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Series GSE248889 Query DataSets for GSE248889
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.
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.
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
Organization name University of California, San Francisco
Department Cell and Tissue Biology
Lab Stephen Floor
Street address 513 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (10)
GSM7921734 RNAseq_K562_118_IGHMBP2_Rep1
GSM7921735 RNAseq_K562_118_IGHMBP2_Rep2
GSM7921736 RNAseq_K562_115_IGHMBP2_Rep1
This SubSeries is part of SuperSeries:
GSE248890 IGHMBP2 deletion suppresses translation and activates the integrated stress response
BioProject PRJNA1046396

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Supplementary file Size Download File type/resource
GSE248889_RAW.tar 207.1 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA

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