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| Status |
Public on May 16, 2024 |
| Title |
PC12-EC1, miRNA-seq |
| Sample type |
SRA |
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| Source name |
PC12
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| Organism |
Rattus norvegicus |
| Characteristics |
cell line: PC12
cell type: rat adrenal pheochromocytoma cells
group: EC
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor_6.0 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw counts for every miRNA and every sample
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| Submission date |
Apr 07, 2024 |
| Last update date |
May 16, 2024 |
| Contact name |
Jinsheng Huang |
| E-mail(s) |
huangjs010926@outlook.com
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| Phone |
+8618539759759
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| Organization name |
Zhengzhou University
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| Street address |
1th, East Jianshe Road
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| City |
Zhengzhou |
| ZIP/Postal code |
450000 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE263389 |
Netrin-1 engineered endothelial cell exosomes induce the formation of pre-regenerative niche to accelerate peripheral nerve repair [miRNA-seq] |
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| Relations |
| BioSample |
SAMN40864119 |
| SRA |
SRX24178662 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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