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Items: 1 to 20 of 31

1.

RNA-seq profiling of A549 cells with sgRNA knockouts that confer prexasertib resistance

(Submitter supplied) A549 cells with FOXM1 or LIN54 sgRNA knockout, which confers resistance to the CHK1 inhibitor prexasertib, were generated. These cells and control (empty vector) cells were synchronized in S phase, released for 1 hour and treated with 100 nM prexasertib or DMSO (vehicle) for 2 hours. RNA-seq profiling was performed to identify drug-induced perturbations in gene expression in these cells.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: TXT
Series
Accession:
GSE154545
ID:
200154545
2.

CHK1 Inhibitor Blocks Phosphorylation of FAM122A and Promotes Replication Stress

(Submitter supplied) While effective anti-cancer drugs targeting the CHK1 kinase are advancing in the clinic, drug resistance is rapidly emerging. Here, we demonstrate that CRISPR-mediated knockout of the little-known gene FAM122A confers cellular resistance to CHK1 inhibitors and cross-resistance to ATR inhibitors. Knockout of FAM122A results in activation of PP2A-B55α, a phosphatase which dephosphorylates the WEE1 protein and rescues WEE1 from Ubiquitin-mediated degradation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: CSV
Series
Accession:
GSE158338
ID:
200158338
3.

Profiling chromatin accessible regions in Merkel cell carcinoma cells

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: BED
Series
Accession:
GSE140505
ID:
200140505
4.

LSD1-RCOR2 binding and LSD1 and BRD9 transcriptome analysis in Merkel cell carcinoma cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
66 Samples
Download data: BED, TXT
Series
Accession:
GSE124864
ID:
200124864
5.

LSD1 and BRD9 transcriptome analysis in the MKL-1 Merkel cell carcinoma (MCC) cell line

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: TXT
Series
Accession:
GSE124861
ID:
200124861
6.

LSD1 transcriptome analysis in Merkel cell carcinoma (MCC) cell lines

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
42 Samples
Download data: TXT
Series
Accession:
GSE124857
ID:
200124857
7.

Genome-wide maps of LSD1-RCOR2 binding in Merkel cell carcinoma cells

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: BED, TXT
Series
Accession:
GSE124856
ID:
200124856
8.

STRIPAK directs PP2A activity to promote oncogenic transformation

(Submitter supplied) We evaluated the effects of suppressing MAP4K4 on transcriptome and YAP1 pathway based on the observation that partial suppression of MAP4K4 leads to transformation through activation of YAP1. Mutations and deletions involving subunits of the serine-threonine phosphatase PP2A occur in a broad range of human cancers, and partial loss of PP2A function contributes to cell transformation. In particular, displacement of regulatory B subunits by the viral oncoprotein SV40 small-t antigen (ST) or mutation or deletion of PP2A subunits alters the abundance and types of PP2A complexes in cells and induces cell transformation in human cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: TSV
Series
Accession:
GSE118272
ID:
200118272
9.

RNA-seq of human foreskin fibroblast cells lacking RB, p130, and p107 treated with doxorubicin.

(Submitter supplied) We used human foreskin fibroblast cells with CRISPR-Cas9 mediated knockout of RB1 and p130 (RBL2) (sgP130, sgRB1+sg130), knocked down p107 using siRNA and measured gene expression changes after doxorubicin treatmnet (24 hr, 350 nM).
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
16 Samples
Download data: XLSX
Series
Accession:
GSE135842
ID:
200135842
10.

RNA-seq of human foreskin fibroblast cells lacking RB and/or p130 after doxorubicin treatment

(Submitter supplied) We used human foreskin fibroblast cells with CRISPR-Cas9 mediated knockout of RB1 and p130 (RBL2) (Control, sgRB1, sgP130, sgRB1+sg130) and measured gene expression changes after doxorubicin treatmnet (24 hr, 350 nM).
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
16 Samples
Download data: TXT
Series
Accession:
GSE128711
ID:
200128711
11.

RNA-seq (PolyA) of RNA from Tet-inducible SaOS2-p21 cells

(Submitter supplied) RNA was extracted from SaOS2 cells harboring a tet-inducible p21 expression vector. 3 replicates from untreated and 3 replicates from 24h doxycycline-treated cells.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
6 Samples
Download data: TXT
Series
Accession:
GSE128669
ID:
200128669
12.

