Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA352390: Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta

Source: NCBI / GSE89497
Submission Date: Nov 03 2016
Release Date: Jul 24 2018
Update Date: May 15 2019

Summary: In this study, we isolated human villous stromal cells (STRs), CTBs, the STB, and EVTs at the first and second trimester of pregnancy and monitored the transcriptome dynamics of 1567 cells at single-cell resolution. We identified 14 subtypes of placental cells and characterized their functions, especially the unexpected secretion of 102 polypeptide hormone using bioinformatics analyses and immnunostaining verifications. Our study builds a strong foundation for understanding how the human placenta develops and functions to maintain a healthy pregnancy.

Overall Design: single cell transcriptome profiles of stomal cells and trophoblast cells from 8 week and 24 week gestation of placenta were generated by next generation sequencing using Illumina Hiseq4000.

GEN Datasets:
GEND000058
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: Extravillous trophoblast of weeks 24 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Cytotrophoblast of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; TMR-positive CD8+ sorted T-cells of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Extravillous trophoblast of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Stromal cell of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h
Extract Protocol: Chrion were scraped from human placenta and the remaining villi were collected and minced into small pieces. The tissue were digested with an enzyme cocktail (0.125% trypsin 0.04% Dnase and 0.05% type Ⅳ collagenase) for 8 min twice at 37℃ Cell suspension were collected by filtering the ezyme mixture with 70 μm cell strainer and the enzyme reaction were stopped by addition of 5% DMEM. cells were centrifuged at 1200 g at 4 ℃ on a percoll gradient (7 layers: 10%, 20%, 30%, 40%, 50%, 60% and 70%) and cells from 30% - 50% percoll gradient were collected and washed with DMEM. EVT and CTB were sorted with MACS with PE-conjucted HLA-G and CDH1 antibody combined with anti-PE beads,STB were purified with mouth pipette based on their big size from the cell population and the remaning HLA-G and CDH1 double negative cells were stromal cells. For isolation of EVT from the basal plate of the 24 w placenta, basal plate were scaped from the placenta, minced and digested with the method as described above,finally 24 w EVT were purified by MACs with HLA-G antibody.
Library Construction Protocol: the single cells were picked into 2ul cell lysis buffer using mouse pipet, then the transcriptome was amplified by modified smart-seq2 protocol which added in barcode for each cell. the amplified cDNAs were sheared into 300bp fragments, the 3' end of the cDNAs were enriched to build library with KAPA Hyper Prep Kits for Illumina
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: paired
Library Strand: Reverse; -
Platform: Illumina
Instrument Model: Illumina HiSeq 4000
Strand-Specific: Specific; Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta.
Cell research . 2018-07-24 [PMID: 30042384]