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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 29, 2020 |
| Title |
Identification of human endogenous retroviruses working as enhancers in cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Human endogenous retroviruses (HERVs) are a sort of transposable elements. HERVs harbor abundant regulatory elements in their sequences and have a potential to work as enhancers modulating the expressions of the adjacent genes. Some HERV-enhancers are particularly activated in cancer cells and suspected to be associated with cancer progression. To verify the enhancer activity of HERVs on the gene expressions in lung adenocarcinoma cells, we established the HERV-excised A549 cell lines using a CRISPR-Cas9 system and performed RNA sequencing (RNA-Seq) analysis of these cells.
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| Overall design |
First, an A549 cell line stably expressing Cas9 (referred to as A549/Cas9 cell) was established. Second, a pair of guide RNAs that are specific to the 5´- and 3´-flanking regions of the target HERV were co-transfected into A549/Cas9 cells. Through limiting dilution, single cell clones were picked up and screened by genotyping PCR. The resultant clones in which the targeted HERV was excised homozygously were obtained. As a control, the A549/Cas9 cells that were transfected with non-target control guide RNA were prepared and cloned as described above. Total RNA was extracted from these cells by QIAamp RNA Blood Mini Kit (QIAGEN #52304) and treated with RNase-Free DNase Set (QIAGEN #79254). Quality check of the purified RNA, library construction, and sequencing were performed by Novogene (https://en.novogene.com). Pair-ended and 150bp read length sequencing was performed by Illumina Novaseq6000.
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| Contributor(s) |
Kimura I, Soper A, Misawa N, Ito J, Sato K |
| Citation(s) |
33087347 |
| Submission date |
Nov 27, 2019 |
| Last update date |
Nov 09, 2020 |
| Contact name |
Kei Sato |
| E-mail(s) |
su9ark@gmail.com
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| Phone |
81364092212
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| Organization name |
The Institute of Medical Science, The University of Tokyo
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| Department |
Department of Microbiology and Immunology
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| Lab |
Division of Systems Virology
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| Street address |
4-6-1 Shiroganedai
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| City |
Minato-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1088639 |
| Country |
Japan |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (20)
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| GSM4196000 |
A549 in which HERV1 was excised, clone 1 |
| GSM4196001 |
A549 in which HERV1 was excised, clone 2 |
| GSM4196002 |
A549 in which HERV1 was excised, clone 3 |
| GSM4196003 |
A549 in which HERV1 was excised, clone 4 |
| GSM4196004 |
A549 in which HERV1 was excised, clone 5 |
| GSM4196005 |
A549 with non-target control gRNA, clone 1 |
| GSM4196006 |
A549 with non-target control gRNA, clone 2 |
| GSM4196007 |
A549 with non-target control gRNA, clone 3 |
| GSM4196008 |
A549 with non-target control gRNA, clone 4 |
| GSM4196009 |
A549 with non-target control gRNA, clone 5 |
| GSM4421221 |
A549 with non-target control gRNA, clone 1, batch2 |
| GSM4421222 |
A549 with non-target control gRNA, clone 2, batch2 |
| GSM4421223 |
A549 with non-target control gRNA, clone 3, batch2 |
| GSM4421224 |
A549 with non-target control gRNA, clone 4, batch2 |
| GSM4421225 |
A549 with non-target control gRNA, clone 5, batch2 |
| GSM4421226 |
A549 in which HERV2 was excised, clone1, batch2 |
| GSM4421227 |
A549 in which HERV2 was excised, clone2, batch2 |
| GSM4421228 |
A549 in which HERV2 was excised, clone3, batch2 |
| GSM4421229 |
A549 in which HERV2 was excised, clone4, batch2 |
| GSM4421230 |
A549 in which HERV2 was excised, clone5, batch2 |
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| This SubSeries is part of SuperSeries: |
| GSE141803 |
Roles of human endogenous retroviruses and KRAB-zinc finger proteins in tumor progression |
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| Relations |
| BioProject |
PRJNA592198 |
| SRA |
SRP233584 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141141_HERV-excised.matrix.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
| GSE141141_HERV-excised2.matrix.csv.gz |
2.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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