GEO DataSets

(Submitter supplied) While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. more...

Organism:

synthetic construct; Mus musculus; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19424 GPL16512 GPL34340

18 Samples

Download data: FA, TXT

(Submitter supplied) Disease causal mechanism remains largely unknown for most Alzheimer’s disease (AD) genome-wide association studies (GWAS) risk loci, including the Clusterin (CLU) locus. Here, leveraging our approach to identify functional GWAS risk variants that show allele-specific open chromatin (ASoC), we nominated a putative AD causal SNP rs1532278 (T/C) of CLU that showed strong ASoC specifically in iPSC-derived excitatory neurons (iGlut). more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

18 Samples

Download data: TSV

(Submitter supplied) Enfortumab vedotin is a Nectin-4-directed antibody–drug conjugate designed to deliver the microtubule-disrupting agent monomethyl auristatin E (MMAE) in tumor cells. Using preclinical models of urothelial cancer (UC), we expand the understanding of the multifaceted mechanism of action for enfortumab vedotin that includes direct cytotoxicity on Nectin-4–positive tumor cells, indirect bystander effect on neighboring Nectin-4–negative tumor cells, and MMAE-mediated induction of immunogenic cell death (ICD) and associated increase in activated immune cells in the tumor microenvironment. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

21 Samples

Download data: TXT

(Submitter supplied) This study is a repository for all RNAseq data obtained from High Throuput Seqeuncing of Patient Derived Xenograft models of Breast Cancer studied at the Baylor College of Medicine Breast Center.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

153 Samples

Download data: RESULTS, TXT

(Submitter supplied) Estrogen receptor-positive (ER+) metastatic tumors contribute to nearly 70% of breast cancer-related deaths. Most patients with ER+ metastatic breast cancer (MBC) undergo treatment with the estrogen receptor agonist fulvestrant (Fulv) as standard of care. Yet, among such patients, metastasis in liver is associated with reduced overall survival compared to other metastasis sites. The factors underlying the reduced responsiveness of liver metastases to ER agonists remain unknown, impeding the development of more effective treatment approaches to improve outcomes for patients with ER+ liver metastases. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL11154 GPL16512

44 Samples

Download data: BW, CSV, TXT

(Submitter supplied) we reported the development of an accurate, easy-to-use and scalable system (SNuBar) for multiplexing single cell ATAC or multi-omics (ATAC&RNA) assays, and applied this method to multiplex therapy combinations in a lung cancer mouse model and macro-spatial regions of normal breast tissues and samples.

Organism:

Homo sapiens; Mus musculus

Type:

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

6 related Platforms

15 Samples

Download data: BED, CSV, MTX, TBI, TSV, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL11154 GPL16512 GPL18573

29 Samples

Download data: H5, NARROWPEAK

(Submitter supplied) Tcf3 is an effector of Wnt canonical pathway and deletion of Tcf3 in mouse embryonic stem cells (mESCs) strongly enhances reprogramming efficiency after fusion. We fused murine Tcf3-/- mESCs with human B-lymphocytes using the Polyethylene glycol (PEG) reagent and isolated heterokaryons at different time points to analyze early reprogramming events starting from 4 hours after fusion. We performed a genome-wide expression profile of the heterokaryons by RNA-sequencing at a high resolution.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16512

15 Samples

Download data: TXT

(Submitter supplied) Tumor progression is recognized as a result of an evolving crosstalk between tumor cells and their surrounding non-transformed stroma. Although Wnt signaling has been intensively studied in colorectal cancer (CRC), it remains unclear whether activity in the tumor-associated stroma contributes to malignancy. To specifically interfere with stromal signals, we generated Wnt-independent tumor organoids that secrete the Wnt antagonist Sfrp1. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16512 GPL13112

30 Samples

Download data: TXT

(Submitter supplied) Dopaminergic neurons (DAn), generated from human pluripotent stem cells (hPSC), are capable of functionally integrating following transplantation and have recently advanced to clinical trials for Parkinson’s disease (PD). However, pre-clinical studies have highlighted the low proportion of DAn within hPSC-derived grafts and their inferior plasticity compared to fetal tissue. Here we examined whether delivery of a developmentally critical protein, glial cell line-derived neurotrophic factor (GDNF), could improve graft outcomes. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

6 Samples

Download data: TAB, TXT

(Submitter supplied) Here we aim to demonstrate a novel approach enabling standardised and rapid characterisation of transplanted xenografts in the rodent brain. The approach employs bulk tissue dissection, inclusive of the grafted human cells and surrounding host (rodent) tissue, and utilises differences in the RNA sequences between the species to discriminate the xenograft from host gene expression. To demonstrate and validate this technique, we assessed grafts of undifferentiated human stem cells, immature neural progenitors and mature neurons following transplantation into the rodent brain. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

9 Samples

Download data: TAB, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

4 related Platforms

32 Samples

Download data: TXT

(Submitter supplied) Resolution of early molecular events preceding endogenous OCT4 activation is critical to understanding the mechanism of reprogramming somatic cells to induced pluripotent stem cells (iPSCs), yet capturing transient regulators at the onset of reprogramming is difficult in heterogeneous populations of asynchronously reprogramming fibroblasts following four-factor transduction. To address this need, we used a heterokaryon system to identify an early and transiently expressed homeobox transcription factor, NKX3-1. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

25 Samples

Download data: TXT

(Submitter supplied) Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16512 GPL11154

67 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with unprecedented sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert fluorocytosine to fluorouracil, covalently labeling nascent RNA for purification and sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16512 GPL11154

27 Samples

Download data: CSV

(Submitter supplied) Understanding the biology of rare cell populations in the context of their microenvironment requires an accurate analysis of the transcriptomes of these cells as expressed in situ. We developed fluorouracil-tagged RNA sequencing (Flura-seq) to characterize the transcriptomes of small cell subpopulations from a whole organ in model systems. The method utilizes cytosine deaminase (CD), which converts the non-natural pyrimidine base fluorocytosine to fluorouracil. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16512 GPL11154

30 Samples

Download data: CSV

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL16512 GPL13112

22 Samples

Download data

(Submitter supplied) RNA sequencing of control or Notch1-expressing mouse cells co-cultured with control, Jag1WT, or Jag1Ndr-expressing human cells. Deep sequencing and bioinformatical separation of mouse and human reads reveals transcripts specifically regulated in mouse receptor-expressing cells.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16512

6 Samples

Download data: TXT

(Submitter supplied) Our study provides a systematic and mechanistic approach for identifying key regulators in directed differentiation of pluripotent stem cells to a variety of somatic cell lineages.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL16512

17 Samples

Download data: FPKM_TRACKING

(Submitter supplied) We studied the synaptic activity-regulated gene expression response in the human genetic background using cultured human iPSC-derived (hiPSCd) neuronal networks and networks of hiPSCd neurons mixed with mouse primary neurons. Our results confirm that genetic changes affect the synaptic activity-regulated gene program, proposing a functional mechanism how they have driven evolution of human cognitive abilities.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16512 GPL19415 GPL11154

22 Samples

Download data: TXT