|
| Status |
Public on Mar 04, 2024 |
| Title |
HEK293,polyA,rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
genotype: WT
|
| Treatment protocol |
SY5Y cells were induced differentiation by treatment with 10 μM retinoic acid (RA) in the presence of 1% FBS.
|
| Growth protocol |
cells were cultured with DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted by Trizol reagent (Invitrogene), according to the standard protocol. The ribosome RNA (rRNA) was removed by Ribominus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For poly(A)+ RNA-seq, raw sequence reads were trimmed for adaptor using cutadapt. Trimmed sequence reads were mapped to GRCh38/hg38 using STAR. Read count for each gene was obtained using RSEM. Intron retention in linear RNAs (LIR) was detected using IRFinder.
For RNase R-treated RNA-seq, raw sequence reads were trimmed for adaptor using cutadapt. Trimmed sequence reads were mapped to GRCh38/hg38 using bwa. Circular RNAs (circRNAs) were detected using CIRI2 and Exon-intron circRNAs (EIciRNAs) were detected using FEICP.
Assembly: hg38
|
| |
|
| Submission date |
Aug 24, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Yan Yang |
| E-mail(s) |
yangyan2015@mail.ustc.edu.cn
|
| Organization name |
University of Science and Technology of China
|
| Lab |
Ge Shan
|
| Street address |
No.373 Huangshan Road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230027 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE241679 |
Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq) |
| GSE241685 |
Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome |
|
| Relations |
| BioSample |
SAMN37146999 |
| SRA |
SRX21481432 |
