Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

ABSTRACT: To compare the performance of Illumina and BGI sequencing technologies for high-throughput single cell sequencing, four Chromium single cell libraries of the following human cell types: Induced Pluripotent Stem Cells (hIPSC), cultured Trabecular MeshWork Cells (TMWC) and Peripheral Blood Mononuclear Cells (PBMCs), were sequenced on Illumina sequencers (NextSeq 500, NovaSeq 6000) and a BGI sequencer (MGISEQ-2000). The technologies were benchmarked based on sequencing quality, characterisation of cell populations within samples and for specific single cell analyses such as variant calling and detection of guide RNAs from pooled CRISPR screens.

INSTRUMENT(S): Illumina NovaSeq 6000, NextSeq 500, BGISEQ-500

ORGANISM(S): Homo sapiens

SUBMITTER: Anne Senabouth

PROVIDER: E-MTAB-9024 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Single Cell RNAseq from IL6R deficient patient and healthy parent

Project description:To determine the phenotypic differences in blood cells that are regulated by the IL-6R

2019-06-19 | E-MTAB-8034 | biostudies-arrayexpress

Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells

Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 2 chemistry) system on ~6,000 mouse endothelial cells derived from aorta.

2019-05-27 | E-MTAB-7149 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract in young, pregnant and aged C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract across the four stages of estrus cycle in young adult mice (ovary, oviduct, uterus, cervix and vagina, with spleen as a comparison) and compared this with similar analyses of decidualization (uterus) and ageing (ovary, oviduct, uterus, cervix, vagina and spleen). Vaginal smears were used to stage the estrus cycle in young mice. To collect the decidualized uteri mice were mated and uterine tissue was collected from pregnant mice at day 5.5 after mating. Tissues of aged mice were collected at the age of 18 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2023-02-01 | E-MTAB-11491 | biostudies-arrayexpress

10X Chromium Single-cell RNA sequencing of the female reproductive tract during aging in C57BL/6 mice

Project description:The aim of the study was to assess the cellular composition and transcriptional changes at single-cell resolution of the female reproductive tract during ageing in ovary, oviduct and uterus. Tissues of aged mice were collected at the age of 9,12 and 15 months. All tissues were collected and digested using a collagenase and trypsin protocol to obtain single cell suspension. Libraries were prepared using the 10x scRNA-seq protocol.

2024-01-31 | E-MTAB-12889 | biostudies-arrayexpress

Single-cell RNA-seq comparing WT, HDAC3 and Dax1 knock-out clones in SL(RA) differentiation conditions

Project description:We performed single-cell RNA-seq in order to characterize in high resolution the transcriptomic profiles, differentiation fates and heterogeneity of wild-type, HDAC3 or Dax1 knock-out cells in SL(RA) differentiation conditions.

2021-03-15 | E-MTAB-10147 | biostudies-arrayexpress

Human pluripotent stem cell-derived ROR1e lens epithelial cell single cell RNA-sequencing

Project description:Detailed transcriptomic analyses of differentiated cell populations derived from human pluripotent stem cells is routinely used to assess the identity and utility of the differentiated cells. In particular, single cell RNA-sequencing (scRNA-seq) can provide insights into both the cellular and transcriptional heterogeneity of differentiated cell populations. Here we provide scRNA-seq data obtained from ROR1-expressing lens epithelial cells (ROR1e LECs) obtained via directed differentiation of CA1 human embryonic stem cells. Through the use of principal component analysis, heat maps and gene ontology assessments, we demonstrate that ROR1e LECs represent a highly purified and large-scale population of lens cells. These data provide a resource for future characterisation of both normal and cataractous human lens biology.

2020-11-27 | E-MTAB-9178 | biostudies-arrayexpress

Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

Project description:We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlexTM and TeSRTM-E8TM media. Single-cell transcriptome sequencing was performed for 20,962 cells from two cell lines grown in the two media. Analysis of transcriptomic profile revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Single cell analysis of the four samples revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that 60-96% of the cells in the ground/naive subpopulations and 98-99% of the cells in the primed subpopulations are similar between all four samples. The single cell RNA sequencing analysis of iPSC lines grown in both media is the first report of the molecular pathways modulated in StemFlex medium and how they compare to those modulated in TeSR-E8 medium.

2019-05-08 | E-MTAB-6524 | biostudies-arrayexpress

Single-cell RNA sequencing of mouse germ cells

Project description:Spermatogenesis is a recurring differentiation process that results in the production of male gametes within the testes. During this process, spermatogonial stem cells differentiate to form spermatocytes, which undergo two rounds of meiotic division to form haploid spermatids. Throughout spermiogenesis, round spermatids elongate to form mature sperm. To profile maturing germ cells during the first wave of spermatogenesis, we generated droplet-based single cell RNAseq from juvenile animals at post-natal day P5-P35 as well as adult animals. Cells were isolated from whole testes. Furthermore, to assay the robustness of the meiotic cell division process, we profiled germ cells of the trans-chromosomal mouse model (Tc1) that carries a copy of the human chromosome 21.

2019-01-25 | E-MTAB-6946 | biostudies-arrayexpress

Single cell RNA sequencing of iPSC and Human dermal fibroblasts

Project description:single cell RNA sequencing of iPSC and Human dermal fibroblasts using 10x Genomics with 3-prime, 5-prime poly(dT) primer, and 5-prime random primer. For comparison in gene, ncRNA and enhancer detection.

2021-05-13 | E-MTAB-10385 | 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