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| Status |
Public on Feb 06, 2024 |
| Title |
Yak-3 |
| Sample type |
SRA |
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| Source name |
testis
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| Organism |
Bos grunniens |
| Characteristics |
tissue: testis
treatment: Four years old
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| Treatment protocol |
The testicular tissue was washed with PBS and quickly placed in a freezer tube, immediately stored in liquid nitrogen.
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| Growth protocol |
Four-year-old cattle, yaks and cattle-yaks ( three each ) were selected from the same cooperative in Gannan Tibetan Autonomous Prefecture for castration.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each testicular sample using TRIzol reagent. RNA quality was assessed using Nanodrop-2000 and 1% agarose gel electrophoresis.
RNA-seq：A total amount of 5μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribozero™ rRNA Removal Kit (Epicentre, USA). Second, the sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Third, the library quality was assessed on the Agilent Bioanalyzer 2100 system. At last, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. And sequencing the library on the Illumina Hiseq 2500 platform and and 125bp.paired -end reads were generated. miRNA-seq：A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA high sensitivity chips. After clustering the samples, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50 bp single-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The raw data in fastq format was removed by Trimmomatic software to remove adapters, remove poly-N reads and low-quality reads, and obtain clean reads. Clean reads were aligned to the cattle genome using HISAT2 (version 2.0.5) (version: Bos_taurus.UMD3.1). The mapped reads of each sample were assembled by StringTie (v1.3.4) in a reference-based approach. Cufflinks was used to calculated FPKM (Fragments Per Kilobase of exon Model per million mapped fragments) values of transcripts.
The raw data in fastq format is used to remove joints and low-quality reads by custom perl and python scripts. Bowtie was used to map small RNAs with a length range of 18-35 nt to the reference genome. Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself. The signature hairpin structure of miRNA precursors can be used to predict new miRNAs, and integrate miREvo and mirdeep2 miRNA prediction software to analyze new miRNAs. miRNA expression levels were estimated by TPM through the criteria。The predicted miRNA target genes were the intersection results of miRanda, PITA and RNAhybrid.
Assembly: Bos_taurus.UMD3.1
Supplementary files format and content: Excle include FPKM/TPM values for each Sample...
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| Submission date |
Feb 01, 2024 |
| Last update date |
Feb 06, 2024 |
| Contact name |
shaoke guo |
| E-mail(s) |
YDKang0901@outlook.com
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| Phone |
15036009308
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Lanzhou institute of husbandry and pharmaceutical sciences
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| Street address |
West Lake Street
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| City |
Lanzhou |
| State/province |
Gansu |
| ZIP/Postal code |
730050 |
| Country |
China |
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| Platform ID |
GPL22950 |
| Series (1) |
| GSE254886 |
Comprehensive analysis of differentially expressed mRNA, circRNA and miRNA and their ceRNA networks in testis of cattle-yak, yak and cattle |
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| Relations |
| BioSample |
SAMN39736376 |
| SRA |
SRX23504886 |
| 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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