Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptome analysis of mouse main olfactory epithelium

ABSTRACT: The goal of scRNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR in a large and unbias scale. Olfactory epithelial single cell suspensions were made using 3 male and 3 female mice. Single-cell sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) according to the manufacturer’s guidelines. Libraries were sequenced using 150 cycles of paired end reads on Illumina Hiseq4000 and Novaseq6000 instruments (Novogene). The sequencing reads were processed using the DolphinNext Single Cell-10X Genomics pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=420, default settings except STAR v2.6.1 was used for alignment).

ORGANISM(S): Mus musculus

PROVIDER: GSE169011 | GEO | 2022/01/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome analysis of mouse olfactory sensory neurons expressing 3 different types of olfactory receptor

Project description:The goal of RNA-seq is to explore whether olfactory sensory neurons (OSNs) that display a specific olfactory receptor (OR) express a distinct transcriptional program from OSNs that display a different OR. The GFP knockin mice (Olfr73-IRES-GFP, Olfr1507-IRES-GFP, and Olfr160-IRES-mCherry) was used to label the OSN expressing specific OR. These cells was then isolate with fluorescence activated cell sorting. For each sample, at least 5000 cells are collected, there biological replicates were collected for each genotype and in total 9 samples were prepared for RNA-seq libraries with using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s guidelines with one alteration, which was to increase the insert length to ~300 base pair. Libraries were sequenced using paired end 150 cycle reads on an Illumina Hiseq4000 (Novogene). The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732). The default settings were employed except STAR v2.6.1 and RSEM v1.3.1 were used for alignment and quantification, respectively. Differential analysis were conducted in DESeq2. The significant genes were deducted by computing Wald test with corrected p < 0.05. Our results shows that different types of OSNs express significantly different patterns of genes, especially the genes involved in axonal guidance.

2022-01-31 | GSE169010 | GEO

Single-cell RNA-sequencing of OMP-GFP mouse olfactory sensory neurons

Project description:We sequenced the transcriptome of 34 single olfactory sensory neurons (OSNs) manually picked from OMP-GFP mice, ensuring the cells expressed high levels of GFP, a marker of mature OSNs. We pooled the olfactory mucosa from 2 male and 2 female animals, to obtain single-cell suspensions for cell picking. We only picked healthy-looking cells. From each, we constructed libraries for single-cell RNA-sequencing, to characterise the diversity of OR genes expressed.

2020-02-04 | E-MTAB-8285 | biostudies-arrayexpress

Single cell RNA-seq of human synovial joints from healthy donors

Project description:Human synovial Single cell RNA-seq was performed on three tissue samples from healthy donors. This experiment was done to explore the heterogeneity of cells in healthy human synovial joint and enabled the comparison of cellular states and composition to those of publicly available single cell RNA-seq datasets from psoriatic arthritis and rheumatoid arthritis patients. Human synovial cells were loaded immediately after tissue dissociation with up to 25,000 cells in a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as paired end (PE) 150 bp by Illumina sequencing to 65-80% saturation. Reads were mapped to the GRCh38 human genome (GENCODE) using the 10x Genomics Cell Ranger pipeline (7.2.0).

2024-08-06 | E-MTAB-14339 | biostudies-arrayexpress

Single cell RNAseq of adoptively transferred Tregs in rhesus macaques

Project description:Animal R.401 was infused with ex-vivo expanded T-regulatory cells. After adoptive transfer, PBMC were obtained and stained with surface antibodies. Single cell libraries from sorted populations were generated using a UMI-based droplet-partitioning platform (10X Genomics) and sequenced using a NextSeq 500 (Illumina). Resulting reads were processed using Cellranger software (10X Genomics) and downstream analysis was performed using Monocle6,7 using a negative binomial model of distribution with fixed variance.

2019-10-24 | GSE139200 | GEO

Single cell RNA-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control

Project description:This study used scRNA-seq to characterise the transcriptome in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using a cold-active protease. Nuclei were extracted and profiled using the 10X Genomics Single-cell 3' V3 kits. Libraries were sequenced using paired-end reads on an Illumina NextSeq 500. Initial processing was performed using CellRanger v3.1.0 (10X Genomics).

2023-04-30 | E-MTAB-11138 | biostudies-arrayexpress

Single cell ATAC-seq of iPSC-derived Kidney Organoids treated with TGF-Beta 1 and GSK343 compared with vehicle treated control

Project description:This study used snATAC-seq to profile Chromatin accessibility in 26 day-old iPSC-derived kidney organoids, treated with TGFB1, the EzH2 inhibitor GSK343, a combination of both or a vehicle control for 48 hours (days 24-26) before harvesting. 2 organoids per condition were pooled and dissociated using a cold-active protease. Nuclei were extracted and profiled using the 10X Genomics Single-cell ATAC reagent kit v1.1. Libraries were sequenced using paired-end reads on an Illumina NovaSeq 6000. Initial processing was performed using CellRanger ATAC v1.2.0 (10X Genomics).

2023-04-30 | E-MTAB-11139 | biostudies-arrayexpress

Single-cell RNA-sequencing analysis for the molecular taxonomy of primate hippocampus after sevoflurane exposure

Project description:We thus isolated hippocampus from rhesus macaques and performed single-cell RNA-sequencing analysis. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

2023-06-12 | GSE153598 | GEO

scRNA-seq of mouse lymph node stromal cells

Project description:C57BL/6 mouse lymph node stromal cells were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip. 5-10 x 104 reads/cell were obtained with characterization of 2-3 x 103 transcripts/cell.

2022-07-01 | GSE202068 | GEO

Analysis of single-cell RNA-seq data from human PBMCs and from in vitro cultures of human cord blood CD34+ progenitors encompassing different DC types

Project description:For both PBMC and cells from the in vitro cultures, RNA purification and library generation was performed using the Chromium Single Cell Controller apparatus and associated protocols (10X Genomics). Libraries were sequenced by 75-bp single-end reading on a NextSeq500 sequencer (Illumina). Reads were aligned on the GRCh38 human genome assembly. Data analysis was performed using the R software package Seurat (https://github.com/satijalab/seurat)

2018-08-14 | GSE115405 | GEO

scRNA-seq of lymph node stromal cells from mouse treated with anti-CD40L

Project description:C57BL/6 mouse lymph node stromal cells treated with anti-CD40L were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip. 5-10 x 104 reads/cell were obtained with characterization of 2-3 x 103 transcripts/cell.

2022-09-17 | GSE213400 | GEO

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