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| Status |
Public on Mar 04, 2024 |
| Title |
Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Exon-intron circRNA (EIciRNA) is a subclass of backsplicing-generated circRNAs featured with intron retention, among which some play roles in transcriptional regulation. We aim to characterize EIciRNAs by developing pipeline and investigate the factors involved in regulating EIciRNA biogenesis using CRISPR-Cas9 screen, as well as the physiology functions of EIciRNAs during neuronal differentiation.
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| Overall design |
To detect EIciRNAs and intron retention in the human transcriptome, we performed both RNase R-treated and poly(A)+ RNA-seq in HEK293 cells. To investigate the regulation of SRSF1 on EIciRNA biogenesis, SRSF1 knockdown cell line was established and both the two types of RNA-seq were performed. To investigate the functional roles of EIciRNAs during neuronal differentiation, differentiated neuronal cell line was established by inducing SH-SY5Y cells using Retinoic acid (RA).
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| Contributor(s) |
Zhong Y, Yang Y, Shan G, Chen L |
| Citation(s) |
38609186 |
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| Submission date |
Aug 24, 2023 |
| Last update date |
May 24, 2024 |
| Contact name |
Yan Yang |
| E-mail(s) |
yangyan2015@mail.ustc.edu.cn
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| Organization name |
University of Science and Technology of China
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| Lab |
Ge Shan
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| Street address |
No.373 Huangshan Road
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| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230027 |
| Country |
China |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (26)
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| GSM7733661 |
HEK293,RNaseR,rep4 |
| GSM7733662 |
HEK293,polyA,rep1 |
| GSM7733663 |
HEK293,polyA,rep2 |
| GSM7733664 |
HEK293,shCtrl,RNaseR,rep1 |
| GSM7733665 |
HEK293,shCtrl,RNaseR,rep2 |
| GSM7733666 |
HEK293,shSRSF1,RNaseR,rep1 |
| GSM7733667 |
HEK293,shSRSF1,RNaseR,rep2 |
| GSM7733668 |
HEK293,shCtrl,polyA,rep1 |
| GSM7733669 |
HEK293,shCtrl,polyA,rep2 |
| GSM7733670 |
HEK293,shSRSF1,polyA,rep1 |
| GSM7733671 |
HEK293,shSRSF1,polyA,rep2 |
| GSM7733672 |
SH-SY5Y,D0,polyA,rep1 |
| GSM7733673 |
SH-SY5Y,D0,polyA,rep2 |
| GSM7733674 |
SH-SY5Y,D3,polyA,rep1 |
| GSM7733675 |
SH-SY5Y,D3,polyA,rep2 |
| GSM7733676 |
SH-SY5Y,D6,polyA,rep1 |
| GSM7733677 |
SH-SY5Y,D6,polyA,rep2 |
| GSM7733678 |
SH-SY5Y,D0,RNaseR,rep1 |
| GSM7733679 |
SH-SY5Y,D0,RNaseR,rep2 |
| GSM7733680 |
SH-SY5Y,D3,RNaseR,rep1 |
| GSM7733681 |
SH-SY5Y,D3,RNaseR,rep2 |
| GSM7733682 |
SH-SY5Y,D6,RNaseR,rep1 |
| GSM7733683 |
SH-SY5Y,D6,RNaseR,rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE241685 |
Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome |
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| Relations |
| BioProject |
PRJNA1009108 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241679_HEK293_EIciRNAs.txt.gz |
31.2 Kb |
(ftp)(http) |
TXT |
| GSE241679_HEK293_IRFinder_LIR.txt.gz |
77.5 Kb |
(ftp)(http) |
TXT |
| GSE241679_HEK293_SRSF1_KD_EIciRNA_GLM_counts.txt.gz |
76.9 Kb |
(ftp)(http) |
TXT |
| GSE241679_HEK293_SRSF1_KD_IRFinder_comparison.txt.gz |
853.9 Kb |
(ftp)(http) |
TXT |
| GSE241679_HEK293_SRSF1_KD_gene_counts.txt.gz |
351.2 Kb |
(ftp)(http) |
TXT |
| GSE241679_HEK293_circRNAs.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE241679_SH_SY5Y_EIciRNAs.txt.gz |
10.6 Kb |
(ftp)(http) |
TXT |
| GSE241679_SH_SY5Y_gene_counts.txt.gz |
452.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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