Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing of in vitro mouse T-cell differentiation via VCAM-1

ABSTRACT: Sample preparation and single-cell RNA-sequencing of in vitro T-cell differentiation Method: 10X Chromium was used to prepare single-cell cDNA libraries, and Illumina Nextseq was used to 3’ sequence the samples

ORGANISM(S): Mus musculus

PROVIDER: GSE196972 | GEO | 2022/02/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Single-Cell Transcriptome Analysis of MAIT Cell Subsets from human normal intestine

Project description:Normal adjacent tissues from colorectal cancer patients were collected for MAIT cell sorting. Sorted MAIT cells from seven individual donors were pooled together. Single-cell RNA sequencing libraries were prepared using the Chromium 5' Single Cell Gene Expression Kit (10x Genomics), following the manufacturer's protocol. Sequencing was performed on a NextSeq 500 platform (Illumina).

2024-11-26 | E-MTAB-14482 | biostudies-arrayexpress

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

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

Single cell profiling of 3 Human Lung Adenocarcinoma cell lines.

Project description:An equal mixture of cells from the 3 Human Lung Adenocarcinoma cell lines (H2228, NCI-H1975 and HCC827) were processed on the Chromium 3' single cell platform (10X Genomics) and sequenced on an Illumina NextSeq 500. FASTQ data were preprocessed using both scPipe and CellRanger.

2018-02-28 | GSE111108 | GEO

snATAC-seq of the developing mouse cerebellum across eleven stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-9765 | biostudies-arrayexpress

Single-cell RNA-seq analysis of subventricular zone-derived neural progenitors mobilized to demyelinated corpus callosum

Project description:NestinCreERT2:RosaYFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. Corpus callosum was then dissected, dissociated and YFP+ subventricular zone-derived cells were isolated by FACS. 1931 cells were then processed for single-cell RNA-seq analysis. Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.

2021-06-04 | GSE144201 | GEO

Single-nucleus RNA-seq of adult female and male mouse livers for sex-biased gene expression analyses

Project description:To obtain new insight into the sexual dimorphism of mammalian livers, single-nucleus RNA-seq was performed on the liver samples from two female and two male adult mice. The single-nucleus libraries were generated on the 10X Chromium Next GEM Single Cell 3ʹ platform and sequenced on Illumina NextSeq 550. We used the data to understand the heterogeneity and sex-biased gene expression of liver cell types. The data revealed significant sex differences primarily focused on hepatocytes. Specifically, from the sex-biased genes detected at the bulk tissue level, we observed that male-biased genes are more highly expressed in male hepatocytes, and female-biased genes are more highly expressed in female hepatocytes.

2023-08-03 | E-MTAB-12180 | biostudies-arrayexpress

Single-cell RNA sequencing of RUNX1-RUNX1T1(9a) transformed mouse bone marrow cells

Project description:Single-cell RNA sequencing analysis of RUNX1-RUNX1T1(9a) transformed c-kit positive cells with (Kat2a WT) and without Kat2a (Kat2a NULL). Lineage negative bone marrow cells were collected from Kat2a fl/fl Mx1-Cre-/- and Kat2a fl/fl Mx1-Cre +/- animals after pIpC treatment and transduced with RUNX1-RUNX1T1(9a) expressing retrovirus (reported by GFP expression). Cells were injected into irradiated C57BL6 mice and GFP positive c-Kit positive bone marrow cells collected 2 and 4 months after transplantation. Cells were processed for single-cell RNA sequencing library preparation (10X chromium single cell) and next gene sequencing following 10X genomics v2 protocol.

2022-08-24 | E-MTAB-10853 | biostudies-arrayexpress

Single cell Transcriptome of In Vitro Meiosis in mouse spermaotogia with NRRA treatment

Project description:Here we performed single cell RNA seq analysis of cultured spermatogonia with NRRA treatment using 10X Genomics Chromium platform. 5 cluster cell populations were identified.

2021-02-16 | GSE153274 | GEO

Role of trisomy 21, GATAs mutation and associated mutations in the development of a DS-AMKL model from IPSC: Single cell RNAseq

Project description:Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modelled this leukemic evolution through stepwise gene editing of GATA1s, SMC3+/- and MPLW515K providing 20 different trisomy or disomy 21 iPSC clones. Single cell analysis was performed on hematopoietic cells obtained from IPSC clones after 13 days of differentiation. Sample preparation was done at room temperature. Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. All samples were processed simultaneously with the Chromium Controller (10X Genomics) and the resulting libraries were prepared in parallel in a single batch. We pooled all of the libraries for sequencing in a single SP Illumina flow cell. All of the libraries were sequenced with an 8-base index read, a 28-base Read1 containing cell-identifying barcodes and unique molecular identifiers (UMIs), and a 91-base Read2 containing transcript sequences on an Illumina NovaSeq 6000.

2022-09-29 | E-MTAB-11036 | 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