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| Status |
Public on Dec 19, 2023 |
| Title |
IGHMBP2 deletion suppresses translation and activates the integrated stress response [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
IGHMBP2 is a non-essential, superfamily 1 DNA/RNA helicase with incompletely understood biological function. Mutagenesis in IGHMBP2 is found in patients with rare neuromuscular diseases SMARD1 and CMT2S. IGHMBP2 is implicated in translational and transcriptional regulation via biochemical association with ribosomal proteins, pre-rRNA processing factors, and tRNA-related species. To uncover the cellular consequences of perturbing IGHMBP2, we generated full and partial IGHMBP2 deletion K562 cell lines. We performed Ribo-seq and RNA-seq and identified diverse gene expression changes due to IGHMBP2 deletion, including ATF4 upregulation.
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| Overall design |
We performed Ribo-seq and RNA-seq using two replicates per samples including K562 CRISPRi parental cells and K562 CRISPRi monoclonal cell lines with partial "HET" (two separate clones) versus full deletion "KO" (two separate clones) of IGHMBP2. We performed differential expression analysis among "HET" and "KO" genotypes relative to parental cell lines as the control.
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| Contributor(s) |
Park J, Floor S |
| Citation(s) |
38168189, 38803225 |
| |
| Submission date |
Nov 29, 2023 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Jesslyn Park |
| E-mail(s) |
jesslyn.park@ucsf.edu, stephen.floor@ucsf.edu
|
| Organization name |
University of California, San Francisco
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| Department |
Cell and Tissue Biology
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| Lab |
Stephen Floor
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE248890 |
IGHMBP2 deletion suppresses translation and activates the integrated stress response |
|
| Relations |
| BioProject |
PRJNA1046396 |
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