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Sample GSM1364031 Query DataSets for GSM1364031
Status Public on Aug 04, 2014
Title d3
Sample type SRA
 
Source name Intermediate reprogrammed cells
Organism Homo sapiens
Characteristics cell type: SOX2-EGFP (+) cells on day 3
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date Apr 07, 2014
Last update date May 15, 2019
Contact name Akira Watanabe
E-mail(s) a.watanabe@cyberomix.com
Organization name CyberomiX Inc
Street address Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 602-8407
Country Japan
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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