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| Status |
Public on Jan 01, 2024 |
| Title |
WGZC7 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Sus scrofa |
| Characteristics |
tissue: liver
breed: Wujin
treatment: NOT PROVIDED; REQUESTED
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAsimple Total RNA Kit (Tiangen Biotech Co., Ltd., Beijing, China). 1.3 ug of total RNA was used for the construction of sequencing libraries. The total of 1 μg RNA in each sample was used as the input material for RNA sample preparation.
According to the manufacturer's suggestion, a NEBNext Ultra RNA Library Prep Kit (Illumina, Nebraska, USA) was used to generate a sequencing library.
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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 |
Raw data in FASTQ format (raw reading) were first processed using a Perl script. Clean data were obtained by removing readings containing adapters, poly-N, and low-quality readings from the original data. Simultaneously, the Q20, Q30, GC content and sequence repetition levels of the clean data were calculated. All downstream analyses were based on clean high-quality data.
Connectors and low-quality sequence reads were removed from the dataset. After data processing, the original sequences were converted to a clean read. These reads were plotted against the reference genome sequence. Hisat2 software was used to compare the reference genomes. and StringTie comparisons were performed to assemble the reads.
Gene functions were annotated based on the following databases: Nr (NCBI non-redundant protein sequences), Nt (NCBI non-redundant nucleotide sequences), Pfam (protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (a manually annotated and reviewed protein sequence database), KO (KEGG Ortholog database), and GO (Gene Ontology).
Assembly: Sscrofa11.1_ncbi
Supplementary files format and content: xls files include RPKM values for each Sample
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| Submission date |
Nov 09, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Peng Ji |
| E-mail(s) |
skytxiang@gmail.com
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| Phone |
18845100163
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| Organization name |
Yunnan Agricultural University
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| Street address |
Fengyuan raod 452
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| City |
Kunming |
| ZIP/Postal code |
650201 |
| Country |
China |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE247384 |
Effect of different dietary iron contents on liver transcriptome characteristics in Wujin pigs |
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| Relations |
| BioSample |
SAMN38180788 |
| SRA |
SRX22453620 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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