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Items: 1 to 20 of 23405

1.

Tet enzymes are essential for embryogenesis and completion of embryonic genome activation

(Submitter supplied) Mammalian embryo development begins in transcriptional silence followed by activation of thousands of genes. Reprogramming of DNA methylation is integral to embryogenesis and linked to Tet enzymes; however, their function in early development is not fully understood. Here, we generated combined deficiencies of all three Tet enzymes in mouse oocytes and observed arrest at 2-cell stage with the most severe phenotype linked to Tet2. more...
Organism:
Mus musculus; synthetic construct
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL15228 GPL13112
48 Samples
Download data: TXT
Series
Accession:
GSE57063
ID:
200057063
2.

Gene-expression profiles of whole blood cells from a Han Chinese population with or without Type-2 Diabetes Mellitus or/and its complications in nephropathy and retinopathy

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
synthetic construct; Homo sapiens
Type:
Expression profiling by array; Non-coding RNA profiling by array
Platform:
GPL5082
40 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE189007
ID:
200189007
3.

Trabecular meshwork cell-derived exosomal microRNA expression

(Submitter supplied) Trabecular meshwork cells in eyes with glaucoma aquire mesenchymal phenotypes. The types of microRNAs in exosomes may differ between static and glaucomatous status and their effects on aqueous humor regulation are still uknown. We used microarrays to identify the differential microRNA expression related to interaction between trabecular meshwork cells and Schlemm's canal endothelial cells.
Organism:
synthetic construct; Macaca mulatta
Type:
Non-coding RNA profiling by array
Platform:
GPL19117
9 Samples
Download data: CEL, CHP
Series
Accession:
GSE175464
ID:
200175464
4.

MapToCleave: high-throughput profiling of microRNA biogenesis in living cells

(Submitter supplied) We here introduce MapToCleave, a new method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors connected to a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from twenty animal species. We systematically compare the importance of known and novel sequence and structural features, and test miRNA precursors from ten animal and plant species in human cells. more...
Organism:
Homo sapiens; Mus musculus; synthetic construct
Type:
Non-coding RNA profiling by high throughput sequencing; Other
6 related Platforms
56 Samples
Download data: TXT
Series
Accession:
GSE169020
ID:
200169020
5.

Expression data of microRNAs from human lung cancer at different clinical types

(Submitter supplied) Brain metastasis is a major complication of lung cancer. An investigation of the pathogenic mechanisms of brain metastasis, as well as the identification of appropriate molecular markers, is necessary. We used microarrays to determine the expression patterns of microRNAs in lung cancer tissue with or without brain metastasis and to investigate the biological role of these miRNAs during tumorigenesis.
Organism:
Homo sapiens; synthetic construct
Type:
Non-coding RNA profiling by array
Platform:
GPL14613
45 Samples
Download data: CEL
Series
Accession:
GSE186666
ID:
200186666
6.

Sequence determinants of human gene regulatory elements

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; synthetic construct
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
8 related Platforms
80 Samples
Download data: BROADPEAK, NARROWPEAK, TSV, TXT
Series
Accession:
GSE180158
ID:
200180158
7.

Sequence determinants of human gene regulatory elements, STARR-seq random enhancer experiments

(Submitter supplied) DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. Here, we measured transcriptional activity of DNA sequences that represent ~100 times larger sequence space than the human genome using massively parallel reporter assays. Machine learning models revealed that transcription factors (TFs) act generally in an additive manner with weak grammar, and that enhancers increase expression from a promoter by a mechanism that does not involve specific TF-TF interactions. more...
Organism:
synthetic construct; Homo sapiens
Type:
Other
Platforms:
GPL19424 GPL18573
4 Samples
Download data: TSV
Series
Accession:
GSE180153
ID:
200180153
8.

Sequence determinants of human gene regulatory elements, STARR-seq motif library experiments

(Submitter supplied) DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. Here, we measured transcriptional activity of DNA sequences that represent ~100 times larger sequence space than the human genome using massively parallel reporter assays. Machine learning models revealed that transcription factors (TFs) act generally in an additive manner with weak grammar, and that enhancers increase expression from a promoter by a mechanism that does not involve specific TF-TF interactions. more...
Organism:
Homo sapiens; synthetic construct
Type:
Other
Platforms:
GPL20301 GPL21616
3 Samples
Download data: TSV
Series
Accession:
GSE180151
ID:
200180151
9.

Sequence determinants of human gene regulatory elements, ATI experiment

(Submitter supplied) DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. Here, we measured transcriptional activity of DNA sequences that represent ~100 times larger sequence space than the human genome using massively parallel reporter assays. Machine learning models revealed that transcription factors (TFs) act generally in an additive manner with weak grammar, and that enhancers increase expression from a promoter by a mechanism that does not involve specific TF-TF interactions. more...
Organism:
synthetic construct
Type:
Other
Platform:
GPL15228
2 Samples
Download data: TSV
Series
Accession:
GSE180144
ID:
200180144
10.

Identifying non-genetic determinants of malignant clonal fitness at single cell resolution

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; synthetic construct
Type:
Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platforms:
GPL19424 GPL19057 GPL24247
271 Samples
Download data: BED, MTX, SEG, TSV, VCF
Series
Accession:
GSE161676
ID:
200161676
11.

