RNA libraries were prepared for sequencing using Illumina TruSeq protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Image files were preprocessed by illumina software, which generates qseq files
qseq files were converted into fastq files by ruby scripts, and only the ones passing illumina quality controls were retained
Reads were mapped onto human reference genome hg19 by Tophat-1.3.0
Counts on Gencode Genes and RepeatMasker annotated repeat elements were calculated
Differentially expressed repeat elements were calculated by ruby scripts
Genome_build: hg19
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| 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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| Platform ID |
GPL11154 |
| Series (2) |
| GSE44646 |
Repeat elements study in pluripotent stem cells [RNA-seq] |
| GSE54726 |
Repeat elements study in pluripotent stem cells |
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| Relations |
| SRA |
SRX245557 |
| BioSample |
SAMN01924851 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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