A genetic murine model of CLL based on B cell-restricted expression of Sf3b1 mutation and Atm deletion

(Submitter supplied) The RNA splicing factor SF3B1 is recurrently mutated in chronic lymphocytic leukemia (CLL), but its functional role in the pathogenesis of this disease has not been firmly established. Here, we show that conditional expression of heterozygous Sf3b1-K700E mutation in mouse B lineage cells disrupts pre-mRNA splicing, alters B-cell development and function, and induces a state of cellular senescence. B-cell restricted expression of this mutation combined with Atm deletion led to the overcoming of cellular senescence, together with enhanced genome instability and the development of clonal B220+CD5+ CLL cells in elderly mice at low penetrance. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9185
17 Samples
Download data: XLSX
Series
Accession:
GSE122668
ID:
200122668
13.

MYCL and EP400 are required for Max and MCPyV mediated gene activation

(Submitter supplied) To determine if MYCL or EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing shMYCL and two different EP400 shRNA -2, -3 and compared to ChIP-seq data using BETA analyses.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
15 Samples
Download data: CSV, TXT
Series
Accession:
GSE100183
ID:
200100183
14.

MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL11154
31 Samples
Download data: BED, FPKM_TRACKING, TXT, WIG
Series
Accession:
GSE69878
ID:
200069878
15.

MCPyV ST, MAX and the TRRAP complex cooperate to bind to Transcription Start Sites

(Submitter supplied) To determine if MCPyV ST was recruited to chromatin together with MAX and the TRRAP complex, we performed chromatin immunoprecipitation (ChIP) using the validated antibodies to MCPyV ST produced in our lab, HA tagged ST, MAX and EP400 followed by next generation sequencing. De novo DNA motif analysis revealed that the canonical E-box MYC target sequence was the most frequently observed motif. Metagene analysis revealed that antibodies to MAX, EP400, ST (Ab5) and HA tagged ST showed strong enrichment in transcription start site (TSS). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL11154
10 Samples
Download data: BED, TXT, WIG
Series
Accession:
GSE69877
ID:
200069877
16.

EP400 is required for Max and MCPyV mediated gene activation

(Submitter supplied) To determine if EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing EP400 shRNA and compared to ChIP-seq data using BETA analyses.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: CSV, FPKM_TRACKING, TXT
Series
Accession:
GSE69876
ID:
200069876
17.

Characterization of human Merkel cells and their response to Merkel cell polyomavirus

(Submitter supplied) Merkel cells are epidermal mechanoreceptor cells responsible for the perception of gentle touch. Merkel cell carcinoma (MCC) is a rare and highly aggressive skin cancer. Although MCC histologically resembles Merkel cells, the cell of origin for MCC is unknown. MCC frequently contains integrated Merkel cell polyomavirus (MCPyV), a small DNA tumor virus with widespread prevalence. Whether MCPyV can transform Merkel cells is unknown. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
3 Samples
Download data: FPKM_TRACKING
Series
Accession:
GSE79657
ID:
200079657
18.

Transcriptional landscape of the human cell cycle

(Submitter supplied) Steady-state gene expression across the cell cycle has been studied extensively. However, 2 transcriptional gene regulation and histone modification dynamics at different cell cycle stages is3 largely unknown. By applying a combination of GRO-seq, RNA-seq and histone modification 4 ChIP-seq, we depicted a comprehensive transcriptional landscape at G0/G1, G1/S and M phases 5 of breast cancer MCF-7 cells. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL11154
13 Samples
Download data: BW, TXT
19.

Merkel cell polyomavirus small T antigen promotes pro-glycolytic metabolic perturbations required for transformation

(Submitter supplied) Merkel cell polyomavirus (MCPyV) is an etiological agent of Merkel cell carcinoma (MCC), a highly aggressive skin cancer. The MCPyV small tumor antigen (ST) is required for maintenance of MCC and can transform normal cells. To gain insight into cellular perturbations induced by MCPyV ST, we performed transcriptome analysis of normal human fibroblasts with inducible expression of ST. MCPyV ST dynamically alters the cellular transcriptome with increased levels of glycolytic genes, including the monocarboxylate lactate transporter SLC16A1 (MCT1). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
78 Samples
Download data: TXT
Series
Accession:
GSE79968
ID:
200079968
20.

mRNA-seq from Nutlin-3a, doxorubicin, and DMSO treated HCT116 p21-/- cells

(Submitter supplied) We sequenced mRNA from HCT116 p21-/- cells treated with Nutlin-3a, doxorubicin, or DMSO for 24 h.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: TXT
Series
Accession:
GSE77841
ID:
200077841
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