GEO DataSets

(Submitter supplied) The efficacy of hepatic arterial infusion chemotherapy (HAIC) with oxaliplatin (OXA) and 5-fluorouracil (5-Fu) for treating advanced perihilar cholangiocarcinoma (pCCA) has been demonstrated, yet the survival benefits of HAIC for pCCA patients vary. Here, we aimed to screen out HAIC resistance-related bile microRNAs (miRNAs) and explore the functions of specific bile miRNAs in pCCA based on high-throughput sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: XLSX

(Submitter supplied) Epigenetic macromolecular enzyme complexes tightly regulate gene expression at the chromatin level and have recently been found to colocalize with RNA splicing machinery during active transcription1; however, the precise functional consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex (LSD1-HDAC1-CoREST) with components of the RNA splicing machinery and their functional consequences in tumorigenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate the DNA-binding property of two tandem AP2 domains of PbSIP2, DNA immunoprecipitation followed by high-throughput sequencing (DIP-seq) analysis were performed. Recombinant AP2 domains fused with maltose-binding protein (MBP) were mixed with the P. berghei genomic DNA fragmented via sonication, and protein-DNA complex was harvested using amylose resin. The obtained DNA fragments were sequenced via the next generation sequencing.

Organism:

Plasmodium berghei

Type:

Other

Platform:

GPL23133

2 Samples

Download data: XLS

(Submitter supplied) Your female patients with cancer will probably become sub-fertile or infertile even though some finally overcome the cancer through various therapies. Cancer immunotherapy is recently emerging as a promising novel therapy against cancer with high malignancy and lethality, but whether or not cancer immunotherapy affect female fertility is rarely known. In the present study, we employed MCA205 cells-xenografted B6 mice as model to investigate whether two popular immunotherapies, PD-1 monoclonal antibody (PD-1) and whole cancer cell vaccine (WCA), affect ovarian function. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28330

12 Samples

Download data: TXT

(Submitter supplied) Behavioral, social, and physical characteristics are posited to distinguish the sexes, yet research on transcription-level sexual differences in the brain is limited. Here, we investigated sexually divergent brain transcriptomics in prepubertal cynomolgus macaques, a commonly used surrogate species to humans. A transcriptomic profile using RNA sequencing was generated for the temporal lobe, ventral midbrain, and cerebellum of 3 female and 3 male cynomolgus macaques previously treated with an Adeno-associated virus vector mix. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

18 Samples

Download data: TXT

(Submitter supplied) Aims:This study used cell line models and patient datasets to investigate the role of YAP1 in B- ALL. Methods: We used RNA-Seq to compare the gene expression levels of the Hippo pathway-related molecules before and after verteporfin (VP) treatment to identify important Hippo pathway-related genes in the NALM6 cell line. Results:we identified a total of 2002 differentially expressed genes in VP and DMSO treatment groups (FC ≥ 1.5, p ≤ 0.05), including 1042 upregulated and 960 downregulated genes, of which 146 were associated with the Hippo signaling pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX

(Submitter supplied) A total of 4276 lncRNAs (1426 upregulated and 2850 down-regulated) and 9230 mRNAs (5187 upregulated and 4043 down-regulated) were differently expressed in SHR-C compared with WKY, whereas 265 lncRNAs (65 up-regulated and 200 down-regulated) and 267 mRNAs (132 upregulated and 135 down-regulated) were differently expressed after BSJY treatment (fold change >2. 0 and P value< 0. 05). Taking the intersection of the two sets, the analysis found that 8 lncRNAs and 35 mRNAs were upregulated, whereas 11 lncRNAs and 15 mRNAs were downregulated in the WKY vs. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL21829

12 Samples

Download data: TXT, XLS

(Submitter supplied) Nicotine withdrawal can diversely affect brain gene expression patterns. In the brain, the dorsal striatum is a hub of nicotine dependence. Previous studies have shown that nicotine dependence leads to functional alterations in the dorsal striatum. miRNAs are small non-coding RNAs that regulates cellular functions and dysfunctions. Here, we performed small RNA sequencing from the dorsal striatum of mice at 7 days after nicotine withdrawal. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: XLSX

(Submitter supplied) Background: Calcific aortic valve disease (CAVD) is the pathological remodeling of valve leaflets. The initial steps in the osteogenic reprogramming of the leaflet are not fully understood. Studies have shown that TERT overexpression primes mesenchymal stem cells to differentiate into osteoblasts, and we investigated whether TERT contributes to the osteogenic reprogramming of valve interstitial cells (VICs). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

