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| Status |
Public on Apr 22, 2022 |
| Title |
kshv-miR-K12-1-5p-1 |
| Sample type |
SRA |
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| Source name |
AC16 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: AC16
transfection: kshv-miR-K12-1-5p mimic
antibody: anti-Ago2
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| Growth protocol |
AC16 cells (ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in medium (ScienCell research laboratories, Cat. #6201), according to the instruction manual. Medium consists of basal medium, foetal bovine serum (FBS), AC16 cells growth supplement, and penicillin/streptomycin solution.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent following the instructions.
All of our RNA-seq projects used strand specific kits to construct the libraries. By using next-generation sequencing (NGS) technology, paired-end (PE) sequencing of these libraries was performed based on Illumina HiSeq sequencing platform.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: Ensembl 38.85
Supplementary files format and content: RPKM.xlsx: Excel file includes counts and RPKM values for each Sample.
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| Submission date |
Apr 19, 2022 |
| Last update date |
Apr 22, 2022 |
| Contact name |
heng zhi du |
| E-mail(s) |
[email protected]
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| Phone |
15671829826
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| Organization name |
Wuhan Tongji Hospital
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| Street address |
1095 Jiefang Dadao, Wuhan City, Hubei Province, China
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| City |
WUHAN |
| ZIP/Postal code |
437000 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE201041 |
RNA immunoprecipitation sequencing (RIP seq) using anti-Argonaute2 (Ago2) antibody to identify the potential targets of kshv-miR-K12-1-5p in AC16 cells |
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| Relations |
| BioSample |
SAMN27631040 |
| SRA |
SRX14909841 |
| 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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