GPL16791[RGSE] - GEO DataSets

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Select item 2002825421.

CD8+MTs+ Effector T Cells from Enlarged Tumor-Draining Lymph Nodes Drive Enhanced Tumor Immunogenicity and Improved Prognosis in Colorectal Cancer Patients

(Submitter supplied) Tumor-draining lymph nodes (TDLNs) play a crucial role in anti-tumor immunity. However, the heterogeneity of TDLNs significantly impacts their immune function. We employed single-cell RNA sequencing to dissect the immune landscape of TDLNs of colorectal cancer (CRC), revealing that enlarged non-metastatic TDLNs (L-TDLNs) are enriched with CD8+ effector T cells (Teff) exhibiting a distinct metallothionein (MT)-positive signature. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
8 Samples

Download data: MTX, TSV

Series

Accession:: GSE282542

ID:: 200282542

Select item 2002487042.

Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression

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

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL24676
14 Samples

Download data: BW

Series

Accession:: GSE248704

ID:: 200248704

Select item 2002487033.

Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and glioma progression [RNA-Seq]

(Submitter supplied) Histone lysine lactylation is a physiologically relevant epigenetic pathway that can be stimulated by the Warburg effect and L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-CoA, the cofactor for the modification, and how this process is regulated remain unknown. Here we report identification of GTPSCS as a robust lactyl-CoA synthetase using biochemistry and cell biology approaches. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE248703

ID:: 200248703

Select item 2002822604.

N6-methyladenosine in DNA promotes genome stability

(Submitter supplied) DNA base lesions, such as incorporation of uracil into DNA or base mismatches, can be mutagenic and toxic to replicating cells. To discover factors in repair of genomic uracil, we performed a CRISPR knockout screen in the presence of floxuridine, a chemotherapeutic agent that incorporates uracil and fluoro-uracil into DNA. We identified known factors, such as uracil DNA N-glycosylase (UNG), but also unknown factors, such as the N6-adenosine methyltransferase, METTL3, as required to overcome floxuridine-driven cytotoxicity. more...

Organism:: Homo sapiens

Type:: Other

Platforms:: GPL18573 GPL16791
24 Samples

Download data: TXT

Series

Accession:: GSE282260

ID:: 200282260

Select item 2002781545.

Bulk and single cell RNA sequencing analyses of GBM Primary and Recurrent, early and late passages, DMSO / TMZ treatment.

(Submitter supplied) We used bulk RNA sequencing to analyze unsupervised clustering of early and late passages of four GBM PDXs. Single cell RNAseq data was used to study transcriptional profiles of DMSO and TMZ, Primary and Recurrent as well as early and late passages of GBM PDXs.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24676 GPL16791
37 Samples

Download data: CSV, RDS

Series

Accession:: GSE278154

ID:: 200278154

PubMed

Select item 2002769736.

Cellular signatures in human blood track bone mineral density in postmenopausal women

(Submitter supplied) Osteoclasts are sole bone-resorbing cells and are formed by the fusion of osteoclast precursor cells (OCPs) derived from myeloid lineage cells. Animal studies reveal that circulating osteoclast precursor cells (cOCPs) in blood travel to bone and fuse with bone-resident osteoclasts. However, the characteristics of human cOCPs and their association with bone diseases remain elusive. We have identified and characterized human cOCPs and found a positive association between cOCPs and osteoporosis. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
4 Samples

Download data: XLSX

Series

Accession:: GSE276973

ID:: 200276973

Select item 2002240297.

Microinjection of human ESC-derived trophoblast cells(BAP cells) to mouse blastocysts

(Submitter supplied) Purpose: 1. Characterize hESCs and hESC-derived trophoblast cells Results: 1. hESCs have high level of most pluripotency markers; 2. hESC-derived trophoblast cells specifically express trophoblast markers.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: XLSX

Series

Accession:: GSE224029

ID:: 200224029

PubMed

Select item 2002723358.

Two pathogenic germline truncating variants of BRCA2 confer different haploinsufficiency phenotypes

(Submitter supplied) Inactivating germline monoallelic mutations in the tumor suppressor BRCA2 predispose to breast and ovarian cancer. BRCA2 is essential in DNA repair via homologous recombination (HR). Tumorigenesis in this setting is thought to require the inactivation of the second allele; however, this event is not always observed suggesting haploinsufficiency. We investigated this question recreating two BRCA2 pathogenic truncating variants in heterozygosis in breast epithelial cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL24676
9 Samples

Download data: TXT

Series

Accession:: GSE272335

ID:: 200272335

Select item 2002078529.

Pa01c cells stable expressing a scramble or shRNA against TRIM21

(Submitter supplied) We make Pa01c cells stable expressing a scramble or shRNA against TRIM21 and performed bulk scRNASeq to assess transcriptomic changes Pa01c cells

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE207852

ID:: 200207852

PubMed

Select item 20016073310.

Aurora-A phosphorylates splicing factors and regulates alternative splicing

(Submitter supplied) The goal of this study is to identify the effect of inhibition of Aurora-A kinase activity on gene expression and RNA splicing. The perturbation of Aurora-A is well known to affect cell cycle distribution. Therefore, we coupled the inhibition of Aurora-A with cell synchronization procedure in order to avoid the indirect effect of cell cycle perturbation on splicing changes. The mRNA -seq libraries were prepared and subjected to paired-end sequencing on Illumina HiSeq 2500 lanes. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
12 Samples

Download data: TAB

Series

Accession:: GSE160733

ID:: 200160733

SRA Run Selector

Select item 20027850511.

