Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq of human first-trimester and term Hofbauer cells before and after in vitro culture for 7 days

ABSTRACT: To establish an in vitro assay using primary human Hofbauer cells, we needed to understand how the cells change in vitro. We therefore profiled and compared the transcriptomes of freshly isolated first-trimester and term Hofbauer cells to those after 7 days in culture. Cells were isolated by fluorescence-activated cell sorting and the RNA library was prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit (Takara Bio).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Qian Li

PROVIDER: E-MTAB-14087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bulk RNA-seq of human macrophages and monocytes from first-trimester and term placentas

Project description:To understand how the human macrophages and monocytes (of both fetal and maternal origin) isolated from first-trimester and term placentas differ, we profiled and compared the transcriptomes of cells freshly isolated by fluorescence-activated cell sorting, including fetal Hofbauer cells, placenta-associated maternal macrophages (PAMM), decidual macrophages, maternal and fetal monocytes using the SMART-Seq® v4 PLUS Kit (Takara Bio).

2025-08-04 | E-MTAB-14088 | biostudies-arrayexpress

Bulk RNA-seq profiling the response of human first-trimester and term Hofbauer cells to Listeria monocytogenes infection in vitro

Project description:To understand the response of human Hofbauer cells to Listeria monocytogenes infection and how it differs between first trimester and term, we established an infection assay using primary human first-trimester and term Hofbauer cells isolated by fluorescence-activated cell sorting and cultured in vitro for 7 days. We then profiled and compared the transcriptomes of control cells (treated with PBS or Heat-Killed Listeria monocytogenes) and cells infected with Listeria monocytogenes for 8 hours using the NEBNext® Ultra II Directional RNA Library Prep Kit (Illumina).

2025-08-04 | E-MTAB-14086 | biostudies-arrayexpress

Human uterine Natural Killer cells regulate differentiation of extravillous trophoblast early in pregnancy - bulk RNA-seq data

Project description:An allorecognition system depending on interactions between uterine Natural Killer (uNK) cells and placental extravillous trophoblast (EVT) during early pregnancy influences reproductive outcomes in humans. Our previous immunogenetic studies show that particular combinations of maternal Killer Immunoglobulin-like Receptors (KIR) in uNK cells with fetal HLA-C variants on EVT are associated with disorders of pregnancy, especially pre-eclampsia. To identify responses stimulated in uNK cells specifically when activating KIR (KIR2DS1) binds to C2+HLA-C, a combination protective against pre-eclampsia, we modelled KIR-HLA interactions by co-culturing uNK cells with the 721.221 HLA-null cell line transfected to express either C1+ or C2+HLA-C molecules, followed by transcriptome profiling by RNA sequencing. We detect the secretion of key cytokines by uNK cells under the protective combination between KIR2DS1 and C2+HLA-C.

2024-01-10 | E-MTAB-13379 | biostudies-arrayexpress

Spatial transcriptomics of human implantation sites, placenta and decidua

Project description:These samples are part of a study to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. Here we profiled with 10x Visium Spatial transcriptomics of the entire maternal-fetal interface including the myometrium, allowing us to resolve the full trajectory of trophoblast differentiation.

2023-02-03 | E-MTAB-12698 | biostudies-arrayexpress

Human uterine Natural Killer cells regulate differentiation of extravillous trophoblast early in pregnancy - scRNA-seq data

Project description:We used trophoblast organoids differentiating to extravillous trophoblast (EVT) to study the effects of key cytokines secreted by uterine Natural Killer (uNK) cells on EVT behaviour. Specifically, we exposed the organoids to four uNK-derived cytokines (CSF1, CSF2, XCL1, CCL5) and collected cells at different time points along the EVT differentiation pathway for scRNA-seq. We observe enhanced EVT differentiation in cytokine-treated organoids demonstrated by the increased proportion of late EVT subtypes and regulation of related pathways such as epithelial-mesenchymal transition. Moreover, uNK cytokines affect other processes important during early pregnancy including dampening of inflammatory and adaptive immune responses, regulation of blood flow, and placental access to nutrients.

2024-01-10 | E-MTAB-13382 | biostudies-arrayexpress

Bulk ATAC-seq experiments on human samples from normal gastric cardia, normal oesophageal submucosal glands and Barrett's oesophagus tissue

Project description:Profiling open chromatin in different tissue types around the gastro-oesophageal junction to allow for clustering of samples and investigation of transcription factor binding site motif enrichment.

2021-08-24 | E-MTAB-10044 | biostudies-arrayexpress

RNA-seq of human first and second trimester placenta

Project description:The study compares expression differences between first and second trimester placenta in humans. RNA-Sequencing was performed on villi obtained at 7-8 (n=8) and 13-14 (n=6) weeks’ gestational age.

2021-06-02 | E-MTAB-9203 | biostudies-arrayexpress

Investigation of placental DNA methylation in obese women exposed to Metformin during pregnancy

Project description:Maternal obesity in pregnancy is associated with increased birth-weight, obesity and premature mortality in adult offspring. The Effect of Metformin on Maternal and Fetal Outcomes in Pregnant Obese Women (EMPOWaR) trial was a randomised, double-blind, placebo-controlled trial carried out to determine whether exposure to Metformin would affect the offspring birth-weight centile. Obese women exposed to Metformin had increased insulin sensitivity at 36 weeks of pregnancy, but there were no differences in offspring birthweight. We obtained the placentas from these women to determine whether there were differences in DNA methylation of genes regulating fetal growth and metabolism. In a related study we investigated the gene expression in the same samples.

2018-11-01 | E-MTAB-6421 | biostudies-arrayexpress

CD74 downregulation in placental macrophages and its influence on trophoblast cells.

Project description:Preeclampsia is a disease of pregnant women, which is characterized by hypertension, proteinuria and chronic inflammation. There is a growing body of evidence that cause of preeclampsia lies within immunological aspect of pregnancy. This study aimed to analyze the role of CD74 in preeclampsia with a focus on its influence on communication between placental macrophages (Hofbauer cells) and trophoblasts. We have found CD74 to be highly dysregulated in preeclamptic placenta by real-time RT-PCR and Western blot methods. We identified Hofbauer cells to express the highest levels of CD74 in placenta by immunofluorescence and flow cytometry and that CD74 in preeclamptic Hofbauer cells is lower than in controls. We have performed a transcriptome analysis on human blood monocyte-derived macrophages that were non- or IL-4-activated and treated with small interfering RNA against CD74 (siRNA CD74) or non-targeting siRNA (siRNA non-targeting) as control.

2015-04-29 | E-MTAB-3309 | biostudies-arrayexpress

Characterization of primary models of human trophoblast

Project description:To understand the human placenta development, we investigated the features of two trophoblast models, trophoblast organoids and trophoblast stem cells, with the aim of identifying which type of trophoblast in vivo they most closely resemble. To this end, we profiled the microRNAs from the two models by using the Bioo Nextflex protocol (NEXTFLEX Small RNA-seq Kit v3 for Illumina Platforms).

2021-10-18 | E-MTAB-10438 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data