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| Status |
Public on Sep 01, 2014 |
| Title |
P006 |
| Sample type |
SRA |
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| Source name |
placenta
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| Organism |
Homo sapiens |
| Characteristics |
person: child
trio: P006
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| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana™ miRNA Isolation Kit (Ambion®, Life Technologies™) according to manufacturer’s instructions
Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) + SOLiD 5500 System; DNA fragment library kit (Life Technologies, Carlsbad, CA, USA), both according to manufacturer's instructions.
45 ng total RNA was used to consruct WT RNA seq library (cDNA synthesis, cDNA amplification, SOLiDi 5500 adaptor ligation and library amplification), barcoded adaptors were applied for multiplex sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| Data processing |
DESeq package in the R statistical language and environment (version 3.0.2) was used to calculate the reads per kilobase per million reads (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts and RPKM values for each sample
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| Submission date |
Apr 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tauno Metsalu |
| Organization name |
University of Tartu
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| Street address |
Liivi 2
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| City |
Tartu |
| ZIP/Postal code |
50409 |
| Country |
Estonia |
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| Platform ID |
GPL16288 |
| Series (2) |
| GSE56524 |
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (RNA-seq) |
| GSE56781 |
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta |
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| Relations |
| BioSample |
SAMN02720946 |
| SRA |
SRX512273 |
| 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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