GEO DataSets

(Submitter supplied) Our previous results from RNA-seq and IP-MS together suggest that SUMOylation may be critical for the DNA-binding capability of HEY1 to enhance its transcriptional repressive activity. To confirm our speculation, we conducted ChIP assays in HUVECs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23227

8 Samples

Download data: XLSX

(Submitter supplied) Feast-Famine Response Proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the E. coli leucine-responsive regulatory protein (Lrp). Lrp senses environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium towards the octameric state. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21222 GPL25368

234 Samples

Download data: BEDGRAPH, CSV

(Submitter supplied) In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages such as multilineage differentiation, angiogenesis, and close cell‒cell interactions. To systematically investigate the multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We inferred 18 cell differentiation trajectories and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30440 GPL29480 GPL26363

23 Samples

Download data: TXT

(Submitter supplied) In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages such as multilineage differentiation, angiogenesis, and close cell‒cell interactions. To systematically investigate the multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We inferred 18 cell differentiation trajectories and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29480

2 Samples

Download data: BED, TAR, TXT

(Submitter supplied) How do neurons match generation of adenosine triphosphate (ATP) by mitochondria to the bioenergetic demands of regenerative activity? Although the subject of speculation, this coupling is still poorly understood, particularly in neurons that are tonically active. To help fill this gap, pacemaking substantia nigra dopaminergic neurons were studied using a combination of optical, electrophysiological and molecular approaches. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT

(Submitter supplied) Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21290 GPL21493

22 Samples

Download data: BW

(Submitter supplied) Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21290 GPL21493

38 Samples

Download data: BW

(Submitter supplied) Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL21290

13 Samples

Download data: RESULTS, TXT

(Submitter supplied) Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: BW

(Submitter supplied) Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21290

6 Samples

Download data: BW

(Submitter supplied) We conducted a genome-wide transcription profiling experiment using Agilent GeneChip S. coelicolor DNA microarrays (custom-specific design) to determine whether OhkA and OrrA function in the same pathway. From the complete transcriptome data, we observed that, totally, 981 and 1242 genes had significantly altered transcription levels (with at least two-fold increases or decreases) in the mutants of ΔohkA and ΔorrA, respectively, compared with the wild-type strain M145. more...

Organism:

Streptomyces coelicolor

Type:

Expression profiling by array

Platform:

GPL29462

8 Samples

Download data: TXT

(Submitter supplied) Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

19 Samples

Download data: CSV, H5, H5AD, TXT

(Submitter supplied) The EBV BRLF1 expression may exert an influence on genome instability. To test this speculation, the long-term experiment of recurrent BRLF1 expression was performed. The NPC cells (TW01-TetER, doxycycline inducible BRLF1 expressing cell line) were used. Experimental samples were derived from different passages of the NPC cells without or with BRLF1 expression. Array CGH (aCGH) was carried out to investigate the copy-number aberrations in response for different frequencies of BRLF1 expression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Genome variation profiling by genome tiling array

Platform:

GPL8737

3 Samples

Download data: TXT

(Submitter supplied) Despite considerable speculation for the role of cytosine (DNA) methylation in biological and molecular processes in insects, direct functional tests are lacking. Here we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi) we successfully post-transcriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). more...

Organism:

Oncopeltus fasciatus; Blattella germanica

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL22038 GPL24515

75 Samples

Download data: TSV, TXT, XLSX

(Submitter supplied) Temporal regulation of gene expression is essential for early embryonic development. With the development of next-generation sequencing technologies, transcriptional profiling of early developmental processes in various vertebrates are already revealed. However, overall transcriptome analysis of early embryonic development in avian have never been investigated. In this study, to our knowledge, we provide comprehensive profiling of pre-oviposited embryos in chicken by whole-transcriptome RNA-seq for the first time. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19787

21 Samples

Download data: TXT

(Submitter supplied) Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL13821

16 Samples

Download data: WIG

(Submitter supplied) In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL11154 GPL13112

17 Samples

Download data: BED, TXT

(Submitter supplied) In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. more...

Organism:

Mus musculus; Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

10 Samples

Download data: TXT

(Submitter supplied) In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL11154 GPL13112

3 Samples

Download data: BED