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| Status |
Public on Sep 24, 2013 |
| Title |
Aneuploid_XO |
| Sample type |
SRA |
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| Source name |
Monosomy X induced pluripotent stem cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: induced pluripotent stem cell
genotype/variation: Monosomy X
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each line was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Poly(A)+ mRNA was isolated from total RNA using Oligotex (QIAGEN). RNA was fragmented with RNase III, preparing for constructing transcriptome libraries of each iPSC cell line.
Applied Biosystems SOLiD Whole Transcriptome Analysis Kit ( http://solid.appliedbiosystems.com) were applied to perform reversed transcription from 140–200 bp isolated RNA fragments into Single-strand cDNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Data processing |
Sequence data were generated using SOLiD3 system (Applied Biosystems) following the manufacturer’s instructions.
RNA-Seq reads were mapped onto the human reference genome (NCBI37/hg19) with Corona_lite_v4.2.2 software (Applied Biosystems), setting the parameters for full-length read mapping (50, 45, 40, 35 bp) with 5, 4, 4, and 3 mismatches. Only reads that uniquely mapped to the genome and reads for genes corresponding to mRNA were chosen for subsequent analysis.
Reads density for each gene (shown as RPKM value) was calculated by the number of uniquely mapped.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID, RPKM values and chromosome coordinates for each Sample
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| Submission date |
Jul 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruosi Zhang |
| Organization name |
Beijing Institute of Genomics, Chinese Academy of Sciences
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| Street address |
NO.1 Beichen West Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL9442 |
| Series (1) |
| GSE49247 |
Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes |
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| Relations |
| BioSample |
SAMN02265243 |
| SRA |
SRX327912 |
| 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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