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| Status |
Public on Mar 12, 2015 |
| Title |
duck 3 |
| Sample type |
SRA |
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| Source name |
primary duck hepatocytes
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| Organism |
Anas platyrhynchos |
| Characteristics |
tissue: liver
age: 1-day-old duckling
genotype: wild type
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| Growth protocol |
Primary duck hepatocytes were cultured in Leibovitz’s L-15 medium supplemented with 5% fetal bovine serum, 100 units/ml penicillin-streptomycin, 1 mg/L insulin, and 10−5 M hydrocortisone-hemisuccinate.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Primary duck hepatocytes were cultured for 24 hours, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (PRJNA46621) using TopHat v2.0.12.
Cufflinks v2.2.1 software (http://cufflinks.cbcb.umd.edu/) was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression.
Genome_build: PRJNA46621
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Mar 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
LIANG YAN |
| E-mail(s) |
henshore@163.com
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| Organization name |
Fudan University
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| Street address |
NO 131, Dongan Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL19739 |
| Series (1) |
| GSE66786 |
Primary duck hepatocyte transcriptome analysis provides insight into the host innate immune response and hepadnavirus infection |
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| Relations |
| BioSample |
SAMN03400165 |
| SRA |
SRX952159 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1632149_PDH3.txt.gz |
161.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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