3 Samples

Download data: CSV

(Submitter supplied) Background & Aims: Chronic HBV patients with concomitant metabolic dysfunction-associated steatohepatitis (MASH) have been shown to develop more advanced fibrosis faster with more severe liver disease as compared to patients with chronic HBV alone. However, our understanding of the underlying mechanisms is limited. Here we study how MASH co-morbidity impact immune activity in the liver of patients with chronic HBV infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

39 Samples

Download data: SF

(Submitter supplied) Palbociclib is a CDK4/6 inhibitor approved for the treatment of breast cancer by suppressing cell proliferation. However, monotherapy with palbociclib was discouraging in prostate cancer, calling for a mechanism-based effective therapy. In this study, we reported in prostate cancer that palbociclib is a potent sensitizer of ferroptosis, which is worked out by downregulating the expression of TRIB3, a gene highly expressed in prostate cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLSX

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. Hence, the characterization of new RNA families with deep sequence and/or structure conservation has the potential to reveal new molecular and biological RNA functions. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25258

12 Samples

Download data: WIG

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts of chemical reactions, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs, such as ribosomal RNAs, display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. more...

Organism:

Clostridioides difficile

Type:

Other

Platform:

GPL30071

28 Samples

Download data: RC, XML

(Submitter supplied) RNA-Seq analysis was carried out to investigate the transcriptomic changes associated with the development of in vivo everolimus resistance and the effects of CDK8/19 inhibition on the development of resistance in MDA-MB-468 TNBC xenografts. In one study (short-term), tumor samples were collected after 30-40 days of treatment with vehicle or everolimus, when the tumor growth was still suppressed by the mTOR inhibitor. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

50 Samples

Download data: TXT

(Submitter supplied) Due to scarcity of effective therapeutic targets, metastatic TNBC (mTNBC) has shorter survival times compared to other advanced breast cancer subtypes. Although chemo-immunotherapy with immune checkpoint inhibitors (ICIs) in PD-L1+ mTNBC has shown promise, survival benefit remains modest. Therefore, it is crucial to gain improved insight into the mechanisms underlying response and resistance to checkpoint inhibition in mTNBC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: RDS

(Submitter supplied) Viral RNA synthesis of mononegaviruses occurs in the cytoplasmic membrane-less organelles called as inclusion body (IB). Here, we reported that the IBs of mumps virus (MuV), which is the causative agent of mumps and belongs to the family Paramyxoviridae, had properties of liquid organelles formed by liquid-liquid phase separation. Super-resolution microscopic analysis of the MuV IBs demonstrated that nucleocapsid and phospho-(P) proteins formed the cage-like structure and that viral polymerase was in a reticular pattern and partially co-localized with viral mRNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) Antibiotic resistance is a major public health threat, and alternatives to antibiotic therapy are urgently needed. Immunotherapy, particularly the blockade of inhibitory immune checkpoints, is a leading treatment option in cancer and autoimmunity. In this study, we used a murine model of Salmonella Typhimurium infection to investigate whether immune checkpoint blockade could be applied to bacterial infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TXT

(Submitter supplied) Purpose: Development of specific and precise RNA base editing toolkit. Methods: The transcriptome-wide off-target sites identification, annotation, and transcriptome-wide genes regulation of each editor were analyzed by RNA-seq data. The raw reads (.fastq) were first processed using Trim Glore (v0.6.7) to remove adapter sequences with default parameters. Then the trimmed data were used to remove rRNA data by Bowtie2 (v2.5.0) with key parameters –no-unal -I 1 -X 1000. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL30209 GPL30215 GPL24676

23 Samples

Download data: DIFF, XLSX

(Submitter supplied) To examine the effects of ERα antagonism (giredestrant) on Esr1-wildtype and Esr1-mutant mammary glands, animals were treated with hormone pellets (E2, P4), then dosed daily with vehicle (MCT) or giredestrant (30 mg/kg, p.o.) for four days. Following dosing, individual mammary epithelial cell populations were FACS-isolated and sequenced. Rare giredestrant-induced novel cells (at least 1000 cells per sample) were collected from WT tissues and compared to mutant-induced novel cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: TAB

(Submitter supplied) To examine the effects of ERα antagonism (giredestrant) on Esr1-wildtype and Esr1-mutant mammary glands, animals were treated with hormone pellets (E2, P4), then dosed daily with vehicle (MCT) or giredestrant (30 mg/kg, p.o.) for four days. Following dosing, individual mammary epithelial cell populations were FACS-isolated and sequenced.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

51 Samples

Download data: NARROWPEAK