Identifying non-genetic determinants of malignant clonal fitness at single cell resolution (primary leukaemia barcode-seq)

(Submitter supplied) All cancers emerge following a period of clonal selection and subsequent clonal expansion. Whilst the evolutionary principles imparted by genetic intra-tumour heterogeneity (ITH) are becoming increasingly clear, little is known about the non-genetic mechanisms that contribute to ITH and malignant clonal fitness. Using SPLINTR, a synthetic expressed barcoding strategy, in three clinically relevant mouse models of acute myeloid leukaemia (AML) we find that malignant clonal dominance is a stable and heritable property that is facilitated by the repression of antigen presentation and the increased expression of Slpi, a leukocyte protease inhibitor that has not previously been characterised in AML. more...
Organism:
Mus musculus; synthetic construct
Type:
Other
Platforms:
GPL19424 GPL19057
14 Samples
Download data: FASTA, TXT
Series
Accession:
GSE161657
ID:
200161657
12.

Spec-seq sequencing data for CTCF [2021 series]

(Submitter supplied) This series is an updated dataset consisting of the Spec-seq and Methyl-Spec-seq samples for human CTCF with a bigger sequencing libraries and different epigenetic modifications. Each sample has replicate to gurantee the reproducibility for each measurement.
Organism:
synthetic construct
Type:
Other
Platform:
GPL19424
6 Samples
Download data: CSV
Series
Accession:
GSE188164
ID:
200188164
13.

CTCF Spec-seq

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
synthetic construct
Type:
Other
Platform:
GPL19424
10 Samples
Download data: CSV
Series
Accession:
GSE188166
ID:
200188166
14.

N1-methyl-pseudouridine found within COVID-19 mRNA vaccines produces faithful protein products

(Submitter supplied) Given the interest in the COVID mRNA vaccines, we sought to investigate how the RNA modification N1-methyl-pseudouridine (and its related modification, pseudouridine) is read by ribosomes and reverse transcriptases. By looking at reverse transcriptase data, we can gain information on how the modification affects duplex stability, which may have important consequences for the tRNA-mRNA interactions found in the ribosome.
Organism:
synthetic construct
Type:
Other
Platform:
GPL19424
10 Samples
Download data: XLSX
Series
Accession:
GSE186464
ID:
200186464
15.

Profiling miRNA transcriptomic changes using Affymetrix miRNA4.0 in 6 regions of postmortem brains of subjects with alcohol use disorder

(Submitter supplied) Chronic alcohol consumption may alter miRNA transcriptome profiles in reward-related brain regions. Given that miRNAs can regulate the expression of their target coding genes (or mRNAs) at the post-transcriptional level, alcohol-induced miRNA expression change may influence the expression of their targets mRNAs that are involved in alcohol use disorder (AUD)-related pathways, leading to increased risk of AUD. more...
Organism:
Homo sapiens; synthetic construct
Type:
Non-coding RNA profiling by array
Platform:
GPL21572
96 Samples
Download data: CEL
Series
Accession:
GSE180700
ID:
200180700
16.

Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

(Submitter supplied) Hairpin-containing pre-miRNAs are precursors of microRNAs (miRNAs) that play important roles in cellular processes and various human diseases. Pre-miRNAs are produced from longer primary transcripts (pri-miRNAs). The falsity in cellular expression and sequences of pre-miRNAs might cause cellular defects or human diseases. However, the current pre-miRNA quantification methods by qPCR cannot discriminate between pre-miRNAs and their parental pri-miRNAs. more...
Organism:
Homo sapiens; synthetic construct
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL19424 GPL18573
11 Samples
Download data: BED
Series
Accession:
GSE185524
ID:
200185524
17.

Analysis of miRNA expression through microarray scan in penile carcinoma samples and normal-adjacent tissues

(Submitter supplied) Penile cancer is a rare disease that has high morbidity and mortality rates. While a few biomarkers related to prognosis have been previously described to date, none of them was adopted in clinical practice. We used microarrays to identify miRNA-based molecular signatures to identify penile carcinoma regions from paired normal-adjacent tissues. We also used microarray information to distinguish patients with a high risk of metastatic penile carcinoma.
Organism:
Homo sapiens; synthetic construct
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL21572
22 Samples
Download data: CEL, CHP
Series
Accession:
GSE172095
ID:
200172095
18.

miRNA and mRNA expression in placental tissue from high altitude pregnant women

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
synthetic construct; Homo sapiens
Type:
Expression profiling by array; Non-coding RNA profiling by array
Platforms:
GPL19117 GPL15207
40 Samples
Download data: CEL
Series
Accession:
GSE168130
ID:
200168130
19.

miRNA expression in Placental Tissue from high altitude European and Tibetan women

(Submitter supplied) We used in silico analyses to identify the distinct transcriptome signatures of two populations living at high altitudes and identified potential mechanisms that underlie high-altitude adaptation. Data generated in this study indicate that placentas from Tibetan women are genetically distinct from European women at high altitudes, and appear to be protected from hypoxia and stress.
Organism:
synthetic construct; Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL19117
20 Samples
Download data: CEL
Series
Accession:
GSE168028
ID:
200168028
20.

MicroRNA microarray of HBE cell exposed to Al2O3 NPs, PM2.5, DEP

(Submitter supplied) miRNAs have been implicated in the regulation of a broad range of biological processes including development, immunity and inflammation We used miRNA microarray to explore the detailed biological processes and mechanisms underlying matter-induced pulmonary toxicity
Organism:
synthetic construct; Homo sapiens
Type:
Non-coding RNA profiling by array
Platform:
GPL17107
15 Samples
Download data: GPR, TXT
Series
Accession:
GSE134430
ID:
200134430
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