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| Status |
Public on Sep 06, 2022 |
| Title |
Brn-1 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Cervus nippon |
| Characteristics |
breed: Shuangyang
developmental stage: juvenile
tissue: brain
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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 small RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
CASAVA bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Assembly: miRBase Release 22.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Aug 31, 2022 |
| Last update date |
Sep 07, 2022 |
| Contact name |
Boyin Jia |
| Organization name |
Jilin Agricultural University
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| Department |
College of Animal Science and Technology
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| Street address |
2888 Xincheng Street
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| City |
Changchun |
| State/province |
Jilin |
| ZIP/Postal code |
130118 |
| Country |
China |
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| Platform ID |
GPL27967 |
| Series (1) |
| GSE212478 |
Comparison of miRNA transcriptomes reveals differential regulation from ten tissues and four development stages of Sika Deer |
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| Relations |
| BioSample |
SAMN30619471 |
| SRA |
SRX17386656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6533562_Brn_1.txt.gz |
1.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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