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| Status |
Public on Aug 04, 2014 |
| Title |
d3 |
| Sample type |
SRA |
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| Source name |
Intermediate reprogrammed cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: SOX2-EGFP (+) cells on day 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiazol reagent (Qiagen) and a miRNeasy mini kit (Qiagen) according to the manufacturer's instruction.
One µg of total RNA was depleted of rRNA using Ribo-Zero gold kit (Epicentre), and then 100 ng of rRNA-depleted RNA fraction was subjected to Illumina’s sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). The library was captured on an Illumina flow cell for cluster generation.
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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 |
Basecalls performed using CASAVA version 1.8.2
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.5 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) for LTR7,7A,7B,7C,7Y in RepeatMasker open-3.3.30-Repeat Libarary 20120124 were calcurated using Partek Genomic Suite version 6.6 with default parameter except changing "Require strict paired-end compatibility" option from "Yes" to "No".
Genome_build: hg19
Supplementary_files_format_and_content: Text files which contain RPKM for LTR7s were calcurated using Partek Genomic Suite version 6.6.
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| Submission date |
Apr 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Akira Watanabe |
| E-mail(s) |
a.watanabe@cyberomix.com
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| Organization name |
CyberomiX Inc
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| Street address |
Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
602-8407 |
| Country |
Japan |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE56568 |
Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (RNA-Seq) |
| GSE56569 |
Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency |
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| Relations |
| BioSample |
SAMN02721094 |
| SRA |
SRX512375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1364031_d3_LTR7_RPKM.txt.gz |
39.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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