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| Status |
Public on Sep 03, 2020 |
| Title |
RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). This set of bulk RNA-sequencing experiments was performed to identify differentially expressed genes and repetitive elements, particularly HERVs, between independent Wild Type and RBM4 KO clones in the KBM-7 derived, near-haploid human cell line, HAP1
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| Overall design |
Multiple replicates are provided for each HAP1 sample: Wild Type ("WT_" ,3 replicates), RBM4 KO Clone 1 ("1B2_", 3 replicates) RBM4 KO Clone 2 ("1B6_", 2 replicates), Single-end Wild Type ("HAP1_WT_", 1 replicate) and Single-end KO Clone (HAP1_RBM4_KO_", 1 replicate)
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| |
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| Contributor(s) |
Foroushani AK, Chim B, Wong M, Hafner M, Muljo SA |
| Citation(s) |
33020268 |
| |
| Submission date |
Apr 01, 2020 |
| Last update date |
Oct 15, 2020 |
| Contact name |
Stefan A Muljo |
| E-mail(s) |
muljos@niaid.nih.gov
|
| Organization name |
NIH/NIAID
|
| Street address |
10 CENTER DR RM 11N306
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE147897 |
Post-transcriptional regulation of human endogenous retroviruses by RNA-Binding Motif Protein 4, RBM4 |
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| Relations |
| BioProject |
PRJNA622500 |
| SRA |
SRP254900 |
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