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| Status |
Public on Sep 01, 2024 |
| Title |
BN02 |
| Sample type |
SRA |
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| Source name |
The longissimus dorsi muscle
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| Organism |
Bos taurus |
| Characteristics |
age: 3.5 ± 0.5-year-old
tissue: m. longissimus dorsi
species: Banna
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| Extracted molecule |
total RNA |
| Extraction protocol |
All the samples were frozen in liquid nitrogen immediately and stored at -80℃ until further processing.Total RNA of each muscle sample was extracted from approximately 50 mg of frozen tissue using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to manufacturer recommendations. The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
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 |
The quality of the RNA samples was evaluated in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After the quality control, the library preparations were sequenced on an Illumina Hiseq2000 platform (Illumina, San Diego, CA, USA) and paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Bos_taurus.ARS-UCD1.2 whole genome using HISAT2 v2.0.4 with parameters -p 8 --dta -x -S
Genome_build: Bos_taurus.ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jan 08, 2021 |
| Last update date |
Sep 01, 2024 |
| Contact name |
Zehui Wei |
| E-mail(s) |
weizehui7848@hotmail.com
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| Organization name |
Northwest A&F University
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| Street address |
No.3 Taicheng Road
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| City |
Yangling |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL15749 |
| Series (1) |
| GSE164462 |
Transcriptome profiling and Co-expression networks of longissimus dorsi muscle in Gayal（Bos frontalis）and Banna cattle（Bos taurus） with different beef qualities |
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| Relations |
| BioSample |
SAMN17260910 |
| SRA |
SRX9807257 |
| 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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