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

Splenic single cell RNA-Seq of WT and Hem1 KO mice

ABSTRACT: The experiment elucidates the development of splenic B- and T lymphocytes in the absence of a vital gene. For this purpose, spleen cells of 5 wild type and 5 full knock-out mice were depleted of red blood cells and prepared for 10x single cell RNA-Seq sequencing. The library was prepared according to the manufacturers instructions.

INSTRUMENT(S): Illumina NovaSeq 6000, Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Kaan Boztug

PROVIDER: E-MTAB-8706 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq profiling of T cells isolated from MC38 mouse tumors

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Tumors were taken one day after group-out (average 150-250 mm3 at day 0), approximately 14-19 days. Tissues were dissociated and flow sorted accordingly to obtain the following groups for 10x Chromium 5' Gene Expression Profiling. Our results indicate that the degree of clonal expansion is correlated with expression of T cell exhaustion markers, and that T cells with strong exhaustion phenotype also express high levels of activation markers, such as interferon gamma.

2019-05-12 | E-MTAB-7919 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - scRNA / GEX / VDJ

Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

2022-01-27 | E-MTAB-11278 | biostudies-arrayexpress

Single cell RNA-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling.

2021-02-16 | E-MTAB-9274 | biostudies-arrayexpress

TCR repertoire profiling of CMV specific and SARS-CoV2 Spike specific CD8+ T cells using single cell sequencing

Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.

2022-01-01 | E-MTAB-11229 | biostudies-arrayexpress

Single cell RNA-seq and VDJ-seq of B cells from sheep red blood cells-primed WT and Stch cKO mice

Project description:Once activated, B cells produce the antibodies needed to fight against infection. B cells are necessary for adaptive or specific immunity, which focuses on the destruction of foreign invaders that have gotten past the bodies initial defenses. Heat shock protein family is a group of highly conserved molecular chaperones with important functions in protein folding such as antibody and in signal transduction. Stch (Heat shock 70 kDa protein 13) is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins. To explore the role of Stch in B-cell activation and antibody production, we evaluated the transcriptional events and the role of stch pathway on the activation and antibody production of B cells by single cell RNAseq. Splenic lymphocytes were isolated from 7-9-week-old female Stchf/f wildtype (WT) mice and B-cell specific Stch knocked-out (CD19creStchf/f) mice (3 mice/group) using Ficoll (Ficoll-Paque Plus, GE Healthcre). B cells were sorted using B220 microbeads (Cat No. 130-049-501, Miltenyi Biotec, Germany). Their transcriptomes were captured using a 10x chromium system.

2021-03-01 | E-MTAB-8280 | biostudies-arrayexpress

Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

2022-08-16 | E-MTAB-9734 | biostudies-arrayexpress

Single cell TCR-seq of T cells isolated from MC38 mouse tumors

2019-05-11 | E-MTAB-7918 | biostudies-arrayexpress

ScRNA-seq of human skeletal muscle macrophages

Project description:in-depth exploration of macrophage phenotypes following an acute bout of exercise

2021-10-31 | E-MTAB-10988 | biostudies-arrayexpress

Single-cell RNA-seq of tumor-infiltrating lymphocytes in metastatic uveal melanoma

Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.

2020-03-16 | E-MTAB-8846 | biostudies-arrayexpress

Single-cell immune repertoire sequencing of bone marrow plasma cells following infection and immunizations

Project description:We performed single-cell transcriptome and antibody repertoire sequencing of bone marrow plasma cells following protein (OVA and TNFR2) immunizations or infection with high dose LCMV clone 13.

2021-12-01 | E-MTAB-11096 | 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