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| Status |
Public on Dec 16, 2019 |
| Title |
Control_RNA_seq_1 |
| Sample type |
SRA |
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| Source name |
control group
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: testis
strain: wistar
age: 8 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the testes with the TRIzol Plus RNA Purification Kit (Invitrogen) according to the instructions of the manufacturer and was finally eluted with 100 μl DNase/RNase-free water. Subsequently, the NanoQ Micro-volume Spectrophotometer (CapitalBio) was used to quantify RNA concentrations and to evaluate the quality of RNA by the detection of A260/A280, A260/A230 (1.8<A260/A280<2.0, 2.0<A260/A230<2.2). The RNA was evaluated using Bioptic Qsep 100 (Bioptic, Taiwan, China) to assure the integrity of the 18S and 28S ribosomal subunits (18S/28S>1.6, RNA Integrity Number (RIN)>8). The mRNA was isolated from total RNA using Poly (A) Beads (Bioo Scientific)
cDNA Library was prepared using a Rapid RNA-Seq Kit (Bioo Scientific) and RNA-Seq Barcodes 12 (Bioo Scientific), according to the instructions of the manufacturer. Each cDNA library was finally eluted with 15 μl of resuspension buffer. The libraries were quantified using a Qubit 3 Fluorometer (Invitrogen) and a dsDNA HS Assay Kit (Invitrogen) and were evaluated by means of Bioptic Qsep 100 (Bioptic).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
control group
CWY-MC1-1
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| Data processing |
Trimmomatic for quality control of RNA-Seq raw data
Hisat2 for data alignment with rn6 genome
StringTie for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
Genome_build: rn6
Supplementary_files_format_and_content: The .txt files report FPKM
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| Submission date |
Dec 09, 2019 |
| Last update date |
Dec 16, 2019 |
| Contact name |
wenyang chen |
| Organization name |
Hebei North University
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| Street address |
zuanshi south street
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| City |
zhangjiakou |
| ZIP/Postal code |
075000 |
| Country |
China |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE141699 |
Transcriptional Alterations of Genes Related to Fertility Decline in Male rats Induced by Chronic Sleep Restriction |
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| Relations |
| BioSample |
SAMN13514329 |
| SRA |
SRX7291262 |
| 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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