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| Status |
Public on Oct 31, 2020 |
| Title |
Thymus GEN1 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Gallus gallus |
| Characteristics |
breed: ROSS 308
tissue: Thymus
age: post natal day 21
genotype: lipopolysaccharide+genistein treated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Thymus were removed, flash frozen on dry ice, 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 NovaSeq 6000 |
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| Data processing |
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Gallus_gallus.GRCg6a.96 whole genome using featureCounts v1.5.0-p3
Expected number of Fragments Per Kilo base of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Gallus_gallus.GRCg6a.96
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Oct 30, 2020 |
| Last update date |
Oct 31, 2020 |
| Contact name |
zengpeng lv |
| E-mail(s) |
lvzengpeng@njau.edu.cn
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| Organization name |
nanjing agricultural university
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| Street address |
weigang
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| City |
nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL26853 |
| Series (1) |
| GSE160489 |
Next Generation Sequencing Facilitates Quantitative Analysis of basic diet-treated (CON)，lipopolysaccharide-treated(LPS), or lipopolysaccharide+genistein treated broiler chicks (GEN) thymic Transcriptomes |
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| Relations |
| BioSample |
SAMN16605088 |
| SRA |
SRX9405179 |
| 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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