GEO DataSets

(Submitter supplied) Purpose: to analyze gene expression changes of iMACs encountering S. pneumoniae. Methods: SMART-seq2 amplified polyA RNA from sorted iMACs in the co-cultures. Results: the transcriptome of iMACs changed after encountering S. pneumoniae. Conclusions: the gene expression profiles of S. pneumoniae stimulated iMACs indicated iMACs undergoing inflammatory response and the immune response was distinct with iMACs encountering other pathogens such as HCV or SARS-CoV-2.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) Purpose: to depict the single-cell map and reveal the heterogeneity of hPSC derived macrophages Methods: Differentiation day 14 iMacs were dissociated to obtain a single-cell suspension. scRNA-seq and scATAC-seq library preparation and sequencing were done by CapitalBio Technology (https://www.capitalbiotech.com/). scRNA-seq, the cell suspension was immediately loaded onto the Chromium Single Cell Controller (10× Genomics) for droplet formation. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

2 Samples

Download data: BED, MTX, TBI, TSV

(Submitter supplied) Purpose: to analyze change in gene expression of hPSC derived macrophages upon co-culture with hepatic cells including Huh7 and primary human hepatocytes Methods: SMART-seq2 amplified polyA RNA from sorted iMacs in the co-cultures. Results: the transcriptome of iMacs changed after co-culture with Huh7 cells or pHHs, and changed after the HCV infection of the co-cultured Huh7 cells. Conclusions: the gene expression profiles of co-cultured iMacs indicated that the culture conditions and the microenvironments could reprogrammed iMacs to adopt tissue-specific features and perform specifc functions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: TXT

(Submitter supplied) We established a co-culture model using cells derived from hPSC and studied the transcriptomes on the lung cells and the co-cultures using scRNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: MTX, TSV

(Submitter supplied) We hypothesize that the different types of macrophages have distinct responses to SARS-CoV-2 infection. To test this hypothesis, we characterized cellular responses to SARS-CoV-2 at 24h- or 48h-post SARS-CoV-2 infection in M0, M1 or M2 macrophages derived from human pluripotent stem cells using high-throughput RNA sequence and other assays

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: TXT, XLS

(Submitter supplied) We report the application of RNA sequencing for transcriptome analysis of SARS-CoV-2-infected and Influenza A-infected Human nasal turbinate and lung tissues, enabling the study of tissue responses to viral infections

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: XLSX

(Submitter supplied) We performed single-cell RNA sequencing (scRNA-Seq) on nasal wash cells freshly collected from adults with COVID-19, influenza A, or no disease (healthy). Major cell types and subtypes were defined using cluster analysis and classic transcriptional markers.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

116 Samples

Download data: TXT

(Submitter supplied) Specialized tissue macrophages arise during embryogenesis from yolk-sac (YS) progenitors that migrate into developing tissues and terminally differentiate in situ. Until recently, it has been impossible to isolate or derive sufficient numbers of YS-derived macrophages for further study, but data now suggest that induced pluripotent stem cells (iPSCs) can be driven to undergo a process reminiscent of YS-hematopoiesis in vitro. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

24 Samples

Download data: TXT

(Submitter supplied) The generation of human macrophages from induced pluripotent stem cells (iMacs) is a rapidly developing approach used to create disease models, screen drugs, study macrophage-pathogen interactions and develop macrophage-based cell therapy. To generate iMacs, different types of protocols have been suggested, all thought to result in the generation of similar iMac populations. However, direct comparison of iMacs generated using different protocols has not been performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL18573

40 Samples

Download data: TXT

(Submitter supplied) Long term cell culture adaptation of hepatitis C virus resulted in increased replication fitness in various human liver cell lines but in a moderate decrease in virus particle production upon infection of primary human hepatocytes (PHH). In order to identify molecular mechanisms conferring phenotypic differences in replicative fitness of the cell culture adapted virus strain p100pop, we infected PHH and Huh-7 cells with HCV, using the cell culture adapted strain p100pop or a Jc1 strain with similar genome organisation (Jc1-SP). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

18 Samples

Download data: XLSX

(Submitter supplied) We report here a modified protocol for generating homogenous populations of macrophage-like cells from human embryonic stem cells. The induced macrophages, referred to as iMAC, presented similar transcriptomic profiles and characteristic immunological features of classical macrophages and were permissive to viral and bacterial infection, in particular Mycobacterium tuberculosis (Mtb). Their production was amenable to scale up and the resulting cells suitable for high-throughput screening.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: TXT

(Submitter supplied) Macrophages are major innate immune cells located in various human organs, and related in disease progression and regression. Therefore, genetic data of human macrophages are considered as a potential resource to understand of human diseases. Here, we performed large-scale transcriptome analysis of 2,931(raw data: 3,323) human embryonic stem cells-derived macrophages (iMACs) using single-cell RNA-sequencing technology, and provided public data resource for better understanding of the human macrophages’ characteristics and their heterogeneity.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

1 Sample

Download data: MTX, TSV

(Submitter supplied) Most individuals exposed to hepatitis C virus (HCV) become persistently infected while a minority spontaneously eliminate the virus. Although early immune events influence infection outcome, the cellular composition, molecular effectors, and timeframe of the host response active shortly after viral exposure remain incompletely understood. Employing specimens collected from people who inject drugs (PWID) with high risk of HCV exposure, we utilized RNA-Seq to characterize immune function in peripheral blood before, during, and after acute HCV infection resulting in spontaneous resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

53 Samples

Download data: TXT

(Submitter supplied) Study transcriptomes on the lung cells and macrophages derived from hESC

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: MTX, TSV

(Submitter supplied) Pluripotent stem cells are being actively studied as a cell source for regenerating damaged liver. For long term survival of engrafting cells in the body, not only do the cells have to execute liverspecific function but also withstand the physical strains and invading pathogens. The cellular innate immune system orchestrated by the interferon (IFN) pathway provides the first line of defense against pathogens. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) We uncovered the global responses of host human heart muscle cells to SARS-CoV-2 genes Nsp6, Nsp8 and M, defined the molecular mechanisms underlying SARS-CoV-2 genes-induced cardiac abnormalities, and explored the potentially therapeutic approaches to ameliorate cardiac dysfunctions in COVID-19 patients.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TSV

(Submitter supplied) Primary human hepatocytes (PHHs) are a liver-specific cell subtype, and we have shown that these cells respond in a unique manner to the introduction of hepatitis C viral RNA (HCV vRNA) derived from different genotypes of the virus. We used microarray to analyze the transcriptional differences between the PHHs exposed to the different genotypes of HCV to further shed light on their differential effects on HCV innate immune responses in vitro

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

3 Samples

Download data: CEL

(Submitter supplied) We have collected nasal cell swab samples from SARS-CoV-2 infected confirmed COVID-19 patients. Both virus and host RNA were extracted and sequenced by RNA-seq. We mapped and assembled virus sequences and in this study transcriptional profile of host due to virus infection.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) Detailed knowledge about dynamics of SARS-CoV-2 infection in vivo is important for unraveling the viral and host response factors that contribute to COVID-19 pathogenesis. The unknown dose and exposure timing in human infections makes the needed well-controlled time course studies impossible and thus animal models of disease are essential to fill in the gaps in our understanding of disease progression. more...

Organism:

Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29061

20 Samples

Download data: TAR

(Submitter supplied) Purpose: RNAseq analysis of hPSC undergoing in vitro hepatic differentiation, to validate proper differentiation at different times of differentiation (D0 to D21)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

13 Samples

Download data: XLSX