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Status |
Public on Feb 17, 2021 |
Title |
submandibular glands, B3 |
Sample type |
SRA |
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Source name |
submandibular gland
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Organism |
Capra hircus |
Characteristics |
tissue: submandibular gland age: 12 month
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Treatment protocol |
All goats were raised under the same conditions, including natural lighting and free access to food.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from the submandibular salivary gland tissues using TRIzol (Invitrogen, Carlsbad, CA, USA). RNA libraries were prepared for sequencing using standard Illumina miRNA protocols
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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 |
Raw reads were filtered with FastQC: Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); removing reads without 3’adapters; removing reads containing 5’adapters; removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; removing reads containing ployA in small RNA fragment; removing reads shorter than 18nt Applied with Bowtie, we aligned our clean reads with small RNAs in GeneBank database (Release 209.0) and Rfam database (11.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA. We also mapped our clean reads with goat reference genome (Capra hircus ARS1), and those reads mapped to exons, introns and repeat sequences were removed. To identify known miRNAs, we mapped clean reads with miRBase database (Release 22) All of the unmapped reads were applied for novel miRNA identification according to their genome positions and hairpin structures predicted by software Mireap_v0.2. The parameters of Mireap_v0.2 were settled as follows: Minimal miRNA sequence length is 18nt, maximal miRNA sequence length is 26nt, minimal miRNA reference sequence length is 20nt, maximal miRNA reference sequence length is 24nt, minimal depth of Drosha/Dicer cutting site is 3, maximal copy number of miRNAs on reference is 20, maximal free energy allowed for a miRNA precursor is 18 kcal/mol, maximal space between miRNA and miRNA* is 35nt, minimal space between miRNA and miRNA* is 14nt, maximal bulge between miRNA and miRNA* is 4nt, maximal asymmetry of miRNA/miRNA* duplex is 5nt, flank sequence length of miRNA precursor is 10nt. Genome_build: Capra hircus ARS1 Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample
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Submission date |
Feb 16, 2021 |
Last update date |
Feb 17, 2021 |
Contact name |
Chao Tianle |
E-mail(s) |
chaotianle@sdau.edu.cn
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Phone |
15153876133
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Organization name |
6/5000 Shandong Agricultural University
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Street address |
Daizong street, no. 61, 6/5000 Shandong Agricultural University
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City |
Tai’an |
State/province |
Shandong |
ZIP/Postal code |
538 |
Country |
China |
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Platform ID |
GPL19149 |
Series (1) |
GSE166842 |
MiRNA Transcriptome sequencing of Lubo goat submandibular glands at different ages |
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Relations |
BioSample |
SAMN17925174 |
SRA |
SRX10109734 |
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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