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| Status |
Public on Jun 12, 2021 |
| Title |
GM3 |
| Sample type |
SRA |
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| Source name |
muscle stem cells
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| Organism |
Bos taurus |
| Characteristics |
cell type: Muscle-derived stem cells
tissue: Muscle
development stage: proliferation
breed: Guangxi
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen，Carlsbad，CA，USA). A total amount of 3 μg RNA per sample was used as an initial material for the RNA sample preparation. The library was prepared according to the method and process of lncRNA sample preparation kit (Illumina, NEB) and Small RNA Sample Preparation Kit (Illumina, RS-200-0048) at Annoroad Gene Technology Corporation (Beijing, China).
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 HiSeq 2000 |
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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 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Million Mapped Fragments (FPKM)were calculated using a protocol from Trapnell, C. et al, 2010.Spliced Reads per Billion Mapping (SRPBM) calculated using a protocol from Li, et al. 2015 . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM/SRPBM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jun 12, 2020 |
| Last update date |
Jun 12, 2021 |
| Contact name |
Ruimen Zhang |
| E-mail(s) |
ruimenzhang@126.com
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| Organization name |
Guangxi University
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| Street address |
NO.100 University Road,Xi xiang tang
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| City |
Nanning |
| ZIP/Postal code |
530004 |
| Country |
China |
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| Platform ID |
GPL15749 |
| Series (1) |
| GSE152398 |
Transcriptomics analysis of proliferation and differentiation of Guangxi cattle muscle stem cells |
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| Relations |
| BioSample |
SAMN15226487 |
| SRA |
SRX8538835 |
| 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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