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SRX1056759: GSM1709022: Cytosol Ribosome profiling Untreated 1; Mus musculus; OTHER
1 ILLUMINA (Illumina HiSeq 2500) run: 4.1M spots, 207.3M bases, 141.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Ribosome profiling analysis of GADD34 null cells
show Abstracthide Abstract
Accumulation of misfolded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), which results in the increased phosphorylation of the eukaryotic initiation factor, eIF2a, and widespread translational repression. Protein synthesis is subsequently restored following the stress-induced transcriptional upregulation of GADD34 (growth arrest and DNA damage transcript 34) protein, a regulator of an eIF2a phosphatase. Genome-wide ribosome foot-printing in WT and GADD34-/- MEFs established that GADD34 mRNA is translated in unstressed cells and identified numerous mRNAs, whose translation was dependent on GADD34 even in the absence of ER stress. Following UPR activation, temporal analyses showed that the translational profile in GADD34-/- MEFs was stalled, displaying a pattern that mirrors the early response to UPR in WT MEFs. Basal GADD34 expression is also required for de-repression of translation and displacement of ER-bound polysomes that occur in early UPR. Thus, the overall UPR response is delayed in the GADD34-/- MEFs, gradually recovering as CReP expression increased. These studies reveal a critical role for basal GADD34 in the propagation of UPR signals in MEFs and mice and suggest that delayed UPR signaling protects GADD34-/- mice from tunicamycin-induced renal toxicity. Overall design: Translational and transcriptional analysis mouse embryonic fibroblasts lacking GADD34 during ER stress
Sample: Cytosol Ribosome profiling Untreated 1
SAMN03770667 • SRS959367 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. Release cytosol with digitonin. Extract remaining sample with dodecyl maltoside. Ribosome profiling: Digest with Mnase (30 min 10 ug/ml, 37C), pellet ribosomes, extract RNA, PNK treat, gel isolation, library generation with NEB Directional Small RNA kit mRNA-seq: RiboMinus, library prepataion using TruSeq RNA Sample Preparation Kit (Illumina)
Experiment attributes:
GEO Accession: GSM1709022
Links:
External link:
Runs: 1 run, 4.1M spots, 207.3M bases, 141.1Mb
Run# of Spots# of BasesSizePublished
SRR20606844,063,729207.3M141.1Mb2015-10-01

ID:
1533682

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