Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: PIPseq T20 v3.0 versus 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 Dual Index

PROVIDER: PRJNA1170298 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30911718_1.fastq.gz	Fastqsanger.gz
	SRR30911718_2.fastq.gz	Fastqsanger.gz
	SRR30911719_1.fastq.gz	Fastqsanger.gz
	SRR30911719_2.fastq.gz	Fastqsanger.gz
	SRR30911720_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Single cell gene expression, immune receptor and cell surface marker expression profiling of Spike-specfic splenic T and B cells of immunized mice

Project description:Spike-specific T and B cells from splenocytes of immunized mice were profiled with 10x sequencing for gene expression (Chromium Next Automated GEM 5’ v2 kit), cell surface marker (Chromium Automated 5’ Feature Barcode kit) and immune receptor (Chromium Automated Mouse BCR/TCR Amplification and Library Construction kit)

2023-08-07 | GSE222403 | GEO

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 nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

Project description:This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

2023-08-07 | GSE233754 | 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

Single cell RNAseq reveal covid19 vaccine response difference

Project description:Single cell RNAseq was performed on PBMC isolated from health workers who received two doses of Pfizer COVID19 vaccine and determined as either normal responders or low responders by antibody test. Each group has 4 patients. Cells from each patient were labeled with Totalseq C hashing antibodies and mixed 1:1:1:1 for each group. Single cells were further captured using 10x chromium Next GEM 5 prime kit.

2022-10-03 | GSE199123 | GEO

An investigation into the effects of ATV:Trem2 on AD model mice using scRNA-seq

Project description:WT hTfR-KI mice and APP/SAA hTfR-KI mice were treated with one of: Isotype control ATV, naked 4D9 (activating Trem2 Ab), or ATV:4D9. Drugs were delivered IV. After 24 hours, mice were sacrificed, and perfused cortices were processed into single-cell suspensions. The suspensions were FACS sorted for Cd45+/Cd11b+ cells. Single-cell suspensions were labeled with CellPlex CMO per 10X Genomics protocol (CG000391 Rev A.) After each sample was labeled with CMO tags, equal numbers of cells per sample were combined into sample pools for single cell capture on the Chromium using Chromium Next GEM Single Cell 3’ v3.1 kit. After RT and cDNA amplification, each sample pool was separated into one gene expression (GE) library and one CMO tag library via dual-sided SPRI bead purification. Library preparation was performed per manufacturer’s protocol (CG000388 Rev A)

2022-11-22 | GSE209912 | GEO

AhR in the amelioration of Autoimmune Hepatitis

Project description:10X Genomics Chromium Next GEM Single cell V(D)J reagent kits v1.1 was used to process single cell suspensions from Naïve or Concanavalin A exposed mice treated with vehicle, TCDD, or FICZ. The V(D)J enrichment was omitted.

2022-05-23 | GSE201006 | GEO

Single-cell transcriptomic analysis reveals hepatic stellate cell activation roadmap and myofibroblast origin during liver fibrosis

Project description:Purpose: analyze the transcriptomic differences in liver of CCL4 and BDL mouse model Methods: Fresh isolated HSC suspensions of CCL4 and BDL were loaded on the 10x Genomics Chromium Single Cell Platform using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 Results: We revealed the HSC activation roadmap and portal fibroblasts are major contributor to myofbroblast in BDL model.

2021-06-09 | GSE171904 | GEO

Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization

Project description:Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants (injected with 10pg ndr2 mRNA) constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery. For single-cell multiomics, zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 4 rxns PN-1000285) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 10,614 single-cell transcriptomes and 4,335 multiomics were collected after stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm, which drives a differential expression of those key regulators, such as gsc and ripply1 in these two cell lineages, and further regulates mesendoderm cell fate separation.

2023-01-28 | GSE223636 | GEO

Single cell RNAseq reveal covid19 patient immune response

Project description:Eighteen patients admitted to CSMC and diagnosed with COVID19 by RT-PCR were stratified into COVID19 mild/moderate, severe, and recovery groups (n=5-6/group). Venous blood was collected into EDTA coated tubes and centrifuged to separate plasma and buffy coat. Plasma was collected and frozen at -80C, and the buffy coat was collected into cryo-preservation media and frozen at -80C. Recovered cells are sorted for live-dead staining, then fixed with methanol. Fixed single cells were further captured using 10x chromium Next GEM 3 prime v3.1 kit. Two patients samples from the same group were mixed, captured and sequenced together.

2020-09-24 | GSE154567 | 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