Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Deconvolving Linked-Reads (e.g. 10x Genomics) for Metagenomics

PROVIDER: PRJNA505182 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8194100_1.fastq.gz	Fastqsanger.gz
	SRR8194100_2.fastq.gz	Fastqsanger.gz
	SRR8194099_1.fastq.gz	Fastqsanger.gz
	SRR8194099_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Project description:10X Genomics linked-reads from Saccopteryx leptura

| PRJNA1089961 | ENA

e331a5e6-7268-4152-b6cc-99c819195f21 - samples

Project description:Matched tumor-normal data for 6 JPAs. Generated using 10X Genomics Linked-reads

| EGAD00001011114 | EGA

Spatial transcriptomics of 3-month-old and 18-month-old mouse ovarian and uterine tissues

Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).

2024-07-23 | E-MTAB-12105 | biostudies-arrayexpress

Single cell RNA sequencing of paired PBMC and synovial tissue cells from Rheumatoid Arthritis (RA) patients naive to treatment

Project description:Live CD45+ cells from the peripheral blood (PB) and synovial tissue (ST) of 3 naive to treatment RA patients were sorted for single cell RNA sequencing (scRNAseq) using 10x Genomics platform. Library preparation was performed using 10X Single Cell 3’ Reagent Kits v2 and libraries were sequenced on the Illumina HiSeq 4000 system to a minimum depth of 50k reads/cell.

2024-12-09 | E-MTAB-14192 | 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-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 transcriptome analysis of mouse main olfactory epithelium

Project description: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).

2022-01-31 | GSE169011 | GEO

Single-cell RNA-seq of total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- and Pou2f3+/+, Pou2f3+/- mice

Project description:Total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- (KO) and Pou2f3+/+, Pou2f3+/- (heterozygous and homozygous WT mice together in WT sample) littermated mice were sorted for live cells on Moflo XDP cell sorter (singlets, FSCAxSSCA, DAPI-). Immediately post-sorting, cells were run on 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry). Libraries were run on the NovaSeq 6000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (Cell Ranger Version 3.0.2, 10X Genomics). Primary assessment with this software for WT DC sample reported 2,441 cell-barcodes with 7,651 median unique molecular identifiers (UMIs, transcripts) per cell and 2,004 median genes per cell sequenced to 61.4% sequencing saturation with 48,559 mean reads per cell. Primary assessment with this software for MARCH1-/- DC sample reported 681 cell-barcodes with 6,309 median unique transcripts per cell and 1,774 median genes per cell sequenced to 73.1% sequencing saturation with 202,410 mean reads per cell.

2022-03-01 | GSE196546 | 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