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Items: 12

1.

Single cell atlas for mammals, reptiles and birds

(Submitter supplied) The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening on animal cells is a powerful tool to reveal the expression patterns of viral entry genes for different hosts. But such exploration for SARS-CoV-2 remained limited. Here, we presented the broadest pan-species single-nucleus RNA sequencing study to date, covering 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer), from which we investigated the co-expression of ACE2 and TMPRSS2. more...
Organism:
Anas platyrhynchos; Canis lupus familiaris; Anolis carolinensis; Panthera tigris altaica; Columba livia; Felis catus; Capra aegagrus; Manis javanica; Cervus nippon taiouanus; Oryctolagus cuniculus; Mesocricetus auratus
Type:
Expression profiling by high throughput sequencing
11 related Platforms
29 Samples
Download data: TXT
Series
Accession:
GSE183300
ID:
200183300
2.

Single cells from adipose and liver

(Submitter supplied) We isolated single cells (using either liberase or collagenase A dissociation) from subcutaneous adipose tissue collected from abdominoplasty surgery, and healthy liver tissue adjacent to tumor from liver resection and ran 10X v2 3' scRNA Seq. We ran 3 channels for adipose (IRB 2007P002165/1(ORSP-3877)) and 4 channels for liver (IRB 02-240; ORSP 1702 and ORSP-2630 under ORSP-2169). Channels were merged and uploaded here. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21697
2 Samples
Download data: CSV, H5AD
Series
Accession:
GSE153643
ID:
200153643
3.

Transcriptional Characterization of healthy lacrimal gland

(Submitter supplied) Transcriptional Characterization of healthy lacrimal gland
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: CSV
4.

Transcriptional Characterization of healthy retina

(Submitter supplied) Transcriptional Characterization of healthy retina
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
6 Samples
Download data: CSV
5.

Transcriptional Characterization of Pterygium

(Submitter supplied) Purpose: To characterize the transcriptome of pterygium and to investigate transcriptional regulation of HIF target genes.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
16 Samples
Download data: CSV
6.

3’ MACE RNA-Sequencing allows for Transcriptome Profiling in Long-Term Stored Human Tissue Samples

(Submitter supplied) This study aims to compare the potential of standard RNA-sequencing (RNA-Seq) and 3’ massive analysis of c-DNA ends (MACE) RNA-sequencing for the analysis of fresh tissue and describes transcriptome profiling of formalin-fixed paraffin-embedded (FFPE) archival human samples by MACE.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
31 Samples
Download data: CSV
7.

Transcriptional Characterization of the Tumor Microenvironment and Prognostic Gene Signatures in Conjunctival Melanoma

(Submitter supplied) Purpose: To characterize the transcriptome and cellular the tumor microenvi-ronment of conjunctival melanoma (CM) compared to healthy conjunctiva and to analyze the transcriptional differences between CM with good and poor clinical outcome. Methods: Twelve formalin-fixed and paraffin-embedded (FFPE) CM of twelve patients were analyzed by Massive Analysis of cDNA Ends (MACE) RNA se-quencing. Six samples each with good and poor clinical outcome were exam-ined, the latter being defined by local recurrence or systemic metastases with a follow-up of at least 24 months. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
20 Samples
Download data: CSV
8.

Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-related Macular Degeneration

(Submitter supplied) Although genome-wide association studies, animal models, and cell culture systems have yielded important insights into the pathogenesis of neovascular age-related macular degeneration (nAMD), the underlying molecular pathways remain ill defined. Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) of body donor eyes and were thus limited by the time span from death to preservation and the associated rapid 5'-RNA degradation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: CSV
Series
Accession:
GSE146887
ID:
200146887
9.

Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. The raw sequencing data is available through dbGaP (controlled access) due to patient privacy concerns. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL18573 GPL20301
20 Samples
Download data: MTX, TSV
Series
Accession:
GSE161383
ID:
200161383
10.

Single Nucleus RNA-Seq Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection [scRNA-Seq]

(Submitter supplied) Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors of ~30 weeks, ~3 years and ~30 years of age. Focusing on genes implicated in SARS-CoV-2 cell entry, we observed an increase in the proportion of alveolar epithelial cells expressing ACE2 and TMPRSS2 in adult compared to young lungs. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
9 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE161382
ID:
200161382
11.

Single Nucleus ATAC-Seq Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection [scATAC-Seq]

(Submitter supplied) Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors of ~30 weeks, ~3 years and ~30 years of age. Focusing on genes implicated in SARS-CoV-2 cell entry, we observed an increase in the proportion of alveolar epithelial cells expressing ACE2 and TMPRSS2 in adult compared to young lungs. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
11 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE161381
ID:
200161381
12.

Gene expression in 1133 HCCs

(Submitter supplied) Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular phenotypes, raising major challenges in clinical management. HCCs detected by surveillance programs at an early stage are candidates for potentially curative therapies (local ablation, resection, or transplantation). In the long term, transplantation provides the lowest recurrence rates. Treatment allocation is based on tumor number, size, vascular invasion, performance status, functional liver reserve, and the prediction of early (<2 years) recurrence, which reflects the intrinsic aggressiveness of the tumor. more...
Organism:
Type:
Expression profiling by array; Third-party reanalysis
Download data: TXT
Series
Accession:
GSE237977
ID:
200237977

Supplemental Content

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