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| Status |
Public on Nov 22, 2013 |
| Title |
UHRF1_hi_A |
| Sample type |
SRA |
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| Source name |
Zebrafish 5 dpf liver
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| Organism |
Danio rerio |
| Characteristics |
genotype/variation: Tg(fabp10:has.UHRF1-GFP)
tissue: liver
developmental stage: 5 dpf
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol and mRNA was purified using poly-A beads
The mRNA was chemically fragmented,and Hi-seq compatible, bar-coded adapters were ligated to both ends.
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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 |
Illumina CASAVA version 1.7 used for basecalling
Mapped to the Danio rerio genome build Zv9/danRer7
Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non-zero expression
Values were quantile-normalized allowing comparisons of the two sets using custom-built software and algorithms as described (Aravin et al., 2008; Olson et al., 2008; Tam et al., 2008)
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: Tab-delimted text file includes genes and their quantile normalized frequencies.
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| Submission date |
Nov 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ravi Sachidanandam |
| E-mail(s) |
ravi.mssm@gmail.com
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| Organization name |
Girihlet Inc.
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| Street address |
2945 Webster St
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| City |
Oakland |
| State/province |
CA |
| ZIP/Postal code |
94609 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE52605 |
Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma |
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| Relations |
| BioSample |
SAMN02418766 |
| SRA |
SRX381134 |
| 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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