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| Status |
Public on May 31, 2023 |
| Title |
Whole blood, CPP-Se group, 30 Days, biol rep 3 |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Whole blood
treatment: fed with CPP-Se
time: Day 30
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using trizol reagent (Ambion). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CPP_Se_3
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| Data processing |
Illumina Casava software (version: 2.19 ) used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software (version: 0.19.7, parameter: fastp -g -q 5 -u 50 -n 15 -l 150)
Trimmed sequence reads were mapped to the reference genome using hisat2 software (version:2.0.5, parameter: hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>] ).
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ROS_Cfam_1.0
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Jan 04, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
wang wen can |
| E-mail(s) |
wencan_wang1208@126.com
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| Organization name |
Sichuan agriculture university
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| Street address |
Huimin Road 211#
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| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL25760 |
| Series (1) |
| GSE222161 |
Transcriptomic and Metabolomic Changes Reveals the Immunomodulatory Function of Casein Phosphopeptide-Selenium Chelate in Beagle Dogs |
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| Relations |
| BioSample |
SAMN32577544 |
| SRA |
SRX18927522 |
| 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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