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| Status |
Public on Sep 04, 2021 |
| Title |
β-alanine rep3 (B3) |
| Sample type |
SRA |
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| Source name |
Breast muscle
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| Organism |
Gallus gallus |
| Characteristics |
genetic line: Korat chicken
tissue: Breast muscle
age: 10 weeks of age
treatment: Supplemented with β-alanine
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the breast muscle of fifteen chickens, one chicken from each replication of the treatment group, using TRIzol Reagent (Thermo Fisher Scientific, Massachusetts, USA).
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~400 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR andP5/ P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
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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 |
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
Low-quality and technical sequences were removed from the raw sequencing reads using Cutadapt version 1.9.1
Hisat2 version 2.0.1 was used to align the clean reads against the chicken reference genome, GRCg6a (GenBank Assembly ID: GCA_000002315.5).
Gene expression levels were estimated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using HTSeq version 0.6.1. The DESeq2 Bioconductor package was used for differential expression analysis between control and supplemented groups.
Genome_build: GRCg6a (GCA_000002315.5)
Supplementary_files_format_and_content: Column 1, gene_id: gene ID; Column 2, Exonic.gene.sizes:exon length; Column 3-17, Sample:count count of each gene; Column 18-32, Sample_FPKM: FPKM of each gene; Column 33-36, Chr, Start, End, Strand: gene location, including chromosome, start position, end position and strand; Column 37, GeneSymbol: gene symbol; Column 38, Description: gene description
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| Submission date |
Jul 07, 2021 |
| Last update date |
Sep 04, 2021 |
| Contact name |
Satoshi Kubota |
| E-mail(s) |
skubota@g.sut.ac.th
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| Organization name |
Suranaree University of Technology
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| Street address |
111 University Avenue, Suranaree Sub-District,
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| City |
Muang District |
| State/province |
Nakhon Ratchasima |
| ZIP/Postal code |
30000 |
| Country |
Thailand |
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| Platform ID |
GPL26853 |
| Series (1) |
| GSE179643 |
RNA Profiles of the Korat Chicken Breast Muscle with Increased Carnosine Content Produced through Dietary Supplementation with β-Alanine or L-Histidine |
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| Relations |
| BioSample |
SAMN20090799 |
| SRA |
SRX11369147 |
| 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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