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Sample GSM1559538 Query DataSets for GSM1559538
Status Public on Jul 20, 2015
Title 3'-Seq mouse Liver
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
age: 8 weeks
tissue: liver
Extracted molecule total RNA
Extraction protocol Sample preparations for 3′-seq was performed as previously reported (Lianoglou et al., Genes & Development, 2013) using total RNA extracted from 8 week-old C57BL/6 male mouse tissue, including testis, liver, brain, and skeletal muscle.
3'-seq libraries were prepared for sequencing using previously reported protocol(Lianoglou et al., Genes & Development, 2013).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Protocol: 3'-seq
Data processing Illumina RTA 1.17 software used for basecalling.
Sequenced reads were mapped to the mouse genome (mm9) with STAR alignment software (Dobin et al., 2013) and the parameter “--outFilterMultimapNmax 1 --alignIntronMax 1” (no multi-hit reads, no splice prediction) to treat poly-A containing reads.
Quantification of each gene was performed by counting the number of reads that were mapped around the 3′-UTR region and then normalizing the number as reads per million (RPM) per region. In the case of novel histone H3 variant genes, the region within 3 kb from the end of a coding sequence was defined as the putative 3'-UTR.
genome build: mm9
processed data files format and content: tab-delimited text files include RPKM values for each Sample
processed data file: 3primeSeq_RPMTable_rep1.txt.gz
Submission date Dec 05, 2014
Last update date May 15, 2019
Contact name Yasuyuki Ohkawa
Organization name Kyushu University
Department Medical Institute of Bioregulation, Medical Institute of Bioregulation
Street address 3-1-1 Maidashi, Higashi-ku, Fukuoka
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL18480
Series (1)
GSE63890 Characterization of mouse histone H3 variants
BioSample SAMD00019536
SRA DRX020529

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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