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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jul 20, 2015 |
Title |
3'-Seq mouse Liver |
Sample type |
SRA |
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Source name |
liver
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 gender: male age: 8 weeks tissue: liver
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
Protocol: 3'-seq
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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
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Submission date |
Dec 05, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Yasuyuki Ohkawa |
E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
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Organization name |
Kyushu University
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Department |
Medical Institute of Bioregulation, Medical Institute of Bioregulation
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Street address |
3-1-1 Maidashi, Higashi-ku, Fukuoka
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City |
Fukuoka |
ZIP/Postal code |
812-8582 |
Country |
Japan |
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Platform ID |
GPL18480 |
Series (1) |
GSE63890 |
Characterization of mouse histone H3 variants |
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Relations |
BioSample |
SAMD00019536 |
SRA |
DRX020529 |
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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