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| Status |
Public on Dec 13, 2022 |
| Title |
WT rep3 |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: lung
age: 8-week old
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
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 NovaSeq 6000 |
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| Description |
Ctrl_3
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus_norvegicus_Ensemble_94 whole genome using HISAT2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Rattus_norvegicus_Ensemble_94
Supplementary_files_format_and_content: text file include FPKM values and statistics.
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| Submission date |
Dec 16, 2019 |
| Last update date |
Dec 13, 2022 |
| Contact name |
Xiaoyan Liu |
| E-mail(s) |
lxycyyy@mail.ccmu.edu.cn, lxy-213@163.com
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| Organization name |
Beijing Chao-Yang Hospital
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| Street address |
8 Gongren Tiyuchang Nanlu, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100020 |
| Country |
China |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE142118 |
Next Generation Sequencing of Wild Type and CMG2-/- Rat Lung Transcriptomes |
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| Relations |
| BioSample |
SAMN13575709 |
| SRA |
SRX7388301 |
| 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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