Krill oil supplementation in vivo promotes increased fuel metabolism and protein synthesis in cultured human skeletal muscle cells

(Submitter supplied) Krill oil is a dietary supplement derived from Antarctic krill; a small crustacean found in the ocean. Krill oil is a rich source of omega-3 fatty acids, specifically eicosapentaenoic acid and docosahexaenoic acid, as well as the antioxidant astaxanthin. The aim of this study was to investigate the effects of krill oil supplementation, compared to placebo oil (high oleic sunflower oil added astaxanthin), in vivo on energy metabolism and substrate turnover in skeletal muscle cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
16 Samples

Download data: TXT

Series

Accession:: GSE278505

ID:: 200278505

PubMed

Select item 20027405312.

microRNA-637/661 ameliorate hypoxic induced pulmonary arterial hypertension by targeting TRIM29 signaling pathway

(Submitter supplied) To investigate the synergistic effect of miR637/miR661 in PAH regulation, we overexpressed these two microRNAs in HPASMC cells cultured in a low oxygen environment.We then performed the RNA-seq assay to analysis gene expression profiles.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
9 Samples

Download data: XLSX

Series

Accession:: GSE274053

ID:: 200274053

PubMed

Select item 20024846013.

The micro RNA expression of 5 nomal breast tissues and 15 breast cancer tissues

(Submitter supplied) MicroRNAs (miRNAs) are short non-coding RNAs that regulate the function of target genes at the post-transcriptional phase. MiRNAs are considered to play roles in the development, progression and metastasis of cancer. Recent studies have indicated that particular miRNA signatures are correlated with tumor aggressiveness, response to drug therapy, and patient outcome in breast cancer. In the present research, we would like to evaluate the morphological and biological characters of breast cancer stratified by miRNAs signature.

Organism:: Homo sapiens

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL16791
20 Samples

Download data: XLSX

Series

Accession:: GSE248460

ID:: 200248460

Select item 20027604414.

Transcriptome regulated by mitochondrial uncouplers in prostate cancer cells

(Submitter supplied) We discovered that mitochondrial uncouplers represented by nitazoxanide and its active metabolite tizoxanide inhibited prostate cancer growth. This RNA-seq study aims to elucidate the mechanism by which mitochondrial uncouplers inhibit prostate cancer growth. The results indicate that mitochondrial uncouplers predominantly downregulated E2F1 target genes and thus likely inhibited prostate cancer growth through impeding E2F1-mediated transcription.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE276044

ID:: 200276044

Select item 20026979115.

The amniote-conserved DNA-binding domain of CGGBP1 restricts cytosine methylation of transcription factor binding sites in proximal promoters to regulate gene expression (HTS)

(Submitter supplied) Truncated forms of CGGBP1 with (N-term) or without (C-term) the DNA-binding domain (DBD) have been used to to assay global cytosine methylation. HEK293T cells with endogenous CGGBP1 knocked down were used to over-express truncated forms of CGGBP1 followed by MeDIP-Seq analysis. Genome-wide analyses of cytosine methylation and binding of CGGBP1 DBD show that CGGBP1 restricts cytosine methylation in a manner that depends on its DBD and its DNA-binding. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL24676 GPL16791
6 Samples

Download data: BW

Series

Accession:: GSE269791

ID:: 200269791

Select item 20026952616.

TSC22D, WNK and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation

(Submitter supplied) The ability to sense and respond to osmotic fluctuations is critical for the maintenance of cellular integrity. We used gene co-essentiality analysis to identify an unappreciated relationship between TSC22D2, WNK1 and NRBP1 in regulating cell volume homeostasis. Each of these genes have paralogs and are functionally buffered for osmo-sensing and cell volume control. Within seconds of hyperosmotic stress, TSC22D, WNK and NRBP family members physically associate into biomolecular condensates, a process that is dependent on intrinsically disordered regions (IDRs). more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL16791
55 Samples

Download data: TXT

Series

Accession:: GSE269526

ID:: 200269526

PubMed

Select item 20028149517.

Transcriptional regulation of adipocyte lipolysis by IRF2BP2 [ChIP-seq]

(Submitter supplied) Adipocyte lipolysis controls systemic energy levels and metabolic homeostasis. Lipolysis is regulated by post-translational modifications of key lipolytic enzymes. However, less is known about the transcriptional mechanisms that regulate lipolysis. Here, we identify the transcriptional factor interferon regulatory factor-2 binding protein 2 (IRF2BP2) as a repressor of adipocyte lipolysis. Deletion of IRF2BP2 in primary human adipocytes increases lipolysis without affecting glucose uptake, whereas IRF2BP2 overexpression decreases lipolysis. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16791
1 Sample

Download data: BIGWIG

Series

Accession:: GSE281495

ID:: 200281495

Select item 20028128018.

Microglia-RPE Cell Communication via the SPP1-ITGAV Axis Drives EMT and Retinal Degeneration in Dry AMD

(Submitter supplied) Age-related macular degeneration (AMD) is a leading cause of vision loss, with its dry form characterized by retinal pigment epithelium (RPE) degeneration and photoreceptor loss. However, the underlying mechanisms driving these pathological changes remain poorly understood. Here, we identify a critical role for microglia-RPE cell interactions mediated by the SPP1-ITGAV signaling axis in dry AMD pathogenesis.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE281280

ID:: 200281280

Select item 20026707819.

Cytosolic N6AMT1-dependent translation supports mitochondrial RNA processing [Ribo-seq]

(Submitter supplied) Mitochondrial biogenesis relies on both the nuclear and mitochondrial genomes, and imbalance in their expression can lead to inborn errors of metabolism, inflammation, and aging. Here, we investigate N6AMT1, a nucleo-cytosolic methyltransferase that exhibits genetic codependency with mitochondria. We determine transcriptional and translational profiles of N6AMT1 and report that it is required for the cytosolic translation of TRMT10C (MRPP1) and PRORP (MRPP3), two subunits of the mitochondrial RNAse P enzyme. more...