GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

10 Samples

Download data: BW

(Submitter supplied) Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a fatal motoneuron disorder in children with unknown etiology. The disease is caused by mutations in the IGHMBP2 gene, encoding a Super Family 1 (SF1)-type RNA/DNA helicase. IGHMBP2 is a cytosolic protein that binds to ribosomes and polysomes, suggesting a role in mRNA metabolism. Here we performed morphological and functional analyses of isolated Ighmbp2-deficient motoneurons to address the question whether the SMARD1 phenotype results from de-regulation of protein biosynthesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: CSV

(Submitter supplied) RNA helicases constitute a large protein family implicated in cellular RNA homeostasis and disease development. Here we show that the RNA helicase Ighmbp2, linked to the neuromuscular disorder SMARD1 (DSMA1) associates with polysomes and impacts on translation of cellular mRNAs containing short, GC-rich and highly structured 5’UTRs. Absence of Ighmbp2 causes ribosome stalling at the start codon of target mRNAs, leading to their reduced translation efficiency. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

25 Samples

Download data: TSV

(Submitter supplied) The integrated stress response (ISR) is a conserved pathway which is activated by cells that are exposed to stress. In lung adenocarcinoma (LUAD), activation of the ATF4 branch of the ISR by particular oncogenic mutations has been linked to the regulation of amino acid metabolism. In the present study, we provide evidence for ATF4 activation across multiple stages and molecular subtypes of human LUAD. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: CSV

(Submitter supplied) In response to a variety of upstream growth and oncogenic signals, the mechanistic target of rapamycin complex 1 (mTORC1) promotes anabolic metabolism, in part, through activation of downstream transcription factors. The transcription factor activating transcription factor 4 (ATF4) has been previously shown to function downstream of mTORC1 signaling to promote de novo purine synthesis and this activation of ATF4 can occur independently of the canonical activation of ATF4 through the integrated stress response (ISR). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

55 Samples

Download data: CSV

(Submitter supplied) Expression analysis in HeLa cells upon treatment with doxycycline, actinonin, FCCP and MitoBloCK-6

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17301

10 Samples

Download data: TXT

(Submitter supplied) Translation efficiency varies 1000-fold between different mRNAs, thereby strongly impacting protein expression. Translation of the master stress response gene ATF4 increases in response to stress, but the molecular mechanisms are not well understood. We discover here that translation initiation factors DENR, MCTS1 and eIF2D are absolutely required to induce ATF4 translation upon stress, by promoting translation reinitiation on the ATF4 5’UTR. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

9 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL11154

44 Samples

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(Submitter supplied) Purpose: Study the changes in cell transcriptome upon overexpression of lncRNA TINCR Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins Results: we found that TINCR overexpression induces partial reversion of invasive phenotype

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Purpose: Identify RNA interactome of lncRNA TINCR Methods: Primary melanoma cell lines WM902B and MMC70 lysates hybridized with TINCR antisense DNA oligos Results: we found that TINCR silencing induces activation of translation of ATF4 and other stress responsive RNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Study the changes in mRNA translation upon silencing of lncRNA TINCR Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins Results: we found that TINCR silencing induces activation of ATF4 translation

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Purpose: Study the changes in gene expression upon silencing of lncRNA TINCR Methods: Primary melanoma cell line WM902B was transduced with lientiviruses expressing Scrambled and TINCR directed shRNA hairpins Results: we found that TINCR silencing induces switch to invasive phenotype in WM902B primary melanoma cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

22 Samples

Download data: TXT

(Submitter supplied) We report the physiological role of ATF4 within mouse liver, under basal and ER stress conditions. With three mice per group, and approximately 30 million reads per sample, we obtained genome-wide role of ATF4 within the liver. We find ATF4 is responsible for a small subset of ER stress genes, and larger than previously thought basal subset.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Thirty-two, seven-week old male C57BL/6J mice were obtained from Jackson Labs. Mice were adapted to a 12h/12h reverse light cycle and put on Control diet at 8 weeks of age for 10 days. Food was removed during lights on and restored at lights off. On the day of the experiment, mice were fed Control or MR diet for either 3 or 6 hours. There were 8 mice in each group. Animals were sacrificed using CO2 inhalation and decapitation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: XLSX

(Submitter supplied) Translational profiling of RAW264.7 cells stimulated with LPS in the presence and absence of 125ng/ml mycolactone: polysomal and subpolysomal RNA isolated by sucrose gradient centrifugation to determine the effect of mycolactone on translation during a proinflammatory response

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

6 Samples

Download data: TXT

(Submitter supplied) Abcb10 is a mitochondrial membrane protein involved in hemoglobinization of red cells. Abcb10 topology and ATPase domain localization suggest it exports a substrate, likely biliverdin (Shum et al Sci Transl Med 13, (2021), PMC8300486), out of mitochondria that is necessary for hemoglobinization. In this study we generated Abcb10 deletion cell lines in both mouse (Murine Erythroleukemia (MEL) and human erythroid precursor (Human Myelogenous Leukemia K562) cells to better understand the consequences of Abcb10 loss. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: TXT

(Submitter supplied) All cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating select gene programs necessary for survival. Here, we show the fundamental integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d which acts as a master effector to control core stress response orchestrators, the translation factor eIF2ɑ and the transcription factor ATF4. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

32 Samples

Download data: TXT

(Submitter supplied) The integrated stress response (ISR) facilitates cellular adaptation to a variety of stress conditions via phosphorylation of the common target eIF2α. During ISR, the translation of certain stress-related mRNAs is upregulated in spite of global suppression of protein synthesis.The selective translation often relieson alternative mechanisms, such as leaky scanning or reinitiation, but the underlying mechanism remains incompletely understood. more...

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9185

29 Samples

Download data: TXT